Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits
We investigated the nuclear simple sequence repeat (SSR) genotypes of 532 rice ( Oryza sativa L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in O. s...
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| Veröffentlicht in: | Scientific reports 2015-06, Vol.5 (1), p.11254-11254, Article 11254 |
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| creator | Dang, Xiaojing Giang Tran Thi, Thu Mawuli Edzesi, Wisdom Liang, Lijun Liu, Qiangming Liu, Erbao Wang, Yang Qiang, Sheng Liu, Linglong Hong, Delin |
| description | We investigated the nuclear simple sequence repeat (SSR) genotypes of 532 rice (
Oryza sativa
L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in
O. sativa
from low to high latitudes, with levels of linkage disequilibrium (LD) in the 6 subpopulations ranging from 10 to 30 cM. We then investigated the phenotypic data for grain length, grain width, grain thickness and 1,000-grain weight over 4 years. Using a genome-wide association analysis, we identified 17 marker-trait associations involving 14 SSR markers on 12 chromosome arms and 8 of the 17 associations were novel. The elite alleles were mined based on the phenotypic effects of the detected quantitative trait loci (QTLs). These elite alleles could be used to improve target traits through optimal cross designs, with the expected results obtained by pyramiding or substituting the elite alleles per QTL (independent of possible epistatic effects). Together, these results provide an in-depth understanding of the genetic diversity pattern among rice-grain traits across a broad geographic scale, which has potential use in future research work, including studies related to germplasm conservation and molecular breeding by design. |
| doi_str_mv | 10.1038/srep11254 |
| format | Article |
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Oryza sativa
L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in
O. sativa
from low to high latitudes, with levels of linkage disequilibrium (LD) in the 6 subpopulations ranging from 10 to 30 cM. We then investigated the phenotypic data for grain length, grain width, grain thickness and 1,000-grain weight over 4 years. Using a genome-wide association analysis, we identified 17 marker-trait associations involving 14 SSR markers on 12 chromosome arms and 8 of the 17 associations were novel. The elite alleles were mined based on the phenotypic effects of the detected quantitative trait loci (QTLs). These elite alleles could be used to improve target traits through optimal cross designs, with the expected results obtained by pyramiding or substituting the elite alleles per QTL (independent of possible epistatic effects). Together, these results provide an in-depth understanding of the genetic diversity pattern among rice-grain traits across a broad geographic scale, which has potential use in future research work, including studies related to germplasm conservation and molecular breeding by design.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/srep11254</identifier><identifier>PMID: 26059752</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>45 ; 631/208 ; 631/208/205/2138 ; Alleles ; Asia ; Association analysis ; Epistasis ; Evolution ; Gene loci ; Genes, Plant ; Genetic diversity ; Genetic structure ; Genomes ; Genotype & phenotype ; Genotypes ; Germplasm ; Humanities and Social Sciences ; Linkage disequilibrium ; multidisciplinary ; Oryza - genetics ; Oryza sativa ; Plant breeding ; Population genetics ; Quantitative Trait Loci ; Science ; Subpopulations</subject><ispartof>Scientific reports, 2015-06, Vol.5 (1), p.11254-11254, Article 11254</ispartof><rights>The Author(s) 2015</rights><rights>Copyright Nature Publishing Group Jun 2015</rights><rights>Copyright © 2015, Macmillan Publishers Limited 2015 Macmillan Publishers