Genetic Diversity and Population Structure in a European Collection of Rice
ABSTRACT In southern Europe, rice (Oryza sativa L.) is grown as an irrigated crop in river deltas where it plays an important role in the agroecological equilibrium through soil desalinization. In these regions, rice is at the northern limit of its natural area of adaptation. Special cultivars are n...
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| Veröffentlicht in: | Crop science 2012-07, Vol.52 (4), p.1663-1675 |
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| creator | Courtois, Brigitte Frouin, Julien Greco, Raffaella Bruschi, Gianluca Droc, Gaëtan Hamelin, Chantal Ruiz, Manuel Clément, Guy Evrard, Jean‐Charles Coppenole, Sylvie Katsantonis, Dimitrios Oliveira, Margarida Negrão, Sónia Matos, Celina Cavigiolo, Stefano Lupotto, Elisabetta Piffanelli, Pietro Ahmadi, Nourollah |
| description | ABSTRACT
In southern Europe, rice (Oryza sativa L.) is grown as an irrigated crop in river deltas where it plays an important role in the agroecological equilibrium through soil desalinization. In these regions, rice is at the northern limit of its natural area of adaptation. Special cultivars are needed for these challenging conditions. Using model‐based and distance‐based approaches, we analyzed the genetic structure of the European Rice Germplasm Collection (ERGC), which is composed of 425 accessions, using 25 simple sequence repeat (SSR) markers. We compared it with a reference set of 50 accessions that are representative of the diversity of O. sativa. Most of the ERGC accessions (89%) clustered with japonica types. The ERGC japonica accessions were classified into three groups: one group close to rice types of tropical origin that are found in the United States and Argentina and two groups of temperate origin showing less differentiation. The three japonica groups could be characterized according to their grain type and maturity class, which are the most strongly selected traits in European breeding programs. We extracted a core collection of 250 japonica accessions and characterized it using 70 single nucleotide polymorphisms (SNPs). The SSR and SNP dissimilarity matrices coincided reasonably well and for the best‐supported structure, the percentages of admixture were highly correlated. The core collection can be used as an association panel to search for alleles of interest for temperate areas or as a training population for genomic selection. |
| doi_str_mv | 10.2135/cropsci2011.11.0588 |
| format | Article |
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In southern Europe, rice (Oryza sativa L.) is grown as an irrigated crop in river deltas where it plays an important role in the agroecological equilibrium through soil desalinization. In these regions, rice is at the northern limit of its natural area of adaptation. Special cultivars are needed for these challenging conditions. Using model‐based and distance‐based approaches, we analyzed the genetic structure of the European Rice Germplasm Collection (ERGC), which is composed of 425 accessions, using 25 simple sequence repeat (SSR) markers. We compared it with a reference set of 50 accessions that are representative of the diversity of O. sativa. Most of the ERGC accessions (89%) clustered with japonica types. The ERGC japonica accessions were classified into three groups: one group close to rice types of tropical origin that are found in the United States and Argentina and two groups of temperate origin showing less differentiation. The three japonica groups could be characterized according to their grain type and maturity class, which are the most strongly selected traits in European breeding programs. We extracted a core collection of 250 japonica accessions and characterized it using 70 single nucleotide polymorphisms (SNPs). The SSR and SNP dissimilarity matrices coincided reasonably well and for the best‐supported structure, the percentages of admixture were highly correlated. The core collection can be used as an association panel to search for alleles of interest for temperate areas or as a training population for genomic selection.