Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication
The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. We report that the black hull of O. rufipogon was contro...
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creator | Zhu, Bo-Feng Si, Lizhen Wang, Zixuan Jingjie Zhu, Yan Zhou Shangguan, Yingying Lu, Danfeng Fan, Danlin Li, Canyang Lin, Hongxuan Qian, Qian Sang, Tao Zhou, Bo Minobe, Yuzo Han, Bin |
description | The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. We report that the black hull of O. rufipogon was controlled by the Black hull4 (Bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between O. rufipogon W1943 (black hull) and O. sativa indica cv Guangluai 4 (straw-white hull). Bh4 encodes an amino acid transporter. A 22-bp deletion within exon 3 of the bh4 variant disrupted the Bh4 function, leading to the straw-white hull in cultivated rice. Transgenic study indicated that Bh4 could restore the black pigment on hulls in cv Guangluai 4 and Kasalath. Bh4 sequence alignment of all taxa with the outgroup Oryza barthii showed that the wild rice maintained comparable levels of nucleotide diversity that were about 70 times higher than those in the cultivated rice. The results from the maximum likelihood Hudson-Kreitman-Aguade test suggested that the significant reduction in nucleotide diversity in rice cultivars could be caused by artificial selection. We propose that the straw-white hull was selected as an important visual phenotype of nonshattered grains during rice domestication. |
doi_str_mv | 10.1104/pp.110.168500 |
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We report that the black hull of O. rufipogon was controlled by the Black hull4 (Bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between O. rufipogon W1943 (black hull) and O. sativa indica cv Guangluai 4 (straw-white hull). Bh4 encodes an amino acid transporter. A 22-bp deletion within exon 3 of the bh4 variant disrupted the Bh4 function, leading to the straw-white hull in cultivated rice. Transgenic study indicated that Bh4 could restore the black pigment on hulls in cv Guangluai 4 and Kasalath. Bh4 sequence alignment of all taxa with the outgroup Oryza barthii showed that the wild rice maintained comparable levels of nucleotide diversity that were about 70 times higher than those in the cultivated rice. The results from the maximum likelihood Hudson-Kreitman-Aguade test suggested that the significant reduction in nucleotide diversity in rice cultivars could be caused by artificial selection. We propose that the straw-white hull was selected as an important visual phenotype of nonshattered grains during rice domestication.</description><identifier>ISSN: 0032-0889</identifier><identifier>ISSN: 1532-2548</identifier><identifier>EISSN: 1532-2548</identifier><identifier>DOI: 10.1104/pp.110.168500</identifier><identifier>PMID: 21263038</identifier><identifier>CODEN: PPHYA5</identifier><language>eng</language><publisher>Rockville, MD: American Society of Plant Biologists</publisher><subject>Agriculture ; Amino Acid Transport Systems ; Biological and medical sciences ; Cloning, Molecular ; Crops, Agricultural - genetics ; Fundamental and applied biological sciences. Psychology ; Gene Expression Regulation, Plant ; Genes, Plant - genetics ; Genetic loci ; Genetic mutation ; GENETICS, GENOMICS, AND MOLECULAR EVOLUTION ; Geography ; Grains ; Inbreeding ; Molecular Sequence Data ; Mutation - genetics ; Nucleotides - genetics ; Organ Specificity - genetics ; Oryza ; Oryza - genetics ; Oryza barthii ; Oryza rufipogon ; Oryza sativa ; Phenotype ; Phylogeny ; Pigmentation - genetics ; Plant domestication ; Plant physiology and development ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Plants ; Plants, Genetically