Understanding Genetic Controls of Capsaicin Content in Capsicum annuum L

Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of domesticated and wild C. annuum to generate 66,960 SNPs using genotyping by sequencing. Principal component analysis and identity by state were used in a mixed linear model of capsaicin and dihydrocapsaicin content and fruit weight to reduce spurious associations because of confounding effects of subpopulations in genome-wide association study (GWAS). Selfed accessions were grown in three replications during two seasons (2011 and 2012).  GWAS revealed 14 SNPs commonly associated with capsaicin and dihydrocapsaicin content and 15 associated with fruit weight in both years. Five associated SNPs for capsaicin and three for fruit weight were nonsynonymous and significant after correction for false discovery rate and were homologous to known fruit-development genes in tomato and other plants. When scanning pairwise fixation index distribution of domesticated and wild accessions across the genome, we identified a segment of 177 Mb on chromosome 11 that was under strong selection sweep. Of 659 genes located in this sweep area, 30 were under high linkage disequilibrium, with reduced nucleotide diversity levels. Annotation of the genes in the sweep coupled with GWAS revealed their important roles in domestication.