Domestication and association analysis of Hd1 in Chinese mini-core collections of rice
Hd1 is one of the major photoperiod genes with high degree of polymorphisms and contributes to rice (Oryza sativa L.) flowering in different light conditions. Ninety-two rice landraces and 111 accessions of common wild rice (O. rufipogon Griff.) from the mini-core collections in China were selected...
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| Veröffentlicht in: | Genetic resources and crop evolution 2014, Vol.61 (1), p.121-142 |
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| creator | Wei, Xin Qiao, Weihua Yuan, Nannan Chen, Youtao Wang, Rongsheng Cao, Lirong Zhang, Wanxia Yang, Qingwen Zeng, Hanlai |
| description | Hd1 is one of the major photoperiod genes with high degree of polymorphisms and contributes to rice (Oryza sativa L.) flowering in different light conditions. Ninety-two rice landraces and 111 accessions of common wild rice (O. rufipogon Griff.) from the mini-core collections in China were selected and sequenced to analyze the domestication process and association of Hd1 with rice flowering. Association analysis revealed that three insertions and two deletions in the coding region of Hd1 are highly correlated with flowering time in the short-day condition. Phylogenetic analysis suggested that the polymorphisms of Hd1 in wild rice are related to the distributions. Haplotype analysis indicated that Hd1 in most O. sativa L. ssp. indica Kato and O. sativa L. ssp. japonica Kato landraces evolved from different O. rufipogon groups containing functional Hd1 and that most aus varieties were domesticated from O. rufipogon containing the long-insertions Hd1, suggesting multiple origins of Hd1. Moreover, O. rufipogon which contained the long-insertions Hd1 could only be found in Southern China, implying that Southern China might be one of the domestication centers of O. sativa. This study provides much significant information to aid further understanding of the domestication process of Hd1. |
| doi_str_mv | 10.1007/s10722-013-0019-8 |
| format | Article |
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Ninety-two rice landraces and 111 accessions of common wild rice (O. rufipogon Griff.) from the mini-core collections in China were selected and sequenced to analyze the domestication process and association of Hd1 with rice flowering. Association analysis revealed that three insertions and two deletions in the coding region of Hd1 are highly correlated with flowering time in the short-day condition. Phylogenetic analysis suggested that the polymorphisms of Hd1 in wild rice are related to the distributions. Haplotype analysis indicated that Hd1 in most O. sativa L. ssp. indica Kato and O. sativa L. ssp. japonica Kato landraces evolved from different O. rufipogon groups containing functional Hd1 and that most aus varieties were domesticated from O. rufipogon containing the long-insertions Hd1, suggesting multiple origins of Hd1. Moreover, O. rufipogon which contained the long-insertions Hd1 could only be found in Southern China, implying that Southern China might be one of the domestication centers of O. sativa. This study provides much significant information to aid further understanding of the domestication process of Hd1.</description><identifier>ISSN: 0925-9864</identifier><identifier>EISSN: 1573-5109</identifier><identifier>DOI: 10.1007/s10722-013-0019-8</identifier><language>eng</language><publisher>Dordrecht: Springer-Verlag</publisher><subject>Agriculture ; Association analysis ; Biomedical and Life Sciences ; Domestication ; Flowering ; genes ; Haplotypes ; landraces ; Life Sciences ; Oryza ; Oryza rufipogon ; Oryza sativa ; Phylogeny ; Plant Genetics and Genomics ; Plant Physiology ; Plant Sciences ; Plant Systematics/Taxonomy/Biogeography ; Research Article ; Rice ; wild rice</subject><ispartof>Genetic resources and crop evolution, 2014, Vol.61 (1), p.121-142</ispartof><rights>The Author(s) 2013</rights><rights>Genetic Resources and Crop Evolution is a copyright of Springer, (2013). