Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing
Identifieur interne : 000032 ( Main/Exploration ); précédent : 000031; suivant : 000033Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing
Auteurs : João Vitor Maldonado Dos Santos ; Babu Valliyodan [États-Unis] ; Trupti Joshi [États-Unis] ; Saad M. Khan [États-Unis] ; Yang Liu [États-Unis] ; Juexin Wang [États-Unis] ; Tri D. Vuong [États-Unis] ; Marcelo Fernandes De Oliveira ; Francismar Corrêa Marcelino-Guimarães ; Dong Xu [États-Unis] ; Henry T. Nguyen [États-Unis] ; Ricardo Vilela AbdelnoorSource :
- BMC Genomics [ 1471-2164 ] ; 2016.
Abstract
Soybean [
We resequenced the genomes of 28 Brazilian soybean cultivars with an average genome coverage of 14.8X. A total of 5,835,185 single nucleotide polymorphisms (SNPs) and 1,329,844 InDels were identified across the 20 soybean chromosomes, with 541,762 SNPs, 98,922 InDels and 1,093 CNVs that were exclusive to the 28 Brazilian cultivars. In addition, 668 allelic variations of 327 genes were shared among all of the Brazilian cultivars, including genes related to DNA-dependent transcription-elongation, photosynthesis, ATP synthesis-coupled electron transport, cellular respiration, and precursors of metabolite generation and energy. A very homogeneous structure was also observed for the Brazilian soybean germplasm, and we observed 41 regions putatively influenced by positive selection. Finally, we detected 3,880 regions with copy-number variations (CNVs) that could help to explain the divergence among the accessions evaluated.
The large number of allelic and structural variations identified in this study can be used in marker-assisted selection programs to detect unique SNPs for cultivar fingerprinting. The results presented here suggest that despite the diversification of modern Brazilian cultivars, the soybean germplasm remains very narrow because of the large number of genome regions that exhibit low diversity. These results emphasize the need to introduce new alleles to increase the genetic diversity of the Brazilian germplasm.
The online version of this article (doi:10.1186/s12864-016-2431-x) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-016-2431-x
PubMed: 26872939
PubMed Central: 4752768
Affiliations:
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Vuong</name><affiliation wicri:level="2"><nlm:aff id="Aff3">National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia</wicri:cityArea></affiliation></author><author><name sortKey="Oliveira, Marcelo Fernandes De" sort="Oliveira, Marcelo Fernandes De" uniqKey="Oliveira M" first="Marcelo Fernandes De" last="Oliveira">Marcelo Fernandes De Oliveira</name><affiliation><nlm:aff id="Aff1">Brazilian Corporation of Agricultural Research (Embrapa Soja), Carlos João Strass road, Warta County, PR Brazil</nlm:aff><wicri:noCountry code="subfield">PR Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Marcelino Guimaraes, Francismar Correa" sort="Marcelino Guimaraes, Francismar Correa" uniqKey="Marcelino Guimaraes F" first="Francismar Corrêa" last="Marcelino-Guimarães">Francismar Corrêa Marcelino-Guimarães</name><affiliation><nlm:aff id="Aff1">Brazilian Corporation of Agricultural Research (Embrapa Soja), Carlos João Strass road, Warta County, PR Brazil</nlm:aff><wicri:noCountry code="subfield">PR Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff5">Department of Computer Science, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>Department of Computer Science, University of Missouri, Columbia</wicri:cityArea></affiliation></author><author><name sortKey="Nguyen, Henry T" sort="Nguyen, Henry T" uniqKey="Nguyen H" first="Henry T." last="Nguyen">Henry T. Nguyen</name><affiliation wicri:level="2"><nlm:aff id="Aff3">National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff4">Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia</wicri:cityArea></affiliation></author><author><name sortKey="Abdelnoor, Ricardo Vilela" sort="Abdelnoor, Ricardo Vilela" uniqKey="Abdelnoor R" first="Ricardo Vilela" last="Abdelnoor">Ricardo Vilela Abdelnoor</name><affiliation><nlm:aff id="Aff1">Brazilian Corporation of Agricultural Research (Embrapa Soja), Carlos João Strass road, Warta County, PR Brazil</nlm:aff><wicri:noCountry code="subfield">PR Brazil</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil</nlm:aff><wicri:noCountry code="subfield">PR Brazil</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26872939</idno><idno type="pmc">4752768</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752768</idno><idno type="RBID">PMC:4752768</idno><idno