Optimal use of SSR markers for varietal identification of upland cotton
Autor(a) principal: | |
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Data de Publicação: | 2015 |
Outros Autores: | , , , , , , |
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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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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1793416665667469312 |