RiceWiki - User contributions [en]

Os08g0105000

2014-06-08T03:39:32Z

QingweiTian:

Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice

==Annotated Information==
===Function===

A number of genes individually controlling number of grains per plant, heading date and plant height have been cloned recently using map-based cloning approaches. Compared with the genes reported previously, Ghd7 is notable in that it has large pleiotropic effects on an array of traits, including grain number,heading date and plant height. Such pleiotropic effects may provide an explanation for QTL hot spots that were observed in many studies.
CCT-domain proteins have been reported to have crucial roles in regulating processes such as photoperiodic ﬂowering, vernalization31, circadian rhythms and light signaling. The results of the present study indicate that GHD7 has a key role in photoperiod ﬂowering by regulating the putative Ehd1-Hd3a pathway. Strong
expression of Ghd7 in the vascular tissues of leaves is consistent with the role of CO-like genes in ﬂowering regulation. However, we also observed expression of Ghd7 in organs that may not be directly related to photoperiod-controlled ﬂowering, such as roots that do not seem to have a role in ﬂowering, leaves and meristems in the early seedling stage that are much too early for ﬂower induction, and the stems and panicles that already passed the stage of phase transition.
Expression in these tissues corresponded well with increases in the various organs leading to an overall increase in plant size, suggesting the possibility that this gene may have a general role in promoting growth, cell proliferation and differentiation, in addition to photoperiod ﬂowering.
Ghd7 controls heading date through its enhanced expression under long-day conditions to repress the expression of Hd3a, likely through Ehd1, thus delaying ﬂowering. Of note, the cereal VRN2 gene, although referred to as a vernalization gene, actually has a day-length control and is only expressed under long-day conditions, when it acts as a repressor of ﬂowering. VRN2 was classiﬁed in the same CCT subfamily as Ghd7. This suggests that tropical short-day plants that do not use vernalization as a ﬂowering cue, and temperate long-day plants that do use vernalization, actually use related genes to repress ﬂowering in long-day conditions. Such similarity in ﬂowering control provides important clues as to how the temperate cereals might have evolved. Moreover, these genes also act as major sources of adaptive variation, and hence are keys to understanding the spread and success of cereals. Sequence analysis of allelic variants at theGhd7 locus indicated that this locus has contributed greatly to both productivity and adaptability of cultivated rice on a global scale. Asian cultivated rice originated in tropical and subtropical regions of Asia. The functional alleles with strong effects (for example,Ghd7-1 andGhd7-3) allow rice plants to fully exploit light and temperature by delaying ﬂowering under long-day conditions in areas with long growing seasons, thus producing large panicles and increasing yield. The mutations giving rise to the Ghd7-0 and Ghd7-2 alleles, with no or reduced effect of delaying heading under long-day conditions, have had crucial roles by enabling rice to be cultivated under conditions with short growth duration and/or temperate regions. Additionally, the substantial dominant effect observed in the heterozygote between NIL(zs7) and NIL(mh7) indicated that theGhd7 locus has also contributed signiﬁcantly to the highlevel of heterosis of Shanyou 63 (refs. 19,40), a widely cultivated hybrid in China in the last more than 20 years.
Yield has been generally regarded as a complex trait that is controlled by multiple genes of small effects. The major effects demonstrated by the NILs and transgenic plants and the cloning of this QTL have fundamental implications for yield improvement,suggesting that yield, like other traits, can also be improved by individually manipulating the component traits using both molecular marker–assisted selection and transformation.
===Expression===
Expression pattern of Ghd7

We investigated the diurnal expression pattern ofGhd7 by quantifying the relative abundance of the mRNA in young leaves of NIL(mh7) using quantitative RT-PCR. The expression of Ghd7 was much higher under long-day conditions than short-day conditions, and the Ghd7 transcript was much more abundant during the light period than in dark period, especially under long-day conditions.We carried out RNA in situ hybridization and Ghd7 promoter–driven GFP transformation to examine sites of Ghd7 expression. The RNA in situ hybridization signals indicated that the gene is expressed in young tissues, such as the apical meristem, developing leaves and the leaf sheaths of the young seedling, the meristem of the root, the epidermal layer of developing stems and the branch-primordia of developing panicles. The GFP signal was strong in the young stem and in vascular tissues in the blades of fully expended leaves, but weak in the root and vascular tissues of the leaf sheath.

===Evolution===
Comparison of the predicted protein sequences identiﬁed ﬁve alleles that showed a clear geographic distribution. Ghd7-1 was found in rice varieties from the tropics, subtropics and areas with hot summers and long growing seasons, including the most popular high-yield cultivars and parents of elite hybrids in China and
Southeast Asia. The wild rice accession also had this allele, indicating that Ghd7-1 is probably the original wild-type allele. Ghd7-2, differing from Ghd7-1 by four amino acids, was found in varieties of temperate japonica from Japan and northern China. This allele seemed to have a smaller phenotypic effect than Ghd7-1. Ghd7-3 occurring in Teqing is distinct from all the other alleles in that it differs by three amino acids from both Ghd7-1 and Ghd7-2, with one variant amino acid found only in this variety. The phenotypic effect ofGhd7-3 seems to be the same magnitude as that of Ghd7-1 (Table 1 and Supplementary Table 4). The remaining two
alleles (Ghd7-0 and Ghd7-0a) were nonfunctional. Ghd7-0, with the Ghd7 locus completely deleted, was found in two varieties grown as early rice in a system with two-rice crops in central and southern China, in which the growth duration for early rice is short. Ghd7-0a, resulting from a premature termination in the predicted coding region, was found in two varieties from the Heilongjiang Province of northeastern China, which has cool summers and a short growing season.

==Labs working on this gene==
National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.

==References==
[1]Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nature Gent 40:761-767

==Structured Information==
{{JaponicaGene|
GeneName = Os08g0105000|
Description = Zinc finger, PHD-type domain containing protein|
Version = NM_001067318.1 GI:115474372 GeneID:4344443|
Length = 4125 bp|
Definition = Oryza sativa Japonica Group Os08g0105000, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 8|Chromosome 8]]|
AP = Chromosome 8:271854..275978|
CDS = 272583..273512,273602..273646,273832..273921,274832..275152,275242..275445 ,275590..275691|
GCID = <gbrowseImage1>
name=NC_008401:271854..275978
source=RiceChromosome08
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008401:271854..275978
source=RiceChromosome08
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggctcccagaaccgccccccaccaccgcgcaagaggcagccgccgccgccggaggaccacctcgtcacctacaagcgccgccgctccaaagaaacacagcctttgccactcatggccaacggcgccaattctaagaaagacgccaaggcccaacattggattagctggagggacactctccacggcttcctccaatcccctgctattagccagggtggaggaattcagacctgcatccgtcatgctctccaacacaatccttgcttgctcaccaatggtgttgttgttcacactgaattcaaaggtaacccagctcattcccaaggagaggaagcaaaagtgcagcaccctaatggtgctgctggaggcaaggtggtttctgcagatgctgctatacaagatgcggctgccgcagcttcttccgaagctaacaaggcaatgtgtaataatgccctcttcgacattttggtctcccagaaatttgccttgttgtgccatttgctacttgggaccttccatgtcaataaacctggtgatgtcatcgacttggaaaaaatcgacgccaagatgagaaatggagactatgcccacaaccctgcactatttgacgatgatatccagcagatgtgggagaagtttgagcaagttggccaagagatgacaggtctagcgagcaacctttcaaccatttcacgagtttcataccaaaagcaggcttctggattttctgaagctgaggtggctgagcacagaatagaggaaataagtttgccgggtgctgtccacgttgtcacaaaggagtcgactaccaccgtgcagttggccccatgtgattctagtcattctacaataccgaaacgaactgtgccacctggacgtgatctgtgcccttgcgatggttgtggcaccaaggtagatgttgaagaaggcctaatctgtgatgaatgtgacaccatgtaccactttgcatgtgtcaagctactcaatcctgatattaagcaagtcccagcaatctggcattgttcaacctgcagcttcaagaaaaaagaattggctgcagataccacgaataatgttgcccatgactgcttgcatggtggtaactgtgttttgtgtgaccagctcgagctggtgaagacagaagaagaagatcccaagcttcccataaaaattgaattagctgaagaaagagaggggagctccgtctcaagcatgggggaagacaatgaaccagacctgtcaacaactgccctgtcaaacttgtgcaaacactgtggcacatgcgaagacgatgacaagagattcatggtatgcggacatccttactgcgtttacaagttctatcatatccgatgcctgaaaacaagccagcttgcaattgagcaacaaaagaagcttggttgctggtactgcccctcttgcctctgcagagggtgcttccaagacaaggatgatgaccagatagtcatgtgtgatggctgtgatgaaggttatcacatatattgcatgagaccagcacgcaacactatccccaaaggtaagtggtactgtacattttgcaagatccgcagggcagcggaaggaatgcataagtatgaggattctgtgctgaaaatacatgggaatagtaagcatgcttgtaatgtgaatcagtcgaaggattctgaaggtgatggtactgaaaagtga</cdnaseq>|
AA = <aaseq>MGSQNRPPPPRKRQPPPPEDHLVTYKRRRSKETQPLPLMANGAN SKKDAKAQHWISWRDTLHGFLQSPAISQGGGIQTCIRHALQHNPCLLTNGVVVHTEFK GNPAHSQGEEAKVQHPNGAAGGKVVSADAAIQDAAAAASSEANKAMCNNALFDILVSQ KFALLCHLLLGTFHVNKPGDVIDLEKIDAKMRNGDYAHNPALFDDDIQQMWEKFEQVG QEMTGLASNLSTISRVSYQKQASGFSEAEVAEHRIEEISLPGAVHVVTKESTTTVQLA PCDSSHSTIPKRTVPPGRDLCPCDGCGTKVDVEEGLICDECDTMYHFACVKLLNPDIK QVPAIWHCSTCSFKKKELAADTTNNVAHDCLHGGNCVLCDQLELVKTEEEDPKLPIKI ELAEEREGSSVSSMGEDNEPDLSTTALSNLCKHCGTCEDDDKRFMVCGHPYCVYKFYH IRCLKTSQLAIEQQKKLGCWYCPSCLCRGCFQDKDDDQIVMCDGCDEGYHIYCMRPAR NTIPKGKWYCTFCKIRRAAEGMHKYEDSVLKIHGNSKHACNVNQSKDSEGDGTEK</aaseq>|
DNA = <dnaseqindica>2467..3396#2333..2377#2058..2147#827..1147#534..737#288..389#agtttccattcccgttccgttataataagaggagagagagagagattttgggtttgtctccggctccgctcgccgcctccaaatcccgctcctccgctgctgctcctctctgccgcggcgaggcgagagatccgaatccaccgccacccgcgcccaccccgcccgcacaaaccctagtttttccggggttttgcttcccctccgcagctccgctccgctccgtccgtcgtctcctcccggcggctcggcttgctgtccatgctgtagccgccccccgcaggtggctgatgggctcccagaaccgccccccaccaccgcgcaagaggcagccgccgccgccggaggaccacctcgtcacctacaagcgccgccgctccaaagaaacacaggtaaccaaccaaccaactccctgcctcttcttcttcttctttctccagatttcctttcgatttctacaagattcgtactctcgcttcttgcctcctcttacaatctctcattacatctacttgttgtgctttcttttcttgcagcctttgccactcatggccaacggcgccaattctaagaaagacgccaaggcccaacattggattagctggagggacactctccacggcttcctccaatcccctgctattagccagggtggaggaattcagacctgcatccgtcatgctctccaacacaatccttgcttgctcaccaatggtgttgttgttcacactgaattcaaagtaacacacaccacctttgtttgcatctaccctatatatatttatgcaatgataattttcctaacacatgacttctttctcattaccagggtaacccagctcattcccaaggagaggaagcaaaagtgcagcaccctaatggtgctgctggaggcaaggtggtttctgcagatgctgctatacaagatgcggctgccgcagcttcttccgaagctaacaaggcaatgtgtaataatgccctcttcgacattttggtctcccagaaatttgccttgttgtgccatttgctacttgggaccttccatgtcaataaacctggtgatgtcatcgacttggaaaaaatcgacgccaagatgagaaatggagactatgcccacaaccctgcactatttgacgatgatatccagcaggtaattgtttctctattgctcccatgaaagtaatttagctactgttgttggagggaaataatactagctagtgtttattcttatcttttatctaataaagatgatgcatattacctgtacttataagcgccctctgtatgctaaagcttaatgtgttctccatctattattgttcacaactccgtaaatcataagagcaaaatgttctacgtacggccagttgatagaatgatgctgatgctcaactgcttatctgagcttcttttgcgtttgctagttaagatcttcccaaattgtttgaaccatccaagcaacagactcctagggagtttatcacaactgaccttctagaactctggttgttagggttggaacgctagtcaacttaaatggtatactagccctgtttctacactatcatgtcttcgcaactttatatgctctatttctatctgtctgcttcatctgctgtccgcaacatgccaactcccttgcgcttcatggttgatgaagtggaccatggataatgtggttgagctggggtatgacacacacaaaattctggaacatctcatgcatgctgcatgtgtaaccactcaatgctgaggtttctgtctaagtcaactagggttttatcacttgttttcttaaatgggcacaacacaaaaaagaaaacttttataatatttagtgctagcacatctcaaagaccgaacaattactcttctatattgatttccttatcagttatcattgatatacttttttcatctgtgagtttttttgtttacattatattgttcatgctctaaacatagaagttgtgtagtaacatctaggaaaaattatacgatactgttgcctgctgagccttcctcttaatacaactctctatttgtttattttgtagatgtgggagaagtttgagcaagttggccaagagatgacaggtctagcgagcaacctttcaaccatttcacgagtttcataccaaaagcaggtaatctgttgctttatctttcaattaatgtctctagcgtcgagatggttatattttgacaatttgagttaagataaatctattactgcacacttggcaaccatgctgcaatttgcaggatgctttagtatattgaaatctttccttttatgctgggcattactaatggataaattattttataggcttctggattttctgaagctgaggtggctgagcacagaatagaggtaagttgtctgtttgaggatgtttgctaatcattgttccacatgcacacttaattaataatggttttactaattgcattcttcattaggaaataagtttgccgggtgctgtccacgttgtcacaaaggagtcgactaccaccgtgcagttggccccatgtgattctagtcattctacaataccgaaacgaactgtgccacctggacgtgatctgtgcccttgcgatggttgtggcaccaaggtagatgttgaagaaggcctaatctgtgatgaatgtgacaccatgtaccactttgcatgtgtcaagctactcaatcctgatattaagcaagtcccagcaatctggcattgttcaacctgcagcttcaagaaaaaagaattggctgcagataccacgaataatgttgcccatgactgcttgcatggtggtaactgtgttttgtgtgaccagctcgagctggtgaagacagaagaagaagatcccaagcttcccataaaaattgaattagctgaagaaagagaggggagctccgtctcaagcatgggggaagacaatgaaccagacctgtcaacaactgccctgtcaaacttgtgcaaacactgtggcacatgcgaagacgatgacaagagattcatggtatgcggacatccttactgcgtttacaagttctatcatatccgatgcctgaaaacaagccagcttgcaattgagcaacaaaagaagcttggttgctggtactgcccctcttgcctctgcagagggtgcttccaagacaaggatgatgaccagatagtcatgtgtgatggctgtgatgaaggttatcacatatattgcatgagaccagcacgcaacactatccccaaaggtaagtggtactgtacattttgcaagatccgcagggcagcggaaggaatgcataagtatgaggattctgtgctgaaaatacatgggaatagtaagcatgcttgtaatgtgaatcagtcgaaggattctgaaggtgatggtactgaaaagtgatcatcacaatagctttgtggattagcttctgagctcgcttggacaagctcaggaaaagagattctttggccccttaggagggctatacaccgactttgatactgaatcagttgtgtagtttatttaattaactgccgttgacatctacaggaagaactcttacctggtgaagatggtgtatgtagtcttttagctgggcggaatgatgtgttgtttacttgttcaccttccttctttaccccctttcagtgaccattgtgaatgttgtcctgtacttgccctgtgatggtattcttaaacgtttttttgggggaaatatgattttgtttttttaatctcctttttattgcttgattcgtcattgtttatagcctgtgatcgatgattgtgaaggtttatagtctgtatgttgtgtatgtaatggtttggttgatcctgaagctttttggaggtcttatttcagtcgaggacaagcatgagagtcaaggaagaaagtggatcttcattttgtcagacaattgtgacagtcatggagcatgtaagtagtactagtatatagtttgagtgtatgactaaccctgaatattcattcctatagtaaatagtactcctatatcatattagagattctgtggttggattaataagtagtgtagctatatctccagatgatgaatttatatgtgtccttgatatgaattaatgatatttgtggtgagtgttgacctc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001067318.1 RefSeq:Os08g0105000]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 8]]
[[Category:Chromosome 8]]

Os08g0105000

2014-06-08T03:38:52Z

QingweiTian:

Please input one-sentence summary here.

