Genome wide association studies (GWAS) in Capsicum core collection

Abstract

Genome-wide association study (GWAS) is an effective approach for identifying genetic variants associated to useful agronomic traits. As we are performing GWAS for various agronomic traits in pepper, a genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>33,000 SNPs) for a 350 pepper core collection. Using GBS platform, a high density haplotype map was constructed and various stratification methods, including principal component analysis (PCA), and bayesian phylogenetic methods (STRUCTURE) were performed to show the genetic diversity and population stratification. Based on the STRUCTURE, four subgroups were identified and each of Q values was estimated. Through these results, MLM using Q values combined with kinship matrix were performed to identify quantitative trait loci controlling the variation of 12 agronomic traits. A set of 37 SNP locus distributed over 12 Capsicum chromosomes was identified for associations. For a validation, the associations were compared with the location of known QTLs which were surveyed from bi-parental population. It showed that, at least two QTLs were matched well with previous study. These results will help to understand associations between phenotype and genotype and also will give more power to validate the candidate genes or quantitative trait loci.