Modified ; Polymerase chain reaction ; Rice ; Rice hulls ; RNA, Messenger - genetics ; RNA, Messenger - metabolism ; Seeds ; Seeds - anatomy & histology ; Seeds - genetics ; Sequence Homology, Nucleic Acid ; Wild rice</subject><ispartof>Plant physiology (Bethesda), 2011-03, Vol.155 (3), p.1301-1311</ispartof><rights>2011 American Society of Plant Biologists</rights><rights>2015 INIST-CNRS</rights><rights>2011 American Society of Plant Biologists 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c560t-fa473ae7ee9c58334fac01d09e4f06c07feb8fc2e51598512709e7823942f12b3</citedby><cites>FETCH-LOGICAL-c560t-fa473ae7ee9c58334fac01d09e4f06c07feb8fc2e51598512709e7823942f12b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/41434200$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/41434200$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,777,781,800,882,27905,27906,57998,58231</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23960966$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21263038$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhu, Bo-Feng</creatorcontrib><creatorcontrib>Si, Lizhen</creatorcontrib><creatorcontrib>Wang, Zixuan</creatorcontrib><creatorcontrib>Jingjie Zhu, Yan Zhou</creatorcontrib><creatorcontrib>Shangguan, Yingying</creatorcontrib><creatorcontrib>Lu, Danfeng</creatorcontrib><creatorcontrib>Fan, Danlin</creatorcontrib><creatorcontrib>Li, Canyang</creatorcontrib><creatorcontrib>Lin, Hongxuan</creatorcontrib><creatorcontrib>Qian, Qian</creatorcontrib><creatorcontrib>Sang, Tao</creatorcontrib><creatorcontrib>Zhou, Bo</creatorcontrib><creatorcontrib>Minobe, Yuzo</creatorcontrib><creatorcontrib>Han, Bin</creatorcontrib><title>Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication</title><title>Plant physiology (Bethesda)</title><addtitle>Plant Physiol</addtitle><description>The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. We report that the black hull of O. rufipogon was controlled by the Black hull4 (Bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between O. rufipogon W1943 (black hull) and O. sativa indica cv Guangluai 4 (straw-white hull). Bh4 encodes an amino acid transporter. A 22-bp deletion within exon 3 of the bh4 variant disrupted the Bh4 function, leading to the straw-white hull in cultivated rice. Transgenic study indicated that Bh4 could restore the black pigment on hulls in cv Guangluai 4 and Kasalath. Bh4 sequence alignment of all taxa with the outgroup Oryza barthii showed that the wild rice maintained comparable levels of nucleotide diversity that were about 70 times higher than those in the cultivated rice. The results from the maximum likelihood Hudson-Kreitman-Aguade test suggested that the significant reduction in nucleotide diversity in rice cultivars could be caused by artificial selection. We propose that the straw-white hull was selected as an important visual phenotype of nonshattered grains during rice domestication.</description><subject>Agriculture</subject><subject>Amino Acid Transport Systems</subject><subject>Biological and medical sciences</subject><subject>Cloning, Molecular</subject><subject>Crops, Agricultural - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genes, Plant - genetics</subject><subject>Genetic loci</subject><subject>Genetic mutation</subject><subject>GENETICS, GENOMICS, AND MOLECULAR EVOLUTION</subject><subject>Geography</subject><subject>Grains</subject><subject>Inbreeding</subject><subject>Molecular Sequence Data</subject><subject>Mutation - genetics</subject><subject>Nucleotides - genetics</subject><subject>Organ Specificity - genetics</subject><subject>Oryza</subject><subject>Oryza - genetics</subject><subject>Oryza barthii</subject><subject>Oryza rufipogon</subject><subject>Oryza