Please input one-sentence summary here.

==Annotated Information==
===Function===
Low temperatures during the booting stage reduce rice yields by causing cold-induced male sterility[1]. Ctb1 is a QTL for cold tolerance, which is located in the introgression on chromosome 4[2]. Researches mapped Ctb1 to a 17-kb region containing two genes that encode an F-box protein and a ser/thr protein kinase. Both genes were cloned from a cold-tolerant variety, Norin-PL8, and introduced into a cold-sensitive variety, Hokkai241, and a cold-sensitive line, BT4-74-8. The cold tolerance of T2 and T3 progenies was assessed by measuring the degree of spikelet fertility in plants treated with cool water irrigation (19◦C, 25 cm) or cool air (12◦C, 4 days).
The results indicated that the F-box protein gene confers cold tolerance. Cold tolerance is associated with greater anther length, which is one of major factors in cold tolerance at the booting stage. Ctb-1 expressed cold tolerance by producing a large anther. The transgenic plants had longer anthers than non-transformed controls. The F-box protein encoded by Ctb1 interact with a subunit of the E3 ubiquitin ligase, Skp1, suggesting that an ubiquitin–proteasome pathway is involved in cold tolerance at the booting stage[1].

[[File:Anther.JPG]]

Table. 1 Cold tolerance, heading date and anther length of the near-isogenic lines(NILs) and parental varieties[2]

[[File:Seed.JPG]]

Fig. 1. Relation between cold tolerance and anther length shown in Table 1. Circles represent the NILs: open circles represent the NILs without either Ctb-1or Ctb-2, and closed circles represent the NILs with Ctb-1and/or Ctb-2. Open and closed triangles represent Kirara397 and Norin-PL8, respectively[2]

'''GO assignment(s)''': GO:0003674 GO:0005634 GO:0008150

===Expression===
[[File:PCR.JPG]]

Fig. 2 RT-PCR and structural analysis of the Ctb1 candidate genes. (a) Expression of genes encoding F-box protein (FB) and a ser/thr protein kinase(PK) in mature leaves (L) and young panicles (YP) from a cold sensitive variety Kirara397 (K) and a cold-tolerant variety Norin-PL8 (N). ACTIN gene was used as a reference. (b) Diagrams of DNA fragments containing the FB and PK genes cloned from Norin-PL8 genomic DNA. Black rectangles, black triangles, and open triangles indicate putative exons, initiation codons, and stop codons, respectively<nowiki>[1]</nowiki>.

Sequence analyses indicated no polymorphism between Norin-PL8 and Kirara397 in the coding regions but several polymorphisms (mostly single nucleotide polymorphisms) in the 5’ upstream regions of both F-box protein (FB) and a ser/thr protein kinase(PK). Comparing the expression of the genes in Norin-PL8 and Kirara397 by RT-PCR analysis, PK was expressed in mature leaves and young panicles. By contrast, FB was expressed preferentially in young panicles, suggesting that FB was a more likely candidate to be Ctb1. No differences were observed in expression levels between Norin-PL8 and Kirara397[1].

===Knowledge Extension===
Rice is a staple crop cultivated worldwide. However, since it is a cold-sensitive plant that evolved in tropical and subtropical areas, rice yields are greatly reduced under low temperature conditions. One of the factors reducing rice yields is cold-induced male sterility (CIMS). In CIMS, the growth stage that is sensitive to cold is the booting stage, especially the young microspore stage just after meiosis[3]. Low temperatures at the young microspore stage cause the degeneration of microspores and hypertrophy of tapetal cells[4].

===Evolution===
K.Saito et al[2] concluded that there are at least two QTLs for cold tolerance in the introgression on chromosome 4 of rice, and tentatively designated as Ctb-1 and Ctb-2.

==Labs working on this gene==

Natl Agr Res Ctr Hokkaido Reg, Hitsujigaoka 1, Sapporo, Hokkaido 0628555, Japan

Univ Florida, IFAS, Ctr Citrus Res & Educ, Lake Alfred, FL 33850 USA

N Carolina State Univ, Dept Bot, Raleigh, NC 27695 USA

==References==
<references>
<ref name="ref1">K. Saito, Y. Hayano-Saito, M. Kuroki, Y. Sato,(2010) Map-based cloning of the rice cold tolerance gene Ctb1, Plant Science, 179:97–102.</ref>

<ref name="ref2">K. Saito, K. Miura, K. Nagano, Y. Hayano-Saito, H. Araki, A. Kato, (2001) Identification of two closely linked quantitative trait loci for cold tolerance on chromosome 4 of rice and their association with anther length, Theor. Appl. Genet. 103: 862–868.</ref>

<ref name="ref3">T. Satake, H. Hayase, (1970) Male sterility caused by cooling treatment at the young microspore stage in rice plants, V. Estimation of pollen developmental stage and the most sensitive stage to coolness, Proc. Crop Sci. Soc. Jpn. 39: 468–473.</ref>

