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Pepper ( Capsicum annuum L. ) is an economically important crop with added nutritional value. Production of capsaicin is an important quantitative trait with high environmental variance, so the development of markers regulating capsaicinoid accumulation is important for pepper breeding programs. In this study, we performed association mapping at the gene level to identify single nucleotide polymorphisms (SNPs) associated with capsaicin pathway metabolites in a diverse  Capsicum annuum  collection during two seasons. The genes  Pun1 ,  CCR, KAS  and  HCT  were sequenced and matched with the whole-genome sequence draft of pepper to identify SNP locations and for further characterization. The identified SNPs for each gene underwent candidate gene association mapping. Association mapping results revealed  Pun1  as a key regulator of major metabolites in the capsaicin pathway mainly affecting capsaicinoids and precursors for acyl moieties of capsaicinoids. Six different SNPs in the promoter sequence of  Pun1  were found associated with capsaicin in plants from both seasons. Our results support that  CCR  is an important control point for the flux of p-coumaric acid to specific biosynthesis pathways.  KAS  was found to regulate the major precursors for acyl moieties of capsaicinoids and may play a key role in capsaicinoid production. Candidate gene association mapping of  Pun1  suggested that the accumulation of capsaicinoids depends on the expression of  Pun1 , as revealed by the most important associated SNPs found in the promoter region of  Pun1 .

Identification of Gene-Specific Polymorphisms and Association with Capsaicin Pathway Metabolites in Capsicum annuum L. Collections