Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection
Identifieur interne : 000055 ( Main/Exploration ); précédent : 000054; suivant : 000056Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection
Auteurs : Jorge Duitama [Colombie] ; Alexander Silva [Colombie] ; Yamid Sanabria [États-Unis] ; Daniel Felipe Cruz [Colombie] ; Constanza Quintero [Colombie] ; Carolina Ballen [Colombie] ; Mathias Lorieux [Colombie, France] ; Brian Scheffler [États-Unis] ; Andrew Farmer [États-Unis] ; Edgar Torres [Colombie] ; James Oard [États-Unis] ; Joe Tohme [Colombie]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of
Url:
DOI: 10.1371/journal.pone.0124617
PubMed: 25923345
PubMed Central: 4414565
Affiliations:
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Tropical Agriculture, Cali</wicri:regionArea><wicri:noRegion>Cali</wicri:noRegion></affiliation></author><author><name sortKey="Silva, Alexander" sort="Silva, Alexander" uniqKey="Silva A" first="Alexander" last="Silva">Alexander Silva</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia</addr-line></nlm:aff><country xml:lang="fr">Colombie</country><wicri:regionArea>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali</wicri:regionArea><wicri:noRegion>Cali</wicri:noRegion></affiliation></author><author><name sortKey="Sanabria, Yamid" sort="Sanabria, Yamid" uniqKey="Sanabria Y" first="Yamid" last="Sanabria">Yamid Sanabria</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Rice Research Station, Louisiana State University Agricultural Center, Rayne, Louisiana, United States of America</addr-line></nlm:aff><country 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id="aff001"><addr-line>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia</addr-line></nlm:aff><country xml:lang="fr">Colombie</country><wicri:regionArea>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali</wicri:regionArea><wicri:noRegion>Cali</wicri:noRegion></affiliation></author><author><name sortKey="Ballen, Carolina" sort="Ballen, Carolina" uniqKey="Ballen C" first="Carolina" last="Ballen">Carolina Ballen</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia</addr-line></nlm:aff><country xml:lang="fr">Colombie</country><wicri:regionArea>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali</wicri:regionArea><wicri:noRegion>Cali</wicri:noRegion></affiliation></author><author><name sortKey="Lorieux, Mathias" sort="Lorieux, Mathias" uniqKey="Lorieux M" first="Mathias" last="Lorieux">Mathias Lorieux</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia</addr-line></nlm:aff><country xml:lang="fr">Colombie</country><wicri:regionArea>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali</wicri:regionArea><wicri:noRegion>Cali</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff005"><addr-line>Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement, Montpellier, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement, Montpellier</wicri:regionArea><placeName><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Scheffler, Brian" sort="Scheffler, Brian" uniqKey="Scheffler B" first="Brian" last="Scheffler">Brian Scheffler</name><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>Genomics and Bioinformatics Research Unit, Agricultural Research Service, United States Department of Agriculture, Jamie Whitten Delta States Research Center, Stoneville, Mississippi, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genomics and Bioinformatics Research Unit, Agricultural Research Service, United States Department of Agriculture, Jamie Whitten Delta States Research Center, Stoneville, Mississippi</wicri:regionArea><placeName><region type="state">État du Mississippi</region></placeName></affiliation></author><author><name sortKey="Farmer, Andrew" sort="Farmer, Andrew" uniqKey="Farmer A" first="Andrew" last="Farmer">Andrew Farmer</name><affiliation wicri:level="2"><nlm:aff id="aff004"><addr-line>National Center for Genome Resources, Santa Fe, New Mexico, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Genome Resources, Santa Fe, New Mexico</wicri:regionArea><placeName><region type="state">Nouveau-Mexique</region></placeName></affiliation></author><author><name