<ref name="ref4">I. Nishiyama, (1976) Male sterility caused by cooling treatment at the young microspore stage in rice plants, XIII. Ultrastructure of tapetal hypertrophy without primary wall, Proc. Crop Sci. Soc. Jpn. 45:270–278.</ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0619300|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001060432.1 GI:115460593 GeneID:4337020|
Length = 3063 bp|
Definition = Oryza sativa Japonica Group Os04g0619300, 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 4|Chromosome 4]]|
AP = Chromosome 4:31857495..31860557|
CDS = 31858937..31860304|
GCID = <gbrowseImage1>
name=NC_008397:31857495..31860557
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:31857495..31860557
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaagatttacaagattgtgactgcaaaagccttgttgctgttcctggttctgtggttctgcacctctttaggctgtttaatcagcaggataattcctggcagaagtacacattagcctactttcttttggtcaggaatgagtacttctctagggattcaaggaagcattcagatgggaagaaccaacttcttgactgctgtgatgattcagaattagatttggatgtgctgtatgctgatttggatagtaaagaactggagcttaagttgcagaaacctgttgtcaagactcaatcaaaaggtgactcaagtgccagtggatcaaatgattgcttctttcctggccttcacgacgacctggctcaggactgccttgcttgggcgagcagatcagactacccatcgctttcttgtttgaataagaagttcaatttgttaatcaacagcgggtatctgtacagactgagaagaaaatatggcattgttgaacactgggtgtatctagcgtgtagcttgatgccctgggaagcatttgatccttcacgcaagcgatggatgaggctcccaagaatgccatgcgacgagtgcttctcttgtgcagacaaggaatcgcttgccgtcgggacacaactgcttgtgtttggccgtgaatatacaggtcttgctatttggatgtacaatttactggcccgtggttggtcccgatgcactccaatgaacctgcctcgctgcctctttgcctcaggaagctttggtgagattgctattgttgctggtgggtgtgataagaatggacaggtgctgaaatctgccgagctgtacaattcagagactggtcattgggagactttgccagacatgaacttgccgaggaggctctcatctggtttcttcatggatggaaagttttatgtcattgggggtgtgtcaagtcagagggattctttgacttgtggagaggaatacaatcttgaaacaaggacatggagaagaatacatgatatgtaccctggagggactagtgcctctcaatctcctcccctagttgctgttgtgaataatcagctttatgcagctgatcaggcaacaaatgtggtaaagaagtacgacaaaggaaataacacctggaacatagtgaagccattgccagtcagagctgactcttccaatggttggggcctagctttcaaggcatgtggtgatagattgcttgttattggtggccatagagtaccccgtggtgaagtaatattgctgcattcttggtgccctgaagatgggaatggtggtgctgactgggaagtgctctcggtgaaggagcgtgctggtgtattcgtttataactgcgcaataatggggtgctga</cdnaseq>|
AA = <aaseq>MEDLQDCDCKSLVAVPGSVVLHLFRLFNQQDNSWQKYTLAYFLL VRNEYFSRDSRKHSDGKNQLLDCCDDSELDLDVLYADLDSKELELKLQKPVVKTQSKG DSSASGSNDCFFPGLHDDLAQDCLAWASRSDYPSLSCLNKKFNLLINSGYLYRLRRKY GIVEHWVYLACSLMPWEAFDPSRKRWMRLPRMPCDECFSCADKESLAVGTQLLVFGRE YTGLAIWMYNLLARGWSRCTPMNLPRCLFASGSFGEIAIVAGGCDKNGQVLKSAELYN SETGHWETLPDMNLPRRLSSGFFMDGKFYVIGGVSSQRDSLTCGEEYNLETRTWRRIH DMYPGGTSASQSPPLVAVVNNQLYAADQATNVVKKYDKGNNTWNIVKPLPVRADSSNG WGLAFKACGDRLLVIGGHRVPRGEVILLHSWCPEDGNGGADWEVLSVKERAGVFVYNC AIMGC</aaseq>|
