Genome-wide association analysis and linkage mapping decipher the genetic control of primary metabolites and quality traits in Capsicum

Pepper (Capsicum spp.) is a rich source of natural compounds, including primary metabolites essential forplants and influencing human nutrition and taste perception. Although pepper represents an important horticulturalcrop, the genetic bases underlying the primary metabolism remain largely unclear. Here, we performeda complementary approach for mapping primary metabolites via quantitative trait loci analysis(mQTL) and genome-wide association studies (mGWAS). Using gas chromatography coupled with massspectrometry we quantified and mapped 80 metabolites, including amino acids, sugars, and organic acids inan interspecific backcross inbred line population and a GWAS panel over three independent trials. We identified263 candidate genes implicated in 91 robust QTL across studies. Additionally, 28 QTL containing 84candidate genes were identified with various pleiotropic effects. We further combined agro-physiologicalcharacteristics determining their relationships with metabolites, both underlying the quality of pepperfruits. We implemented plasticity analysis to investigate candidate genes causal for metabolic dispersion.Eighty-six genes were identified; among these, a previously reported UDP-glycosyltransferase responsiblefor capsianosides biosynthesis was found to be associated with a cluster of sugars, organic, and aminoacids, which are the main precursors of sensory taste in vegetables. This study provides the first attempt tocomprehend the genetic basis of Capsicum primary metabolism, which will further support assisted breedingfor fruit quality.