==Annotated Information==
===Function===

A number of genes individually controlling number of grains per plant, heading date and plant height have been cloned recently using map-based cloning approaches. Compared with the genes reported previously, Ghd7 is notable in that it has large pleiotropic effects on an array of traits, including grain number,heading date and plant height. Such pleiotropic effects may provide an explanation for QTL hot spots that were observed in many studies.
CCT-domain proteins have been reported to have crucial roles in regulating processes such as photoperiodic ﬂowering, vernalization31, circadian rhythms and light signaling. The results of the present study indicate that GHD7 has a key role in photoperiod ﬂowering by regulating the putative Ehd1-Hd3a pathway. Strong
expression of Ghd7 in the vascular tissues of leaves is consistent with the role of CO-like genes in ﬂowering regulation. However, we also observed expression of Ghd7 in organs that may not be directly related to photoperiod-controlled ﬂowering, such as roots that do not seem to have a role in ﬂowering, leaves and meristems in the early seedling stage that are much too early for ﬂower induction, and the stems and panicles that already passed the stage of phase transition.
Expression in these tissues corresponded well with increases in the various organs leading to an overall increase in plant size, suggesting the possibility that this gene may have a general role in promoting growth, cell proliferation and differentiation, in addition to photoperiod ﬂowering.
Ghd7 controls heading date through its enhanced expression under long-day conditions to repress the expression of Hd3a, likely through Ehd1, thus delaying ﬂowering. Of note, the cereal VRN2 gene, although referred to as a vernalization gene, actually has a day-length control and is only expressed under long-day conditions, when it acts as a repressor of ﬂowering. VRN2 was classiﬁed in the same CCT subfamily as Ghd7. This suggests that tropical short-day plants that do not use vernalization as a ﬂowering cue, and temperate long-day plants that do use vernalization, actually use related genes to repress ﬂowering in long-day conditions. Such similarity in ﬂowering control provides important clues as to how the temperate cereals might have evolved. Moreover, these genes also act as major sources of adaptive variation, and hence are keys to understanding the spread and success of cereals. Sequence analysis of allelic variants at theGhd7 locus indicated that this locus has contributed greatly to both productivity and adaptability of cultivated rice on a global scale. Asian cultivated rice originated in tropical and subtropical regions of Asia. The functional alleles with strong effects (for example,Ghd7-1 andGhd7-3) allow rice plants to fully exploit light and temperature by delaying ﬂowering under long-day conditions in areas with long growing seasons, thus producing large panicles and increasing yield. The mutations giving rise to the Ghd7-0 and Ghd7-2 alleles, with no or reduced effect of delaying heading under long-day conditions, have had crucial roles by enabling rice to be cultivated under conditions with short growth duration and/or temperate regions. Additionally, the substantial dominant effect observed in the heterozygote between NIL(zs7) and NIL(mh7) indicated that theGhd7 locus has also contributed signiﬁcantly to the highlevel of heterosis of Shanyou 63 (refs. 19,40), a widely cultivated hybrid in China in the last more than 20 years.
Yield has been generally regarded as a complex trait that is controlled by multiple genes of small effects. The major effects demonstrated by the NILs and transgenic plants and the cloning of this QTL have fundamental implications for yield improvement,suggesting that yield, like other traits, can also be improved by individually manipulating the component traits using both molecular marker–assisted selection and transformation.
===Expression===
Expression pattern of Ghd7

We investigated the diurnal expression pattern ofGhd7 by quantifying the relative abundance of the mRNA in young leaves of NIL(mh7) using quantitative RT-PCR. The expression of Ghd7 was much higher under long-day conditions than short-day conditions, and the Ghd7 transcript was much more abundant during the light period than in dark period, especially under long-day conditions.We carried out RNA in situ hybridization and Ghd7 promoter–driven GFP transformation to examine sites of Ghd7 expression. The RNA in situ hybridization signals indicated that the gene is expressed in young tissues, such as the apical meristem, developing leaves and the leaf sheaths of the young seedling, the meristem of the root, the epidermal layer of developing stems and the branch-primordia of developing panicles. The GFP signal was strong in the young stem and in vascular tissues in the blades of fully expended leaves, but weak in the root and vascular tissues of the leaf sheath.

===Evolution===
Comparison of the predicted protein sequences identiﬁed ﬁve alleles that showed a clear geographic distribution. Ghd7-1 was found in rice varieties from the tropics, subtropics and areas with hot summers and long growing seasons, including the most popular high-yield cultivars and parents of elite hybrids in China and
Southeast Asia. The wild rice accession also had this allele, indicating that Ghd7-1 is probably the original wild-type allele. Ghd7-2, differing from Ghd7-1 by four amino acids, was found in varieties of temperate japonica from Japan and northern China. This allele seemed to have a smaller phenotypic effect than Ghd7-1. Ghd7-3 occurring in Teqing is distinct from all the other alleles in that it differs by three amino acids from both Ghd7-1 and Ghd7-2, with one variant amino acid found only in this variety. The phenotypic effect ofGhd7-3 seems to be the same magnitude as that of Ghd7-1 (Table 1 and Supplementary Table 4). The remaining two
alleles (Ghd7-0 and Ghd7-0a) were nonfunctional. Ghd7-0, with the Ghd7 locus completely deleted, was found in two varieties grown as early rice in a system with two-rice crops in central and southern China, in which the growth duration for early rice is short. Ghd7-0a, resulting from a premature termination in the predicted coding region, was found in two varieties from the Heilongjiang Province of northeastern China, which has cool summers and a short growing season.

==Labs working on this gene==
National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.

==References==
[1]Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nature Gent 40:761-767

==Structured Information==
{{JaponicaGene|
GeneName = Os08g0105000|
Description = Zinc finger, PHD-type domain containing protein|
Version = NM_001067318.1 GI:115474372 GeneID:4344443|
Length = 4125 bp|
Definition = Oryza sativa Japonica Group Os08g0105000, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 8|Chromosome 8]]|
AP = Chromosome 8:271854..275978|
CDS = 272583..273512,273602..273646,273832..273921,274832..275152,275242..275445 ,275590..275691|
GCID = <gbrowseImage1>
name=NC_008401:271854..275978
source=RiceChromosome08
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008401:271854..275978
source=RiceChromosome08
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggctcccagaaccgccccccaccaccgcgcaagaggcagccgccgccgccggaggaccacctcgtcacctacaagcgccgccgctccaaagaaacacagcctttgccactcatggccaacggcgccaattctaagaaagacgccaaggcccaacattggattagctggagggacactctccacggcttcctccaatcccctgctattagccagggtggaggaattcagacctgcatccgtcatgctctccaacacaatccttgcttgctcaccaatggtgttgttgttcacactgaattcaaaggtaacccagctcattcccaaggagaggaagcaaaagtgcagcaccctaatggtgctgctggaggcaaggtggtttctgcagatgctgctatacaagatgcggctgccgcagcttcttccgaagctaacaaggcaatgtgtaataatgccctcttcgacattttggtctcccagaaatttgccttgttgtgccatttgctacttgggaccttccatgtcaataaacctggtgatgtcatcgacttggaaaaaatcgacgccaagatgagaaatggagactatgcccacaaccctgcactatttgacgatgatatccagcagatgtgggagaagtttgagcaagttggccaagagatgacaggtctagcgagcaacctttcaaccatttcacgagtttcataccaaaagcaggcttctggattttctgaagctgaggtggctgagcacagaatagaggaaataagtttgccgggtgctgtccacgttgtcacaaaggagtcgactaccaccgtgcagttggccccatgtgattctagtcattctacaataccgaaacgaactgtgccacctggacgtgatctgtgcccttgcgatggttgtggcaccaaggtagatgttgaagaaggcctaatctgtgatgaatgtgacaccatgtaccactttgcatgtgtcaagctactcaatcctgatattaagcaagtcccagcaatctggcattgttcaacctgcagcttcaagaaaaaagaattggctgcagataccacgaataatgttgcccatgactgcttgcatggtggtaactgtgttttgtgtgaccagctcgagctggtgaagacagaagaagaagatcccaagcttcccataaaaattgaattagctgaagaaagagaggggagctccgtctcaagcatgggggaagacaatgaaccagacctgtcaacaactgccctgtcaaacttgtgcaaacactgtggcacatgcgaagacgatgacaagagattcatggtatgcggacatccttactgcgtttacaagttctatcatatccgatgcctgaaaacaagccagcttgcaattgagcaacaaaagaagcttggttgctggtactgcccctcttgcctctgcagagggtgcttccaagacaaggatgatgaccagatagtcatgtgtgatggctgtgatgaaggttatcacatatattgcatgagaccagcacgcaacactatccccaaaggtaagtggtactgtacattttgcaagatccgcagggcagcggaaggaatgcataagtatgaggattctgtgctgaaaatacatgggaatagtaagcatgcttgtaatgtgaatcagtcgaaggattctgaaggtgatggtactgaaaagtga</cdnaseq>|
AA = <aaseq>MGSQNRPPPPRKRQPPPPEDHLVTYKRRRSKETQPLPLMANGAN SKKDAKAQHWISWRDTLHGFLQSPAISQGGGIQTCIRHALQHNPCLLTNGVVVHTEFK GNPAHSQGEEAKVQHPNGAAGGKVVSADAAIQDAAAAASSEANKAMCNNALFDILVSQ KFALLCHLLLGTFHVNKPGDVIDLEKIDAKMRNGDYAHNPALFDDDIQQMWEKFEQVG QEMTGLASNLSTISRVSYQKQASGFSEAEVAEHRIEEISLPGAVHVVTKESTTTVQLA PCDSSHSTIPKRTVPPGRDLCPCDGCGTKVDVEEGLICDECDTMYHFACVKLLNPDIK QVPAIWHCSTCSFKKKELAADTTNNVAHDCLHGGNCVLCDQLELVKTEEEDPKLPIKI ELAEEREGSSVSSMGEDNEPDLSTTALSNLCKHCGTCEDDDKRFMVCGHPYCVYKFYH IRCLKTSQLAIEQQKKLGCWYCPSCLCRGCFQDKDDDQIVMCDGCDEGYHIYCMRPAR NTIPKGKWYCTFCKIRRAAEGMHKYEDSVLKIHGNSKHACNVNQSKDSEGDGTEK</aaseq>|
DNA = <dnaseqindica>2467..3396#2333..2377#2058..2147#827..1147#534..737#288..389#agtttccattcccgttccgttataataagaggagagagagagagattttgggtttgtctccggctccgctcgccgcctccaaatcccgctcctccgctgctgctcctctctgccgcggcgaggcgagagatccgaatccaccgccacccgcgcccaccccgcccgcacaaaccctagtttttccggggttttgcttcccctccgcagctccgctccgctccgtccgtcgtctcctcccggcggctcggcttgctgtccatgctgtagccgccccccgcaggtggctgatgggctcccagaaccgccccccaccaccgcgcaagaggcagccgccgccgccggaggaccacctcgtcacctacaagcgccgccgctccaaagaaacacaggtaaccaaccaaccaactccctgcctcttcttcttcttctttctccagatttcctttcgatttctacaagattcgtactctcgcttcttgcctcctcttacaatctctcattacatctacttgttgtgctttcttttcttgcagcctttgccactcatggccaacggcgccaattctaagaaagacgccaaggcccaacattggattagctggagggacactctccacggcttcctccaatcccctgctattagccagggtggaggaattcagacctgcatccgtcatgctctccaacacaatccttgcttgctcaccaatggtgttgttgttcacactgaattcaaagtaacacacaccacctttgtttgcatctaccctatatatatttatgcaatgataattttcctaacacatgacttctttctcattaccagggtaacccagctcattcccaaggagaggaagcaaaagtgcagcaccctaatggtgctgctggaggcaaggtggtttctgcagatgctgctatacaagatgcggctgccgcagcttcttccgaagctaacaaggcaatgtgtaataatgccctcttcgacattttggtctcccagaaatttgccttgttgtgccatttgctacttgggaccttccatgtcaataaacctggtgatgtcatcgacttggaaaaaatcgacgccaagatgagaaatggagactatgcccacaaccctgcactatttgacgatgatatccagcaggtaattgtttctctattgctcccatgaaagtaatttagctactgttgttggagggaaataatactagctagtgtttattcttatcttttatctaataaagatgatgcatattacctgtacttataagcgccctctgtatgctaaagcttaatgtgttctccatctattattgttcacaactccgtaaatcataagagcaaaatgttctacgtacggccagttgatagaatgatgctgatgctcaactgcttatctgagcttcttttgcgtttgctagttaagatcttcccaaattgtttgaaccatccaagcaacagactcctagggagtttatcacaactgaccttctagaactctggttgttagggttggaacgctagtcaacttaaatggtatactagccctgtttctacactatcatgtcttcgcaactttatatgctctatttctatctgtctgcttcatctgctgtccgcaacatgccaactcccttgcgcttcatggttgatgaagtggaccatggataatgtggttgagctggggtatgacacacacaaaattctggaacatctcatgcatgctgcatgtgtaaccactcaatgctgaggtttctgtctaagtcaactagggttttatcacttgttttcttaaatgggcacaacacaaaaaagaaaacttttataatatttagtgctagcacatctcaaagaccgaacaattactcttctatattgatttccttatcagttatcattgatatacttttttcatctgtgagtttttttgtttacattatattgttcatgctctaaacatagaagttgtgtagtaacatctaggaaaaattatacgatactgttgcctgctgagccttcctcttaatacaactctctatttgtttattttgtagatgtgggagaagtttgagcaagttggccaagagatgacaggtctagcgagcaacctttcaaccatttcacgagtttcataccaaaagcaggtaatctgttgctttatctttcaattaatgtctctagcgtcgagatggttatattttgacaatttgagttaagataaatctattactgcacacttggcaaccatgctgcaatttgcaggatgctttagtatattgaaatctttccttttatgctgggcattactaatggataaattattttataggcttctggattttctgaagctgaggtggctgagcacagaatagaggtaagttgtctgtttgaggatgtttgctaatcattgttccacatgcacacttaattaataatggttttactaattgcattcttcattaggaaataagtttgccgggtgctgtccacgttgtcacaaaggagtcgactaccaccgtgcagttggccccatgtgattctagtcattctacaataccgaaacgaactgtgccacctggacgtgatctgtgcccttgcgatggttgtggcaccaaggtagatgttgaagaaggcctaatctgtgatgaatgtgacaccatgtaccactttgcatgtgtcaagctactcaatcctgatattaagcaagtcccagcaatctggcattgttcaacctgcagcttcaagaaaaaagaattggctgcagataccacgaataatgttgcccatgactgcttgcatggtggtaactgtgttttgtgtgaccagctcgagctggtgaagacagaagaagaagatcccaagcttcccataaaaattgaattagctgaagaaagagaggggagctccgtctcaagcatgggggaagacaatgaaccagacctgtcaacaactgccctgtcaaacttgtgcaaacactgtggcacatgcgaagacgatgacaagagattcatggtatgcggacatccttactgcgtttacaagttctatcatatccgatgcctgaaaacaagccagcttgcaattgagcaacaaaagaagcttggttgctggtactgcccctcttgcctctgcagagggtgcttccaagacaaggatgatgaccagatagtcatgtgtgatggctgtgatgaaggttatcacatatattgcatgagaccagcacgcaacactatccccaaaggtaagtggtactgtacattttgcaagatccgcagggcagcggaaggaatgcataagtatgaggattctgtgctgaaaatacatgggaatagtaagcatgcttgtaatgtgaatcagtcgaaggattctgaaggtgatggtactgaaaagtgatcatcacaatagctttgtggattagcttctgagctcgcttggacaagctcaggaaaagagattctttggccccttaggagggctatacaccgactttgatactgaatcagttgtgtagtttatttaattaactgccgttgacatctacaggaagaactcttacctggtgaagatggtgtatgtagtcttttagctgggcggaatgatgtgttgtttacttgttcaccttccttctttaccccctttcagtgaccattgtgaatgttgtcctgtacttgccctgtgatggtattcttaaacgtttttttgggggaaatatgattttgtttttttaatctcctttttattgcttgattcgtcattgtttatagcctgtgatcgatgattgtgaaggtttatagtctgtatgttgtgtatgtaatggtttggttgatcctgaagctttttggaggtcttatttcagtcgaggacaagcatgagagtcaaggaagaaagtggatcttcattttgtcagacaattgtgacagtcatggagcatgtaagtagtactagtatatagtttgagtgtatgactaaccctgaatattcattcctatagtaaatagtactcctatatcatattagagattctgtggttggattaataagtagtgtagctatatctccagatgatgaatttatatgtgtccttgatatgaattaatgatatttgtggtgagtgttgacctc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001067318.1 RefSeq:Os08g0105000]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 8]]
[[Category:Chromosome 8]]

Os08g0105000

2014-06-08T03:36:53Z

QingweiTian:

Please input one-sentence summary here.

