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

<div><p>Pepper (<i>Capsicum annuum L.</i>) 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 <i>Capsicum annuum</i> collection during two seasons. The genes <i>Pun1</i>, <i>CCR, KAS</i> and <i>HCT</i> 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 <i>Pun1</i> 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 <i>Pun1</i> were found associated with capsaicin in plants from both seasons. Our results support that <i>CCR</i> is an important control point for the flux of p-coumaric acid to specific biosynthesis pathways. <i>KAS</i> 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 <i>Pun1</i> suggested that the accumulation of capsaicinoids depends on the expression of <i>Pun1</i>, as revealed by the most important associated SNPs found in the promoter region of <i>Pun1</i>.</p></div

Principal component analysis of transformed concentrations of capsaicin pathway metabolites.

<p>Accessions are labeled by their <i>pun</i>gency level (EV  =  eigenvalue).</p