Os07g0261200 - Revision history

Lily at 09:56, 1 June 2014

2014-06-01T09:56:22Z

Lily at 15:41, 31 May 2014

2014-05-31T15:41:15Z

Lily at 15:33, 31 May 2014

2014-05-31T15:33:19Z

Lily at 13:48, 31 May 2014

2014-05-31T13:48:27Z

Lily at 13:43, 31 May 2014

2014-05-31T13:43:06Z

Lily at 13:05, 31 May 2014

2014-05-31T13:05:07Z

Lily: /* Localization */

2014-05-31T13:02:30Z

‎Localization

Lily: /* Localization */

2014-05-31T13:01:20Z

‎Localization

Lily: /* Function */

2014-05-31T12:27:35Z

‎Function

Lily: /* Function */

2014-05-31T12:26:42Z

‎Function

← Older revision		Revision as of 09:56, 1 June 2014
Line 73:		Line 73:

	== Structured Information ==		== Structured Information ==
		+	{{JaponicaGene\|
		+	GeneName = Os07g0261200\|
		+	Description = XXX\|
		+	Version = XXX \|
		+	Length = XXX bp\|
		+	Definition = Oryza sativa Japonica Group Os07g0261200, 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 7\|Chromosome 7]]\|
		+	AP = Chromosome 7:XXX..XXX\|
		+	CDS = start1...end1, start2..end2\|
		+	GCID = <gbrowseImage1>
		+	name=NC_008400:start..end
		+	source=RiceChromosome07
		+	preset=GeneLocation
		+	</gbrowseImage1>\|
		+	GSID = <gbrowseImage2>
		+	name=NC_008400:start..end
		+	source=RiceChromosome07
		+	preset=GeneLocation
		+	</gbrowseImage2>\|
		+	CDNA = <cdnaseq>XXX</cdnaseq>\|
		+	AA = <aaseq>XXX</aaseq>\|
		+	DNA =<dnaseqindica>XXX</dnaseqindica>\|
		+	Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_XXX RefSeq:Os07g0261200]\|
		+	}}

← Older revision		Revision as of 15:41, 31 May 2014
Line 73:		Line 73:

