Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR)

Several studies have confirmed that popcorn (Zea mays L. var. everta) has a narrow genetic basis, which affects the quality of breeding programs. In this study, we present a genetic characterization of 420 individuals representing 28 popcorn populations from Brazilian germplasm banks. All individual...

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Autores principales:	Saavedra,Javier, Silva,Tereza Aparecida, Mora,Freddy, Scapim,Carlos Alberto
Lenguaje:	English
Publicado:	Instituto de Investigaciones Agropecuarias, INIA 2013
Materias:	Genetic differentiation microsatellite markers Bayesian clustering Monte Carlo Markov chains
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-58392013000200003
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spelling	oai:scielo:S0718-583920130002000032018-10-01Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR)Saavedra,JavierSilva,Tereza AparecidaMora,FreddyScapim,Carlos Alberto Genetic differentiation microsatellite markers Bayesian clustering Monte Carlo Markov chains Several studies have confirmed that popcorn (Zea mays L. var. everta) has a narrow genetic basis, which affects the quality of breeding programs. In this study, we present a genetic characterization of 420 individuals representing 28 popcorn populations from Brazilian germplasm banks. All individuals were genotyped using 11 microsatellite markers from the Maize Genetics and Genomics Database. A Bayesian clustering approach via Monte Carlo Markov chains was performed to examine the genetic differentiation (Fst values) among different clusters. The results indicate the existence of three distinct and strongly differentiated genetic groups (K = 3). Moreover, the Fst values (calculated among clusters) were significantly different according to Bayesian credible intervals of the posterior Fst values. The estimates of posterior mean (and 95% credible interval) of the Fst values were 0.086 (0.04-0.14), 0.49 (0.376-0.624) and 0.243 (0.173-0.324) for clusters 1, 2, and 3, respectively. Clusters 1 and 3 showed a high level of genetic diversity in terms of expected heterozygosity and number of alleles, indicating their potential for broadening the genetic basis of popcorn in future breeding programs. Additionally, the 11 microsatellites were informative and presented a suitable number of alleles for determining parameters related to genetic diversity and genetic structure. This information is important for increasing our knowledge regarding genetic relationships, for the identification of heterotic groups, and for developing strategies of gene introgression in popcorn.info:eu-repo/semantics/openAccessInstituto de Investigaciones Agropecuarias, INIAChilean journal of agricultural research v.73 n.2 20132013-06-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-58392013000200003en10.4067/S0718-58392013000200003
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Genetic differentiation microsatellite markers Bayesian clustering Monte Carlo Markov chains
spellingShingle	Genetic differentiation microsatellite markers Bayesian clustering Monte Carlo Markov chains Saavedra,Javier Silva,Tereza Aparecida Mora,Freddy Scapim,Carlos Alberto Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR)
description	Several studies have confirmed that popcorn (Zea mays L. var. everta) has a narrow genetic basis, which affects the quality of breeding programs. In this study, we present a genetic characterization of 420 individuals representing 28 popcorn populations from Brazilian germplasm banks. All individuals were genotyped using 11 microsatellite markers from the Maize Genetics and Genomics Database. A Bayesian clustering approach via Monte Carlo Markov chains was performed to examine the genetic differentiation (Fst values) among different clusters. The results indicate the existence of three distinct and strongly differentiated genetic groups (K = 3). Moreover, the Fst values (calculated among clusters) were significantly different according to Bayesian credible intervals of the posterior Fst values. The estimates of posterior mean (and 95% credible interval) of the Fst values were 0.086 (0.04-0.14), 0.49 (0.376-0.624) and 0.243 (0.173-0.324) for clusters 1, 2, and 3, respectively. Clusters 1 and 3 showed a high level of genetic diversity in terms of expected heterozygosity and number of alleles, indicating their potential for broadening the genetic basis of popcorn in future breeding programs. Additionally, the 11 microsatellites were informative and presented a suitable number of alleles for determining parameters related to genetic diversity and genetic structure. This information is important for increasing our knowledge regarding genetic relationships, for the identification of heterotic groups, and for developing strategies of gene introgression in popcorn.
author	Saavedra,Javier Silva,Tereza Aparecida Mora,Freddy Scapim,Carlos Alberto
author_facet	Saavedra,Javier Silva,Tereza Aparecida Mora,Freddy Scapim,Carlos Alberto
author_sort	Saavedra,Javier
title	Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR)
title_short	Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR)
title_full	Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR)
title_fullStr	Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR)
title_full_unstemmed	Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR)
title_sort	bayesian analysis of the genetic structure of a brazilian popcorn germplasm using data from simple sequence repeats (ssr)
publisher	Instituto de Investigaciones Agropecuarias, INIA
publishDate	2013
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-58392013000200003
work_keys_str_mv	AT saavedrajavier bayesiananalysisofthegeneticstructureofabrazilianpopcorngermplasmusingdatafromsimplesequencerepeatsssr AT silvaterezaaparecida bayesiananalysisofthegeneticstructureofabrazilianpopcorngermplasmusingdatafromsimplesequencerepeatsssr AT morafreddy bayesiananalysisofthegeneticstructureofabrazilianpopcorngermplasmusingdatafromsimplesequencerepeatsssr AT scapimcarlosalberto bayesiananalysisofthegeneticstructureofabrazilianpopcorngermplasmusingdatafromsimplesequencerepeatsssr
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Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR)

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