Genetic divergence among cupuaçu accessions by multiscale bootstrap resampling

Detalhes bibliográficos
Autor(a) principal: Santos,Vinicius Silva dos
Data de Publicação: 2015
Outros Autores: Martins Filho,Sebastião, Alves,Rafael Moysés, Resende,Marcos Deon Vilela de, Silva,Fabyano Fonseca e
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Bragantia
Texto Completo: http://old.scielo.br/scielo.php?script=sci_arttext&pid=S0006-87052015000200169
Resumo: This study aimed at investigating the genetic divergence of eighteen accessions of cupuaçu trees based on fruit morphometric traits and comparing usual methods of cluster analysis with the proposed multiscale bootstrap resampling methodology. The data were obtained from an experiment conducted in Tomé-Açu city (PA, Brazil), arranged in a completely randomized design with eighteen cupuaçu accessions and 10 repetitions, from 2004 to 2011. Genetic parameters were estimated by restricted maximum likelihood/best linear unbiased prediction (REML/BLUP) methodology. The predicted breeding values were used in the study on genetic divergence through Unweighted Pair Cluster Method with Arithmetic Mean (UPGMA) hierarchical clustering and Tocher’s optimization method based on standardized Euclidean distance. Clustering consistency and optimal number of clusters in the UPGMA method were verified by the cophenetic correlation coefficient (CCC) and Mojena’s criterion, respectively, besides the multiscale bootstrap resampling technique. The use of the clustering UPGMA method in situations with and without multiscale bootstrap resulted in four and five clusters, respectively, while the Tocher’s method resulted in seven clusters. The multiscale bootstrap resampling technique proves to be efficient to assess the consistency of clustering in hierarchical methods and, consequently, the optimal number of clusters.
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spelling Genetic divergence among cupuaçu accessions by multiscale bootstrap resamplingclusteringUPGMAtocherTheobroma grandiflorumThis study aimed at investigating the genetic divergence of eighteen accessions of cupuaçu trees based on fruit morphometric traits and comparing usual methods of cluster analysis with the proposed multiscale bootstrap resampling methodology. The data were obtained from an experiment conducted in Tomé-Açu city (PA, Brazil), arranged in a completely randomized design with eighteen cupuaçu accessions and 10 repetitions, from 2004 to 2011. Genetic parameters were estimated by restricted maximum likelihood/best linear unbiased prediction (REML/BLUP) methodology. The predicted breeding values were used in the study on genetic divergence through Unweighted Pair Cluster Method with Arithmetic Mean (UPGMA) hierarchical clustering and Tocher’s optimization method based on standardized Euclidean distance. Clustering consistency and optimal number of clusters in the UPGMA method were verified by the cophenetic correlation coefficient (CCC) and Mojena’s criterion, respectively, besides the multiscale bootstrap resampling technique. The use of the clustering UPGMA method in situations with and without multiscale bootstrap resulted in four and five clusters, respectively, while the Tocher’s method resulted in seven clusters. The multiscale bootstrap resampling technique proves to be efficient to assess the consistency of clustering in hierarchical methods and, consequently, the optimal number of clusters.Instituto Agronômico de Campinas2015-06-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersiontext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S0006-87052015000200169Bragantia v.74 n.2 2015reponame:Bragantiainstname:Instituto Agronômico de Campinas (IAC)instacron:IAC10.1590/1678-4499.0431info:eu-repo/semantics/openAccessSantos,Vinicius Silva dosMartins Filho,SebastiãoAlves,Rafael MoysésResende,Marcos Deon Vilela deSilva,Fabyano Fonseca eeng2015-06-11T00:00:00Zoai:scielo:S0006-87052015000200169Revistahttps://www.scielo.br/j/brag/https://old.scielo.br/oai/scielo-oai.phpbragantia@iac.sp.gov.br||bragantia@iac.sp.gov.br1678-44990006-8705opendoar:2015-06-11T00:00Bragantia - Instituto Agronômico de Campinas (IAC)false