	== Structured Information ==		== Structured Information ==
−	~~[[File:Ncfetch.png\|middle\|thumb\|300px\|]]~~
−	~~LOCUS EU286800 1028 bp mRNA linear PLN 04-JUN-2008~~
−	~~DEFINITION Oryza sativa Indica Group cultivar Minghui 63 GHD7 (Ghd7) mRNA,~~
−	~~complete cds.~~
−	~~ACCESSION EU286800~~
−	~~VERSION EU286800.1 GI:168188196~~
−	~~KEYWORDS .~~
−	~~SOURCE Oryza sativa Indica Group (long-grained rice)~~
−	~~ORGANISM Oryza sativa Indica Group~~
−	~~Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;~~
−	~~Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP~~
−	~~clade; Ehrhartoideae; Oryzeae; Oryza.~~
−	~~REFERENCE 1 (bases 1 to 1028)~~
−	~~AUTHORS Xue,W., Xing,Y., Weng,X., Zhao,Y., Tang,W., Wang,L., Zhou,H.,~~
−	~~Yu,S., Xu,C., Li,X. and Zhang,Q.~~
−	~~TITLE Natural variation in Ghd7 is an important regulator of heading date~~
−	~~and yield potential in rice~~
−	~~JOURNAL Nat. Genet. 40 (6), 761-767 (2008)~~
−	~~PUBMED 18454147~~
−	~~REFERENCE 2 (bases 1 to 1028)~~
−	~~AUTHORS Xue,W., Xing,Y., Weng,X. and Zhang,Q.~~
−	~~TITLE A major QTL for productivity and adaptability of rice~~
−	~~JOURNAL Unpublished~~
−	~~REFERENCE 3 (bases 1 to 1028)~~
−	~~AUTHORS Xue,W., Xing,Y., Weng,X. and Zhang,Q.~~
−	~~TITLE Direct Submission~~
−	~~JOURNAL Submitted (17-NOV-2007) National Key Laboratory of Crop Genetic~~
−	~~Improvement, National Center of Plant Gene Research (Wuhan),~~
−	~~Huazhong Agricultural University, Wuhan, Hubei 430070, China~~
−	~~FEATURES Location/Qualifiers~~
−	~~source 1..1028~~
−	~~/organism="Oryza sativa Indica Group"~~
−	~~/mol_type="mRNA"~~
−	~~/cultivar="Minghui 63"~~
−	~~/db_xref="taxon:39946"~~
−	~~gene 1..1028~~
−	~~/gene="Ghd7"~~
−	~~/note="CCT"~~
−	~~CDS 211..984~~
−	~~/gene="Ghd7"~~
−	~~/codon_start=1~~
−	~~/product="GHD7"~~
−	~~/protein_id="ACA14488.1"~~
−	~~/db_xref="GI:168188197"~~
−	~~/translation="MSMGPAAGEGCGLCGADGGGCCSRHRHDDDGFPFVFPPSACQGI~~
−	~~GAPAPPVHEFQFFGNDGGGDDGESVAWLFDDYPPPSPVAAAAGMHHRQPPYDGVVAPP~~
−	~~SLFRRNTGAGGLTFDVSLGGRPDLDAGLGLGGGSGRHAEAAASATIMSYCGSTFTDAA~~
−	~~SSMPKEMVAAMADVGESLNPNTVVGAMVEREAKLMRYKEKRKKRCYEKQIRYASRKAY~~
−	~~AEMRPRVRGRFAKEADQEAVAPPSTYVDPSRLELGQWFR"~~
−	~~ORIGIN~~
−	~~1 caacttgccc tgtcttcttc ttcttcttct tcttgtacct atattattac aagtcatcga~~
−	~~61 tctcgctgat cgatcagtga tcacaagcat ttcacaaccc tagctagctg agctgatcga~~
−	~~121 gctcaagtga cctcacctgc tatagctaac ttactagcta gctctagcta gttgttgttt~~
−	~~181 gtagctcgat cgagtttgat ttatccgttc atgtcgatgg gaccagcagc cggagaagga~~
−	~~241 tgtggcctgt gcggcgccga cggtggcggc tgttgctccc gccatcgcca cgatgatgat~~
−	~~301 ggattcccct tcgtcttccc gccgagtgcg tgccagggga tcggcgcccc ggcgccaccg~~
−	~~361 gtgcacgagt tccagttctt cggcaacgac ggcggcggcg acgacggcga gagcgtggcc~~
−	~~421 tggctgttcg atgactaccc gccgccgtcg cccgttgctg ccgccgccgg gatgcatcat~~
−	~~481 cggcagccgc cgtacgacgg cgtcgtggcg ccgccgtcgc tgttcaggag gaacaccggc~~
−	~~541 gccggcgggc tcacgttcga cgtctccctc ggcggacggc ccgacctgga cgccgggctc~~
−	~~601 ggcctcggcg gcggcagcgg ccggcacgcc gaggccgcgg ccagcgccac catcatgtca~~
−	~~661 tattgtggga gcacgttcac tgacgcagcg agctcgatgc ccaaggagat ggtggccgcc~~
−	~~721 atggccgatg ttggggagag cttgaaccca aacacggtgg ttggcgcaat ggtggagagg~~
−	~~781 gaggccaagc tgatgaggta caaggagaag aggaagaaga ggtgctacga gaagcaaatc~~
−	~~841 cggtacgcgt ccagaaaagc ctatgccgag atgaggcccc gagtgagagg tcgcttcgcc~~
−	~~901 aaagaagctg atcaggaagc tgtcgcaccg ccatccacct atgtcgatcc tagtaggctt~~
−	~~961 gagcttggac aatggttcag atagataatt acagtgcgta tataccacta actaaaaaaa~~
−	~~1021 aaaaaaaa~~
−	//

@@ Line 71: / Line 71: @@
 <ref name="ref12">Griffiths S, Dunford RP, Coupland G,etal.(2003) The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis. Plant Physiol 131:1855–1867.</ref>
 <ref name="ref13">Yang L, Liu T, Li B,et al. (2012) Comparative Sequence Analysis of the Ghd7 Orthologous Regions Revealed Movement of Ghd7 in the Grass Genomes. PLoS ONE 7(11): e50236. doi:10.1371/journal.pone.0050236.</ref>
 == Structured Information ==