sortKey="Torres, Edgar" sort="Torres, Edgar" uniqKey="Torres E" first="Edgar" last="Torres">Edgar Torres</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia</addr-line></nlm:aff><country xml:lang="fr">Colombie</country><wicri:regionArea>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali</wicri:regionArea><wicri:noRegion>Cali</wicri:noRegion></affiliation></author><author><name sortKey="Oard, James" sort="Oard, James" uniqKey="Oard J" first="James" last="Oard">James Oard</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Rice Research Station, Louisiana State University Agricultural Center, Rayne, Louisiana, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Rice Research Station, Louisiana State University Agricultural Center, Rayne, Louisiana</wicri:regionArea><placeName><region type="state">Louisiane</region></placeName></affiliation></author><author><name sortKey="Tohme, Joe" sort="Tohme, Joe" uniqKey="Tohme J" first="Joe" last="Tohme">Joe Tohme</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia</addr-line></nlm:aff><country xml:lang="fr">Colombie</country><wicri:regionArea>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali</wicri:regionArea><wicri:noRegion>Cali</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of <italic>Oryza sativa</italic>. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within <italic>O. sativa</italic> allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene <italic>GBSSI</italic>, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Abe, A" uniqKey="Abe A">A Abe</name></author><author><name sortKey="Kosugi, S" uniqKey="Kosugi S">S Kosugi</name></author><author><name sortKey="Yoshida, K" uniqKey="Yoshida K">K Yoshida</name></author><author><name sortKey="Natsume, S" uniqKey="Natsume S">S Natsume</name></author><author><name sortKey="Takagi, H" uniqKey="Takagi H">H Takagi</name></author><author><name sortKey="Kanzaki, H" uniqKey="Kanzaki H">H Kanzaki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="He, Z" uniqKey="He Z">Z He</name></author><author><name sortKey="Zhai, W" uniqKey="Zhai W">W Zhai</name></author><author><name sortKey="Wen, H" uniqKey="Wen H">H 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Mississippi</li></region><settlement><li>Montpellier</li></settlement></list><tree><country name="Colombie"><noRegion><name sortKey="Duitama, Jorge" sort="Duitama, Jorge" uniqKey="Duitama J" first="Jorge" last="Duitama">Jorge Duitama</name></noRegion><name sortKey="Ballen, Carolina" sort="Ballen, Carolina" uniqKey="Ballen C" first="Carolina" last="Ballen">Carolina Ballen</name><name sortKey="Cruz, Daniel Felipe" sort="Cruz, Daniel Felipe" uniqKey="Cruz D" first="Daniel Felipe" last="Cruz">Daniel Felipe Cruz</name><name sortKey="Lorieux, Mathias" sort="Lorieux, Mathias" uniqKey="Lorieux M" first="Mathias" last="Lorieux">Mathias Lorieux</name><name sortKey="Quintero, Constanza" sort="Quintero, Constanza" uniqKey="Quintero C" first="Constanza" last="Quintero">Constanza Quintero</name><name sortKey="Silva, Alexander" sort="Silva, Alexander" uniqKey="Silva A" first="Alexander" last="Silva">Alexander Silva</name><name sortKey="Tohme, Joe" sort="Tohme, Joe" uniqKey="Tohme J" first="Joe" last="Tohme">Joe Tohme</name><name sortKey="Torres, Edgar" sort="Torres, Edgar" uniqKey="Torres E" first="Edgar" last="Torres">Edgar Torres</name></country><country name="États-Unis"><region name="Louisiane"><name sortKey="Sanabria, Yamid" sort="Sanabria, Yamid" uniqKey="Sanabria Y" first="Yamid" last="Sanabria">Yamid Sanabria</name></region><name sortKey="Farmer, Andrew" sort="Farmer, Andrew" uniqKey="Farmer A" first="Andrew" last="Farmer">Andrew Farmer</name><name sortKey="Oard, James" sort="Oard, James" uniqKey="Oard J" first="James" last="Oard">James Oard</name><name sortKey="Scheffler, Brian" sort="Scheffler, Brian" uniqKey="Scheffler B" first="Brian" last="Scheffler">Brian Scheffler</name></country><country name="France"><noRegion><name sortKey="Lorieux, Mathias" sort="Lorieux, Mathias" uniqKey="Lorieux M" first="Mathias" last="Lorieux">Mathias Lorieux</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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