DNA = <dnaseqindica>1443..2810#gctctccatgccctccccgtctcactgacggtggtcccaccgccccacgctccccccccgtgggccccgttcgtcggcgaccgaccgctagctccggcgaccccctccccgccgacgagatccggccgtctccggtgagctccccccccccactctctctcctccccggcgcgcggcgcgttgtcccacgagaaacccgcgtaaccgctctcctctcttgcttccttgtggcccgtgcgccaacgcgcaggttttcttggagccgctcgtcgtggctggggtggcgccggggggaatggaggcggccggcgctcgcgcgggcggtggcggccgggatctcgccggcggcgcgcctcggtgaggtcaggatgtggctcaattctctcgtttggttgcgaaggtctttctgttctttttttctctctttttgtttggtgagtgcttgagctgaagtcgtggctcgtagatttagaggaaagttaattctgttttgttgtgagttagtggttggtgaattagttggggaaaacgtctgcattttttttctgtttggttcagagcgagaaaaattcgagatttttggagagctttgtgtcatggagagcagcaaccagatgtggccgtttcttttgcttgcggatgtttctttttttttgggtgagaatagagaggtttttttgcttgcattctgcaaatcttggggttattttctgttttgctggattttcctttttgttaggatagataattagttgtcgtcttccgtgtgaattggtcaggtcagatagccaccttagaggttatttttttcttgtgttgaatccaaatctagaactagcagatgatagtagtaatgtactagccggtgctttggtacaaagtctaattattcctctgttttagatgaaacttgatggtagaaatgttttggatataatttgtttcttgaggcaaatgcttttttggatcaagttggctaagaagcagaaaccagtttggatgcccaggctagcagaatcagccatgtaggcaaatatttttttgttggtatcaacaataaaaaatgattgcatatgattactaacggaagatttggaatcgttggtcttagtggtacaaaattttagttgtttacttgattctgaatacgccaaagctgggggaaatatatatttttccatcaaatcaactctgaagatttttttagtgaaataaatgtacctattaagacgaacatgcctagatgagtccattgtttaactctgtagtggtatctgagctaaaattatgtatattgtttgctctgttcttgatccagaaatttagtgcatttcaaatacgctgtgctcattttgctatttatctcaaaatattttccagatgtgatctgtgatctgtccaacctttgtgtactcgggctcattccacagttaacaaaaaagatggaagatttacaagattgtgactgcaaaagccttgttgctgttcctggttctgtggttctgcacctctttaggctgtttaatcagcaggataattcctggcagaagtacacattagcctactttcttttggtcaggaatgagtacttctctagggattcaaggaagcattcagatgggaagaaccaacttcttgactgctgtgatgattcagaattagatttggatgtgctgtatgctgatttggatagtaaagaactggagcttaagttgcagaaacctgttgtcaagactcaatcaaaaggtgactcaagtgccagtggatcaaatgattgcttctttcctggccttcacgacgacctggctcaggactgccttgcttgggcgagcagatcagactacccatcgctttcttgtttgaataagaagttcaatttgttaatcaacagcgggtatctgtacagactgagaagaaaatatggcattgttgaacactgggtgtatctagcgtgtagcttgatgccctgggaagcatttgatccttcacgcaagcgatggatgaggctcccaagaatgccatgcgacgagtgcttctcttgtgcagacaaggaatcgcttgccgtcgggacacaactgcttgtgtttggccgtgaatatacaggtcttgctatttggatgtacaatttactggcccgtggttggtcccgatgcactccaatgaacctgcctcgctgcctctttgcctcaggaagctttggtgagattgctattgttgctggtgggtgtgataagaatggacaggtgctgaaatctgccgagctgtacaattcagagactggtcattgggagactttgccagacatgaacttgccgaggaggctctcatctggtttcttcatggatggaaagttttatgtcattgggggtgtgtcaagtcagagggattctttgacttgtggagaggaatacaatcttgaaacaaggacatggagaagaatacatgatatgtaccctggagggactagtgcctctcaatctcctcccctagttgctgttgtgaataatcagctttatgcagctgatcaggcaacaaatgtggtaaagaagtacgacaaaggaaataacacctggaacatagtgaagccattgccagtcagagctgactcttccaatggttggggcctagctttcaaggcatgtggtgatagattgcttgttattggtggccatagagtaccccgtggtgaagtaatattgctgcattcttggtgccctgaagatgggaatggtggtgctgactgggaagtgctctcggtgaaggagcgtgctggtgtattcgtttataactgcgcaataatggggtgctgaattacatttctttcggtataatccgtatatgcctcttgtttagcaacccacccatttcttgctgctgcttagctaccccctataatgacctgtaattcagaaaaatgacaccccccttttcgtggagctctcaatgaaatgtttgggagagagcatagagcattcagttcagtttacctggaacttcttttaactcgttcaaaatttgttcttcttgtccagtatgaaatttatgcagtattctttattcatc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060432.1 RefSeq:Os04g0619300]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0619300