</description><identifier>ISSN: 0011-183X</identifier><identifier>EISSN: 1435-0653</identifier><identifier>DOI: 10.2135/cropsci2011.11.0588</identifier><identifier>CODEN: CRPSAY</identifier><language>eng</language><publisher>Madison, WI: The Crop Science Society of America, Inc</publisher><subject>Agronomy. Soil science and plant productions ; Biological and medical sciences ; Collections ; Cultivars ; Deltas ; Fundamental and applied biological sciences. Psychology ; Generalities. Genetics. Plant material ; Genetic diversity ; Genetic resources, diversity ; Genetic structure ; Genetics and breeding of economic plants ; Grain ; Plant material ; Population structure ; Rice ; Rural development ; Salinity</subject><ispartof>Crop science, 2012-07, Vol.52 (4), p.1663-1675</ispartof><rights>Copyright © by the Crop Science Society of America, Inc.</rights><rights>2015 INIST-CNRS</rights><rights>Copyright American Society of Agronomy Jul/Aug 2012</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4368-236f5facb4fa22fbf064f6a47adb2fd0782627cd442d81957d5c34e90f0a9a8f3</citedby><cites>FETCH-LOGICAL-c4368-236f5facb4fa22fbf064f6a47adb2fd0782627cd442d81957d5c34e90f0a9a8f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.2135%2Fcropsci2011.11.0588$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.2135%2Fcropsci2011.11.0588$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=26106980$$DView record in Pascal Francis$$Hfree_for_read</backlink></links><search><creatorcontrib>Courtois, Brigitte</creatorcontrib><creatorcontrib>Frouin, Julien</creatorcontrib><creatorcontrib>Greco, Raffaella</creatorcontrib><creatorcontrib>Bruschi, Gianluca</creatorcontrib><creatorcontrib>Droc, Gaëtan</creatorcontrib><creatorcontrib>Hamelin, Chantal</creatorcontrib><creatorcontrib>Ruiz, Manuel</creatorcontrib><creatorcontrib>Clément, Guy</creatorcontrib><creatorcontrib>Evrard, Jean‐Charles</creatorcontrib><creatorcontrib>Coppenole, Sylvie</creatorcontrib><creatorcontrib>Katsantonis, Dimitrios</creatorcontrib><creatorcontrib>Oliveira, Margarida</creatorcontrib><creatorcontrib>Negrão, Sónia</creatorcontrib><creatorcontrib>Matos, Celina</creatorcontrib><creatorcontrib>Cavigiolo, Stefano</creatorcontrib><creatorcontrib>Lupotto, Elisabetta</creatorcontrib><creatorcontrib>Piffanelli, Pietro</creatorcontrib><creatorcontrib>Ahmadi, Nourollah</creatorcontrib><title>Genetic Diversity and Population Structure in a European Collection of Rice</title><title>Crop science</title><description>ABSTRACT
In southern Europe, rice (Oryza sativa L.) is grown as an irrigated crop in river deltas where it plays an important role in the agroecological equilibrium through soil desalinization. In these regions, rice is at the northern limit of its natural area of adaptation. Special cultivars are needed for these challenging conditions. Using model‐based and distance‐based approaches, we analyzed the genetic structure of the European Rice Germplasm Collection (ERGC), which is composed of 425 accessions, using 25 simple sequence repeat (SSR) markers. We compared it with a reference set of 50 accessions that are representative of the diversity of O. sativa. Most of the ERGC accessions (89%) clustered with japonica types. The ERGC japonica accessions were classified into three groups: one group close to rice types of tropical origin that are found in the United States and Argentina and two groups of temperate origin showing less differentiation. The three japonica groups could be characterized according to their grain type and maturity class, which are the most strongly selected traits in European breeding programs. We extracted a core collection of 250 japonica accessions and characterized it using 70 single nucleotide polymorphisms (SNPs). The SSR and SNP dissimilarity matrices coincided reasonably well and for the best‐supported structure, the percentages of admixture were highly correlated. The core collection can be used as an association panel to search for alleles of interest for temperate areas or as a training population for genomic selection.