==Annotated Information==
===Function===

A number of genes individually controlling number of grains per plant, heading date and plant height have been cloned recently using map-based cloning approaches. Compared with the genes reported previously, Ghd7 is notable in that it has large pleiotropic effects on an array of traits, including grain number,heading date and plant height. Such pleiotropic effects may provide an explanation for QTL hot spots that were observed in many studies.
CCT-domain proteins have been reported to have crucial roles in regulating processes such as photoperiodic ﬂowering, vernalization31, circadian rhythms and light signaling. The results of the present study indicate that GHD7 has a key role in photoperiod ﬂowering by regulating the putative Ehd1-Hd3a pathway. Strong
expression of Ghd7 in the vascular tissues of leaves is consistent with the role of CO-like genes in ﬂowering regulation. However, we also observed expression of Ghd7 in organs that may not be directly related to photoperiod-controlled ﬂowering, such as roots that do not seem to have a role in ﬂowering, leaves and meristems in the early seedling stage that are much too early for ﬂower induction, and the stems and panicles that already passed the stage of phase transition.
Expression in these tissues corresponded well with increases in the various organs leading to an overall increase in plant size, suggesting the possibility that this gene may have a general role in promoting growth, cell proliferation and differentiation, in addition to photoperiod ﬂowering.
Ghd7 controls heading date through its enhanced expression under long-day conditions to repress the expression of Hd3a, likely through Ehd1, thus delaying ﬂowering. Of note, the cereal VRN2 gene, although referred to as a vernalization gene, actually has a day-length control and is only expressed under long-day conditions, when it acts as a repressor of ﬂowering. VRN2 was classiﬁed in the same CCT subfamily as Ghd7. This suggests that tropical short-day plants that do not use vernalization as a ﬂowering cue, and temperate long-day plants that do use vernalization, actually use related genes to repress ﬂowering in long-day conditions. Such similarity in ﬂowering control provides important clues as to how the temperate cereals might have evolved. Moreover, these genes also act as major sources of adaptive variation, and hence are keys to understanding the spread and success of cereals. Sequence analysis of allelic variants at theGhd7 locus indicated that this locus has contributed greatly to both productivity and adaptability of cultivated rice on a global scale. Asian cultivated rice originated in tropical and subtropical regions of Asia. The functional alleles with strong effects (for example,Ghd7-1 andGhd7-3) allow rice plants to fully exploit light and temperature by delaying ﬂowering under long-day conditions in areas with long growing seasons, thus producing large panicles and increasing yield. The mutations giving rise to the Ghd7-0 and Ghd7-2 alleles, with no or reduced effect of delaying heading under long-day conditions, have had crucial roles by enabling rice to be cultivated under conditions with short growth duration and/or temperate regions. Additionally, the substantial dominant effect observed in the heterozygote between NIL(zs7) and NIL(mh7) indicated that theGhd7 locus has also contributed signiﬁcantly to the highlevel of heterosis of Shanyou 63 (refs. 19,40), a widely cultivated hybrid in China in the last more than 20 years.
Yield has been generally regarded as a complex trait that is controlled by multiple genes of small effects. The major effects demonstrated by the NILs and transgenic plants and the cloning of this QTL have fundamental implications for yield improvement,suggesting that yield, like other traits, can also be improved by individually manipulating the component traits using both molecular marker–assisted selection and transformation.
===Expression===
Expression pattern of Ghd7

We investigated the diurnal expression pattern ofGhd7 by quantifying the relative abundance of the mRNA in young leaves of NIL(mh7) using quantitative RT-PCR. The expression of Ghd7 was much higher under long-day conditions than short-day conditions, and the Ghd7 transcript was much more abundant during the light period than in dark period, especially under long-day conditions.We carried out RNA in situ hybridization and Ghd7 promoter–driven GFP transformation to examine sites of Ghd7 expression. The RNA in situ hybridization signals indicated that the gene is expressed in young tissues, such as the apical meristem, developing leaves and the leaf sheaths of the young seedling, the meristem of the root, the epidermal layer of developing stems and the branch-primordia of developing panicles. The GFP signal was strong in the young stem and in vascular tissues in the blades of fully expended leaves, but weak in the root and vascular tissues of the leaf sheath.

===Evolution===
Comparison of the predicted protein sequences identiﬁed ﬁve alleles that showed a clear geographic distribution. Ghd7-1 was found in rice varieties from the tropics, subtropics and areas with hot summers and long growing seasons, including the most popular high-yield cultivars and parents of elite hybrids in China and
Southeast Asia. The wild rice accession also had this allele, indicating that Ghd7-1 is probably the original wild-type allele. Ghd7-2, differing from Ghd7-1 by four amino acids, was found in varieties of temperate japonica from Japan and northern China. This allele seemed to have a smaller phenotypic effect than Ghd7-1. Ghd7-3 occurring in Teqing is distinct from all the other alleles in that it differs by three amino acids from both Ghd7-1 and Ghd7-2, with one variant amino acid found only in this variety. The phenotypic effect ofGhd7-3 seems to be the same magnitude as that of Ghd7-1 (Table 1 and Supplementary Table 4). The remaining two
alleles (Ghd7-0 and Ghd7-0a) were nonfunctional. Ghd7-0, with the Ghd7 locus completely deleted, was found in two varieties grown as early rice in a system with two-rice crops in central and southern China, in which the growth duration for early rice is short. Ghd7-0a, resulting from a premature termination in the predicted coding region, was found in two varieties from the Heilongjiang Province of northeastern China, which has cool summers and a short growing season.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os08g0105000|
Description = Zinc finger, PHD-type domain containing protein|
Version = NM_001067318.1 GI:115474372 GeneID:4344443|
Length = 4125 bp|
Definition = Oryza sativa Japonica Group Os08g0105000, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 8|Chromosome 8]]|
AP = Chromosome 8:271854..275978|
CDS = 272583..273512,273602..273646,273832..273921,274832..275152,275242..275445 ,275590..275691|
GCID = <gbrowseImage1>
name=NC_008401:271854..275978
source=RiceChromosome08
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008401:271854..275978
source=RiceChromosome08
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggctcccagaaccgccccccaccaccgcgcaagaggcagccgccgccgccggaggaccacctcgtcacctacaagcgccgccgctccaaagaaacacagcctttgccactcatggccaacggcgccaattctaagaaagacgccaaggcccaacattggattagctggagggacactctccacggcttcctccaatcccctgctattagccagggtggaggaattcagacctgcatccgtcatgctctccaacacaatccttgcttgctcaccaatggtgttgttgttcacactgaattcaaaggtaacccagctcattcccaaggagaggaagcaaaagtgcagcaccctaatggtgctgctggaggcaaggtggtttctgcagatgctgctatacaagatgcggctgccgcagcttcttccgaagctaacaaggcaatgtgtaataatgccctcttcgacattttggtctcccagaaatttgccttgttgtgccatttgctacttgggaccttccatgtcaataaacctggtgatgtcatcgacttggaaaaaatcgacgccaagatgagaaatggagactatgcccacaaccctgcactatttgacgatgatatccagcagatgtgggagaagtttgagcaagttggccaagagatgacaggtctagcgagcaacctttcaaccatttcacgagtttcataccaaaagcaggcttctggattttctgaagctgaggtggctgagcacagaatagaggaaataagtttgccgggtgctgtccacgttgtcacaaaggagtcgactaccaccgtgcagttggccccatgtgattctagtcattctacaataccgaaacgaactgtgccacctggacgtgatctgtgcccttgcgatggttgtggcaccaaggtagatgttgaagaaggcctaatctgtgatgaatgtgacaccatgtaccactttgcatgtgtcaagctactcaatcctgatattaagcaagtcccagcaatctggcattgttcaacctgcagcttcaagaaaaaagaattggctgcagataccacgaataatgttgcccatgactgcttgcatggtggtaactgtgttttgtgtgaccagctcgagctggtgaagacagaagaagaagatcccaagcttcccataaaaattgaattagctgaagaaagagaggggagctccgtctcaagcatgggggaagacaatgaaccagacctgtcaacaactgccctgtcaaacttgtgcaaacactgtggcacatgcgaagacgatgacaagagattcatggtatgcggacatccttactgcgtttacaagttctatcatatccgatgcctgaaaacaagccagcttgcaattgagcaacaaaagaagcttggttgctggtactgcccctcttgcctctgcagagggtgcttccaagacaaggatgatgaccagatagtcatgtgtgatggctgtgatgaaggttatcacatatattgcatgagaccagcacgcaacactatccccaaaggtaagtggtactgtacattttgcaagatccgcagggcagcggaaggaatgcataagtatgaggattctgtgctgaaaatacatgggaatagtaagcatgcttgtaatgtgaatcagtcgaaggattctgaaggtgatggtactgaaaagtga</cdnaseq>|
AA = <aaseq>MGSQNRPPPPRKRQPPPPEDHLVTYKRRRSKETQPLPLMANGAN SKKDAKAQHWISWRDTLHGFLQSPAISQGGGIQTCIRHALQHNPCLLTNGVVVHTEFK GNPAHSQGEEAKVQHPNGAAGGKVVSADAAIQDAAAAASSEANKAMCNNALFDILVSQ KFALLCHLLLGTFHVNKPGDVIDLEKIDAKMRNGDYAHNPALFDDDIQQMWEKFEQVG QEMTGLASNLSTISRVSYQKQASGFSEAEVAEHRIEEISLPGAVHVVTKESTTTVQLA PCDSSHSTIPKRTVPPGRDLCPCDGCGTKVDVEEGLICDECDTMYHFACVKLLNPDIK QVPAIWHCSTCSFKKKELAADTTNNVAHDCLHGGNCVLCDQLELVKTEEEDPKLPIKI ELAEEREGSSVSSMGEDNEPDLSTTALSNLCKHCGTCEDDDKRFMVCGHPYCVYKFYH IRCLKTSQLAIEQQKKLGCWYCPSCLCRGCFQDKDDDQIVMCDGCDEGYHIYCMRPAR NTIPKGKWYCTFCKIRRAAEGMHKYEDSVLKIHGNSKHACNVNQSKDSEGDGTEK</aaseq>|
DNA = <dnaseqindica>2467..3396#2333..2377#2058..2147#827..1147#534..737#288..389#agtttccattcccgttccgttataataagaggagagagagagagattttgggtttgtctccggctccgctcgccgcctccaaatcccgctcctccgctgctgctcctctctgccgcggcgaggcgagagatccgaatccaccgccacccgcgcccaccccgcccgcacaaaccctagtttttccggggttttgcttcccctccgcagctccgctccgctccgtccgtcgtctcctcccggcggctcggcttgctgtccatgctgtagccgccccccgcaggtggctgatgggctcccagaaccgccccccaccaccgcgcaagaggcagccgccgccgccggaggaccacctcgtcacctacaagcgccgccgctccaaagaaacacaggtaaccaaccaaccaactccctgcctcttcttcttcttctttctccagatttcctttcgatttctacaagattcgtactctcgcttcttgcctcctcttacaatctctcattacatctacttgttgtgctttcttttcttgcagcctttgccactcatggccaacggcgccaattctaagaaagacgccaaggcccaacattggattagctggagggacactctccacggcttcctccaatcccctgctattagccagggtggaggaattcagacctgcatccgtcatgctctccaacacaatccttgcttgctcaccaatggtgttgttgttcacactgaattcaaagtaacacacaccacctttgtttgcatctaccctatatatatttatgcaatgataattttcctaacacatgacttctttctcattaccagggtaacccagctcattcccaaggagaggaagcaaaagtgcagcaccctaatggtgctgctggaggcaaggtggtttctgcagatgctgctatacaagatgcggctgccgcagcttcttccgaagctaacaaggcaatgtgtaataatgccctcttcgacattttggtctcccagaaatttgccttgttgtgccatttgctacttgggaccttccatgtcaataaacctggtgatgtcatcgacttggaaaaaatcgacgccaagatgagaaatggagactatgcccacaaccctgcactatttgacgatgatatccagcaggtaattgtttctctattgctcccatgaaagtaatttagctactgttgttggagggaaataatactagctagtgtttattcttatcttttatctaataaagatgatgcatattacctgtacttataagcgccctctgtatgctaaagcttaatgtgttctccatctattattgttcacaactccgtaaatcataagagcaaaatgttctacgtacggccagttgatagaatgatgctgatgctcaactgcttatctgagcttcttttgcgtttgctagttaagatcttcccaaattgtttgaaccatccaagcaacagactcctagggagtttatcacaactgaccttctagaactctggttgttagggttggaacgctagtcaacttaaatggtatactagccctgtttctacactatcatgtcttcgcaactttatatgctctatttctatctgtctgcttcatctgctgtccgcaacatgccaactcccttgcgcttcatggttgatgaagtggaccatggataatgtggttgagctggggtatgacacacacaaaattctggaacatctcatgcatgctgcatgtgtaaccactcaatgctgaggtttctgtctaagtcaactagggttttatcacttgttttcttaaatgggcacaacacaaaaaagaaaacttttataatatttagtgctagcacatctcaaagaccgaacaattactcttctatattgatttccttatcagttatcattgatatacttttttcatctgtgagtttttttgtttacattatattgttcatgctctaaacatagaagttgtgtagtaacatctaggaaaaattatacgatactgttgcctgctgagccttcctcttaatacaactctctatttgtttattttgtagatgtgggagaagtttgagcaagttggccaagagatgacaggtctagcgagcaacctttcaaccatttcacgagtttcataccaaaagcaggtaatctgttgctttatctttcaattaatgtctctagcgtcgagatggttatattttgacaatttgagttaagataaatctattactgcacacttggcaaccatgctgcaatttgcaggatgctttagtatattgaaatctttccttttatgctgggcattactaatggataaattattttataggcttctggattttctgaagctgaggtggctgagcacagaatagaggtaagttgtctgtttgaggatgtttgctaatcattgttccacatgcacacttaattaataatggttttactaattgcattcttcattaggaaataagtttgccgggtgctgtccacgttgtcacaaaggagtcgactaccaccgtgcagttggccccatgtgattctagtcattctacaataccgaaacgaactgtgccacctggacgtgatctgtgcccttgcgatggttgtggcaccaaggtagatgttgaagaaggcctaatctgtgatgaatgtgacaccatgtaccactttgcatgtgtcaagctactcaatcctgatattaagcaagtcccagcaatctggcattgttcaacctgcagcttcaagaaaaaagaattggctgcagataccacgaataatgttgcccatgactgcttgcatggtggtaactgtgttttgtgtgaccagctcgagctggtgaagacagaagaagaagatcccaagcttcccataaaaattgaattagctgaagaaagagaggggagctccgtctcaagcatgggggaagacaatgaaccagacctgtcaacaactgccctgtcaaacttgtgcaaacactgtggcacatgcgaagacgatgacaagagattcatggtatgcggacatccttactgcgtttacaagttctatcatatccgatgcctgaaaacaagccagcttgcaattgagcaacaaaagaagcttggttgctggtactgcccctcttgcctctgcagagggtgcttccaagacaaggatgatgaccagatagtcatgtgtgatggctgtgatgaaggttatcacatatattgcatgagaccagcacgcaacactatccccaaaggtaagtggtactgtacattttgcaagatccgcagggcagcggaaggaatgcataagtatgaggattctgtgctgaaaatacatgggaatagtaagcatgcttgtaatgtgaatcagtcgaaggattctgaaggtgatggtactgaaaagtgatcatcacaatagctttgtggattagcttctgagctcgcttggacaagctcaggaaaagagattctttggccccttaggagggctatacaccgactttgatactgaatcagttgtgtagtttatttaattaactgccgttgacatctacaggaagaactcttacctggtgaagatggtgtatgtagtcttttagctgggcggaatgatgtgttgtttacttgttcaccttccttctttaccccctttcagtgaccattgtgaatgttgtcctgtacttgccctgtgatggtattcttaaacgtttttttgggggaaatatgattttgtttttttaatctcctttttattgcttgattcgtcattgtttatagcctgtgatcgatgattgtgaaggtttatagtctgtatgttgtgtatgtaatggtttggttgatcctgaagctttttggaggtcttatttcagtcgaggacaagcatgagagtcaaggaagaaagtggatcttcattttgtcagacaattgtgacagtcatggagcatgtaagtagtactagtatatagtttgagtgtatgactaaccctgaatattcattcctatagtaaatagtactcctatatcatattagagattctgtggttggattaataagtagtgtagctatatctccagatgatgaatttatatgtgtccttgatatgaattaatgatatttgtggtgagtgttgacctc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001067318.1 RefSeq:Os08g0105000]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 8]]
[[Category:Chromosome 8]]