2014-05-25T15:18:41Z

Lixueliuwei: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Low temperatures during the booting stage reduce rice yields by causing cold-induced male sterility[1]. Ctb1 is a QTL for cold tolerance, which is located in the introgression on chromosome 4[2]. Researches mapped Ctb1 to a 17-kb region containing two genes that encode an F-box protein and a ser/thr protein kinase. Both genes were cloned from a cold-tolerant variety, Norin-PL8, and introduced into a cold-sensitive variety, Hokkai241, and a cold-sensitive line, BT4-74-8. The cold tolerance of T2 and T3 progenies was assessed by measuring the degree of spikelet fertility in plants treated with cool water irrigation (19◦C, 25 cm) or cool air (12◦C, 4 days).
The results indicated that the F-box protein gene confers cold tolerance. Cold tolerance is associated with greater anther length, which is one of major factors in cold tolerance at the booting stage. Ctb-1 expressed cold tolerance by producing a large anther. The transgenic plants had longer anthers than non-transformed controls. The F-box protein encoded by Ctb1 interact with a subunit of the E3 ubiquitin ligase, Skp1, suggesting that an ubiquitin–proteasome pathway is involved in cold tolerance at the booting stage[1].

[[File:Anther.JPG]]

Table. 1 Cold tolerance, heading date and anther length of the near-isogenic lines(NILs) and parental varieties[2]

[[File:Seed.JPG]]

Fig. 1. Relation between cold tolerance and anther length shown in Table 1. Circles represent the NILs: open circles represent the NILs without either Ctb-1or Ctb-2, and closed circles represent the NILs with Ctb-1and/or Ctb-2. Open and closed triangles represent Kirara397 and Norin-PL8, respectively[2]

'''GO assignment(s)''': GO:0003674 GO:0005634 GO:0008150

===Expression===
[[File:PCR.JPG]]

Fig. 2 RT-PCR and structural analysis of the Ctb1 candidate genes. (a) Expression of genes encoding F-box protein (FB) and a ser/thr protein kinase(PK) in mature leaves (L) and young panicles (YP) from a cold sensitive variety Kirara397 (K) and a cold-tolerant variety Norin-PL8 (N). ACTIN gene was used as a reference. (b) Diagrams of DNA fragments containing the FB and PK genes cloned from Norin-PL8 genomic DNA. Black rectangles, black triangles, and open triangles indicate putative exons, initiation codons, and stop codons, respectively<nowiki>[1]</nowiki>.

Sequence analyses indicated no polymorphism between Norin-PL8 and Kirara397 in the coding regions but several polymorphisms (mostly single nucleotide polymorphisms) in the 5’ upstream regions of both F-box protein (FB) and a ser/thr protein kinase(PK). Comparing the expression of the genes in Norin-PL8 and Kirara397 by RT-PCR analysis, PK was expressed in mature leaves and young panicles. By contrast, FB was expressed preferentially in young panicles, suggesting that FB was a more likely candidate to be Ctb1. No differences were observed in expression levels between Norin-PL8 and Kirara397[1].

===Knowledge Extension===
Rice is a staple crop cultivated worldwide. However, since it is a cold-sensitive plant that evolved in tropical and subtropical areas, rice yields are greatly reduced under low temperature conditions. One of the factors reducing rice yields is cold-induced male sterility (CIMS). In CIMS, the growth stage that is sensitive to cold is the booting stage, especially the young microspore stage just after meiosis[3]. Low temperatures at the young microspore stage cause the degeneration of microspores and hypertrophy of tapetal cells[4].

===Evolution===
K.Saito et al[2] concluded that there are at least two QTLs for cold tolerance in the introgression on chromosome 4 of rice, and tentatively designated as Ctb-1 and Ctb-2.

==Labs working on this gene==

Natl Agr Res Ctr Hokkaido Reg, Hitsujigaoka 1, Sapporo, Hokkaido 0628555, Japan

Univ Florida, IFAS, Ctr Citrus Res & Educ, Lake Alfred, FL 33850 USA

N Carolina State Univ, Dept Bot, Raleigh, NC 27695 USA

==References==
<ref name="ref1">K. Saito, Y. Hayano-Saito, M. Kuroki, Y. Sato,(2010) Map-based cloning of the rice cold tolerance gene Ctb1, Plant Science, 179:97–102.</ref>

<ref name="ref2">K. Saito, K. Miura, K. Nagano, Y. Hayano-Saito, H. Araki, A. Kato, (2001) Identification of two closely linked quantitative trait loci for cold tolerance on chromosome 4 of rice and their association with anther length, Theor. Appl. Genet. 103: 862–868.</ref>

<ref name="ref3">T. Satake, H. Hayase, (1970) Male sterility caused by cooling treatment at the young microspore stage in rice plants, V. Estimation of pollen developmental stage and the most sensitive stage to coolness, Proc. Crop Sci. Soc. Jpn. 39: 468–473.</ref>