type="doi">10.1186/s12864-016-2431-x</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000172</idno><idno type="wicri:Area/Pmc/Curation">000172</idno><idno type="wicri:Area/Pmc/Checkpoint">000030</idno><idno type="wicri:Area/Ncbi/Merge">000712</idno><idno type="wicri:Area/Ncbi/Curation">000712</idno><idno type="wicri:Area/Ncbi/Checkpoint">000712</idno><idno type="wicri:Area/Main/Merge">000032</idno><idno type="wicri:Area/Main/Curation">000032</idno><idno type="wicri:Area/Main/Exploration">000032</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing</title><author><name sortKey="Maldonado Dos Santos, Joao Vitor" sort="Maldonado Dos Santos, Joao Vitor" uniqKey="Maldonado Dos Santos J" first="João Vitor" last="Maldonado Dos Santos">João Vitor Maldonado Dos Santos</name><affiliation><nlm:aff id="Aff1">Brazilian Corporation of Agricultural Research (Embrapa Soja), Carlos João Strass road, Warta County, PR Brazil</nlm:aff><wicri:noCountry code="subfield">PR Brazil</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil</nlm:aff><wicri:noCountry code="subfield">PR Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Valliyodan, Babu" sort="Valliyodan, Babu" uniqKey="Valliyodan B" first="Babu" last="Valliyodan">Babu Valliyodan</name><affiliation wicri:level="2"><nlm:aff id="Aff3">National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia</wicri:cityArea></affiliation></author><author><name sortKey="Joshi, Trupti" sort="Joshi, Trupti" uniqKey="Joshi T" first="Trupti" last="Joshi">Trupti Joshi</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff5">Department of Computer Science, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>Department of Computer Science, University of Missouri, Columbia</wicri:cityArea></affiliation></author><author><name sortKey="Khan, Saad M" sort="Khan, Saad M" uniqKey="Khan S" first="Saad M." last="Khan">Saad M. Khan</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia</wicri:cityArea></affiliation></author><author><name sortKey="Liu, Yang" sort="Liu, Yang" uniqKey="Liu Y" first="Yang" last="Liu">Yang Liu</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia</wicri:cityArea></affiliation></author><author><name sortKey="Wang, Juexin" sort="Wang, Juexin" uniqKey="Wang J" first="Juexin" last="Wang">Juexin Wang</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia</wicri:cityArea></affiliation></author><author><name sortKey="Vuong, Tri D" sort="Vuong, Tri D" uniqKey="Vuong T" first="Tri D." last="Vuong">Tri D. Vuong</name><affiliation wicri:level="2"><nlm:aff id="Aff3">National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia</wicri:cityArea></affiliation></author><author><name sortKey="Oliveira, Marcelo Fernandes De" sort="Oliveira, Marcelo Fernandes De" uniqKey="Oliveira M" first="Marcelo Fernandes De" last="Oliveira">Marcelo Fernandes De Oliveira</name><affiliation><nlm:aff id="Aff1">Brazilian Corporation of Agricultural Research (Embrapa Soja), Carlos João Strass road, Warta County, PR Brazil</nlm:aff><wicri:noCountry code="subfield">PR Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Marcelino Guimaraes, Francismar Correa" sort="Marcelino Guimaraes, Francismar Correa" uniqKey="Marcelino Guimaraes F" first="Francismar Corrêa" last="Marcelino-Guimarães">Francismar Corrêa Marcelino-Guimarães</name><affiliation><nlm:aff id="Aff1">Brazilian Corporation of Agricultural Research (Embrapa Soja), Carlos João Strass road, Warta County, PR Brazil</nlm:aff><wicri:noCountry code="subfield">PR Brazil</wicri:noCountry></affiliation></author><author><name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff5">Department of Computer Science, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>Department of Computer Science, University of Missouri, Columbia</wicri:cityArea></affiliation></author><author><name sortKey="Nguyen, Henry T" sort="Nguyen, Henry T" uniqKey="Nguyen H" first="Henry T." last="Nguyen">Henry T. Nguyen</name><affiliation wicri:level="2"><nlm:aff id="Aff3">National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff4">Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Missouri (État)</region></placeName><wicri:cityArea>Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia</wicri:cityArea></affiliation></author><author><name sortKey="Abdelnoor, Ricardo Vilela" sort="Abdelnoor, Ricardo Vilela" uniqKey="Abdelnoor R" first="Ricardo Vilela" last="Abdelnoor">Ricardo Vilela Abdelnoor</name><affiliation><nlm:aff id="Aff1">Brazilian Corporation of Agricultural Research (Embrapa Soja), Carlos João Strass road, Warta