@@ Line 40: / Line 40: @@
 Ghd7, a CCT domain-containing gene located on the short arm of rice chromosome 7, controls the number of grains per panicle, plant height and heading date<ref name="ref2"/>.Ghd7 is thought to be an evolutionarily new gene, because it does not have homologs in Arabidopsis thaliana, and the protein sequence lacks a B-box domain, and the non-CCT portion differs from other CCT domain-containing proteins<ref name="ref2"/><ref name="ref12" />.
-[[File:Figure 4.jpg|right|thumb|300px|'''Figure 4. Unrooted phylogenetic tree for Ghd7 and its homologous genes from rice, B. distachyon, sorghum and maize.'''The tree was built using the Neighbor-Joining method. The conserved motifs were shaded in different colors. The two clades can be distinguished by the motif distribution. doi:10.1371/journal.pone.0050236.g003((from reference<ref name="ref13" />)]]
+[[File:F4Unrooted phylogenetic tree for Ghd7 and its homologous genes from rice, B. distachyon, sorghum and maize.jpg|right|thumb|300px|'''Figure 4. Unrooted phylogenetic tree for Ghd7 and its homologous genes from rice, B. distachyon, sorghum and maize.'''The tree was built using the Neighbor-Joining method. The conserved motifs were shaded in different colors. The two clades can be distinguished by the motif distribution. doi:10.1371/journal.pone.0050236.g003((from reference<ref name="ref13" />)]]
 Ghd7 is a pleiotropic gene that controls the traits of Plant height, heading date, and yield.In this study<ref name="ref11" />, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise p and h in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that '''Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively.''' In addition to the previously reported '''premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits''', we found another functional C/T mutation (SNP S_555) by structure-based association analysis. '''SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression'''. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs.

@@ Line 38: / Line 38: @@
 ==Localization and Evolution==
 Ghd7 is located in rice chromosome 7 between markers R1440 and C1023; Further,percisely it is located between RM5436 and RM2256 range ,the length of which is 79 KB.
-Ghd7, a CCT domain-containing gene located on the short arm of rice chromosome 7, controls the number of grains per panicle, plant height and heading date<ref name="ref2"/>.
+Ghd7, a CCT domain-containing gene located on the short arm of rice chromosome 7, controls the number of grains per panicle, plant height and heading date<ref name="ref2"/>.Ghd7 is thought to be an evolutionarily new gene, because it does not have homologs in Arabidopsis thaliana, and the protein sequence lacks a B-box domain, and the non-CCT portion differs from other CCT domain-containing proteins<ref name="ref2"/><ref name="ref12" />.
 Ghd7 is a pleiotropic gene that controls the traits of Plant height, heading date, and yield.In this study<ref name="ref11" />, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise p and h in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that '''Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively.''' In addition to the previously reported '''premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits''', we found another functional C/T mutation (SNP S_555) by structure-based association analysis. '''SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression'''. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs.
 ==Labs working on this gene==
@@ Line 64: / Line 69: @@
 <ref name="ref10">Osugi A, Itoh H,Ikeda-Kawakatsu K, et al.(2011)Molecular dissection of the roles of phytochrome in photoperiodic flowering in rice. Plant Physiology 157(3): 1128-1137</ref>
 <ref name="ref11">Lu L, Yan WH, Xue WY; et al.(2012)Evolution and Association Analysis of Ghd7 in Rice.  PLoS ONE, 2012, 7(5): e34021</ref>
 . Xiaoyu Weng;Lei Wang;Jia Wang;Yong Hu;Hao Du;Caiguo Xu;Yongzhong Xing;Xianghua Li;Jinghua Xiao;Qifa Zhang

@@ Line 17: / Line 17: @@
 Hd3a in the rice flowering pathway. Association analysis of 19 rice cultivars identified five allelic variants of Ghd7. The Ghd7 alleles
 with strong genetic effects were shown to increase grain yield by adapting to the long growing season of tropical regions and the Ghd7 alleles with no or reduced effect found in temperate regions shortened the rice life cycle to ensure seed setting<ref name="ref2"/>.
 == Expression ==
@@ Line 41: / Line 36: @@
 SNPs in exons, Ghd7 protein diversity was analyzed in the present study.Ghd7 has a partial-dominant effecton flowering time, plant height, and yield traits;The phenotypic effect of Ghd7 is quantitatively related to the abundance of its transcript, and the enhanced transcript level of Ghd7 caused delayed flowering, increased plant height, and yield traits<ref name="ref1" />.
-==Evolution==
+==Localization and Evolution==
 Ghd7 is a pleiotropic gene that controls the traits of Plant height, heading date, and yield.In this study<ref name="ref11" />, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise p and h in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that '''Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively.''' In addition to the previously reported '''premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits''', we found another functional C/T mutation (SNP S_555) by structure-based association analysis. '''SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression'''. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs.