<ref name="ref4">I. Nishiyama, (1976) Male sterility caused by cooling treatment at the young microspore stage in rice plants, XIII. Ultrastructure of tapetal hypertrophy without primary wall, Proc. Crop Sci. Soc. Jpn. 45:270–278.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0619300|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001060432.1 GI:115460593 GeneID:4337020|
Length = 3063 bp|
Definition = Oryza sativa Japonica Group Os04g0619300, 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 4|Chromosome 4]]|
AP = Chromosome 4:31857495..31860557|
CDS = 31858937..31860304|
GCID = <gbrowseImage1>
name=NC_008397:31857495..31860557
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:31857495..31860557
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaagatttacaagattgtgactgcaaaagccttgttgctgttcctggttctgtggttctgcacctctttaggctgtttaatcagcaggataattcctggcagaagtacacattagcctactttcttttggtcaggaatgagtacttctctagggattcaaggaagcattcagatgggaagaaccaacttcttgactgctgtgatgattcagaattagatttggatgtgctgtatgctgatttggatagtaaagaactggagcttaagttgcagaaacctgttgtcaagactcaatcaaaaggtgactcaagtgccagtggatcaaatgattgcttctttcctggccttcacgacgacctggctcaggactgccttgcttgggcgagcagatcagactacccatcgctttcttgtttgaataagaagttcaatttgttaatcaacagcgggtatctgtacagactgagaagaaaatatggcattgttgaacactgggtgtatctagcgtgtagcttgatgccctgggaagcatttgatccttcacgcaagcgatggatgaggctcccaagaatgccatgcgacgagtgcttctcttgtgcagacaaggaatcgcttgccgtcgggacacaactgcttgtgtttggccgtgaatatacaggtcttgctatttggatgtacaatttactggcccgtggttggtcccgatgcactccaatgaacctgcctcgctgcctctttgcctcaggaagctttggtgagattgctattgttgctggtgggtgtgataagaatggacaggtgctgaaatctgccgagctgtacaattcagagactggtcattgggagactttgccagacatgaacttgccgaggaggctctcatctggtttcttcatggatggaaagttttatgtcattgggggtgtgtcaagtcagagggattctttgacttgtggagaggaatacaatcttgaaacaaggacatggagaagaatacatgatatgtaccctggagggactagtgcctctcaatctcctcccctagttgctgttgtgaataatcagctttatgcagctgatcaggcaacaaatgtggtaaagaagtacgacaaaggaaataacacctggaacatagtgaagccattgccagtcagagctgactcttccaatggttggggcctagctttcaaggcatgtggtgatagattgcttgttattggtggccatagagtaccccgtggtgaagtaatattgctgcattcttggtgccctgaagatgggaatggtggtgctgactgggaagtgctctcggtgaaggagcgtgctggtgtattcgtttataactgcgcaataatggggtgctga</cdnaseq>|
AA = <aaseq>MEDLQDCDCKSLVAVPGSVVLHLFRLFNQQDNSWQKYTLAYFLL VRNEYFSRDSRKHSDGKNQLLDCCDDSELDLDVLYADLDSKELELKLQKPVVKTQSKG DSSASGSNDCFFPGLHDDLAQDCLAWASRSDYPSLSCLNKKFNLLINSGYLYRLRRKY GIVEHWVYLACSLMPWEAFDPSRKRWMRLPRMPCDECFSCADKESLAVGTQLLVFGRE YTGLAIWMYNLLARGWSRCTPMNLPRCLFASGSFGEIAIVAGGCDKNGQVLKSAELYN SETGHWETLPDMNLPRRLSSGFFMDGKFYVIGGVSSQRDSLTCGEEYNLETRTWRRIH DMYPGGTSASQSPPLVAVVNNQLYAADQATNVVKKYDKGNNTWNIVKPLPVRADSSNG WGLAFKACGDRLLVIGGHRVPRGEVILLHSWCPEDGNGGADWEVLSVKERAGVFVYNC AIMGC</aaseq>|
DNA = <dnaseqindica>1443..2810#gctctccatgccctccccgtctcactgacggtggtcccaccgccccacgctccccccccgtgggccccgttcgtcggcgaccgaccgctagctccggcgaccccctccccgccgacgagatccggccgtctccggtgagctccccccccccactctctctcctccccggcgcgcggcgcgttgtcccacgagaaacccgcgtaaccgctctcctctcttgcttccttgtggcccgtgcgccaacgcgcaggttttcttggagccgctcgtcgtggctggggtggcgccggggggaatggaggcggccggcgctcgcgcgggcggtggcggccgggatctcgccggcggcgcgcctcggtgaggtcaggatgtggctcaattctctcgtttggttgcgaaggtctttctgttctttttttctctctttttgtttggtgagtgcttgagctgaagtcgtggctcgtagatttagaggaaagttaattctgttttgttgtgagttagtggttggtgaattagttggggaaaacgtctgcattttttttctgtttggttcagagcgagaaaaattcgagatttttggagagctttgtgtcatggagagcagcaaccagatgtggccgtttcttttgcttgcggatgtttctttttttttgggtgagaatagagaggtttttttgcttgcattctgcaaatcttggggttattttctgttttgctggattttcctttttgttaggatagataattagttgtcgtcttccgtgtgaattggtcaggtcagatagccaccttagaggttatttttttcttgtgttgaatccaaatctagaactagcagatgatagtagtaatgtactagccggtgctttggtacaaagtctaattattcctctgttttagatgaaacttgatggtagaaatgttttggatataatttgtttcttgaggcaaatgcttttttggatcaagttggctaagaagcagaaaccagtttggatgcccaggctagcagaatcagccatgtaggcaaatatttttttgttggtatcaacaataaaaaatgattgcatatgattactaacggaagatttggaatcgttggtcttagtggtacaaaattttagttgtttacttgattctgaatacgccaaagctgggggaaatatatatttttccatcaaatcaactctgaagatttttttagtgaaataaatgtacctattaagacgaacatgcctagatgagtccattgtttaactctgtagtggtatctgagctaaaattatgtatattgtttgctctgttcttgatccagaaatttagtgcatttcaaatacgctgtgctcattttgctatttatctcaaaatattttccagatgtgatctgtgatctgtccaacctttgtgtactcgggctcattccacagttaacaaaaaagatggaagatttacaagattgtgactgcaaaagccttgttgctgttcctggttctgtggttctgcacctctttaggctgtttaatcagcaggataattcctggcagaagtacacattagcctactttcttttggtcaggaatgagtacttctctagggattcaaggaagcattcagatgggaagaaccaacttcttgactgctgtgatgattcagaattagatttggatgtgctgtatgctgatttggatagtaaagaactggagcttaagttgcagaaacctgttgtcaagactcaatcaaaaggtgactcaagtgccagtggatcaaatgattgcttctttcctggccttcacgacgacctggctcaggactgccttgcttgggcgagcagatcagactacccatcgctttcttgtttgaataagaagttcaatttgttaatcaacagcgggtatctgtacagactgagaagaaaatatggcattgttgaacactgggtgtatctagcgtgtagcttgatgccctgggaagcatttgatccttcacgcaagcgatggatgaggctcccaagaatgccatgcgacgagtgcttctcttgtgcagacaaggaatcgcttgccgtcgggacacaactgcttgtgtttggccgtgaatatacaggtcttgctatttggatgtacaatttactggcccgtggttggtcccgatgcactccaatgaacctgcctcgctgcctctttgcctcaggaagctttggtgagattgctattgttgctggtgggtgtgataagaatggacaggtgctgaaatctgccgagctgtacaattcagagactggtcattgggagactttgccagacatgaacttgccgaggaggctctcatctggtttcttcatggatggaaagttttatgtcattgggggtgtgtcaagtcagagggattctttgacttgtggagaggaatacaatcttgaaacaaggacatggagaagaatacatgatatgtaccctggagggactagtgcctctcaatctcctcccctagttgctgttgtgaataatcagctttatgcagctgatcaggcaacaaatgtggtaaagaagtacgacaaaggaaataacacctggaacatagtgaagccattgccagtcagagctgactcttccaatggttggggcctagctttcaaggcatgtggtgatagattgcttgttattggtggccatagagtaccccgtggtgaagtaatattgctgcattcttggtgccctgaagatgggaatggtggtgctgactgggaagtgctctcggtgaaggagcgtgctggtgtattcgtttataactgcgcaataatggggtgctgaattacatttctttcggtataatccgtatatgcctcttgtttagcaacccacccatttcttgctgctgcttagctaccccctataatgacctgtaattcagaaaaatgacaccccccttttcgtggagctctcaatgaaatgtttgggagagagcatagagcattcagttcagtttacctggaacttcttttaactcgttcaaaatttgttcttcttgtccagtatgaaatttatgcagtattctttattcatc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060432.1 RefSeq:Os04g0619300]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0619300