Os08g0105000

2014-06-08T03:34:19Z

QingweiTian:

Please input one-sentence summary here.

==Annotated Information==
===Function===

A number of genes individually controlling number of grains per plant, heading date and plant height have been cloned recently using map-based cloning approaches. Compared with the genes reported previously, Ghd7 is notable in that it has large pleiotropic effects on an array of traits, including grain number,heading date and plant height. Such pleiotropic effects may provide an explanation for QTL hot spots that were observed in many studies.
CCT-domain proteins have been reported to have crucial roles in regulating processes such as photoperiodic ﬂowering, vernalization31, circadian rhythms and light signaling. The results of the present study indicate that GHD7 has a key role in photoperiod ﬂowering by regulating the putative Ehd1-Hd3a pathway. Strong
expression of Ghd7 in the vascular tissues of leaves is consistent with the role of CO-like genes in ﬂowering regulation. However, we also observed expression of Ghd7 in organs that may not be directly related to photoperiod-controlled ﬂowering, such as roots that do not seem to have a role in ﬂowering, leaves and meristems in the early seedling stage that are much too early for ﬂower induction, and the stems and panicles that already passed the stage of phase transition.
Expression in these tissues corresponded well with increases in the various organs leading to an overall increase in plant size, suggesting the possibility that this gene may have a general role in promoting growth, cell proliferation and differentiation, in addition to photoperiod ﬂowering.
Ghd7 controls heading date through its enhanced expression under long-day conditions to repress the expression of Hd3a, likely through Ehd1, thus delaying ﬂowering. Of note, the cereal VRN2 gene, although referred to as a vernalization gene, actually has a day-length control and is only expressed under long-day conditions, when it acts as a repressor of ﬂowering. VRN2 was classiﬁed in the same CCT subfamily as Ghd7. This suggests that tropical short-day plants that do not use vernalization as a ﬂowering cue, and temperate long-day plants that do use vernalization, actually use related genes to repress ﬂowering in long-day conditions. Such similarity in ﬂowering control provides important clues as to how the temperate cereals might have evolved. Moreover, these genes also act as major sources of adaptive variation, and hence are keys to understanding the spread and success of cereals. Sequence analysis of allelic variants at theGhd7 locus indicated that this locus has contributed greatly to both productivity and adaptability of cultivated rice on a global scale. Asian cultivated rice originated in tropical and subtropical regions of Asia. The functional alleles with strong effects (for example,Ghd7-1 andGhd7-3) allow rice plants to fully exploit light and temperature by delaying ﬂowering under long-day conditions in areas with long growing seasons, thus producing large panicles and increasing yield. The mutations giving rise to the Ghd7-0 and Ghd7-2 alleles, with no or reduced effect of delaying heading under long-day conditions, have had crucial roles by enabling rice to be cultivated under conditions with short growth duration and/or temperate regions. Additionally, the substantial dominant effect observed in the heterozygote between NIL(zs7) and NIL(mh7) indicated that theGhd7 locus has also contributed signiﬁcantly to the highlevel of heterosis of Shanyou 63 (refs. 19,40), a widely cultivated hybrid in China in the last more than 20 years.
Yield has been generally regarded as a complex trait that is controlled by multiple genes of small effects. The major effects demonstrated by the NILs and transgenic plants and the cloning of this QTL have fundamental implications for yield improvement,suggesting that yield, like other traits, can also be improved by individually manipulating the component traits using both molecular marker–assisted selection and transformation.
===Expression===
Expression pattern of Ghd7

We investigated the diurnal expression pattern ofGhd7 by quantifying the relative abundance of the mRNA in young leaves of NIL(mh7) using quantitative RT-PCR. The expression of Ghd7 was much higher under long-day conditions than short-day conditions, and the Ghd7 transcript was much more abundant during the light period than in dark period, especially under long-day conditions.We carried out RNA in situ hybridization and Ghd7 promoter–driven GFP transformation to examine sites of Ghd7 expression. The RNA in situ hybridization signals indicated that the gene is expressed in young tissues, such as the apical meristem, developing leaves and the leaf sheaths of the young seedling, the meristem of the root, the epidermal layer of developing stems and the branch-primordia of developing panicles. The GFP signal was strong in the young stem and in vascular tissues in the blades of fully expended leaves, but weak in the root and vascular tissues of the leaf sheath.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os08g0105000|
Description = Zinc finger, PHD-type domain containing protein|
Version = NM_001067318.1 GI:115474372 GeneID:4344443|
Length = 4125 bp|
Definition = Oryza sativa Japonica Group Os08g0105000, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 8|Chromosome 8]]|
AP = Chromosome 8:271854..275978|
CDS = 272583..273512,273602..273646,273832..273921,274832..275152,275242..275445 ,275590..275691|
GCID = <gbrowseImage1>
name=NC_008401:271854..275978
source=RiceChromosome08
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008401:271854..275978
source=RiceChromosome08
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggctcccagaaccgccccccaccaccgcgcaagaggcagccgccgccgccggaggaccacctcgtcacctacaagcgccgccgctccaaagaaacacagcctttgccactcatggccaacggcgccaattctaagaaagacgccaaggcccaacattggattagctggagggacactctccacggcttcctccaatcccctgctattagccagggtggaggaattcagacctgcatccgtcatgctctccaacacaatccttgcttgctcaccaatggtgttgttgttcacactgaattcaaaggtaacccagctcattcccaaggagaggaagcaaaagtgcagcaccctaatggtgctgctggaggcaaggtggtttctgcagatgctgctatacaagatgcggctgccgcagcttcttccgaagctaacaaggcaatgtgtaataatgccctcttcgacattttggtctcccagaaatttgccttgttgtgccatttgctacttgggaccttccatgtcaataaacctggtgatgtcatcgacttggaaaaaatcgacgccaagatgagaaatggagactatgcccacaaccctgcactatttgacgatgatatccagcagatgtgggagaagtttgagcaagttggccaagagatgacaggtctagcgagcaacctttcaaccatttcacgagtttcataccaaaagcaggcttctggattttctgaagctgaggtggctgagcacagaatagaggaaataagtttgccgggtgctgtccacgttgtcacaaaggagtcgactaccaccgtgcagttggccccatgtgattctagtcattctacaataccgaaacgaactgtgccacctggacgtgatctgtgcccttgcgatggttgtggcaccaaggtagatgttgaagaaggcctaatctgtgatgaatgtgacaccatgtaccactttgcatgtgtcaagctactcaatcctgatattaagcaagtcccagcaatctggcattgttcaacctgcagcttcaagaaaaaagaattggctgcagataccacgaataatgttgcccatgactgcttgcatggtggtaactgtgttttgtgtgaccagctcgagctggtgaagacagaagaagaagatcccaagcttcccataaaaattgaattagctgaagaaagagaggggagctccgtctcaagcatgggggaagacaatgaaccagacctgtcaacaactgccctgtcaaacttgtgcaaacactgtggcacatgcgaagacgatgacaagagattcatggtatgcggacatccttactgcgtttacaagttctatcatatccgatgcctgaaaacaagccagcttgcaattgagcaacaaaagaagcttggttgctggtactgcccctcttgcctctgcagagggtgcttccaagacaaggatgatgaccagatagtcatgtgtgatggctgtgatgaaggttatcacatatattgcatgagaccagcacgcaacactatccccaaaggtaagtggtactgtacattttgcaagatccgcagggcagcggaaggaatgcataagtatgaggattctgtgctgaaaatacatgggaatagtaagcatgcttgtaatgtgaatcagtcgaaggattctgaaggtgatggtactgaaaagtga</cdnaseq>|
AA = <aaseq>MGSQNRPPPPRKRQPPPPEDHLVTYKRRRSKETQPLPLMANGAN SKKDAKAQHWISWRDTLHGFLQSPAISQGGGIQTCIRHALQHNPCLLTNGVVVHTEFK GNPAHSQGEEAKVQHPNGAAGGKVVSADAAIQDAAAAASSEANKAMCNNALFDILVSQ KFALLCHLLLGTFHVNKPGDVIDLEKIDAKMRNGDYAHNPALFDDDIQQMWEKFEQVG QEMTGLASNLSTISRVSYQKQASGFSEAEVAEHRIEEISLPGAVHVVTKESTTTVQLA PCDSSHSTIPKRTVPPGRDLCPCDGCGTKVDVEEGLICDECDTMYHFACVKLLNPDIK QVPAIWHCSTCSFKKKELAADTTNNVAHDCLHGGNCVLCDQLELVKTEEEDPKLPIKI ELAEEREGSSVSSMGEDNEPDLSTTALSNLCKHCGTCEDDDKRFMVCGHPYCVYKFYH IRCLKTSQLAIEQQKKLGCWYCPSCLCRGCFQDKDDDQIVMCDGCDEGYHIYCMRPAR NTIPKGKWYCTFCKIRRAAEGMHKYEDSVLKIHGNSKHACNVNQSKDSEGDGTEK</aaseq>|
DNA = <dnaseqindica>2467..3396#2333..2377#2058..2147#827..1147#534..737#288..389#agtttccattcccgttccgttataataagaggagagagagagagattttgggtttgtctccggctccgctcgccgcctccaaatcccgctcctccgctgctgctcctctctgccgcggcgaggcgagagatccgaatccaccgccacccgcgcccaccccgcccgcacaaaccctagtttttccggggttttgcttcccctccgcagctccgctccgctccgtccgtcgtctcctcccggcggctcggcttgctgtccatgctgtagccgccccccgcaggtggctgatgggctcccagaaccgccccccaccaccgcgcaagaggcagccgccgccgccggaggaccacctcgtcacctacaagcgccgccgctccaaagaaacacaggtaaccaaccaaccaactccctgcctcttcttcttcttctttctccagatttcctttcgatttctacaagattcgtactctcgcttcttgcctcctcttacaatctctcattacatctacttgttgtgctttcttttcttgcagcctttgccactcatggccaacggcgccaattctaagaaagacgccaaggcccaacattggattagctggagggacactctccacggcttcctccaatcccctgctattagccagggtggaggaattcagacctgcatccgtcatgctctccaacacaatccttgcttgctcaccaatggtgttgttgttcacactgaattcaaagtaacacacaccacctttgtttgcatctaccctatatatatttatgcaatgataattttcctaacacatgacttctttctcattaccagggtaacccagctcattcccaaggagaggaagcaaaagtgcagcaccctaatggtgctgctggaggcaaggtggtttctgcagatgctgctatacaagatgcggctgccgcagcttcttccgaagctaacaaggcaatgtgtaataatgccctcttcgacattttggtctcccagaaatttgccttgttgtgccatttgctacttgggaccttccatgtcaataaacctggtgatgtcatcgacttggaaaaaatcgacgccaagatgagaaatggagactatgcccacaaccctgcactatttgacgatgatatccagcaggtaattgtttctctattgctcccatgaaagtaatttagctactgttgttggagggaaataatactagctagtgtttattcttatcttttatctaataaagatgatgcatattacctgtacttataagcgccctctgtatgctaaagcttaatgtgttctccatctattattgttcacaactccgtaaatcataagagcaaaatgttctacgtacggccagttgatagaatgatgctgatgctcaactgcttatctgagcttcttttgcgtttgctagttaagatcttcccaaattgtttgaaccatccaagcaacagactcctagggagtttatcacaactgaccttctagaactctggttgttagggttggaacgctagtcaacttaaatggtatactagccctgtttctacactatcatgtcttcgcaactttatatgctctatttctatctgtctgcttcatctgctgtccgcaacatgccaactcccttgcgcttcatggttgatgaagtggaccatggataatgtggttgagctggggtatgacacacacaaaattctggaacatctcatgcatgctgcatgtgtaaccactcaatgctgaggtttctgtctaagtcaactagggttttatcacttgttttcttaaatgggcacaacacaaaaaagaaaacttttataatatttagtgctagcacatctcaaagaccgaacaattactcttctatattgatttccttatcagttatcattgatatacttttttcatctgtgagtttttttgtttacattatattgttcatgctctaaacatagaagttgtgtagtaacatctaggaaaaattatacgatactgttgcctgctgagccttcctcttaatacaactctctatttgtttattttgtagatgtgggagaagtttgagcaagttggccaagagatgacaggtctagcgagcaacctttcaaccatttcacgagtttcataccaaaagcaggtaatctgttgctttatctttcaattaatgtctctagcgtcgagatggttatattttgacaatttgagttaagataaatctattactgcacacttggcaaccatgctgcaatttgcaggatgctttagtatattgaaatctttccttttatgctgggcattactaatggataaattattttataggcttctggattttctgaagctgaggtggctgagcacagaatagaggtaagttgtctgtttgaggatgtttgctaatcattgttccacatgcacacttaattaataatggttttactaattgcattcttcattaggaaataagtttgccgggtgctgtccacgttgtcacaaaggagtcgactaccaccgtgcagttggccccatgtgattctagtcattctacaataccgaaacgaactgtgccacctggacgtgatctgtgcccttgcgatggttgtggcaccaaggtagatgttgaagaaggcctaatctgtgatgaatgtgacaccatgtaccactttgcatgtgtcaagctactcaatcctgatattaagcaagtcccagcaatctggcattgttcaacctgcagcttcaagaaaaaagaattggctgcagataccacgaataatgttgcccatgactgcttgcatggtggtaactgtgttttgtgtgaccagctcgagctggtgaagacagaagaagaagatcccaagcttcccataaaaattgaattagctgaagaaagagaggggagctccgtctcaagcatgggggaagacaatgaaccagacctgtcaacaactgccctgtcaaacttgtgcaaacactgtggcacatgcgaagacgatgacaagagattcatggtatgcggacatccttactgcgtttacaagttctatcatatccgatgcctgaaaacaagccagcttgcaattgagcaacaaaagaagcttggttgctggtactgcccctcttgcctctgcagagggtgcttccaagacaaggatgatgaccagatagtcatgtgtgatggctgtgatgaaggttatcacatatattgcatgagaccagcacgcaacactatccccaaaggtaagtggtactgtacattttgcaagatccgcagggcagcggaaggaatgcataagtatgaggattctgtgctgaaaatacatgggaatagtaagcatgcttgtaatgtgaatcagtcgaaggattctgaaggtgatggtactgaaaagtgatcatcacaatagctttgtggattagcttctgagctcgcttggacaagctcaggaaaagagattctttggccccttaggagggctatacaccgactttgatactgaatcagttgtgtagtttatttaattaactgccgttgacatctacaggaagaactcttacctggtgaagatggtgtatgtagtcttttagctgggcggaatgatgtgttgtttacttgttcaccttccttctttaccccctttcagtgaccattgtgaatgttgtcctgtacttgccctgtgatggtattcttaaacgtttttttgggggaaatatgattttgtttttttaatctcctttttattgcttgattcgtcattgtttatagcctgtgatcgatgattgtgaaggtttatagtctgtatgttgtgtatgtaatggtttggttgatcctgaagctttttggaggtcttatttcagtcgaggacaagcatgagagtcaaggaagaaagtggatcttcattttgtcagacaattgtgacagtcatggagcatgtaagtagtactagtatatagtttgagtgtatgactaaccctgaatattcattcctatagtaaatagtactcctatatcatattagagattctgtggttggattaataagtagtgtagctatatctccagatgatgaatttatatgtgtccttgatatgaattaatgatatttgtggtgagtgttgacctc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001067318.1 RefSeq:Os08g0105000]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 8]]
[[Category:Chromosome 8]]

Os08g0105000

2014-06-08T03:31:52Z

QingweiTian:

Please input one-sentence summary here.

