Optimal use of SSR markers for varietal identification of upland cotton

Detalhes bibliográficos
Autor(a) principal: Pereira, Guilherme da Silva
Data de Publicação: 2015
Outros Autores: Cazé, Ana Luiza Ramos, Silva, Michelle Garcia da, Almeida, Vanessa Cavalcante, Magalhães, Fernanda Oliveira da Cunha, Silva Filho, João Luís da, Barroso, Paulo Augusto Vianna, Hoffmann, Lucia Vieira
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Pesquisa Agropecuária Brasileira (Online)
Texto Completo: https://seer.sct.embrapa.br/index.php/pab/article/view/20789
Resumo: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.
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spelling Optimal use of SSR markers for varietal identification of upland cottonUso otimizado de marcadores SSR para identificação varietal de algodoeiro herbáceoGossypium hirsutum; cultivar discrimination; intraspecific polymorphism; microsatelliteGossypium hirsutum; discriminação de cultivares; polimorfismo intraespecífico; microssatéliteThe objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.O objetivo deste trabalho foi identificar marcadores polimórficos de sequências simples repetidas (SSR) para identificação varietal de algodão e avaliação da distância genética entre as variedades. Inicialmente, 92 marcadores SSR foram genotipados em 20 cultivares de algodão do Brasil. Desse total, 38 locos foram polimórficos, dos quais dois deles foram amplificados por um único par de iniciadores; o número médio de alelos por loco foi 2,2. Os conteúdos de informação polimórfica (PIC) e de poder de discriminação (DP) foram, em média, 0,374 e 0,433, respectivamente. A distância genética média foi de 0,397 (mínima de 0,092 e máxima de 0,641). Um painel de 96 variedades originárias de diversas regiões do mundo foi avaliado por 21 locos polimórficos derivados a partir de 17 pares de iniciadores selecionados. Entre essas variedades, a distância genética média foi de 0,387 (mínima de 0 e máxima de 0,786). Os dendrogramas elaborados a partir de média aritmética não ponderada (UPGMA) não refletiram as regiões do Brasil (20 genótipos) ou do mundo (96 genótipos), onde as variedades ou linhagens foram selecionadas. O procedimento de reamostragem bootstrap mostra que a identificação dos genótipos é viável com 19 locos. Os marcadores polimórficos avaliados são úteis na identificação varietal de um painel amplo de variedades de algodão e podem ser aplicados em estudos de diversidade da espécie.Pesquisa Agropecuaria BrasileiraPesquisa Agropecuária BrasileiraEmbrapaPereira, Guilherme da SilvaCazé, Ana Luiza RamosSilva, Michelle Garcia daAlmeida, Vanessa CavalcanteMagalhães, Fernanda Oliveira da CunhaSilva Filho, João Luís daBarroso, Paulo Augusto ViannaHoffmann, Lucia Vieira2015-07-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://seer.sct.embrapa.br/index.php/pab/article/view/20789Pesquisa Agropecuaria Brasileira; v.50, n.7, jul. 2015; 571-581Pesquisa Agropecuária Brasileira; v.50, n.7, jul. 2015; 571-5811678-39210100-104xreponame:Pesquisa Agropecuária Brasileira (Online)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPAenghttps://seer.sct.embrapa.br/index.php/pab/article/view/20789/12972https://seer.sct.embrapa.br/index.php/pab/article/downloadSuppFile/20789/12958https://seer.sct.embrapa.br/index.php/pab/article/downloadSuppFile/20789/13050https://seer.sct.embrapa.br/index.php/pab/article/downloadSuppFile/20789/13056info:eu-repo/semantics/openAccess2015-07-30T14:43:17Zoai:ojs.seer.sct.embrapa.br:article/20789Revistahttp://seer.sct.embrapa.br/index.php/pabPRIhttps://old.scielo.br/oai/scielo-oai.phppab@sct.embrapa.br || sct.pab@embrapa.br1678-39210100-204Xopendoar:2015-07-30T14:43:17Pesquisa Agropecuária Brasileira (Online) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false