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c416t-fb0e228389ffbac7f7214f5dc5e5996da8c6320e68e9017836662dd2edf9e4053</citedby><cites>FETCH-LOGICAL-c416t-fb0e228389ffbac7f7214f5dc5e5996da8c6320e68e9017836662dd2edf9e4053</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10722-013-0019-8$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10722-013-0019-8$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>314,776,780,4010,27900,27901,27902,41464,42533,51294</link.rule.ids></links><search><creatorcontrib>Wei, Xin</creatorcontrib><creatorcontrib>Qiao, Weihua</creatorcontrib><creatorcontrib>Yuan, Nannan</creatorcontrib><creatorcontrib>Chen, Youtao</creatorcontrib><creatorcontrib>Wang, Rongsheng</creatorcontrib><creatorcontrib>Cao, Lirong</creatorcontrib><creatorcontrib>Zhang, Wanxia</creatorcontrib><creatorcontrib>Yang, Qingwen</creatorcontrib><creatorcontrib>Zeng, Hanlai</creatorcontrib><title>Domestication and association analysis of Hd1 in Chinese mini-core collections of rice</title><title>Genetic resources and crop evolution</title><addtitle>Genet Resour Crop Evol</addtitle><description>Hd1 is one of the major photoperiod genes with high degree of polymorphisms and contributes to rice (Oryza sativa L.) flowering in different light conditions. Ninety-two rice landraces and 111 accessions of common wild rice (O. rufipogon Griff.) from the mini-core collections in China were selected and sequenced to analyze the domestication process and association of Hd1 with rice flowering. Association analysis revealed that three insertions and two deletions in the coding region of Hd1 are highly correlated with flowering time in the short-day condition. Phylogenetic analysis suggested that the polymorphisms of Hd1 in wild rice are related to the distributions. Haplotype analysis indicated that Hd1 in most O. sativa L. ssp. indica Kato and O. sativa L. ssp. japonica Kato landraces evolved from different O. rufipogon groups containing functional Hd1 and that most aus varieties were domesticated from O. rufipogon containing the long-insertions Hd1, suggesting multiple origins of Hd1. Moreover, O. rufipogon which contained the long-insertions Hd1 could only be found in Southern China, implying that Southern China might be one of the domestication centers of O. sativa. This study provides much significant information to aid further understanding of the domestication process of Hd1.</description><subject>Agriculture</subject><subject>Association analysis</subject><subject>Biomedical and Life Sciences</subject><subject>Domestication</subject><subject>Flowering</subject><subject>genes</subject><subject>Haplotypes</subject><subject>landraces</subject><subject>Life Sciences</subject><subject>Oryza</subject><subject>Oryza rufipogon</subject><subject>Oryza sativa</subject><subject>Phylogeny</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Physiology</subject><subject>Plant Sciences</subject><subject>Plant Systematics/Taxonomy/Biogeography</subject><subject>Research Article</subject><subject>Rice</subject><subject>wild rice</subject><issn>0925-9864</issn><issn>1573-5109</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>BENPR</sourceid><recordid>eNp9kbFuFDEQhi0EEkfgAahYiYbGYcZee-0SHZAgRaIgSWs53nFwtLcOnrsib88emwiJgmo00vf90vwjxFuEUwQYPjLCoJQE1BIAvXTPxAbNoKVB8M_FBrwy0jvbvxSvmO8AwA_WbcT157oj3pcU96XOXZzHLjLXVJ72OD1w4a7m7nzErszd9meZianblbnIVBt1qU4TpSP_h2sl0WvxIseJ6c3jPBFXX79cbs_lxfezb9tPFzL1aPcy3wAp5bTzOd_ENORBYZ_NmAwZ7-0YXbJaAVlHHnBw2lqrxlHRmD31YPSJ-LDm3rf667AcEnaFE01TnKkeOKCxgKD9cETf_4Pe1UNb7uOglNewpKNdKFyp1CpzoxzuW9nF9hAQwrHpsDYdlqbDsengFketDi_sfEvtb_L_pHerlGMN8bYVDlc_FGC_vMYaY53-DV3SiQA</recordid><startdate>2014</startdate><enddate>2014</enddate><creator>Wei, Xin</creator><creator>Qiao, Weihua</creator><creator>Yuan, Nannan</creator><creator>Chen, Youtao</creator><creator>Wang, Rongsheng</creator><creator>Cao, Lirong</creator><creator>Zhang, Wanxia</creator><creator>Yang, Qingwen</creator><creator>Zeng, Hanlai</creator><general>Springer-Verlag</general><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>FBQ</scope><scope>C6C</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X2</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M0K</scope><scope>M7P</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>2014</creationdate><title>Domestication and association analysis of Hd1 in Chinese mini-core collections