Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.

Detalhes bibliográficos
Autor(a) principal: SANTOS, J. V. M. dos
Data de Publicação: 2016
Outros Autores: VALLIYODAN, B., JOSHI, T., KHAN, S. M., LIU, YANG., WANG, J., VUONG, T. D., OLIVEIRA, M. F. de, MARCELINO-GUIMARÃES, F. C., XU, D., NGUYEN, H. T., ABDELNOOR, R. V.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
Texto Completo: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1037089
Resumo: Soybean [Glycine max (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. 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.
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spelling Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.SojaVariedadeGenomaVariação genéticaSoybeansCultivarsHigh-throughput nucleotide sequencingGenetic variationSoybean [Glycine max (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. 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.JOÃO VITOR MALDONADO DOS SANTOS, UEL; BABU VALLIYODAN, UNIVERSITY OF MISSOURI; TRUPTI JOSHI, UNIVERSITY OF MISSOURI; SAAD M. KHAN, UNIVERSITY OF MISSOURI; LIU, Y., UNIVERSITY OF MISSOURI; JUEXIN WANG, UNIVERSITY OF MISSOURI; TRI D. VUONG, UNIVERSITY OF MISSOURI; MARCELO FERNANDES DE OLIVEIRA, CNPSO; FRANCISMAR CORREA MARCELINO GUIMARA, CNPSO; DONG XU., UNIVERSITY OF MISSOURI; HENRY T. NGUYEN., UNIVERSITY OF MISSOURI; RICARDO VILELA ABDELNOOR, CNPSO.SANTOS, J. V. M. dosVALLIYODAN, B.JOSHI, T.KHAN, S. M.LIU, YANG.WANG, J.VUONG, T. D.OLIVEIRA, M. F. deMARCELINO-GUIMARÃES, F. C.XU, D.NGUYEN, H. T.ABDELNOOR, R. V.2016-02-16T11:11:11Z2016-02-16T11:11:11Z2016-02-1620162017-06-19T11:11:11Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleBMC Genomics, v. 17, n. 110, 18 p., Feb. 2016.1471-2164http://www.alice.cnptia.embrapa.br/alice/handle/doc/103708910.1186/s12864-016-2431-xenginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2017-08-16T03:27:10Zoai:www.alice.cnptia.embrapa.br:doc/1037089Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542017-08-16T03:27:10falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542017-08-16T03:27:10Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false
dc.title.none.fl_str_mv Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.
title Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.
spellingShingle Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.
SANTOS, J. V. M. dos
Soja
Variedade
Genoma
Variação genética
Soybeans
Cultivars
High-throughput nucleotide sequencing
Genetic variation
title_short Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.
title_full Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.
title_fullStr Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.
title_full_unstemmed Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.
title_sort Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.
author SANTOS, J. V. M. dos
author_facet SANTOS, J. V. M. dos
VALLIYODAN, B.
JOSHI, T.
KHAN, S. M.
LIU, YANG.
WANG, J.
VUONG, T. D.
OLIVEIRA, M. F. de
MARCELINO-GUIMARÃES, F. C.
XU, D.
NGUYEN, H. T.
ABDELNOOR, R. V.
author_role author
author2 VALLIYODAN, B.
JOSHI, T.
KHAN, S. M.
LIU, YANG.
WANG, J.
VUONG, T. D.
OLIVEIRA, M. F. de
MARCELINO-GUIMARÃES, F. C.
XU, D.
NGUYEN, H. T.
ABDELNOOR, R. V.
author2_role author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv JOÃO VITOR MALDONADO DOS SANTOS, UEL; BABU VALLIYODAN, UNIVERSITY OF MISSOURI; TRUPTI JOSHI, UNIVERSITY OF MISSOURI; SAAD M. KHAN, UNIVERSITY OF MISSOURI; LIU, Y., UNIVERSITY OF MISSOURI; JUEXIN WANG, UNIVERSITY OF MISSOURI; TRI D. VUONG, UNIVERSITY OF MISSOURI; MARCELO FERNANDES DE OLIVEIRA, CNPSO; FRANCISMAR CORREA MARCELINO GUIMARA, CNPSO; DONG XU., UNIVERSITY OF MISSOURI; HENRY T. NGUYEN., UNIVERSITY OF MISSOURI; RICARDO VILELA ABDELNOOR, CNPSO.
dc.contributor.author.fl_str_mv SANTOS, J. V. M. dos
VALLIYODAN, B.
JOSHI, T.
KHAN, S. M.
LIU, YANG.
WANG, J.
VUONG, T. D.
OLIVEIRA, M. F. de
MARCELINO-GUIMARÃES, F. C.
XU, D.
NGUYEN, H. T.
ABDELNOOR, R. V.
dc.subject.por.fl_str_mv Soja
Variedade
Genoma
Variação genética
Soybeans
Cultivars
High-throughput nucleotide sequencing
Genetic variation
topic Soja
Variedade
Genoma
Variação genética
Soybeans
Cultivars
High-throughput nucleotide sequencing
Genetic variation
description Soybean [Glycine max (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. 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.
publishDate 2016
dc.date.none.fl_str_mv 2016-02-16T11:11:11Z
2016-02-16T11:11:11Z
2016-02-16
2016
2017-06-19T11:11:11Z
dc.type.driver.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv BMC Genomics, v. 17, n. 110, 18 p., Feb. 2016.
1471-2164
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1037089
10.1186/s12864-016-2431-x
identifier_str_mv BMC Genomics, v. 17, n. 110, 18 p., Feb. 2016.
1471-2164
10.1186/s12864-016-2431-x
url http://www.alice.cnptia.embrapa.br/alice/handle/doc/1037089
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron:EMBRAPA
instname_str Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron_str EMBRAPA
institution EMBRAPA
reponame_str Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
collection Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
repository.name.fl_str_mv Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
repository.mail.fl_str_mv cg-riaa@embrapa.br
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