Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm

Abstract

BackgroundConservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum.ResultsTo explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (HE = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (HE = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection ‘CC240’ with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher genetic diversity (I = 0.95) and genetic evenness (J’ = 0.80), and represented a wider range of phenotypic variation (MD = 9.45 %, CR = 98.40 %).ConclusionsA total of 240 accessions were selected from 3,821 Capsicum accessions based on transcriptome-based 48 SNP markers with genome-wide distribution and 32 traits using a systematic approach. This core collection will be a primary resource for pepper breeders and researchers for further genetic association and functional analyses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0452-8) contains supplementary material, which is available to authorized users.

Genetic Diversity Analysis of Capsicum Genus by SSR Markers

“…Lee found that C. galapagoense was close to C. annuum (Lee et al, 2016). Our results also support this conclusion, but we also found an interesting conclusion that C. tovarii was also close to C. annuum.…”

QTLmapping andGWASreveal candidate genes controlling capsaicinoid content inCapsicum

“…To reduce the effect of the major gene controlling pungency, Pun1 , all accessions were genotyped using the MAP1 marker (Rodríguez‐Maza et al ., ; Stewart et al ., ). A total of 208 accessions were selected, including 140 from the CC240 core collection (Lee et al ., ) and 68 additional accessions (Table S6). Five plants of each accession were grown in plastic greenhouses at the RDA‐GenBank in Jeonju, Republic of Korea.…”

“…A subpopulation of Capsicum core collections was used for GWAS (Lee et al, 2016a). To reduce the effect of the major gene controlling pungency, Pun1, all accessions were genotyped using the MAP1 marker (Rodr ıguez-Maza et al, 2012;Stewart et al, 2005).…”

Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites

“…Phylogenetic reconstruction confirms clustering of accessions in species (Figure 3a), as observed in similar studies based on plant morphological characteristics [27,28] or a smaller number of genetic markers. [3,29,2] Nevertheless, this is to date the largest phylogenetic study in terms of genomic markers analyzed in Capsicum species. We used principal components analysis (PCA) to summarize the observed genetic variation among accessions and species.…”

“…inferred from genetic markers mostly reflects the known taxonomic grouping, however it highlights sub-groups within C. annuum and admixture between C. chinense and C. frutescens. [2,3] Even if these studies were carried out on a large number of accessions, both are based on small number of markers (28 simple sequence repeats, SSR, on 1,400 accessions and 48 simple nucleotide polymorphisms, SNP, on 3,800 accessions), therefore the population structure of the different Capsicum species has never been investigated deeply.…”