2014-05-25T15:18:14Z

Lixueliuwei: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Low temperatures during the booting stage reduce rice yields by causing cold-induced male sterility[1]. Ctb1 is a QTL for cold tolerance, which is located in the introgression on chromosome 4[2]. Researches mapped Ctb1 to a 17-kb region containing two genes that encode an F-box protein and a ser/thr protein kinase. Both genes were cloned from a cold-tolerant variety, Norin-PL8, and introduced into a cold-sensitive variety, Hokkai241, and a cold-sensitive line, BT4-74-8. The cold tolerance of T2 and T3 progenies was assessed by measuring the degree of spikelet fertility in plants treated with cool water irrigation (19◦C, 25 cm) or cool air (12◦C, 4 days).
The results indicated that the F-box protein gene confers cold tolerance. Cold tolerance is associated with greater anther length, which is one of major factors in cold tolerance at the booting stage. Ctb-1 expressed cold tolerance by producing a large anther. The transgenic plants had longer anthers than non-transformed controls. The F-box protein encoded by Ctb1 interact with a subunit of the E3 ubiquitin ligase, Skp1, suggesting that an ubiquitin–proteasome pathway is involved in cold tolerance at the booting stage[1].

[[File:Anther.JPG]]

Table. 1 Cold tolerance, heading date and anther length of the near-isogenic lines(NILs) and parental varieties[2]

[[File:Seed.JPG]]

Fig. 1. Relation between cold tolerance and anther length shown in Table 1. Circles represent the NILs: open circles represent the NILs without either Ctb-1or Ctb-2, and closed circles represent the NILs with Ctb-1and/or Ctb-2. Open and closed triangles represent Kirara397 and Norin-PL8, respectively[2]

'''GO assignment(s)''': GO:0003674 GO:0005634 GO:0008150

===Expression===
[[File:PCR.JPG]]

Fig. 2 RT-PCR and structural analysis of the Ctb1 candidate genes. (a) Expression of genes encoding F-box protein (FB) and a ser/thr protein kinase(PK) in mature leaves (L) and young panicles (YP) from a cold sensitive variety Kirara397 (K) and a cold-tolerant variety Norin-PL8 (N). ACTIN gene was used as a reference. (b) Diagrams of DNA fragments containing the FB and PK genes cloned from Norin-PL8 genomic DNA. Black rectangles, black triangles, and open triangles indicate putative exons, initiation codons, and stop codons, respectively<nowiki>[1]</nowiki>.

Sequence analyses indicated no polymorphism between Norin-PL8 and Kirara397 in the coding regions but several polymorphisms (mostly single nucleotide polymorphisms) in the 5’ upstream regions of both F-box protein (FB) and a ser/thr protein kinase(PK). Comparing the expression of the genes in Norin-PL8 and Kirara397 by RT-PCR analysis, PK was expressed in mature leaves and young panicles. By contrast, FB was expressed preferentially in young panicles, suggesting that FB was a more likely candidate to be Ctb1. No differences were observed in expression levels between Norin-PL8 and Kirara397[1].

===Knowledge Extension===
Rice is a staple crop cultivated worldwide. However, since it is a cold-sensitive plant that evolved in tropical and subtropical areas, rice yields are greatly reduced under low temperature conditions. One of the factors reducing rice yields is cold-induced male sterility (CIMS). In CIMS, the growth stage that is sensitive to cold is the booting stage, especially the young microspore stage just after meiosis[3]. Low temperatures at the young microspore stage cause the degeneration of microspores and hypertrophy of tapetal cells[4].