==Annotated Information==
===Function===

A number of genes individually controlling number of grains per plant, heading date and plant height have been cloned recently using map-based cloning approaches. Compared with the genes reported previously, Ghd7 is notable in that it has large pleiotropic effects on an array of traits, including grain number,heading date and plant height. Such pleiotropic effects may provide an explanation for QTL hot spots that were observed in many studies.
CCT-domain proteins have been reported to have crucial roles in regulating processes such as photoperiodic ﬂowering, vernalization31, circadian rhythms and light signaling. The results of the present study indicate that GHD7 has a key role in photoperiod ﬂowering by regulating the putative Ehd1-Hd3a pathway. Strong
expression of Ghd7 in the vascular tissues of leaves is consistent with the role of CO-like genes in ﬂowering regulation. However, we also observed expression of Ghd7 in organs that may not be directly related to photoperiod-controlled ﬂowering, such as roots that do not seem to have a role in ﬂowering, leaves and meristems in the early seedling stage that are much too early for ﬂower induction, and the stems and panicles that already passed the stage of phase transition.
Expression in these tissues corresponded well with increases in the various organs leading to an overall increase in plant size, suggesting the possibility that this gene may have a general role in promoting growth, cell proliferation and differentiation, in addition to photoperiod ﬂowering.
Ghd7 controls heading date through its enhanced expression under long-day conditions to repress the expression of Hd3a, likely through Ehd1, thus delaying ﬂowering. Of note, the cereal VRN2 gene, although referred to as a vernalization gene, actually has a day-length control and is only expressed under long-day conditions, when it acts as a repressor of ﬂowering. VRN2 was classiﬁed in the same CCT subfamily as Ghd7. This suggests that tropical short-day plants that do not use vernalization as a ﬂowering cue, and temperate long-day plants that do use vernalization, actually use related genes to repress ﬂowering in long-day conditions. Such similarity in ﬂowering control provides important clues as to how the temperate cereals might have evolved. Moreover, these genes also act as major sources of adaptive variation, and hence are keys to understanding the spread and success of cereals. Sequence analysis of allelic variants at theGhd7 locus indicated that this locus has contributed greatly to both productivity and adaptability of cultivated rice on a global scale. Asian cultivated rice originated in tropical and subtropical regions of Asia. The functional alleles with strong effects (for example,Ghd7-1 andGhd7-3) allow rice plants to fully exploit light and temperature by delaying ﬂowering under long-day conditions in areas with long growing seasons, thus producing large panicles and increasing yield. The mutations giving rise to the Ghd7-0 and Ghd7-2 alleles, with no or reduced effect of delaying heading under long-day conditions, have had crucial roles by enabling rice to be cultivated under conditions with short growth duration and/or temperate regions. Additionally, the substantial dominant effect observed in the heterozygote between NIL(zs7) and NIL(mh7) indicated that theGhd7 locus has also contributed signiﬁcantly to the highlevel of heterosis of Shanyou 63 (refs. 19,40), a widely cultivated hybrid in China in the last more than 20 years.
Yield has been generally regarded as a complex trait that is controlled by multiple genes of small effects. The major effects demonstrated by the NILs and transgenic plants and the cloning of this QTL have fundamental implications for yield improvement,suggesting that yield, like other traits, can also be improved by individually manipulating the component traits using both molecular marker–assisted selection and transformation.
===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os08g0105000|
Description = Zinc finger, PHD-type domain containing protein|
Version = NM_001067318.1 GI:115474372 GeneID:4344443|
Length = 4125 bp|
Definition = Oryza sativa Japonica Group Os08g0105000, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 8|Chromosome 8]]|
AP = Chromosome 8:271854..275978|
CDS = 272583..273512,273602..273646,273832..273921,274832..275152,275242..275445 ,275590..275691|
GCID = <gbrowseImage1>
name=NC_008401:271854..275978
source=RiceChromosome08
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008401:271854..275978
source=RiceChromosome08
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggctcccagaaccgccccccaccaccgcgcaagaggcagccgccgccgccggaggaccacctcgtcacctacaagcgccgccgctccaaagaaacacagcctttgccactcatggccaacggcgccaattctaagaaagacgccaaggcccaacattggattagctggagggacactctccacggcttcctccaatcccctgctattagccagggtggaggaattcagacctgcatccgtcatgctctccaacacaatccttgcttgctcaccaatggtgttgttgttcacactgaattcaaaggtaacccagctcattcccaaggagaggaagcaaaagtgcagcaccctaatggtgctgctggaggcaaggtggtttctgcagatgctgctatacaagatgcggctgccgcagcttcttccgaagctaacaaggcaatgtgtaataatgccctcttcgacattttggtctcccagaaatttgccttgttgtgccatttgctacttgggaccttccatgtcaataaacctggtgatgtcatcgacttggaaaaaatcgacgccaagatgagaaatggagactatgcccacaaccctgcactatttgacgatgatatccagcagatgtgggagaagtttgagcaagttggccaagagatgacaggtctagcgagcaacctttcaaccatttcacgagtttcataccaaaagcaggcttctggattttctgaagctgaggtggctgagcacagaatagaggaaataagtttgccgggtgctgtccacgttgtcacaaaggagtcgactaccaccgtgcagttggccccatgtgattctagtcattctacaataccgaaacgaactgtgccacctggacgtgatctgtgcccttgcgatggttgtggcaccaaggtagatgttgaagaaggcctaatctgtgatgaatgtgacaccatgtaccactttgcatgtgtcaagctactcaatcctgatattaagcaagtcccagcaatctggcattgttcaacctgcagcttcaagaaaaaagaattggctgcagataccacgaataatgttgcccatgactgcttgcatggtggtaactgtgttttgtgtgaccagctcgagctggtgaagacagaagaagaagatcccaagcttcccataaaaattgaattagctgaagaaagagaggggagctccgtctcaagcatgggggaagacaatgaaccagacctgtcaacaactgccctgtcaaacttgtgcaaacactgtggcacatgcgaagacgatgacaagagattcatggtatgcggacatccttactgcgtttacaagttctatcatatccgatgcctgaaaacaagccagcttgcaattgagcaacaaaagaagcttggttgctggtactgcccctcttgcctctgcagagggtgcttccaagacaaggatgatgaccagatagtcatgtgtgatggctgtgatgaaggttatcacatatattgcatgagaccagcacgcaacactatccccaaaggtaagtggtactgtacattttgcaagatccgcagggcagcggaaggaatgcataagtatgaggattctgtgctgaaaatacatgggaatagtaagcatgcttgtaatgtgaatcagtcgaaggattctgaaggtgatggtactgaaaagtga</cdnaseq>|
AA = <aaseq>MGSQNRPPPPRKRQPPPPEDHLVTYKRRRSKETQPLPLMANGAN SKKDAKAQHWISWRDTLHGFLQSPAISQGGGIQTCIRHALQHNPCLLTNGVVVHTEFK GNPAHSQGEEAKVQHPNGAAGGKVVSADAAIQDAAAAASSEANKAMCNNALFDILVSQ KFALLCHLLLGTFHVNKPGDVIDLEKIDAKMRNGDYAHNPALFDDDIQQMWEKFEQVG QEMTGLASNLSTISRVSYQKQASGFSEAEVAEHRIEEISLPGAVHVVTKESTTTVQLA PCDSSHSTIPKRTVPPGRDLCPCDGCGTKVDVEEGLICDECDTMYHFACVKLLNPDIK QVPAIWHCSTCSFKKKELAADTTNNVAHDCLHGGNCVLCDQLELVKTEEEDPKLPIKI ELAEEREGSSVSSMGEDNEPDLSTTALSNLCKHCGTCEDDDKRFMVCGHPYCVYKFYH IRCLKTSQLAIEQQKKLGCWYCPSCLCRGCFQDKDDDQIVMCDGCDEGYHIYCMRPAR NTIPKGKWYCTFCKIRRAAEGMHKYEDSVLKIHGNSKHACNVNQSKDSEGDGTEK</aaseq>|
DNA = <dnaseqindica>2467..3396#2333..2377#2058..2147#827..1147#534..737#288..389#agtttccattcccgttccgttataataagaggagagagagagagattttgggtttgtctccggctccgctcgccgcctccaaatcccgctcctccgctgctgctcctctctgccgcggcgaggcgagagatccgaatccaccgccacccgcgcccaccccgcccgcacaaaccctagtttttccggggttttgcttcccctccgcagctccgctccgctccgtccgtcgtctcctcccggcggctcggcttgctgtccatgctgtagccgccccccgcaggtggctgatgggctcccagaaccgccccccaccaccgcgcaagaggcagccgccgccgccggaggaccacctcgtcacctacaagcgccgccgctccaaagaaacacaggtaaccaaccaaccaactccctgcctcttcttcttcttctttctccagatttcctttcgatttctacaagattcgtactctcgcttcttgcctcctcttacaatctctcattacatctacttgttgtgctttcttttcttgcagcctttgccactcatggccaacggcgccaattctaagaaagacgccaaggcccaacattggattagctggagggacactctccacggcttcctccaatcccctgctattagccagggtggaggaattcagacctgcatccgtcatgctctccaacacaatccttgcttgctcaccaatggtgttgttgttcacactgaattcaaagtaacacacaccacctttgtttgcatctaccctatatatatttatgcaatgataattttcctaacacatgacttctttctcattaccagggtaacccagctcattcccaaggagaggaagcaaaagtgcagcaccctaatggtgctgctggaggcaaggtggtttctgcagatgctgctatacaagatgcggctgccgcagcttcttccgaagctaacaaggcaatgtgtaataatgccctcttcgacattttggtctcccagaaatttgccttgttgtgccatttgctacttgggaccttccatgtcaataaacctggtgatgtcatcgacttggaaaaaatcgacgccaagatgagaaatggagactatgcccacaaccctgcactatttgacgatgatatccagcaggtaattgtttctctattgctcccatgaaagtaatttagctactgttgttggagggaaataatactagctagtgtttattcttatcttttatctaataaagatgatgcatattacctgtacttataagcgccctctgtatgctaaagcttaatgtgttctccatctattattgttcacaactccgtaaatcataagagcaaaatgttctacgtacggccagttgatagaatgatgctgatgctcaactgcttatctgagcttcttttgcgtttgctagttaagatcttcccaaattgtttgaaccatccaagcaacagactcctagggagtttatcacaactgaccttctagaactctggttgttagggttggaacgctagtcaacttaaatggtatactagccctgtttctacactatcatgtcttcgcaactttatatgctctatttctatctgtctgcttcatctgctgtccgcaacatgccaactcccttgcgcttcatggttgatgaagtggaccatggataatgtggttgagctggggtatgacacacacaaaattctggaacatctcatgcatgctgcatgtgtaaccactcaatgctgaggtttctgtctaagtcaactagggttttatcacttgttttcttaaatgggcacaacacaaaaaagaaaacttttataatatttagtgctagcacatctcaaagaccgaacaattactcttctatattgatttccttatcagttatcattgatatacttttttcatctgtgagtttttttgtttacattatattgttcatgctctaaacatagaagttgtgtagtaacatctaggaaaaattatacgatactgttgcctgctgagccttcctcttaatacaactctctatttgtttattttgtagatgtgggagaagtttgagcaagttggccaagagatgacaggtctagcgagcaacctttcaaccatttcacgagtttcataccaaaagcaggtaatctgttgctttatctttcaattaatgtctctagcgtcgagatggttatattttgacaatttgagttaagataaatctattactgcacacttggcaaccatgctgcaatttgcaggatgctttagtatattgaaatctttccttttatgctgggcattactaatggataaattattttataggcttctggattttctgaagctgaggtggctgagcacagaatagaggtaagttgtctgtttgaggatgtttgctaatcattgttccacatgcacacttaattaataatggttttactaattgcattcttcattaggaaataagtttgccgggtgctgtccacgttgtcacaaaggagtcgactaccaccgtgcagttggccccatgtgattctagtcattctacaataccgaaacgaactgtgccacctggacgtgatctgtgcccttgcgatggttgtggcaccaaggtagatgttgaagaaggcctaatctgtgatgaatgtgacaccatgtaccactttgcatgtgtcaagctactcaatcctgatattaagcaagtcccagcaatctggcattgttcaacctgcagcttcaagaaaaaagaattggctgcagataccacgaataatgttgcccatgactgcttgcatggtggtaactgtgttttgtgtgaccagctcgagctggtgaagacagaagaagaagatcccaagcttcccataaaaattgaattagctgaagaaagagaggggagctccgtctcaagcatgggggaagacaatgaaccagacctgtcaacaactgccctgtcaaacttgtgcaaacactgtggcacatgcgaagacgatgacaagagattcatggtatgcggacatccttactgcgtttacaagttctatcatatccgatgcctgaaaacaagccagcttgcaattgagcaacaaaagaagcttggttgctggtactgcccctcttgcctctgcagagggtgcttccaagacaaggatgatgaccagatagtcatgtgtgatggctgtgatgaaggttatcacatatattgcatgagaccagcacgcaacactatccccaaaggtaagtggtactgtacattttgcaagatccgcagggcagcggaaggaatgcataagtatgaggattctgtgctgaaaatacatgggaatagtaagcatgcttgtaatgtgaatcagtcgaaggattctgaaggtgatggtactgaaaagtgatcatcacaatagctttgtggattagcttctgagctcgcttggacaagctcaggaaaagagattctttggccccttaggagggctatacaccgactttgatactgaatcagttgtgtagtttatttaattaactgccgttgacatctacaggaagaactcttacctggtgaagatggtgtatgtagtcttttagctgggcggaatgatgtgttgtttacttgttcaccttccttctttaccccctttcagtgaccattgtgaatgttgtcctgtacttgccctgtgatggtattcttaaacgtttttttgggggaaatatgattttgtttttttaatctcctttttattgcttgattcgtcattgtttatagcctgtgatcgatgattgtgaaggtttatagtctgtatgttgtgtatgtaatggtttggttgatcctgaagctttttggaggtcttatttcagtcgaggacaagcatgagagtcaaggaagaaagtggatcttcattttgtcagacaattgtgacagtcatggagcatgtaagtagtactagtatatagtttgagtgtatgactaaccctgaatattcattcctatagtaaatagtactcctatatcatattagagattctgtggttggattaataagtagtgtagctatatctccagatgatgaatttatatgtgtccttgatatgaattaatgatatttgtggtgagtgttgacctc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001067318.1 RefSeq:Os08g0105000]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 8]]
[[Category:Chromosome 8]]

Os01g0578500

2014-06-06T14:08:09Z

QingweiTian:

SaF+/SaF- is an important gene impact the fertility in hybrids between indica and japonica subspecies of Asian cultivated rice(Oryza sativa).