County, PR Brazil</nlm:aff><wicri:noCountry code="subfield">PR Brazil</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil</nlm:aff><wicri:noCountry code="subfield">PR Brazil</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Soybean [<italic>Glycine max</italic> (L.) Merrill] is one of the most important legumes cultivated worldwide, and Brazil is one of the main producers of this crop. Since the sequencing of its reference genome, interest in structural and allelic variations of cultivated and wild soybean germplasm has grown. To investigate the genetics of the Brazilian soybean germplasm, we selected soybean cultivars based on the year of commercialization, geographical region and maturity group and resequenced their genomes.</p></sec><sec><title>Results</title><p>We resequenced the genomes of 28 Brazilian soybean cultivars with an average genome coverage of 14.8X. A total of 5,835,185 single nucleotide polymorphisms (SNPs) and 1,329,844 InDels were identified across the 20 soybean chromosomes, with 541,762 SNPs, 98,922 InDels and 1,093 CNVs that were exclusive to the 28 Brazilian cultivars. In addition, 668 allelic variations of 327 genes were shared among all of the Brazilian cultivars, including genes related to DNA-dependent transcription-elongation, photosynthesis, ATP synthesis-coupled electron transport, cellular respiration, and precursors of metabolite generation and energy. A very homogeneous structure was also observed for the Brazilian soybean germplasm, and we observed 41 regions putatively influenced by positive selection. Finally, we detected 3,880 regions with copy-number variations (CNVs) that could help to explain the divergence among the accessions evaluated.</p></sec><sec><title>Conclusions</title><p>The large number of allelic and structural variations identified in this study can be used in marker-assisted selection programs to detect unique SNPs for cultivar fingerprinting. The results presented here suggest that despite the diversification of modern Brazilian cultivars, the soybean germplasm remains very narrow because of the large number of genome regions that exhibit low diversity. These results emphasize the need to introduce new alleles to increase the genetic diversity of the Brazilian germplasm.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-016-2431-x) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Hiromoto, Dm" uniqKey="Hiromoto D">DM Hiromoto</name></author><author><name sortKey="Vello, Na" uniqKey="Vello N">NA Vello</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wysmierski, Pt" uniqKey="Wysmierski P">PT Wysmierski</name></author><author><name sortKey="Vello, Na" uniqKey="Vello N">NA Vello</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lam, H M" uniqKey="Lam H">H-M Lam</name></author><author><name sortKey="Xu, X" uniqKey="Xu X">X 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sort="Marcelino Guimaraes, Francismar Correa" uniqKey="Marcelino Guimaraes F" first="Francismar Corrêa" last="Marcelino-Guimarães">Francismar Corrêa Marcelino-Guimarães</name><name sortKey="Oliveira, Marcelo Fernandes De" sort="Oliveira, Marcelo Fernandes De" uniqKey="Oliveira M" first="Marcelo Fernandes De" last="Oliveira">Marcelo Fernandes De Oliveira</name></noCountry><country name="États-Unis"><region name="Missouri (État)"><name sortKey="Valliyodan, Babu" sort="Valliyodan, Babu" uniqKey="Valliyodan B" first="Babu" last="Valliyodan">Babu Valliyodan</name></region><name sortKey="Joshi, Trupti" sort="Joshi, Trupti" uniqKey="Joshi T" first="Trupti" last="Joshi">Trupti Joshi</name><name sortKey="Joshi, Trupti" sort="Joshi, Trupti" uniqKey="Joshi T" first="Trupti" last="Joshi">Trupti Joshi</name><name sortKey="Khan, Saad M" sort="Khan, Saad M" uniqKey="Khan S" first="Saad M." last="Khan">Saad M. Khan</name><name sortKey="Liu, Yang" sort="Liu, Yang" uniqKey="Liu Y" first="Yang" last="Liu">Yang Liu</name><name sortKey="Nguyen, Henry T" sort="Nguyen, Henry T" uniqKey="Nguyen H" first="Henry T." last="Nguyen">Henry T. Nguyen</name><name sortKey="Nguyen, Henry T" sort="Nguyen, Henry T" uniqKey="Nguyen H" first="Henry T." last="Nguyen">Henry T. Nguyen</name><name sortKey="Vuong, Tri D" sort="Vuong, Tri D" uniqKey="Vuong T" first="Tri D." last="Vuong">Tri D. Vuong</name><name sortKey="Wang, Juexin" sort="Wang, Juexin" uniqKey="Wang J" first="Juexin" last="Wang">Juexin Wang</name><name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name><name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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