dc.title.none.fl_str_mv Genetic divergence among cupuaçu accessions by multiscale bootstrap resampling
title Genetic divergence among cupuaçu accessions by multiscale bootstrap resampling
spellingShingle Genetic divergence among cupuaçu accessions by multiscale bootstrap resampling
Santos,Vinicius Silva dos
clustering
UPGMA
tocher
Theobroma grandiflorum
title_short Genetic divergence among cupuaçu accessions by multiscale bootstrap resampling
title_full Genetic divergence among cupuaçu accessions by multiscale bootstrap resampling
title_fullStr Genetic divergence among cupuaçu accessions by multiscale bootstrap resampling
title_full_unstemmed Genetic divergence among cupuaçu accessions by multiscale bootstrap resampling
title_sort Genetic divergence among cupuaçu accessions by multiscale bootstrap resampling
author Santos,Vinicius Silva dos
author_facet Santos,Vinicius Silva dos
Martins Filho,Sebastião
Alves,Rafael Moysés
Resende,Marcos Deon Vilela de
Silva,Fabyano Fonseca e
author_role author
author2 Martins Filho,Sebastião
Alves,Rafael Moysés
Resende,Marcos Deon Vilela de
Silva,Fabyano Fonseca e
author2_role author
author
author
author
dc.contributor.author.fl_str_mv Santos,Vinicius Silva dos
Martins Filho,Sebastião
Alves,Rafael Moysés
Resende,Marcos Deon Vilela de
Silva,Fabyano Fonseca e
dc.subject.por.fl_str_mv clustering
UPGMA
tocher
Theobroma grandiflorum
topic clustering
UPGMA
tocher
Theobroma grandiflorum
description This study aimed at investigating the genetic divergence of eighteen accessions of cupuaçu trees based on fruit morphometric traits and comparing usual methods of cluster analysis with the proposed multiscale bootstrap resampling methodology. The data were obtained from an experiment conducted in Tomé-Açu city (PA, Brazil), arranged in a completely randomized design with eighteen cupuaçu accessions and 10 repetitions, from 2004 to 2011. Genetic parameters were estimated by restricted maximum likelihood/best linear unbiased prediction (REML/BLUP) methodology. The predicted breeding values were used in the study on genetic divergence through Unweighted Pair Cluster Method with Arithmetic Mean (UPGMA) hierarchical clustering and Tocher’s optimization method based on standardized Euclidean distance. Clustering consistency and optimal number of clusters in the UPGMA method were verified by the cophenetic correlation coefficient (CCC) and Mojena’s criterion, respectively, besides the multiscale bootstrap resampling technique. The use of the clustering UPGMA method in situations with and without multiscale bootstrap resulted in four and five clusters, respectively, while the Tocher’s method resulted in seven clusters. The multiscale bootstrap resampling technique proves to be efficient to assess the consistency of clustering in hierarchical methods and, consequently, the optimal number of clusters.
publishDate 2015
dc.date.none.fl_str_mv 2015-06-01
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://old.scielo.br/scielo.php?script=sci_arttext&pid=S0006-87052015000200169
url http://old.scielo.br/scielo.php?script=sci_arttext&pid=S0006-87052015000200169
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 10.1590/1678-4499.0431
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv text/html
dc.publisher.none.fl_str_mv Instituto Agronômico de Campinas
publisher.none.fl_str_mv Instituto Agronômico de Campinas
dc.source.none.fl_str_mv Bragantia v.74 n.2 2015
reponame:Bragantia
instname:Instituto Agronômico de Campinas (IAC)
instacron:IAC
instname_str Instituto Agronômico de Campinas (IAC)
instacron_str IAC
institution IAC
reponame_str Bragantia
collection Bragantia
repository.name.fl_str_mv Bragantia - Instituto Agronômico de Campinas (IAC)
repository.mail.fl_str_mv bragantia@iac.sp.gov.br||bragantia@iac.sp.gov.br
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