===Evolution===
K.Saito et al[2] concluded that there are at least two QTLs for cold tolerance in the introgression on chromosome 4 of rice, and tentatively designated as Ctb-1 and Ctb-2.

==Labs working on this gene==

Natl Agr Res Ctr Hokkaido Reg, Hitsujigaoka 1, Sapporo, Hokkaido 0628555, Japan

Univ Florida, IFAS, Ctr Citrus Res & Educ, Lake Alfred, FL 33850 USA

N Carolina State Univ, Dept Bot, Raleigh, NC 27695 USA

==References==
<ref name="ref1">K. Saito, Y. Hayano-Saito, M. Kuroki, Y. Sato,(2010) Map-based cloning of the rice cold tolerance gene Ctb1, Plant Science, 179:97–102.</ref>
<ref name="ref1">K. Saito, K. Miura, K. Nagano, Y. Hayano-Saito, H. Araki, A. Kato, (2001) Identification of two closely linked quantitative trait loci for cold tolerance on chromosome 4 of rice and their association with anther length, Theor. Appl. Genet. 103: 862–868.</ref>
<ref name="ref1">T. Satake, H. Hayase, (1970) Male sterility caused by cooling treatment at the young microspore stage in rice plants, V. Estimation of pollen developmental stage and the most sensitive stage to coolness, Proc. Crop Sci. Soc. Jpn. 39: 468–473.</ref>
<ref name="ref1">I. Nishiyama, (1976) Male sterility caused by cooling treatment at the young microspore stage in rice plants, XIII. Ultrastructure of tapetal hypertrophy without primary wall, Proc. Crop Sci. Soc. Jpn. 45:270–278.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0619300|
Description = Cyclin-like F-box domain containing protein|
Version = NM_001060432.1 GI:115460593 GeneID:4337020|
Length = 3063 bp|
Definition = Oryza sativa Japonica Group Os04g0619300, 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 4|Chromosome 4]]|
AP = Chromosome 4:31857495..31860557|
CDS = 31858937..31860304|
GCID = <gbrowseImage1>
name=NC_008397:31857495..31860557
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:31857495..31860557
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaagatttacaagattgtgactgcaaaagccttgttgctgttcctggttctgtggttctgcacctctttaggctgtttaatcagcaggataattcctggcagaagtacacattagcctactttcttttggtcaggaatgagtacttctctagggattcaaggaagcattcagatgggaagaaccaacttcttgactgctgtgatgattcagaattagatttggatgtgctgtatgctgatttggatagtaaagaactggagcttaagttgcagaaacctgttgtcaagactcaatcaaaaggtgactcaagtgccagtggatcaaatgattgcttctttcctggccttcacgacgacctggctcaggactgccttgcttgggcgagcagatcagactacccatcgctttcttgtttgaataagaagttcaatttgttaatcaacagcgggtatctgtacagactgagaagaaaatatggcattgttgaacactgggtgtatctagcgtgtagcttgatgccctgggaagcatttgatccttcacgcaagcgatggatgaggctcccaagaatgccatgcgacgagtgcttctcttgtgcagacaaggaatcgcttgccgtcgggacacaactgcttgtgtttggccgtgaatatacaggtcttgctatttggatgtacaatttactggcccgtggttggtcccgatgcactccaatgaacctgcctcgctgcctctttgcctcaggaagctttggtgagattgctattgttgctggtgggtgtgataagaatggacaggtgctgaaatctgccgagctgtacaattcagagactggtcattgggagactttgccagacatgaacttgccgaggaggctctcatctggtttcttcatggatggaaagttttatgtcattgggggtgtgtcaagtcagagggattctttgacttgtggagaggaatacaatcttgaaacaaggacatggagaagaatacatgatatgtaccctggagggactagtgcctctcaatctcctcccctagttgctgttgtgaataatcagctttatgcagctgatcaggcaacaaatgtggtaaagaagtacgacaaaggaaataacacctggaacatagtgaagccattgccagtcagagctgactcttccaatggttggggcctagctttcaaggcatgtggtgatagattgcttgttattggtggccatagagtaccccgtggtgaagtaatattgctgcattcttggtgccctgaagatgggaatggtggtgctgactgggaagtgctctcggtgaaggagcgtgctggtgtattcgtttataactgcgcaataatggggtgctga</cdnaseq>|