@@ Line 9: / Line 9: @@
 Grain number, plant height, and heading date7 (''Ghd7'') has been regarded as '''an important regulator of heading date and yield potential in rice''';As a long-day dependent negative regulator of heading date, the degree of phenotypic effect of ''Ghd7'' on heading date and yield traits is quantitatively related to the transcript level and is also influenced by both environmental conditions and genetic backgrounds. ''Ghd7'' regulates yield traits through modulating panicle branching independent of heading date. ''Ghd7'' also regulates plasticity of tiller branching by mediating the PHYTOCHROME B-TEOSINTE BRANCHED1 pathway;so,''Ghd7'' functions to integrate the dynamic environmental inputs with phase transition, architecture regulation, and stress response to maximize the reproductive success of the rice plant<ref name="ref1"/>.
-Grain number, plant height, andheading date7 (''Ghd7'') encoding a CCT (CONSTANS,CONSTANS-LIKE, and TIMING OF CHLOROPHYLL A/B BINDING1) domain protein is considered to be a key regulator of the rice-specific flowering pathway and also contributes to rice yield potential<ref name="ref2"/>;Ghd7 controls the critical daylength response of Early heading date1 (Ehd1) and florigen expression through circadian gating and phytochrome action<ref name="ref3"/><ref name="ref4"/>.Ghd7 showed pleiotropic effects on heading date,plant height, and yield traits, and its expression was regulated by light signal and photoperiod<ref name="ref2"/><ref name="ref3"/>.
+Grain number, plant height, andheading date7 (''Ghd7'') encoding a CCT (CONSTANS,CONSTANS-LIKE, and TIMING OF CHLOROPHYLL A/B BINDING1) domain protein is considered to be '''a key regulator of the rice-specific flowering pathway and also contributes to rice yield potential'''<ref name="ref2"/>;Ghd7 controls the critical daylength response of Early heading date1 (Ehd1) and florigen expression through circadian gating and phytochrome action<ref name="ref3"/><ref name="ref4"/>.Ghd7 showed pleiotropic effects on heading date,plant height, and yield traits, and its expression was regulated by light signal and photoperiod<ref name="ref2"/><ref name="ref3"/>.
 [[File:F1 .jpg|right|thumb|300px|'''Figure 1. The effect of Ghd7 on tillering in different density conditions.'''A, Tillers of NIL(zs7) and NIL(mh7) under low- and high-density conditions under natural long-day conditions in Wuhan. Bar = 10 cm. B, Tiller number of NIL(zs7) and NIL(mh7) at 68 days after germination (DAG; the heading date of NIL(zs7)) and 91 DAG (the heading date of NIL(mh7); three different plantings with 30 plants each). Error bars indicate SE.<ref name="ref1" />)]]