Limited</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c504t-5c03485a05a4ce3de844b5d1588e11c1d0277c71f486a770aae82e1787416a6c3</citedby><cites>FETCH-LOGICAL-c504t-5c03485a05a4ce3de844b5d1588e11c1d0277c71f486a770aae82e1787416a6c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4462027/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4462027/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,41120,42189,51576,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26059752$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dang, Xiaojing</creatorcontrib><creatorcontrib>Giang Tran Thi, Thu</creatorcontrib><creatorcontrib>Mawuli Edzesi, Wisdom</creatorcontrib><creatorcontrib>Liang, Lijun</creatorcontrib><creatorcontrib>Liu, Qiangming</creatorcontrib><creatorcontrib>Liu, Erbao</creatorcontrib><creatorcontrib>Wang, Yang</creatorcontrib><creatorcontrib>Qiang, Sheng</creatorcontrib><creatorcontrib>Liu, Linglong</creatorcontrib><creatorcontrib>Hong, Delin</creatorcontrib><title>Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>We investigated the nuclear simple sequence repeat (SSR) genotypes of 532 rice (
Oryza sativa
L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in
O. sativa
from low to high latitudes, with levels of linkage disequilibrium (LD) in the 6 subpopulations ranging from 10 to 30 cM. We then investigated the phenotypic data for grain length, grain width, grain thickness and 1,000-grain weight over 4 years. Using a genome-wide association analysis, we identified 17 marker-trait associations involving 14 SSR markers on 12 chromosome arms and 8 of the 17 associations were novel. The elite alleles were mined based on the phenotypic effects of the detected quantitative trait loci (QTLs). These elite alleles could be used to improve target traits through optimal cross designs, with the expected results obtained by pyramiding or substituting the elite alleles per QTL (independent of possible epistatic effects). Together, these results provide an in-depth understanding of the genetic diversity pattern among rice-grain traits across a broad geographic scale, which has potential use in future research work, including studies related to germplasm conservation and molecular breeding by design.</description><subject>45</subject><subject>631/208</subject><subject>631/208/205/2138</subject><subject>Alleles</subject><subject>Asia</subject><subject>Association analysis</subject><subject>Epistasis</subject><subject>Evolution</subject><subject>Gene loci</subject><subject>Genes, Plant</subject><subject>Genetic diversity</subject><subject>Genetic structure</subject><subject>Genomes</subject><subject>Genotype & phenotype</subject><subject>Genotypes</subject><subject>Germplasm</subject><subject>Humanities and Social Sciences</subject><subject>Linkage disequilibrium</subject><subject>multidisciplinary</subject><subject>Oryza - genetics</subject><subject>Oryza sativa</subject><subject>Plant breeding</subject><subject>Population genetics</subject><subject>Quantitative Trait Loci</subject><subject>Science</subject><subject>Subpopulations</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNplkV1rVDEQhoMottRe-Ack4I0V1iY5-To3QinVFgotqNchzZmzTckma5KzsPrnzXbrstpcJJnMk3dmeBF6S8knSjp9WjIsKWWCv0CHjHAxYx1jL_fuB-i4lAfSlmA9p_1rdMAkEb0S7BD9vk3LKdjqU8RziFC9w6XmydUpA04jvsnrXxaXRqws9hFf2FKxjQP-lqZ6D5vorHj7-NRiPPji0gryevMZgq-AbQgQoOAxZTzPtonUttfyBr0abShw_HQeoR9fLr6fX86ub75enZ9dz5wgvM6EIx3XwhJhuYNuAM35nRio0BoodXQgTCmn6Mi1tEoRa0EzoEorTqWVrjtCn7e6y-luAYOD2OoHs8x-YfPaJOvNv5no7808rQznkjXxJvDhSSCnnxOUahZtSgjBRkhTMVRqJYUQXDf0_X_oQ5pybOMZqvteSC4Vb9TJlnI5lWbguGuGErNx1excbey7_e535F8PG_BxC5SWinPIeyWfqf0BV56s8A</recordid><startdate>20150610</startdate><enddate>20150610</enddate><creator>Dang, Xiaojing</creator><creator>Giang Tran Thi, Thu</creator><creator>Mawuli Edzesi, Wisdom</creator><creator>Liang, Lijun</creator><creator>Liu, Qiangming</creator><creator>Liu, Erbao</creator><creator>Wang, Yang</creator><creator>Qiang, Sheng</creator><creator>Liu, Linglong</creator><creator>Hong, Delin</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</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>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20150610</creationdate><title>Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits</title><author>Dang, Xiaojing ; Giang Tran Thi, Thu ; Mawuli Edzesi, Wisdom ; Liang, Lijun ; Liu, Qiangming ; Liu, Erbao ; Wang, Yang ; Qiang, Sheng ; Liu, Linglong ; Hong, Delin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c504t-5c03485a05a4ce3de844b5d1588e11c1d0277c71f486a770aae82e1787416a6c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>45</topic><topic>631/208</topic><topic>631/208/205/2138</topic><topic>Alleles</topic><topic>Asia</topic><topic>Association analysis</topic><topic>Epistasis</topic><topic>Evolution</topic><topic>Gene loci</topic><topic>Genes, Plant</topic><topic>Genetic diversity</topic><topic>Genetic structure</topic><topic>Genomes</topic><topic>Genotype & phenotype</topic><topic>Genotypes</topic><topic>Germplasm</topic><topic>Humanities and Social Sciences</topic><topic>Linkage disequilibrium</topic><topic>multidisciplinary</topic><topic>Oryza - genetics</topic><topic>Oryza sativa</topic><topic>Plant breeding</topic><topic>Population genetics</topic><topic>Quantitative Trait Loci</topic><topic>Science</topic><topic>Subpopulations</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dang, Xiaojing</creatorcontrib><creatorcontrib>Giang Tran Thi, Thu</creatorcontrib><creatorcontrib>Mawuli Edzesi, Wisdom</creatorcontrib><creatorcontrib>Liang, Lijun</creatorcontrib><creatorcontrib>Liu, Qiangming</creatorcontrib><creatorcontrib>Liu, Erbao</creatorcontrib><creatorcontrib>Wang, Yang</creatorcontrib><creatorcontrib>Qiang, Sheng</creatorcontrib><creatorcontrib>Liu, Linglong</creatorcontrib><creatorcontrib>Hong, Delin</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</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>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content 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>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dang, Xiaojing</au><au>Giang Tran Thi, Thu</au><au>Mawuli Edzesi, Wisdom</au><au>Liang, Lijun</au><au>Liu, Qiangming</au><au>Liu, Erbao</au><au>Wang, Yang</au><au>Qiang, Sheng</au><au>Liu, Linglong</au><au>Hong, Delin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2015-06-10</date><risdate>2015</risdate><volume>5</volume><issue>1</issue><spage>11254</spage><epage>11254</epage><pages>11254-11254</pages><artnum>11254</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>We investigated the nuclear simple sequence repeat (SSR) genotypes of 532 rice (
Oryza sativa
L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in
O. sativa
from low to high latitudes, with levels of linkage disequilibrium (LD) in the 6 subpopulations ranging from 10 to 30 cM. We then investigated the phenotypic data for grain length, grain width, grain thickness and 1,000-grain weight over 4 years. Using a genome-wide association analysis, we identified 17 marker-trait associations involving 14 SSR markers on 12 chromosome arms and 8 of the 17 associations were novel. The elite alleles were mined based on the phenotypic effects of the detected quantitative trait loci (QTLs). These elite alleles could be used to improve target traits through optimal cross designs, with the expected results obtained by pyramiding or substituting the elite alleles per QTL (independent of possible epistatic effects). Together, these results provide an in-depth understanding of the genetic diversity pattern among rice-grain traits across a broad geographic scale, which has potential use in future research work, including studies related to germplasm conservation and molecular breeding by design.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>26059752</pmid><doi>10.1038/srep11254</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 45 631/208 631/208/205/2138 Alleles Asia Association analysis Epistasis Evolution Gene loci Genes, Plant Genetic diversity Genetic structure Genomes Genotype & phenotype Genotypes Germplasm Humanities and Social Sciences Linkage disequilibrium multidisciplinary Oryza - genetics Oryza sativa Plant breeding Population genetics Quantitative Trait Loci Science Subpopulations |
| title | Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits |
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