of rice</title><author>Wei, Xin ; Qiao, Weihua ; Yuan, Nannan ; Chen, Youtao ; Wang, Rongsheng ; Cao, Lirong ; Zhang, Wanxia ; Yang, Qingwen ; Zeng, Hanlai</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c416t-fb0e228389ffbac7f7214f5dc5e5996da8c6320e68e9017836662dd2edf9e4053</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Agriculture</topic><topic>Association analysis</topic><topic>Biomedical and Life Sciences</topic><topic>Domestication</topic><topic>Flowering</topic><topic>genes</topic><topic>Haplotypes</topic><topic>landraces</topic><topic>Life Sciences</topic><topic>Oryza</topic><topic>Oryza rufipogon</topic><topic>Oryza sativa</topic><topic>Phylogeny</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Physiology</topic><topic>Plant Sciences</topic><topic>Plant Systematics/Taxonomy/Biogeography</topic><topic>Research Article</topic><topic>Rice</topic><topic>wild rice</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wei, Xin</creatorcontrib><creatorcontrib>Qiao, Weihua</creatorcontrib><creatorcontrib>Yuan, Nannan</creatorcontrib><creatorcontrib>Chen, Youtao</creatorcontrib><creatorcontrib>Wang, Rongsheng</creatorcontrib><creatorcontrib>Cao, Lirong</creatorcontrib><creatorcontrib>Zhang, Wanxia</creatorcontrib><creatorcontrib>Yang, Qingwen</creatorcontrib><creatorcontrib>Zeng, Hanlai</creatorcontrib><collection>AGRIS</collection><collection>Springer Nature OA Free Journals</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Agricultural Science Collection</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Biological Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Genetic resources and crop evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wei, Xin</au><au>Qiao, Weihua</au><au>Yuan, Nannan</au><au>Chen, Youtao</au><au>Wang, Rongsheng</au><au>Cao, Lirong</au><au>Zhang, Wanxia</au><au>Yang, Qingwen</au><au>Zeng, Hanlai</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Domestication and association analysis of Hd1 in Chinese mini-core collections of rice</atitle><jtitle>Genetic resources and crop evolution</jtitle><stitle>Genet Resour Crop Evol</stitle><date>2014</date><risdate>2014</risdate><volume>61</volume><issue>1</issue><spage>121</spage><epage>142</epage><pages>121-142</pages><issn>0925-9864</issn><eissn>1573-5109</eissn><abstract>Hd1 is one of the major photoperiod genes with high degree of polymorphisms and contributes to rice (Oryza sativa L.) flowering in different light conditions. Ninety-two rice landraces and 111 accessions of common wild rice (O. rufipogon Griff.) from the mini-core collections in China were selected and sequenced to analyze the domestication process and association of Hd1 with rice flowering. Association analysis revealed that three insertions and two deletions in the coding region of Hd1 are highly correlated with flowering time in the short-day condition. Phylogenetic analysis suggested that the polymorphisms of Hd1 in wild rice are related to the distributions. Haplotype analysis indicated that Hd1 in most O. sativa L. ssp. indica Kato and O. sativa L. ssp. japonica Kato landraces evolved from different O. rufipogon groups containing functional Hd1 and that most aus varieties were domesticated from O. rufipogon containing the long-insertions Hd1, suggesting multiple origins of Hd1. Moreover, O. rufipogon which contained the long-insertions Hd1 could only be found in Southern China, implying that Southern China might be one of the domestication centers of O. sativa. This study provides much significant information to aid further understanding of the domestication process of Hd1.</abstract><cop>Dordrecht</cop><pub>Springer-Verlag</pub><doi>10.1007/s10722-013-0019-8</doi><tpages>22</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Agriculture Association analysis Biomedical and Life Sciences Domestication Flowering genes Haplotypes landraces Life Sciences Oryza Oryza rufipogon Oryza sativa Phylogeny Plant Genetics and Genomics Plant Physiology Plant Sciences Plant Systematics/Taxonomy/Biogeography Research Article Rice wild rice |
| title | Domestication and association analysis of Hd1 in Chinese mini-core collections of rice |
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