AA = <aaseq>MEDLQDCDCKSLVAVPGSVVLHLFRLFNQQDNSWQKYTLAYFLL VRNEYFSRDSRKHSDGKNQLLDCCDDSELDLDVLYADLDSKELELKLQKPVVKTQSKG DSSASGSNDCFFPGLHDDLAQDCLAWASRSDYPSLSCLNKKFNLLINSGYLYRLRRKY GIVEHWVYLACSLMPWEAFDPSRKRWMRLPRMPCDECFSCADKESLAVGTQLLVFGRE YTGLAIWMYNLLARGWSRCTPMNLPRCLFASGSFGEIAIVAGGCDKNGQVLKSAELYN SETGHWETLPDMNLPRRLSSGFFMDGKFYVIGGVSSQRDSLTCGEEYNLETRTWRRIH DMYPGGTSASQSPPLVAVVNNQLYAADQATNVVKKYDKGNNTWNIVKPLPVRADSSNG WGLAFKACGDRLLVIGGHRVPRGEVILLHSWCPEDGNGGADWEVLSVKERAGVFVYNC AIMGC</aaseq>|
DNA = <dnaseqindica>1443..2810#gctctccatgccctccccgtctcactgacggtggtcccaccgccccacgctccccccccgtgggccccgttcgtcggcgaccgaccgctagctccggcgaccccctccccgccgacgagatccggccgtctccggtgagctccccccccccactctctctcctccccggcgcgcggcgcgttgtcccacgagaaacccgcgtaaccgctctcctctcttgcttccttgtggcccgtgcgccaacgcgcaggttttcttggagccgctcgtcgtggctggggtggcgccggggggaatggaggcggccggcgctcgcgcgggcggtggcggccgggatctcgccggcggcgcgcctcggtgaggtcaggatgtggctcaattctctcgtttggttgcgaaggtctttctgttctttttttctctctttttgtttggtgagtgcttgagctgaagtcgtggctcgtagatttagaggaaagttaattctgttttgttgtgagttagtggttggtgaattagttggggaaaacgtctgcattttttttctgtttggttcagagcgagaaaaattcgagatttttggagagctttgtgtcatggagagcagcaaccagatgtggccgtttcttttgcttgcggatgtttctttttttttgggtgagaatagagaggtttttttgcttgcattctgcaaatcttggggttattttctgttttgctggattttcctttttgttaggatagataattagttgtcgtcttccgtgtgaattggtcaggtcagatagccaccttagaggttatttttttcttgtgttgaatccaaatctagaactagcagatgatagtagtaatgtactagccggtgctttggtacaaagtctaattattcctctgttttagatgaaacttgatggtagaaatgttttggatataatttgtttcttgaggcaaatgcttttttggatcaagttggctaagaagcagaaaccagtttggatgcccaggctagcagaatcagccatgtaggcaaatatttttttgttggtatcaacaataaaaaatgattgcatatgattactaacggaagatttggaatcgttggtcttagtggtacaaaattttagttgtttacttgattctgaatacgccaaagctgggggaaatatatatttttccatcaaatcaactctgaagatttttttagtgaaataaatgtacctattaagacgaacatgcctagatgagtccattgtttaactctgtagtggtatctgagctaaaattatgtatattgtttgctctgttcttgatccagaaatttagtgcatttcaaatacgctgtgctcattttgctatttatctcaaaatattttccagatgtgatctgtgatctgtccaacctttgtgtactcgggctcattccacagttaacaaaaaagatggaagatttacaagattgtgactgcaaaagccttgttgctgttcctggttctgtggttctgcacctctttaggctgtttaatcagcaggataattcctggcagaagtacacattagcctactttcttttggtcaggaatgagtacttctctagggattcaaggaagcattcagatgggaagaaccaacttcttgactgctgtgatgattcagaattagatttggatgtgctgtatgctgatttggatagtaaagaactggagcttaagttgcagaaacctgttgtcaagactcaatcaaaaggtgactcaagtgccagtggatcaaatgattgcttctttcctggccttcacgacgacctggctcaggactgccttgcttgggcgagcagatcagactacccatcgctttcttgtttgaataagaagttcaatttgttaatcaacagcgggtatctgtacagactgagaagaaaatatggcattgttgaacactgggtgtatctagcgtgtagcttgatgccctgggaagcatttgatccttcacgcaagcgatggatgaggctcccaagaatgccatgcgacgagtgcttctcttgtgcagacaaggaatcgcttgccgtcgggacacaactgcttgtgtttggccgtgaatatacaggtcttgctatttggatgtacaatttactggcccgtggttggtcccgatgcactccaatgaacctgcctcgctgcctctttgcctcaggaagctttggtgagattgctattgttgctggtgggtgtgataagaatggacaggtgctgaaatctgccgagctgtacaattcagagactggtcattgggagactttgccagacatgaacttgccgaggaggctctcatctggtttcttcatggatggaaagttttatgtcattgggggtgtgtcaagtcagagggattctttgacttgtggagaggaatacaatcttgaaacaaggacatggagaagaatacatgatatgtaccctggagggactagtgcctctcaatctcctcccctagttgctgttgtgaataatcagctttatgcagctgatcaggcaacaaatgtggtaaagaagtacgacaaaggaaataacacctggaacatagtgaagccattgccagtcagagctgactcttccaatggttggggcctagctttcaaggcatgtggtgatagattgcttgttattggtggccatagagtaccccgtggtgaagtaatattgctgcattcttggtgccctgaagatgggaatggtggtgctgactgggaagtgctctcggtgaaggagcgtgctggtgtattcgtttataactgcgcaataatggggtgctgaattacatttctttcggtataatccgtatatgcctcttgtttagcaacccacccatttcttgctgctgcttagctaccccctataatgacctgtaattcagaaaaatgacaccccccttttcgtggagctctcaatgaaatgtttgggagagagcatagagcattcagttcagtttacctggaacttcttttaactcgttcaaaatttgttcttcttgtccagtatgaaatttatgcagtattctttattcatc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060432.1 RefSeq:Os04g0619300]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]