dc.title.none.fl_str_mv Optimal use of SSR markers for varietal identification of upland cotton
Uso otimizado de marcadores SSR para identificação varietal de algodoeiro herbáceo
title Optimal use of SSR markers for varietal identification of upland cotton
spellingShingle Optimal use of SSR markers for varietal identification of upland cotton
Pereira, Guilherme da Silva
Gossypium hirsutum; cultivar discrimination; intraspecific polymorphism; microsatellite
Gossypium hirsutum; discriminação de cultivares; polimorfismo intraespecífico; microssatélite
title_short Optimal use of SSR markers for varietal identification of upland cotton
title_full Optimal use of SSR markers for varietal identification of upland cotton
title_fullStr Optimal use of SSR markers for varietal identification of upland cotton
title_full_unstemmed Optimal use of SSR markers for varietal identification of upland cotton
title_sort Optimal use of SSR markers for varietal identification of upland cotton
author Pereira, Guilherme da Silva
author_facet Pereira, Guilherme da Silva
Cazé, Ana Luiza Ramos
Silva, Michelle Garcia da
Almeida, Vanessa Cavalcante
Magalhães, Fernanda Oliveira da Cunha
Silva Filho, João Luís da
Barroso, Paulo Augusto Vianna
Hoffmann, Lucia Vieira
author_role author
author2 Cazé, Ana Luiza Ramos
Silva, Michelle Garcia da
Almeida, Vanessa Cavalcante
Magalhães, Fernanda Oliveira da Cunha
Silva Filho, João Luís da
Barroso, Paulo Augusto Vianna
Hoffmann, Lucia Vieira
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Embrapa
dc.contributor.author.fl_str_mv Pereira, Guilherme da Silva
Cazé, Ana Luiza Ramos
Silva, Michelle Garcia da
Almeida, Vanessa Cavalcante
Magalhães, Fernanda Oliveira da Cunha
Silva Filho, João Luís da
Barroso, Paulo Augusto Vianna
Hoffmann, Lucia Vieira
dc.subject.por.fl_str_mv Gossypium hirsutum; cultivar discrimination; intraspecific polymorphism; microsatellite
Gossypium hirsutum; discriminação de cultivares; polimorfismo intraespecífico; microssatélite
topic Gossypium hirsutum; cultivar discrimination; intraspecific polymorphism; microsatellite
Gossypium hirsutum; discriminação de cultivares; polimorfismo intraespecífico; microssatélite
description The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.
publishDate 2015
dc.date.none.fl_str_mv 2015-07-10
dc.type.none.fl_str_mv
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv https://seer.sct.embrapa.br/index.php/pab/article/view/20789
url https://seer.sct.embrapa.br/index.php/pab/article/view/20789
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv https://seer.sct.embrapa.br/index.php/pab/article/view/20789/12972
https://seer.sct.embrapa.br/index.php/pab/article/downloadSuppFile/20789/12958
https://seer.sct.embrapa.br/index.php/pab/article/downloadSuppFile/20789/13050
https://seer.sct.embrapa.br/index.php/pab/article/downloadSuppFile/20789/13056
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Pesquisa Agropecuaria Brasileira
Pesquisa Agropecuária Brasileira
publisher.none.fl_str_mv Pesquisa Agropecuaria Brasileira
Pesquisa Agropecuária Brasileira
dc.source.none.fl_str_mv Pesquisa Agropecuaria Brasileira; v.50, n.7, jul. 2015; 571-581
Pesquisa Agropecuária Brasileira; v.50, n.7, jul. 2015; 571-581
1678-3921
0100-104x
reponame:Pesquisa Agropecuária Brasileira (Online)
instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron:EMBRAPA
instname_str Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron_str EMBRAPA
institution EMBRAPA
reponame_str Pesquisa Agropecuária Brasileira (Online)
collection Pesquisa Agropecuária Brasileira (Online)
repository.name.fl_str_mv Pesquisa Agropecuária Brasileira (Online) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
repository.mail.fl_str_mv pab@sct.embrapa.br || sct.pab@embrapa.br
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