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.[[File:fig.2.jpg]]

SaF Interacts with SaM- but not with SaM+. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+ and SaF- interacted physically with SaM- but not with SaM+.Therefore, the amino acid substitution in SaF- did not affect its physical interaction with SaM- but impaired the biological function of SaF-for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM+ blocks the interaction, probably by affecting the protein’s structure.[[File:fig.4.jpg]]

Functional analysis of SaM+,SaM-,and SaF+ in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.[[File:fig.5.jpg]]

A Molecular Genetic Model for Rice Hybrid Male Sterility.

The absence of any one of the three alleles, SaM+,SaM-,or SaF+, fails to produce male sterility.In an F1 plant, the linked allelesets (SaM+SaF+, SaM-SaF-) are separated from each other in the haploid microspores. Therefore, the SaF+ and SaM+ proteins may need to be transported from their own microspores to those carrying SaM- for interaction. The SaF+ -SaM- complex may interact further with SaM+ indirectly to trigger a specific sterility process. Because the male developmental defect appears at the early uni-nucleate microspore stage, the protein transport may occur at the tetrad stage, through cytoplasmic channels existing between tetrad cells. However, SaM- should be unable to move to the microspores carrying SaM+ to cause sterility, probably because of the loss of a necessary domain in the truncated region. The selective protein transport and the specific SaF+ -SaM- interaction restrict the sterility process in the SaM--containing microspores, thereby resulting in allele-specific pollen killing. This model also can explain the induction of male sterility in other recombinants and in the transgenic plants.In some of these plants, SaF+(tSaF+) and/or SaM+ (tSaM+) co-exist with SaM- (tSaM-) in microspores, and the transgenes can function by ectopic expression to cause male sterility. Therefore, the molecular effect of the ‘‘allelic interaction’’ of gene sets does not necessarily require genetic allelism (i.e., location at the same position of the chromosomes). In conclusion, SaM- acts as a gametophytic factor in the male sterility system, whereas SaM+ and SaF+ play their roles in any microspores in which they are located. On the other hand, the blocking of the SaF+–SaM- interaction by the self-inhibitory domain in SaM+ may be an important mechanism to prevent triggering the sterility process in SaM+-carrying microspores, thus facilitating its transmission to hybrid progenies and avoiding male sterility in indica cultivars.[[File:fig.3.jpg]]

===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively. About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF+, which results in a Phe-to-Ser substitution in position 287. SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels.This analysis showed that only the cDNA of SaF was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaF-carrying pollen.[[File:fig.1.jpg]][[File:fig9.jpg]]

===Evolution===
Divergence of SaM and SaF Arose in Wild Rice Species.

To trace the origins of the variation in SaF and SaM,the SNPs G02-69.8 and G02-74.6 was investigated in 13 wild species and in cultivated rice.
The nucleotides "T" and "C" at G02-69.8 were variably present in populations of nine wild species (including the common wild rice, O.rufipogon Griff) and in indica cultivars. For G02-74.6, only the nucleotide "G" was detected in all tested wild species and indica, with the exception of O.rufipogon, which was"G"-only in accessions distributing in South and Southeast Asia but contained both "G" and "T" (54 of 110 accessions carried "T") in the accessions from southern China.[[File:fig.8.jpg]]

In summary, three haplotypes of the linked orthologs, SaM+SaF+, SaM+SaF-, and SaM-SaF-, were present in the O.rufipogon populations. Most indica cultivars (95 of 106 accessions) contained SaM+SaF+, but 11 accessions carried SaM+SaF-. All the tested 108 japonica cultivars possessed SaM-SaF-. These results indicate that the variation in SaF occurred before the split of most, if not all, of the Oryza species, whereas the mutation in SaM most likely arose in an O. rufipogon population with SaM+SaF- in southern China and generated the haplotype SaM-SaF- .[[File:fig.7.jpg]]

==Labs working on this gene==
Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University,
Wushan, Guangzhou 510642, China

==References==
[1] Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Wu H and Liu Y-G* . 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. USA. 105(48):18871-18876.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0578500

2014-06-06T14:04:46Z

QingweiTian:

SaF+/SaF- is an important gene impact the fertility in hybrids between indica and japonica subspecies of Asian cultivated rice(Oryza sativa).

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.[[File:fig.Os01g05785002.jpg]]

SaF Interacts with SaM- but not with SaM+. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+ and SaF- interacted physically with SaM- but not with SaM+.Therefore, the amino acid substitution in SaF- did not affect its physical interaction with SaM- but impaired the biological function of SaF-for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM+ blocks the interaction, probably by affecting the protein’s structure.[[File:fig.Os01g05785004.jpg]]

Functional analysis of SaM+,SaM-,and SaF+ in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.[[File:fig.Os01g05785005.jpg]]

A Molecular Genetic Model for Rice Hybrid Male Sterility.

The absence of any one of the three alleles, SaM+,SaM-,or SaF+, fails to produce male sterility.In an F1 plant, the linked allelesets (SaM+SaF+, SaM-SaF-) are separated from each other in the haploid microspores. Therefore, the SaF+ and SaM+ proteins may need to be transported from their own microspores to those carrying SaM- for interaction. The SaF+ -SaM- complex may interact further with SaM+ indirectly to trigger a specific sterility process. Because the male developmental defect appears at the early uni-nucleate microspore stage, the protein transport may occur at the tetrad stage, through cytoplasmic channels existing between tetrad cells. However, SaM- should be unable to move to the microspores carrying SaM+ to cause sterility, probably because of the loss of a necessary domain in the truncated region. The selective protein transport and the specific SaF+ -SaM- interaction restrict the sterility process in the SaM--containing microspores, thereby resulting in allele-specific pollen killing. This model also can explain the induction of male sterility in other recombinants and in the transgenic plants.In some of these plants, SaF+(tSaF+) and/or SaM+ (tSaM+) co-exist with SaM- (tSaM-) in microspores, and the transgenes can function by ectopic expression to cause male sterility. Therefore, the molecular effect of the ‘‘allelic interaction’’ of gene sets does not necessarily require genetic allelism (i.e., location at the same position of the chromosomes). In conclusion, SaM- acts as a gametophytic factor in the male sterility system, whereas SaM+ and SaF+ play their roles in any microspores in which they are located. On the other hand, the blocking of the SaF+–SaM- interaction by the self-inhibitory domain in SaM+ may be an important mechanism to prevent triggering the sterility process in SaM+-carrying microspores, thus facilitating its transmission to hybrid progenies and avoiding male sterility in indica cultivars.[[File:fig.Os01g05785003.jpg]]

===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively. About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF+, which results in a Phe-to-Ser substitution in position 287. SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels.This analysis showed that only the cDNA of SaF was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaF-carrying pollen.[[File:fig.Os01g05785001.jpg]][[File:fig.Os01g05785009.jpg]]

===Evolution===
Divergence of SaM and SaF Arose in Wild Rice Species.

To trace the origins of the variation in SaF and SaM,the SNPs G02-69.8 and G02-74.6 was investigated in 13 wild species and in cultivated rice.
The nucleotides "T" and "C" at G02-69.8 were variably present in populations of nine wild species (including the common wild rice, O.rufipogon Griff) and in indica cultivars. For G02-74.6, only the nucleotide "G" was detected in all tested wild species and indica, with the exception of O.rufipogon, which was"G"-only in accessions distributing in South and Southeast Asia but contained both "G" and "T" (54 of 110 accessions carried "T") in the accessions from southern China.[[File:fig.Os01g05785008.jpg]]

In summary, three haplotypes of the linked orthologs, SaM+SaF+, SaM+SaF-, and SaM-SaF-, were present in the O.rufipogon populations. Most indica cultivars (95 of 106 accessions) contained SaM+SaF+, but 11 accessions carried SaM+SaF-. All the tested 108 japonica cultivars possessed SaM-SaF-. These results indicate that the variation in SaF occurred before the split of most, if not all, of the Oryza species, whereas the mutation in SaM most likely arose in an O. rufipogon population with SaM+SaF- in southern China and generated the haplotype SaM-SaF- .[[File:fig.Os01g05785007.jpg]]

==Labs working on this gene==
Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University,
Wushan, Guangzhou 510642, China

==References==
[1] Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Wu H and Liu Y-G* . 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. USA. 105(48):18871-18876.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0578500

2014-06-06T12:55:23Z

QingweiTian: Blanked the page

Os01g0578500

2014-06-06T12:47:06Z

QingweiTian: /* Expression */

Os01g0578500

2014-06-06T12:46:39Z

QingweiTian: /* Expression */

SaF+/SaF- is an important gene impact the fertility in hybrids between indica and japonica subspecies of Asian cultivated rice(Oryza sativa).

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.[[File:fig.2.jpg]]

SaF Interacts with SaM- but not with SaM+. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+ and SaF- interacted physically with SaM- but not with SaM+.Therefore, the amino acid substitution in SaF- did not affect its physical interaction with SaM- but impaired the biological function of SaF-for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM+ blocks the interaction, probably by affecting the protein’s structure.[[File:fig.4.jpg]]

Functional analysis of SaM+,SaM-,and SaF+ in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.[[File:fig.5.jpg]]

A Molecular Genetic Model for Rice Hybrid Male Sterility.

The absence of any one of the three alleles, SaM+,SaM-,or SaF+, fails to produce male sterility.In an F1 plant, the linked allelesets (SaM+SaF+, SaM-SaF-) are separated from each other in the haploid microspores. Therefore, the SaF+ and SaM+ proteins may need to be transported from their own microspores to those carrying SaM- for interaction. The SaF+ -SaM- complex may interact further with SaM+ indirectly to trigger a specific sterility process. Because the male developmental defect appears at the early uni-nucleate microspore stage, the protein transport may occur at the tetrad stage, through cytoplasmic channels existing between tetrad cells. However, SaM- should be unable to move to the microspores carrying SaM+ to cause sterility, probably because of the loss of a necessary domain in the truncated region. The selective protein transport and the specific SaF+ -SaM- interaction restrict the sterility process in the SaM--containing microspores, thereby resulting in allele-specific pollen killing. This model also can explain the induction of male sterility in other recombinants and in the transgenic plants.In some of these plants, SaF+(tSaF+) and/or SaM+ (tSaM+) co-exist with SaM- (tSaM-) in microspores, and the transgenes can function by ectopic expression to cause male sterility. Therefore, the molecular effect of the ‘‘allelic interaction’’ of gene sets does not necessarily require genetic allelism (i.e., location at the same position of the chromosomes). In conclusion, SaM- acts as a gametophytic factor in the male sterility system, whereas SaM+ and SaF+ play their roles in any microspores in which they are located. On the other hand, the blocking of the SaF+–SaM- interaction by the self-inhibitory domain in SaM+ may be an important mechanism to prevent triggering the sterility process in SaM+-carrying microspores, thus facilitating its transmission to hybrid progenies and avoiding male sterility in indica cultivars.[[File:fig.3.jpg]]

===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively. About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF+, which results in a Phe-to-Ser substitution in position 287. SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels.This analysis showed that only the cDNA of SaF was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaF-carrying pollen.[[File:fig.1.jpg]][[Filefig9.jpg]]

===Evolution===
Divergence of SaM and SaF Arose in Wild Rice Species.

To trace the origins of the variation in SaF and SaM,the SNPs G02-69.8 and G02-74.6 was investigated in 13 wild species and in cultivated rice.
The nucleotides "T" and "C" at G02-69.8 were variably present in populations of nine wild species (including the common wild rice, O.rufipogon Griff) and in indica cultivars. For G02-74.6, only the nucleotide "G" was detected in all tested wild species and indica, with the exception of O.rufipogon, which was"G"-only in accessions distributing in South and Southeast Asia but contained both "G" and "T" (54 of 110 accessions carried "T") in the accessions from southern China.[[File:fig.8.jpg]]

In summary, three haplotypes of the linked orthologs, SaM+SaF+, SaM+SaF-, and SaM-SaF-, were present in the O.rufipogon populations. Most indica cultivars (95 of 106 accessions) contained SaM+SaF+, but 11 accessions carried SaM+SaF-. All the tested 108 japonica cultivars possessed SaM-SaF-. These results indicate that the variation in SaF occurred before the split of most, if not all, of the Oryza species, whereas the mutation in SaM most likely arose in an O. rufipogon population with SaM+SaF- in southern China and generated the haplotype SaM-SaF- .[[File:fig.7.jpg]]

==Labs working on this gene==
Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University,
Wushan, Guangzhou 510642, China

==References==
[1] Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Wu H and Liu Y-G* . 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. USA. 105(48):18871-18876.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Fig9.jpg

2014-06-06T12:45:41Z

QingweiTian: uploaded a new version of "File:Fig9.jpg"

Working model of long-day flowering signal pathway in rice. OsMADS50 promotes transition to reproductive stage by suppressing expression of OsLFL1 that is a repressor of Ehd1. OsMADS56 inhibits flowering by binding to OsMADS50. Ehd1 is also controlled by other genes, e.g. OsID1 and Ghd7.

Os01g0578500

2014-06-06T12:42:23Z

QingweiTian: /* Annotated Information */

SaF+/SaF- is an important gene impact the fertility in hybrids between indica and japonica subspecies of Asian cultivated rice(Oryza sativa).

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.[[File:fig.2.jpg]]

SaF Interacts with SaM- but not with SaM+. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+ and SaF- interacted physically with SaM- but not with SaM+.Therefore, the amino acid substitution in SaF- did not affect its physical interaction with SaM- but impaired the biological function of SaF-for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM+ blocks the interaction, probably by affecting the protein’s structure.[[File:fig.4.jpg]]

Functional analysis of SaM+,SaM-,and SaF+ in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.[[File:fig.5.jpg]]

A Molecular Genetic Model for Rice Hybrid Male Sterility.

The absence of any one of the three alleles, SaM+,SaM-,or SaF+, fails to produce male sterility.In an F1 plant, the linked allelesets (SaM+SaF+, SaM-SaF-) are separated from each other in the haploid microspores. Therefore, the SaF+ and SaM+ proteins may need to be transported from their own microspores to those carrying SaM- for interaction. The SaF+ -SaM- complex may interact further with SaM+ indirectly to trigger a specific sterility process. Because the male developmental defect appears at the early uni-nucleate microspore stage, the protein transport may occur at the tetrad stage, through cytoplasmic channels existing between tetrad cells. However, SaM- should be unable to move to the microspores carrying SaM+ to cause sterility, probably because of the loss of a necessary domain in the truncated region. The selective protein transport and the specific SaF+ -SaM- interaction restrict the sterility process in the SaM--containing microspores, thereby resulting in allele-specific pollen killing. This model also can explain the induction of male sterility in other recombinants and in the transgenic plants.In some of these plants, SaF+(tSaF+) and/or SaM+ (tSaM+) co-exist with SaM- (tSaM-) in microspores, and the transgenes can function by ectopic expression to cause male sterility. Therefore, the molecular effect of the ‘‘allelic interaction’’ of gene sets does not necessarily require genetic allelism (i.e., location at the same position of the chromosomes). In conclusion, SaM- acts as a gametophytic factor in the male sterility system, whereas SaM+ and SaF+ play their roles in any microspores in which they are located. On the other hand, the blocking of the SaF+–SaM- interaction by the self-inhibitory domain in SaM+ may be an important mechanism to prevent triggering the sterility process in SaM+-carrying microspores, thus facilitating its transmission to hybrid progenies and avoiding male sterility in indica cultivars.[[File:fig.3.jpg]]

===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively. About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF+, which results in a Phe-to-Ser substitution in position 287. SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels.This analysis showed that only the cDNA of SaF was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaF-carrying pollen.[[File:fig.1.jpg]]

===Evolution===
Divergence of SaM and SaF Arose in Wild Rice Species.

