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

Abstract

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.

Genetic diversity of Dacryodes edulis provenances used in controlled breeding trials

“…The number of alleles at a determined SSR locus (allelic richness) is the simplest measure of genetic diversity (Saavedra et al, 2013). The six SSR markers used in this study produced a total of 61 alleles, with an average of 11.1667 alleles per marker.…”

SSR-based genetic analysis of sweet corn inbred lines using artificial neural networks

“…Consequently, several breeding programs have been undertaken to achieve genetic gains in several traits of interest (e.g., Kulka et al 2018). Studies of diversity and genetic structure allow plant breeders to investigate the population variability and thus provide basic information at the molecular level (Ballesta et al 2015, Contreras-Soto et al 2017); a key aspect in maize breeding programs (Saavedra et al 2013, Amaral et al 2016.…”

UPOV morphological versus molecular markers for maize inbred lines variability determination

“…Special difficulties arise when choosing the pairs of parental lines within a relatively narrow genetic base, for example in popcorn, sweet maize or in white grain maize (Saavedra et al, 2013;Babic et al, 2014). The white grain line L22, developed by crossing the unrelated white line and white line from BSSS group, with lines L21 and L17 gave realized hybrids.…”