sativa</subject><subject>Phenotype</subject><subject>Phylogeny</subject><subject>Pigmentation - genetics</subject><subject>Plant domestication</subject><subject>Plant physiology and development</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Plants</subject><subject>Plants, Genetically Modified</subject><subject>Polymerase chain reaction</subject><subject>Rice</subject><subject>Rice hulls</subject><subject>RNA, Messenger - genetics</subject><subject>RNA, Messenger - metabolism</subject><subject>Seeds</subject><subject>Seeds - anatomy & histology</subject><subject>Seeds - genetics</subject><subject>Sequence Homology, Nucleic Acid</subject><subject>Wild rice</subject><issn>0032-0889</issn><issn>1532-2548</issn><issn>1532-2548</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFks1vEzEUxC0EoqFw5Aj4gjhtef5c-1IJArRIlZBIK8TJchy7ddldL_YGxH-Pw4YAJ07P0vw8fqMxQo8JnBAC_OU47uYJkUoA3EELIhhtqODqLloA1DMopY_Qg1JuAYAwwu-jI0qoZMDUAn0-84OfosPLNEw5dTgFbPFltkOJU0wDDjn1-HVn3Rc8Jbyasv3efLqJk8cr7zf4fNt1OA74Y3Qev0m9L9XM7m4-RPeC7Yp_tJ_H6Ord28vleXPx4ez98tVF44SEqQmWt8z61nvthGKMB-uAbEB7HkA6aINfq-CoF0RoJQhtq9QqyjSngdA1O0ans--4Xfd-43zNYTsz5tjb_MMkG82_yhBvzHX6ZhhwKVRbDV7sDXL6uq0BTB-L811nB5-2xWipiGSKkf-SSgiiW611JZuZdDmVkn047EPA7Hoz47ibZu6t8k__DnGgfxdVged7wBZnu1ALcrH84ZiWoKWs3JOZuy1TygedE844_fXQs1kPNhl7navH1YrWfwFEc6VBsp9Xo7K4</recordid><startdate>20110301</startdate><enddate>20110301</enddate><creator>Zhu, Bo-Feng</creator><creator>Si, Lizhen</creator><creator>Wang, Zixuan</creator><creator>Jingjie Zhu, Yan Zhou</creator><creator>Shangguan, Yingying</creator><creator>Lu, Danfeng</creator><creator>Fan, Danlin</creator><creator>Li, Canyang</creator><creator>Lin, Hongxuan</creator><creator>Qian, Qian</creator><creator>Sang, Tao</creator><creator>Zhou, Bo</creator><creator>Minobe, Yuzo</creator><creator>Han, Bin</creator><general>American Society of Plant Biologists</general><scope>FBQ</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>20110301</creationdate><title>Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication</title><author>Zhu, Bo-Feng ; Si, Lizhen ; Wang, Zixuan ; Jingjie Zhu, Yan Zhou ; Shangguan, Yingying ; Lu, Danfeng ; Fan, Danlin ; Li, Canyang ; Lin, Hongxuan ; Qian, Qian ; Sang, Tao ; Zhou, Bo ; Minobe, Yuzo ; Han, Bin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c560t-fa473ae7ee9c58334fac01d09e4f06c07feb8fc2e51598512709e7823942f12b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Agriculture</topic><topic>Amino Acid Transport Systems</topic><topic>Biological and medical sciences</topic><topic>Cloning, Molecular</topic><topic>Crops, Agricultural - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Expression Regulation, Plant</topic><topic>Genes, Plant - genetics</topic><topic>Genetic loci</topic><topic>Genetic mutation</topic><topic>GENETICS, GENOMICS, AND MOLECULAR EVOLUTION</topic><topic>Geography</topic><topic>Grains</topic><topic>Inbreeding</topic><topic>Molecular Sequence Data</topic><topic>Mutation - genetics</topic><topic>Nucleotides - genetics</topic><topic>Organ Specificity - genetics</topic><topic>Oryza</topic><topic>Oryza - genetics</topic><topic>Oryza barthii</topic><topic>Oryza rufipogon</topic><topic>Oryza sativa</topic><topic>Phenotype</topic><topic>Phylogeny</topic><topic>Pigmentation - genetics</topic><topic>Plant domestication</topic><topic>Plant physiology and development</topic><topic>Plant Proteins - genetics</topic><topic>Plant Proteins - metabolism</topic><topic>Plants</topic><topic>Plants, Genetically Modified</topic><topic>Polymerase chain reaction</topic><topic>Rice</topic><topic>Rice hulls</topic><topic>RNA, Messenger - genetics</topic><topic>RNA, Messenger - metabolism</topic><topic>Seeds</topic><topic>Seeds - anatomy & histology</topic><topic>Seeds - genetics</topic><topic>Sequence Homology, Nucleic