To trace the origins of the variation in SaF and SaM,the SNPs G02-69.8 and G02-74.6 was investigated in 13 wild species and in cultivated rice.
The nucleotides "T" and "C" at G02-69.8 were variably present in populations of nine wild species (including the common wild rice, O.rufipogon Griff) and in indica cultivars. For G02-74.6, only the nucleotide "G" was detected in all tested wild species and indica, with the exception of O.rufipogon, which was"G"-only in accessions distributing in South and Southeast Asia but contained both "G" and "T" (54 of 110 accessions carried "T") in the accessions from southern China.[[File:fig.8.jpg]]

In summary, three haplotypes of the linked orthologs, SaM+SaF+, SaM+SaF-, and SaM-SaF-, were present in the O.rufipogon populations. Most indica cultivars (95 of 106 accessions) contained SaM+SaF+, but 11 accessions carried SaM+SaF-. All the tested 108 japonica cultivars possessed SaM-SaF-. These results indicate that the variation in SaF occurred before the split of most, if not all, of the Oryza species, whereas the mutation in SaM most likely arose in an O. rufipogon population with SaM+SaF- in southern China and generated the haplotype SaM-SaF- .[[File:fig.7.jpg]]

==Labs working on this gene==
Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University,
Wushan, Guangzhou 510642, China

==References==
[1] Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Wu H and Liu Y-G* . 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. USA. 105(48):18871-18876.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Fig.8.jpg

2014-06-06T12:32:13Z

QingweiTian:

File:Fig.7.jpg

2014-06-06T12:31:38Z

QingweiTian: uploaded a new version of "File:Fig.7.jpg"

Semiquantitative RT-PCR analysis of the iron (Fe)-responsive genes. RNA was isolated from roots and leaves of 2-wk-old seedlings grown in culture solution with Fe(III) or Fe(II) supply, or without Fe ()Fe). OsActin primers were used as an endogenous control. WL, wild-type leaf; WR, wild-type root; SL, spr1 leaf; SR, spr1 root; NAS, nicotianamine synthase; NRAMP, natural resistanceassociated macrophage protein; YSL, yellow stripe-like.

File:Fig.6.jpg

2014-06-06T12:31:14Z

QingweiTian:

File:Fig.3.jpg

2014-06-06T12:30:58Z

QingweiTian: uploaded a new version of "File:Fig.3.jpg"

The Oryza sativa short postembryonic roots 1 (OsSPR1) expression pattern revealed by GUS staining and RT-PCR. The images show the GUS staining pattern obtained in OsSPR1 promoter:GUS transgenic plants in (a) a primary root; (b) a primary root elongation zone; (c) a primary root tip; (d) a mature lateral root; (e) the base of a mature lateral root; (f) a mature lateral root tip; (g) an elongating lateral root; (h) an elongating lateral root tip; (i) the node region of a young uppermost internode; (j) an auricle; (k) a cross-section of an uppermost node; (l) a cross-section of a stem; (m) young spikelets; (n) flowering spikelets; (o) the pedicel of a young panicle; (p) pistils; (q) a stem; (r) a leaf. Bars: (a, d, g, k–p) 100 lm; (i, j, q, r) 200 lm; (b, c, e, f, h) 50 lm. (s) Expression pattern of OsSPR1 obtained using RT-PCR. cDNA was amplified from the root (R), stem base (SB), stem (S), leaf (L), and panicles (P) for the wild type (WT) and spr1 mutant (mutant), respectively.

Os01g0578500

2014-06-06T12:19:10Z

QingweiTian: /* Evolution */

SaF+/SaF- is an important gene impact the fertility in hybrids between indica and japonica subspecies of Asian cultivated rice(Oryza sativa).

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.[[File:fig.2.jpg]]

SaF Interacts with SaM- but not with SaM+. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+ and SaF- interacted physically with SaM- but not with SaM+.Therefore, the amino acid substitution in SaF- did not affect its physical interaction with SaM- but impaired the biological function of SaF-for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM+ blocks the interaction, probably by affecting the protein’s structure.[[File:fig.4.jpg]]

Functional analysis of SaM+,SaM-,and SaF+ in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.[[File:fig.5.jpg]]

A Molecular Genetic Model for Rice Hybrid Male Sterility.

The absence of any one of the three alleles, SaM+,SaM-,or SaF+, fails to produce male sterility.In an F1 plant, the linked allelesets (SaM+SaF+, SaM-SaF-) are separated from each other in the haploid microspores. Therefore, the SaF+ and SaM+ proteins may need to be transported from their own microspores to those carrying SaM- for interaction. The SaF+ -SaM- complex may interact further with SaM+ indirectly to trigger a specific sterility process. Because the male developmental defect appears at the early uni-nucleate microspore stage, the protein transport may occur at the tetrad stage, through cytoplasmic channels existing between tetrad cells. However, SaM- should be unable to move to the microspores carrying SaM+ to cause sterility, probably because of the loss of a necessary domain in the truncated region. The selective protein transport and the specific SaF+ -SaM- interaction restrict the sterility process in the SaM--containing microspores, thereby resulting in allele-specific pollen killing. This model also can explain the induction of male sterility in other recombinants and in the transgenic plants.In some of these plants, SaF+(tSaF+) and/or SaM+ (tSaM+) co-exist with SaM- (tSaM-) in microspores, and the transgenes can function by ectopic expression to cause male sterility. Therefore, the molecular effect of the ‘‘allelic interaction’’ of gene sets does not necessarily require genetic allelism (i.e., location at the same position of the chromosomes). In conclusion, SaM- acts as a gametophytic factor in the male sterility system, whereas SaM+ and SaF+ play their roles in any microspores in which they are located. On the other hand, the blocking of the SaF+–SaM- interaction by the self-inhibitory domain in SaM+ may be an important mechanism to prevent triggering the sterility process in SaM+-carrying microspores, thus facilitating its transmission to hybrid progenies and avoiding male sterility in indica cultivars.

===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively. About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF+, which results in a Phe-to-Ser substitution in position 287. SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels.This analysis showed that only the cDNA of SaF was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaF-carrying pollen.[[File:fig.1.jpg]]

===Evolution===
Divergence of SaM and SaF Arose in Wild Rice Species.

To trace the origins of the variation in SaF and SaM,the SNPs G02-69.8 and G02-74.6 was investigated(see Fig. 2A) in 13 wild species and in cultivated rice. The nucleotides ‘‘T’’ and ‘‘C’’ at G02-69.8 were variably present in populations of nine wild species (including the common wild rice, O. rufipogon Griff) and in indica cultivars. For G02-74.6, only the nucleotide ‘‘G’’ was detected in all tested wild species and indica, with the exception of O.rufipogon, which was‘‘G’’-only in accessions distributing in South and Southeast Asia but contained both ‘‘G’’ and ‘‘T’’ (54 of 110 accessions carried ‘‘T’’) in the accessions from southern China.

In summary, three haplotypes of the linked orthologs, SaM�SaF�, SaM�SaF�, and SaM�SaF�, were present in the O.rufipogon populations (Fig. 5A). Most indica cultivars (95 of 106 accessions) contained SaM�SaF�, but 11 accessions carried SaM�SaF�. All the tested 108 japonica cultivars possessed SaM�SaF�. These results indicate that the variation in SaF occurred before the split of most, if not all, of the Oryza species, whereas the mutation in SaM most likely arose in an O. rufipogon population with SaM�SaF� in southern China and generated the haplotype SaM�SaF� (Fig. 5A).

==Labs working on this gene==
Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University,
Wushan, Guangzhou 510642, China

==References==
[1] Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Wu H and Liu Y-G* . 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. USA. 105(48):18871-18876.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0578500

2014-06-06T12:14:11Z

QingweiTian: /* Function */

SaF+/SaF- is an important gene impact the fertility in hybrids between indica and japonica subspecies of Asian cultivated rice(Oryza sativa).

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.[[File:fig.2.jpg]]

SaF Interacts with SaM- but not with SaM+. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+ and SaF- interacted physically with SaM- but not with SaM+.Therefore, the amino acid substitution in SaF- did not affect its physical interaction with SaM- but impaired the biological function of SaF-for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM+ blocks the interaction, probably by affecting the protein’s structure.[[File:fig.4.jpg]]

Functional analysis of SaM+,SaM-,and SaF+ in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.[[File:fig.5.jpg]]

A Molecular Genetic Model for Rice Hybrid Male Sterility.

The absence of any one of the three alleles, SaM+,SaM-,or SaF+, fails to produce male sterility.In an F1 plant, the linked allelesets (SaM+SaF+, SaM-SaF-) are separated from each other in the haploid microspores. Therefore, the SaF+ and SaM+ proteins may need to be transported from their own microspores to those carrying SaM- for interaction. The SaF+ -SaM- complex may interact further with SaM+ indirectly to trigger a specific sterility process. Because the male developmental defect appears at the early uni-nucleate microspore stage, the protein transport may occur at the tetrad stage, through cytoplasmic channels existing between tetrad cells. However, SaM- should be unable to move to the microspores carrying SaM+ to cause sterility, probably because of the loss of a necessary domain in the truncated region. The selective protein transport and the specific SaF+ -SaM- interaction restrict the sterility process in the SaM--containing microspores, thereby resulting in allele-specific pollen killing. This model also can explain the induction of male sterility in other recombinants and in the transgenic plants.In some of these plants, SaF+(tSaF+) and/or SaM+ (tSaM+) co-exist with SaM- (tSaM-) in microspores, and the transgenes can function by ectopic expression to cause male sterility. Therefore, the molecular effect of the ‘‘allelic interaction’’ of gene sets does not necessarily require genetic allelism (i.e., location at the same position of the chromosomes). In conclusion, SaM- acts as a gametophytic factor in the male sterility system, whereas SaM+ and SaF+ play their roles in any microspores in which they are located. On the other hand, the blocking of the SaF+–SaM- interaction by the self-inhibitory domain in SaM+ may be an important mechanism to prevent triggering the sterility process in SaM+-carrying microspores, thus facilitating its transmission to hybrid progenies and avoiding male sterility in indica cultivars.

===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively. About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF+, which results in a Phe-to-Ser substitution in position 287. SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels.This analysis showed that only the cDNA of SaF was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaF-carrying pollen.[[File:fig.1.jpg]]

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University,
Wushan, Guangzhou 510642, China

==References==
[1] Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Wu H and Liu Y-G* . 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. USA. 105(48):18871-18876.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Fig.4.jpg

2014-06-06T12:11:46Z

QingweiTian: uploaded a new version of "File:Fig.4.jpg"

File:Fig.5.jpg

2014-06-06T12:11:13Z

QingweiTian:

File:Fig.2.jpg

2014-06-06T12:10:25Z

QingweiTian: uploaded a new version of "File:Fig.2.jpg"

Os01g0578500

2014-06-06T12:06:42Z

QingweiTian: /* Expression */

SaF+/SaF- is an important gene impact the fertility in hybrids between indica and japonica subspecies of Asian cultivated rice(Oryza sativa).

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.

SaF Interacts with SaM- but not with SaM+. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+ and SaF- interacted physically with SaM- but not with SaM+.Therefore, the amino acid substitution in SaF- did not affect its physical interaction with SaM- but impaired the biological function of SaF-for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM+ blocks the interaction, probably by affecting the protein’s structure.

Functional analysis of SaM+,SaM-,and SaF+ in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.

A Molecular Genetic Model for Rice Hybrid Male Sterility.

The absence of any one of the three alleles, SaM+,SaM-,or SaF+, fails to produce male sterility.In an F1 plant, the linked allelesets (SaM+SaF+, SaM-SaF-) are separated from each other in the haploid microspores. Therefore, the SaF+ and SaM+ proteins may need to be transported from their own microspores to those carrying SaM- for interaction. The SaF+ -SaM- complex may interact further with SaM+ indirectly to trigger a specific sterility process. Because the male developmental defect appears at the early uni-nucleate microspore stage, the protein transport may occur at the tetrad stage, through cytoplasmic channels existing between tetrad cells. However, SaM- should be unable to move to the microspores carrying SaM+ to cause sterility, probably because of the loss of a necessary domain in the truncated region. The selective protein transport and the specific SaF+ -SaM- interaction restrict the sterility process in the SaM--containing microspores, thereby resulting in allele-specific pollen killing. This model also can explain the induction of male sterility in other recombinants and in the transgenic plants.In some of these plants, SaF+(tSaF+) and/or SaM+ (tSaM+) co-exist with SaM- (tSaM-) in microspores, and the transgenes can function by ectopic expression to cause male sterility. Therefore, the molecular effect of the ‘‘allelic interaction’’ of gene sets does not necessarily require genetic allelism (i.e., location at the same position of the chromosomes). In conclusion, SaM- acts as a gametophytic factor in the male sterility system, whereas SaM+ and SaF+ play their roles in any microspores in which they are located. On the other hand, the blocking of the SaF+–SaM- interaction by the self-inhibitory domain in SaM+ may be an important mechanism to prevent triggering the sterility process in SaM+-carrying microspores, thus facilitating its transmission to hybrid progenies and avoiding male sterility in indica cultivars.

===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively. About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF+, which results in a Phe-to-Ser substitution in position 287. SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels.This analysis showed that only the cDNA of SaF was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaF-carrying pollen.[[File:fig.1.jpg]]

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University,
Wushan, Guangzhou 510642, China

==References==
[1] Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Wu H and Liu Y-G* . 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. USA. 105(48):18871-18876.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Fig.1.jpg

2014-06-06T12:05:23Z

QingweiTian: uploaded a new version of "File:Fig.1.jpg"

oul1 has increased bulliform cell number and size. A and B, Adaxial epidermal peels abutting the small veins of the wild type (wt; A) and oul1 (B). C to F, Cross sections of wild-type (C) and oul1 (D) mature leaf blades show significantly increased oul1 bulliform cell number (E) and area (F) between vascular bundle ridges. ab, Abaxial; ad, adaxial.
Red lines (C and D) show the bulliform cells. Data show means and SD values of biological replicates (n . 23) and statistical analysis by heteroscedastic t test indicating significant differences (** P , 0.01). Bars = 20 mm (A–D). G, Relative water content of the 10th leaf of 120- d-old greenhouse plants grown in the soil. oul1 had higher water content than the wild type. The data are means and SD (n . 5), with statistical analysis using the heteroscedastic t test showing significant differences (** P , 0.01).

Os01g0578500

2014-06-06T11:54:08Z

QingweiTian: /* Expression */

SaF+/SaF- is an important gene impact the fertility in hybrids between indica and japonica subspecies of Asian cultivated rice(Oryza sativa).

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.

SaF Interacts with SaM- but not with SaM+. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+ and SaF- interacted physically with SaM- but not with SaM+.Therefore, the amino acid substitution in SaF- did not affect its physical interaction with SaM- but impaired the biological function of SaF-for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM+ blocks the interaction, probably by affecting the protein’s structure.

Functional analysis of SaM+,SaM-,and SaF+ in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.

A Molecular Genetic Model for Rice Hybrid Male Sterility.

The absence of any one of the three alleles, SaM+,SaM-,or SaF+, fails to produce male sterility.In an F1 plant, the linked allelesets (SaM+SaF+, SaM-SaF-) are separated from each other in the haploid microspores. Therefore, the SaF+ and SaM+ proteins may need to be transported from their own microspores to those carrying SaM- for interaction. The SaF+ -SaM- complex may interact further with SaM+ indirectly to trigger a specific sterility process. Because the male developmental defect appears at the early uni-nucleate microspore stage, the protein transport may occur at the tetrad stage, through cytoplasmic channels existing between tetrad cells. However, SaM- should be unable to move to the microspores carrying SaM+ to cause sterility, probably because of the loss of a necessary domain in the truncated region. The selective protein transport and the specific SaF+ -SaM- interaction restrict the sterility process in the SaM--containing microspores, thereby resulting in allele-specific pollen killing. This model also can explain the induction of male sterility in other recombinants and in the transgenic plants.In some of these plants, SaF+(tSaF+) and/or SaM+ (tSaM+) co-exist with SaM- (tSaM-) in microspores, and the transgenes can function by ectopic expression to cause male sterility. Therefore, the molecular effect of the ‘‘allelic interaction’’ of gene sets does not necessarily require genetic allelism (i.e., location at the same position of the chromosomes). In conclusion, SaM- acts as a gametophytic factor in the male sterility system, whereas SaM+ and SaF+ play their roles in any microspores in which they are located. On the other hand, the blocking of the SaF+–SaM- interaction by the self-inhibitory domain in SaM+ may be an important mechanism to prevent triggering the sterility process in SaM+-carrying microspores, thus facilitating its transmission to hybrid progenies and avoiding male sterility in indica cultivars.