</description><subject>Agronomy. Soil science and plant productions</subject><subject>Biological and medical sciences</subject><subject>Collections</subject><subject>Cultivars</subject><subject>Deltas</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Generalities. Genetics. Plant material</subject><subject>Genetic diversity</subject><subject>Genetic resources, diversity</subject><subject>Genetic structure</subject><subject>Genetics and breeding of economic plants</subject><subject>Grain</subject><subject>Plant material</subject><subject>Population structure</subject><subject>Rice</subject><subject>Rural development</subject><subject>Salinity</subject><issn>0011-183X</issn><issn>1435-0653</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqNkN1LwzAUxYMoOKd_gS8B8bEz300fpW5zONjYFHwrWZpARm1r0ir7780-EB-FCxfu_Z1z4ABwi9GIYMoftG_aoB1BGI_iIC7lGRhgRnmCBKfnYIDiK8GSvl-CqxC2CKE0S_kAvExNbTqn4ZP7Mj64bgdVXcJl0_aV6lxTw3Xne9313kBXQwXHfcwyqoZ5U1VGH5DGwpXT5hpcWFUFc3PaQ_A2Gb_mz8l8MZ3lj_NEMypkQqiw3Cq9YVYRYjcWCWaFYqkqN8SWKJVEkFSXjJFS4oynJdeUmQxZpDIlLR2Cu6Nv65vP3oSu2Da9r2NkgRGJMk4yFil6pGI5IXhji9a7D-V3ESr2rRV_Wivi7FuLqvuTtwpaVdarWrvwKyUCI5FJFLnJkft2ldn9x7rI1znJV4vlOp_t7xgfAn8AKCKD4Q</recordid><startdate>201207</startdate><enddate>201207</enddate><creator>Courtois, Brigitte</creator><creator>Frouin, Julien</creator><creator>Greco, Raffaella</creator><creator>Bruschi, Gianluca</creator><creator>Droc, Gaëtan</creator><creator>Hamelin, Chantal</creator><creator>Ruiz, Manuel</creator><creator>Clément, Guy</creator><creator>Evrard, Jean‐Charles</creator><creator>Coppenole, Sylvie</creator><creator>Katsantonis, Dimitrios</creator><creator>Oliveira, Margarida</creator><creator>Negrão, Sónia</creator><creator>Matos, Celina</creator><creator>Cavigiolo, Stefano</creator><creator>Lupotto, Elisabetta</creator><creator>Piffanelli, Pietro</creator><creator>Ahmadi, Nourollah</creator><general>The Crop Science Society of America, Inc</general><general>Crop Science Society of America</general><general>American Society of Agronomy</general><scope>IQODW</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X2</scope><scope>7XB</scope><scope>88I</scope><scope>8AF</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FK</scope><scope>8G5</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>L6V</scope><scope>M0K</scope><scope>M2O</scope><scope>M2P</scope><scope>M7S</scope><scope>MBDVC</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>R05</scope><scope>S0X</scope></search><sort><creationdate>201207</creationdate><title>Genetic Diversity and Population Structure in a European Collection of Rice</title><author>Courtois, Brigitte ; Frouin, Julien ; Greco, Raffaella ; Bruschi, Gianluca ; Droc, Gaëtan ; Hamelin, Chantal ; Ruiz, Manuel ; Clément, Guy ; Evrard, Jean‐Charles ; Coppenole, Sylvie ; Katsantonis, Dimitrios ; Oliveira, Margarida ; Negrão, Sónia ; Matos, Celina ; Cavigiolo, Stefano ; Lupotto, Elisabetta ; Piffanelli, Pietro ; Ahmadi, Nourollah</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4368-236f5facb4fa22fbf064f6a47adb2fd0782627cd442d81957d5c34e90f0a9a8f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Agronomy. 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Plant material</topic><topic>Genetic diversity</topic><topic>Genetic resources, diversity</topic><topic>Genetic structure</topic><topic>Genetics and breeding of economic plants</topic><topic>Grain</topic><topic>Plant material</topic><topic>Population structure</topic><topic>Rice</topic><topic>Rural development</topic><topic>Salinity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Courtois, Brigitte</creatorcontrib><creatorcontrib>Frouin, Julien</creatorcontrib><creatorcontrib>Greco, Raffaella</creatorcontrib><creatorcontrib>Bruschi, Gianluca</creatorcontrib><creatorcontrib>Droc, Gaëtan</creatorcontrib><creatorcontrib>Hamelin, Chantal</creatorcontrib><creatorcontrib>Ruiz, Manuel</creatorcontrib><creatorcontrib>Clément, Guy</creatorcontrib><creatorcontrib>Evrard, Jean‐Charles</creatorcontrib><creatorcontrib>Coppenole, Sylvie</creatorcontrib><creatorcontrib>Katsantonis, Dimitrios</creatorcontrib><creatorcontrib>Oliveira, Margarida</creatorcontrib><creatorcontrib>Negrão, Sónia</creatorcontrib><creatorcontrib>Matos, Celina</creatorcontrib><creatorcontrib>Cavigiolo, Stefano</creatorcontrib><creatorcontrib>Lupotto, Elisabetta</creatorcontrib><creatorcontrib>Piffanelli, Pietro</creatorcontrib><creatorcontrib>Ahmadi, Nourollah</creatorcontrib><collection>Pascal-Francis</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Agricultural