Acid</topic><topic>Wild rice</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhu, Bo-Feng</creatorcontrib><creatorcontrib>Si, Lizhen</creatorcontrib><creatorcontrib>Wang, Zixuan</creatorcontrib><creatorcontrib>Jingjie Zhu, Yan Zhou</creatorcontrib><creatorcontrib>Shangguan, Yingying</creatorcontrib><creatorcontrib>Lu, Danfeng</creatorcontrib><creatorcontrib>Fan, Danlin</creatorcontrib><creatorcontrib>Li, Canyang</creatorcontrib><creatorcontrib>Lin, Hongxuan</creatorcontrib><creatorcontrib>Qian, Qian</creatorcontrib><creatorcontrib>Sang, Tao</creatorcontrib><creatorcontrib>Zhou, Bo</creatorcontrib><creatorcontrib>Minobe, Yuzo</creatorcontrib><creatorcontrib>Han, Bin</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Plant physiology (Bethesda)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhu, Bo-Feng</au><au>Si, Lizhen</au><au>Wang, Zixuan</au><au>Jingjie Zhu, Yan Zhou</au><au>Shangguan, Yingying</au><au>Lu, Danfeng</au><au>Fan, Danlin</au><au>Li, Canyang</au><au>Lin, Hongxuan</au><au>Qian, Qian</au><au>Sang, Tao</au><au>Zhou, Bo</au><au>Minobe, Yuzo</au><au>Han, Bin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication</atitle><jtitle>Plant physiology (Bethesda)</jtitle><addtitle>Plant Physiol</addtitle><date>2011-03-01</date><risdate>2011</risdate><volume>155</volume><issue>3</issue><spage>1301</spage><epage>1311</epage><pages>1301-1311</pages><issn>0032-0889</issn><issn>1532-2548</issn><eissn>1532-2548</eissn><coden>PPHYA5</coden><abstract>The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. We report that the black hull of O. rufipogon was controlled by the Black hull4 (Bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between O. rufipogon W1943 (black hull) and O. sativa indica cv Guangluai 4 (straw-white hull). Bh4 encodes an amino acid transporter. A 22-bp deletion within exon 3 of the bh4 variant disrupted the Bh4 function, leading to the straw-white hull in cultivated rice. Transgenic study indicated that Bh4 could restore the black pigment on hulls in cv Guangluai 4 and Kasalath. Bh4 sequence alignment of all taxa with the outgroup Oryza barthii showed that the wild rice maintained comparable levels of nucleotide diversity that were about 70 times higher than those in the cultivated rice. The results from the maximum likelihood Hudson-Kreitman-Aguade test suggested that the significant reduction in nucleotide diversity in rice cultivars could be caused by artificial selection. We propose that the straw-white hull was selected as an important visual phenotype of nonshattered grains during rice domestication.</abstract><cop>Rockville, MD</cop><pub>American Society of Plant Biologists</pub><pmid>21263038</pmid><doi>10.1104/pp.110.168500</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Agriculture Amino Acid Transport Systems Biological and medical sciences Cloning, Molecular Crops, Agricultural - genetics Fundamental and applied biological sciences. Psychology Gene Expression Regulation, Plant Genes, Plant - genetics Genetic loci Genetic mutation GENETICS, GENOMICS, AND MOLECULAR EVOLUTION Geography Grains Inbreeding Molecular Sequence Data Mutation - genetics Nucleotides - genetics Organ Specificity - genetics Oryza Oryza - genetics Oryza barthii Oryza rufipogon Oryza sativa Phenotype Phylogeny Pigmentation - genetics Plant domestication Plant physiology and development Plant Proteins - genetics Plant Proteins - metabolism Plants Plants, Genetically Modified Polymerase chain reaction Rice Rice hulls RNA, Messenger - genetics RNA, Messenger - metabolism Seeds Seeds - anatomy & histology Seeds - genetics Sequence Homology, Nucleic Acid Wild rice |
title | Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication |
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