===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively. About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF+, which results in a Phe-to-Ser substitution in position 287. SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels.This analysis showed that only the cDNA of SaF was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaF-carrying pollen.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University,
Wushan, Guangzhou 510642, China

==References==
[1] Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Wu H and Liu Y-G* . 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. USA. 105(48):18871-18876.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0578500

2014-06-06T11:49:31Z

QingweiTian: /* Function */

SaF+/SaF- is an important gene impact the fertility in hybrids between indica and japonica subspecies of Asian cultivated rice(Oryza sativa).

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.

SaF Interacts with SaM- but not with SaM+. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+ and SaF- interacted physically with SaM- but not with SaM+.Therefore, the amino acid substitution in SaF- did not affect its physical interaction with SaM- but impaired the biological function of SaF-for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM+ blocks the interaction, probably by affecting the protein’s structure.

Functional analysis of SaM+,SaM-,and SaF+ in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.

A Molecular Genetic Model for Rice Hybrid Male Sterility.

The absence of any one of the three alleles, SaM+,SaM-,or SaF+, fails to produce male sterility.In an F1 plant, the linked allelesets (SaM+SaF+, SaM-SaF-) are separated from each other in the haploid microspores. Therefore, the SaF+ and SaM+ proteins may need to be transported from their own microspores to those carrying SaM- for interaction. The SaF+ -SaM- complex may interact further with SaM+ indirectly to trigger a specific sterility process. Because the male developmental defect appears at the early uni-nucleate microspore stage, the protein transport may occur at the tetrad stage, through cytoplasmic channels existing between tetrad cells. However, SaM- should be unable to move to the microspores carrying SaM+ to cause sterility, probably because of the loss of a necessary domain in the truncated region. The selective protein transport and the specific SaF+ -SaM- interaction restrict the sterility process in the SaM--containing microspores, thereby resulting in allele-specific pollen killing. This model also can explain the induction of male sterility in other recombinants and in the transgenic plants.In some of these plants, SaF+(tSaF+) and/or SaM+ (tSaM+) co-exist with SaM- (tSaM-) in microspores, and the transgenes can function by ectopic expression to cause male sterility. Therefore, the molecular effect of the ‘‘allelic interaction’’ of gene sets does not necessarily require genetic allelism (i.e., location at the same position of the chromosomes). In conclusion, SaM- acts as a gametophytic factor in the male sterility system, whereas SaM+ and SaF+ play their roles in any microspores in which they are located. On the other hand, the blocking of the SaF+–SaM- interaction by the self-inhibitory domain in SaM+ may be an important mechanism to prevent triggering the sterility process in SaM+-carrying microspores, thus facilitating its transmission to hybrid progenies and avoiding male sterility in indica cultivars.

===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively (Fig. 2C). About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF�+, which results in a Phe-to-Ser substitution in position 287 (Fig. 2 A and B).
SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels (Fig. 3A). This analysis showed that only the cDNA of SaF� was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaM�-carrying pollen.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University,
Wushan, Guangzhou 510642, China

==References==
[1] Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Wu H and Liu Y-G* . 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. USA. 105(48):18871-18876.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0578500

2014-06-06T11:30:38Z

QingweiTian: /* Function */

SaF+/SaF- is an important gene impact the fertility in hybrids between indica and japonica subspecies of Asian cultivated rice(Oryza sativa).

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.

SaF Interacts with SaM-� but not with SaM+�. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+� and SaF�- interacted physically with SaM�- but not with SaM+�.Therefore, the amino acid substitution in SaF-� did not affect its physical interaction with SaM-� but impaired the biological function of SaF-� for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM�+ blocks the interaction, probably by affecting the protein’s structure.

Functional analysis of SaM+,SaM-,and SaF+ in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.

A Molecular Genetic Model for Rice Hybrid Male Sterility.

The absence of any one of the three alleles, SaM+�, SaM-�, or SaF+�, fails to produce male sterility.In an F1 plant, the linked allelesets (SaM�SaF�, SaM�SaF�) are separated from each other in the haploid microspores. Therefore, the SaF� and SaM� proteins may need to be transported from their own microspores to those carrying SaM� for interaction. The SaF�-SaM� complex may interact further with SaM� indirectly to trigger a specific sterility process. Because the male developmental defect appears at the early uni-nucleate microspore stage, the protein transport may occur at the tetrad stage, through cytoplasmic channels existing between tetrad cells. However, SaM� should be unable to move to the microspores carrying SaM� to cause sterility, probably because of the loss of a necessary domain in the truncated region. The selective protein transport and the specific SaF�-SaM� interaction restrict the sterility process in the SaM�-containing microspores, thereby
resulting in allele-specific pollen killing. This model also can explain the induction of male sterility in other recombinants and in the transgenic plants.In some of these plants, SaF�(tSaF�) and/or SaM� (tSaM�) co-exist with SaM� (tSaM�) in microspores, and the transgenes can function by ectopic expression
to cause male sterility. Therefore, the molecular effect of the ‘‘allelic interaction’’ of gene sets does not necessarily require genetic allelism (i.e., location at the same position of the chromosomes). In conclusion, SaM� acts as a gametophytic factor in the male sterility system, whereas SaM� and SaF� play
their roles in any microspores in which they are located. On the other hand, the blocking of the SaF�–SaM� interaction by the self-inhibitory domain in SaM� may be an important mechanism to prevent triggering the sterility process in SaM�-carrying microspores, thus facilitating its transmission to hybrid progenies and avoiding male sterility in indica cultivars.

===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively (Fig. 2C). About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF�+, which results in a Phe-to-Ser substitution in position 287 (Fig. 2 A and B).
SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels (Fig. 3A). This analysis showed that only the cDNA of SaF� was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaM�-carrying pollen.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University,
Wushan, Guangzhou 510642, China

==References==
[1] Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Wu H and Liu Y-G* . 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. USA. 105(48):18871-18876.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0578500

2014-06-06T11:24:46Z

QingweiTian: /* Labs working on this gene */

SaF+/SaF- is an important gene impact the fertility in hybrids between indica and japonica subspecies of Asian cultivated rice(Oryza sativa).

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.

SaF Interacts with SaM-� but not with SaM+�. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+� and SaF�- interacted physically with SaM�- but not with SaM+�.Therefore, the amino acid substitution in SaF-� did not affect its physical interaction with SaM-� but impaired the biological function of SaF-� for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM�+ blocks the interaction, probably by affecting the protein’s structure.

Functional analysis of SaM+,SaM-,and SaF+ in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.
===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively (Fig. 2C). About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF�+, which results in a Phe-to-Ser substitution in position 287 (Fig. 2 A and B).
SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels (Fig. 3A). This analysis showed that only the cDNA of SaF� was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaM�-carrying pollen.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University,
Wushan, Guangzhou 510642, China

==References==
[1] Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Wu H and Liu Y-G* . 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. USA. 105(48):18871-18876.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0578500

2014-06-06T11:22:22Z

QingweiTian: /* References */

SaF+/SaF- is an important gene impact the fertility in hybrids between indica and japonica subspecies of Asian cultivated rice(Oryza sativa).

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.

SaF Interacts with SaM-� but not with SaM+�. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+� and SaF�- interacted physically with SaM�- but not with SaM+�.Therefore, the amino acid substitution in SaF-� did not affect its physical interaction with SaM-� but impaired the biological function of SaF-� for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM�+ blocks the interaction, probably by affecting the protein’s structure.

Functional analysis of SaM+,SaM-,and SaF+ in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.
===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively (Fig. 2C). About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF�+, which results in a Phe-to-Ser substitution in position 287 (Fig. 2 A and B).
SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels (Fig. 3A). This analysis showed that only the cDNA of SaF� was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaM�-carrying pollen.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
[1] Long Y, Zhao L, Niu B, Su J, Wu H, Chen Y, Zhang Q, Guo J, Zhuang C, Mei M, Xia J, Wang L, Wu H and Liu Y-G* . 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc. Natl. Acad. Sci. USA. 105(48):18871-18876.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0578500

2014-06-06T11:20:19Z

QingweiTian:

Os01g0578500

2014-06-06T11:15:39Z

QingweiTian: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.
SaF Interacts with SaM-� but not with SaM+�. A bacterial two-hybrid(B2H) interaction assay demonstrated that both SaF+� and SaF�- interacted physically with SaM�- but not with SaM+�.Therefore, the amino acid substitution in SaF-� did not affect its physical interaction with SaM-� but impaired the biological function of SaF-� for male sterility.There is a self-inhibitory domain within the 203–218 region of SaM�+ blocks the interaction, probably by affecting the protein’s structure.
Functional analysis of SaM+�, SaM-�, and SaF+� in rice by transformation indicate that the segregation distortion of the Sa region is a consequence of hybrid male sterility caused by the allele-specific gamete selection.
===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively (Fig. 2C). About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF�+, which results in a Phe-to-Ser substitution in position 287 (Fig. 2 A and B).
SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels (Fig. 3A). This analysis showed that only the cDNA of SaF� was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaM�-carrying pollen.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0578500

2014-06-06T09:07:22Z

QingweiTian: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars
contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.

===Expression===
SaF encodes a 476-aa protein with an F-box and a plantspecific F-box protein domain (FBD). F-box proteins mediate protein–protein interactions, but the function of the FBD is unclear. The SaF protein is homologous to a ribosomal RNA apurinic site-specific lyase (RALyase) in wheat (23) with 33% identity in the overall sequences and 64% and 44% identities in the F-box and FBD, respectively (Fig. 2C). About 20 members of the F-box/FBD subfamily are predicted in rice, and they have up to 75% identity to RALyase and up to 40% identity to SaF.In the coding region of SaF, only one SNP was found between SaF-and SaF�+, which results in a Phe-to-Ser substitution in position 287 (Fig. 2 A and B).
SaF was expressed in all tissues tested as examined by RT-PCR, albeit at different levels (Fig. 3A). This analysis showed that only the cDNA of SaF� was detectable in the purified pollen of the F1 plants, providing molecular evidence for the selective abortion of SaM�-carrying pollen.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0578500

2014-06-06T09:04:42Z

QingweiTian: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Sterility is common in hybrids between divergent populations,such as the indica and japonica subspecies of Asian cultivated rice(Oryza sativa).SaF is one gene of the Sa locus,which include two adjacent genes SaF and SaM.SaM encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein. Most indica cultivars
contain a haplotype SaM+SaF+,whereas all japonica cultivars have SaM-SaF- that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM-. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM-, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility.

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0578500

2014-06-06T08:58:43Z

QingweiTian: /* Annotated Information */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Most indica cultivars
contain a haplotype SaM�SaF�, whereas all japonica cultivars have
SaM�SaF� that diverged by nucleotide variations in wild rice. Male
semi-sterility in this heterozygous complex locus is caused by
abortion of pollen carrying SaM�. This allele-specific gamete elimination
results from a selective interaction of SaF� with SaM�, a
truncated protein, but not with SaM� because of the presence of
an inhibitory domain, although SaM� is required for this male
sterility. Lack of any one of the three alleles in recombinant plants
does not produce male sterility.

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0578500|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001185502.1 GI:297720138 GeneID:9266343|
Length = 1733 bp|
Definition = Oryza sativa Japonica Group Os01g0578500, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:24032420..24034152|
CDS = 24032420..24033334,24033421..24033564,24033781..24034152|
GCID = <gbrowseImage1>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:24032420..24034152
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</cdnaseq>|
AA = <aaseq>MEAVIAECRPKPLFTTGPFLSAVGGGGGGVDRISGLPDDLLFVI LSKLPVRDAVATSALSPRWKSLWSSVPLRLDDAGLLHRRDGTRLGREGVAATVSAVLA AHPGPVPAASVGCCLSSDDQGYQLGGWLRALAAKGVRQLCLMGAPWSPRAALPSAVFS CSSLRRLFLGSVQCNWDLIPDHACFPELREIQICNALMKSQDLSLVLAVCPALETVEI LASRNKIPTVRMSSHTIRNTLLWKSVAKEVNVLDTPCLSRVVLWQDLLLPHSRYNSKV TISRATKMRISGYLDTGINTLVINETTVKVNTNISFKTLIPSVKVLGLSVHFGVRKEA LMSISFLRCFPEVETLHITSKTDKASEAEQFSFWGKVDPVECVTSHLKKLVFHGMPWC PGNLEFLKFIVEGAYLLEKVLIVLPKGTYTSMHSVITKLKLAPLTSASWASHICKMEV VQSSQGTLSYQRASDHSVDDPLDYSL</aaseq>|
DNA = <dnaseqindica>1..915#1002..1145#1362..1733#atggaggcggtcatcgcggagtgccgccccaagcctctcttcaccaccgggcccttcctctccgccgtcggcggcggcggcggcggcgtcgaccgcatctccgggctccccgacgacctcctctttgtcatcctctccaagctccccgtcagggatgccgtggcgacgtccgccctctccccccgctggaagagcctctggtccagcgtcccgctccgcctcgacgacgccggcctcctccaccgccgcgacggcacgcgcctcggccgggaaggcgtcgccgccaccgtctccgccgtcctcgccgcccacccaggccccgtgcccgcggcctccgttgggtgctgcctctcctccgacgaccagggctaccagctgggaggctggctccgagccctcgccgccaagggcgttcggcaactgtgcctgatgggcgcgccatggtcgccgcgcgctgctctcccctccgctgtgttctcctgctcatccctgcggcgcctcttccttggttccgtgcaatgcaactgggacctcataccagaccatgcctgcttccctgagctacgagagatccagatatgcaacgccctaatgaagagccaggatctgtcccttgttttggctgtctgcccagcgcttgagacagtggagattcttgcgagccgtaacaaaatccccaccgtgcgaatgagtagccatactatccgcaatactttgctatggaagtcggtggccaaggaagtgaacgttttggacaccccttgcctcagcagggttgttttgtggcaggatcttctgctgccccactcaagatataattctaaggtcacaatcagccgtgccaccaaaatgcgcatttccggttacctggacaccggcatcaacactttggtgatcaacgaaaccacagttaaggtatttgtccctttgttggatatatatctctaatcatatcgaatctgtgaaactgtgttaacgcgttttaatcgttgaatttgaaggtaaacacaaatataagcttcaagacacttatccccagcgtgaaggttttgggtctctctgttcatttcggagtacgaaaggaggctttgatgtccatcagcttccttaggtgttttccagaggttgagacactacatataactgtgagatttctttccttctttcattcccgacatatatatacataaatgtgagattgcgagatagctgtctttcttctttcattcctgacatatgcatcattttacacactcactgcagccattctttcattcccgacatatgcatcattttacacactcactgcagccatatgttcctttgatagctggaggtgatcaatttttcttcttgtgcagagcaaaacggacaaggcttcagaagccgaacaattcagtttctggggaaaggttgatcctgttgagtgtgtgacctctcatctcaagaagttagtgttccatgggatgccatggtgtcctggaaaccttgagtttctcaaattcatcgtggaaggggcatacttgctagagaaggtgttgattgttcttcctaaaggaacttacactagcatgcatagcgttatcaccaaactcaagttagcacctttgacctctgcaagttgggctagtcacatctgtaaaatggaggttgtccaatccagtcaaggaactttgagctaccaaagggcatctgatcattccgtcgatgatcctttagattattccctgtag</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185502.1 RefSeq:Os01g0578500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]