Association Mapping for Fruit Traits in Capsicum chinense

Among the five domesticated species of pepper in the genus Capsicum, chinense is recognized as the most pungent fruit. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) is of great importance and a prerequisite for association mapping. Association mapping has become one of the most important tools in understanding the dynamics of the domestication processes as well as identification of important genes and genomic areas that are the targets for selection. Data is recorded for fruit traits viz. fruit weight, pedicel length, fruit length, fruit-width and pericarp thickness as well as capsaicin and dihydrocapsaicin content in Capsicum chinense for association mapping to identify markers also referred to as QTLs (Quantitative trait loci). This study is an attempt to understand the genetic diversity and relatedness of Capsicum chinense using 126 mapped SSR (Simple Sequence Repeats) loci and 250 germplasm accessions of C. chinense belonging to various countries representing a wide geographical area. In this study, molecular-genetic diversity is estimated by genetic diversity and heterozygosity (h). F_IS and F_ST are estimated by Wright’s F-statistics. Analysis of gene flow (Nm) based on the private allele method is estimated with Genepop 4. We resolved the population structure of Capsicum chinense using genome-wide SSRs in to 4 clusters. This analysis will be of use for future association-mapping studies to identify markers for various complex traits in C. chinense.