The Plant Journal

SUMMARY Pepper (Capsicum spp.) is a rich source of natural compounds, including primary metabolites essential for plants and influencing human nutrition and taste perception. Although pepper represents an important horticultural crop, the genetic bases underlying the primary metabolism remain largely unclear. Here, we performed a complementary approach for mapping primary metabolites via quantitative trait loci analysis (mQTL) and genome-wide association studies (mGWAS). Using gas chromatography coupled with mass spectrometry we quantified and mapped 80 metabolites, including amino acids, sugars, and organic acids in an interspecific backcross inbred line population and a GWAS panel over three independent trials. We identified 263 candidate genes implicated in 91 robust QTL across studies. Additionally, 28 QTL containing 84 candidate genes were identified with various pleiotropic effects. We further combined agro-physiological characteristics determining their relationships with metabolites, both underlying the quality of pepper fruits. We implemented plasticity analysis to investigate candidate genes causal for metabolic dispersion. Eighty-six genes were identified; among these, a previously reported UDP-glycosyltransferase responsible for capsianosides biosynthesis was found to be associated with a cluster of sugars, organic, and amino acids, which are the main precursors of sensory taste in vegetables. This study provides the first attempt to comprehend the genetic basis of Capsicum primary metabolism, which will further support assisted breeding for fruit quality.