@@ Line 7: / Line 7: @@
 Hd2 and Hd16, Hd2 and genetic interactions between Ghd7. Hd2 and its genetic interactions has a very important role for heading stage by controlling the condition of long sunshine.
-Grain number, plant height, and heading date7 (''Ghd7'') has been regarded as an important regulator of heading date and yield potential in rice;As a long-day dependent negative regulator of heading date, the degree of phenotypic effect of ''Ghd7'' on heading date and yield traits is quantitatively related to the transcript level and is also influenced by both environmental conditions and genetic backgrounds. ''Ghd7'' regulates yield traits through modulating panicle branching independent of heading date. ''Ghd7'' also regulates plasticity of tiller branching by mediating the PHYTOCHROME B-TEOSINTE BRANCHED1 pathway;so,''Ghd7'' functions to integrate the dynamic environmental inputs with phase transition, architecture regulation, and stress response to maximize the reproductive success of the rice plant<ref name="ref1"/>.
+Grain number, plant height, and heading date7 (''Ghd7'') has been regarded as '''an important regulator of heading date and yield potential in rice''';As a long-day dependent negative regulator of heading date, the degree of phenotypic effect of ''Ghd7'' on heading date and yield traits is quantitatively related to the transcript level and is also influenced by both environmental conditions and genetic backgrounds. ''Ghd7'' regulates yield traits through modulating panicle branching independent of heading date. ''Ghd7'' also regulates plasticity of tiller branching by mediating the PHYTOCHROME B-TEOSINTE BRANCHED1 pathway;so,''Ghd7'' functions to integrate the dynamic environmental inputs with phase transition, architecture regulation, and stress response to maximize the reproductive success of the rice plant<ref name="ref1"/>.
 Grain number, plant height, andheading date7 (''Ghd7'') encoding a CCT (CONSTANS,CONSTANS-LIKE, and TIMING OF CHLOROPHYLL A/B BINDING1) domain protein is considered to be a key regulator of the rice-specific flowering pathway and also contributes to rice yield potential<ref name="ref2"/>;Ghd7 controls the critical daylength response of Early heading date1 (Ehd1) and florigen expression through circadian gating and phytochrome action<ref name="ref3"/><ref name="ref4"/>.Ghd7 showed pleiotropic effects on heading date,plant height, and yield traits, and its expression was regulated by light signal and photoperiod<ref name="ref2"/><ref name="ref3"/>.
 [[File:F1 .jpg|right|thumb|300px|'''Figure 1. The effect of Ghd7 on tillering in different density conditions.'''A, Tillers of NIL(zs7) and NIL(mh7) under low- and high-density conditions under natural long-day conditions in Wuhan. Bar = 10 cm. B, Tiller number of NIL(zs7) and NIL(mh7) at 68 days after germination (DAG; the heading date of NIL(zs7)) and 91 DAG (the heading date of NIL(mh7); three different plantings with 30 plants each). Error bars indicate SE.<ref name="ref1" />)]]
-Researchers designated NIL(zs7) and NIL(mh7), with almost all of the genetic background of Zhenshan 97 except the introgressed segment, which contained the Ghd7; NIL(mh7) plants had significantly more tillers than NIL(zs7) plants at low-density conditions (Fig. 1), demonstrating that Ghd7 regulates tiller number in a density-dependent manner. Interestingly, there was also a significant increase in secondary branches of the panicles in NIL(mh7) relative to NIL(zs7) at low density, leading to an increased grain number without compromising the number of primary branches;These results suggest that Ghd7 regulates the plasticity of branch development of the plant to adapt to the neighborhood environment<ref name="ref1" />.
+'''The effect of Ghd7 on tillering in different density conditions:''' Researchers designated NIL(zs7) and NIL(mh7), with almost all of the genetic background of Zhenshan 97 except the introgressed segment, which contained the Ghd7; NIL(mh7) plants had significantly more tillers than NIL(zs7) plants at low-density conditions (Fig. 1), demonstrating that Ghd7 regulates tiller number in a density-dependent manner. Interestingly, there was also a significant increase in secondary branches of the panicles in NIL(mh7) relative to NIL(zs7) at low density, leading to an increased grain number without compromising the number of primary branches;These results suggest that Ghd7 regulates the plasticity of branch development of the plant to adapt to the neighborhood environment<ref name="ref1" />.
-Ghd7 has pleiotropic effects on three agronomic traits (PH, HD and spikelets per panicle [SPP]) . Ghd7 delays HD, increases PH and panicle size, and results in enhanced gene expression of Ehd1 and Hd3a under long-day conditions. Expression pattern analysis suggested that Ghd7 may function upstream of Ehd1 and
+'''Ghd7 has pleiotropic effects on three agronomic traits---plant height(PH), Heading date (HD) and spikelets per panicle(SPP).''' Ghd7 delays HD, increases PH and panicle size, and results in enhanced gene expression of Ehd1 and Hd3a under long-day conditions. Expression pattern analysis suggested that Ghd7 may function upstream of Ehd1 and
 Hd3a in the rice flowering pathway. Association analysis of 19 rice cultivars identified five allelic variants of Ghd7. The Ghd7 alleles
 with strong genetic effects were shown to increase grain yield by adapting to the long growing season of tropical regions and the Ghd7 alleles with no or reduced effect found in temperate regions shortened the rice life cycle to ensure seed setting<ref name="ref2"/>.