GWAS of fruit related quantitative traits in Capsicum

Pepper (Capsicum spp.) is one of the most popular vegetable that has medicinal and health benefits due to secondary metabolites such as capsaicinoid and carotenoid. In order to improve the power of the beneficial effects, many breeders and scientist have put efforts to identity genes controlling diverse phytochemicals. GWAS (Genome-wide association study) has become the most effective approach for identifying genetic loci associated with quantitative trait loci. We have constructed a core collection as a natural population consisting of 350 accessions for GWAS study in pepper. A genotyping-by-sequencing (GBS) approach was used to obtain dense genome-wide marker coverage (>384,000 SNPs) for the core collection. Using GBS platform, a high density haplotype map was constructed, and MLM using Q values combined with kinship matrix were performed to identify association with 12 carotenoids and 4 agronomic traits related to fruit. As a results, almost 100 QTLs distributing over 12 Capsicum chromosomes were identified. For a validation, the associations were compared with the locations of known QTLs which were surveyed using bi-parental population. These approach will help to understand associations between phytochemicals and genetic variations and also will give more power to validate the candidate genes or quantitative trait loci.