Science Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Engineering Collection</collection><collection>Agricultural Science Database</collection><collection>Research Library</collection><collection>Science Database</collection><collection>Engineering Database</collection><collection>Research Library (Corporate)</collection><collection>Environmental 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>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>University of Michigan</collection><collection>SIRS Editorial</collection><jtitle>Crop science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Courtois, Brigitte</au><au>Frouin, Julien</au><au>Greco, Raffaella</au><au>Bruschi, Gianluca</au><au>Droc, Gaëtan</au><au>Hamelin, Chantal</au><au>Ruiz, Manuel</au><au>Clément, Guy</au><au>Evrard, Jean‐Charles</au><au>Coppenole, Sylvie</au><au>Katsantonis, Dimitrios</au><au>Oliveira, Margarida</au><au>Negrão, Sónia</au><au>Matos, Celina</au><au>Cavigiolo, Stefano</au><au>Lupotto, Elisabetta</au><au>Piffanelli, Pietro</au><au>Ahmadi, Nourollah</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic Diversity and Population Structure in a European Collection of Rice</atitle><jtitle>Crop science</jtitle><date>2012-07</date><risdate>2012</risdate><volume>52</volume><issue>4</issue><spage>1663</spage><epage>1675</epage><pages>1663-1675</pages><issn>0011-183X</issn><eissn>1435-0653</eissn><coden>CRPSAY</coden><abstract>ABSTRACT
In southern Europe, rice (Oryza sativa L.) is grown as an irrigated crop in river deltas where it plays an important role in the agroecological equilibrium through soil desalinization. In these regions, rice is at the northern limit of its natural area of adaptation. Special cultivars are needed for these challenging conditions. Using model‐based and distance‐based approaches, we analyzed the genetic structure of the European Rice Germplasm Collection (ERGC), which is composed of 425 accessions, using 25 simple sequence repeat (SSR) markers. We compared it with a reference set of 50 accessions that are representative of the diversity of O. sativa. Most of the ERGC accessions (89%) clustered with japonica types. The ERGC japonica accessions were classified into three groups: one group close to rice types of tropical origin that are found in the United States and Argentina and two groups of temperate origin showing less differentiation. The three japonica groups could be characterized according to their grain type and maturity class, which are the most strongly selected traits in European breeding programs. We extracted a core collection of 250 japonica accessions and characterized it using 70 single nucleotide polymorphisms (SNPs). The SSR and SNP dissimilarity matrices coincided reasonably well and for the best‐supported structure, the percentages of admixture were highly correlated. The core collection can be used as an association panel to search for alleles of interest for temperate areas or as a training population for genomic selection.</abstract><cop>Madison, WI</cop><pub>The Crop Science Society of America, Inc</pub><doi>10.2135/cropsci2011.11.0588</doi><tpages>13</tpages></addata></record> |
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| subjects | Agronomy. Soil science and plant productions Biological and medical sciences Collections Cultivars Deltas Fundamental and applied biological sciences. Psychology Generalities. Genetics. Plant material Genetic diversity Genetic resources, diversity Genetic structure Genetics and breeding of economic plants Grain Plant material Population structure Rice Rural development Salinity |
| title | Genetic Diversity and Population Structure in a European Collection of Rice |
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