Genome-wide Association Study Reveals Candidate Genes Controlling Flavone Biosynthesis in Pepper Leaves (Capsicum annuum L.)

Pepper ( Capsicum spp.) leaves contain a range of flavone derivatives that occur in glycosylated, apiosylated, and/or malonylated forms. These compounds confer human health benefits and protect the plant from biotic and abiotic stress. However, to date, information on the genetic regulation of flavones in pepper leaves remains limited. Hence, a genome-wide association study (GWAS) was conducted to identify SNPs associated with pepper leaf flavone accumulation. Two multi-locus models, Blink and FarmCPU, were used in the GWAS analysis; both identified regions that may be responsible for flavone biosynthesis. The study identified several significant SNPs in linkage disequilibrium (LD) with candidate genes involved in flavonoid biosynthesis. Notably, on chromosome 3, we identified a SNP in LD with a candidate gene encoding flavonoid 3’-hydroxylase (F3’H). Cross-validation across the two mapping models (Blink and FarmCPU) indicated that F3'H could be a branch-point regulator controlling the divergence between apigenin- and luteolin-derived flavone derivatives. Other candidate genes include UGT29-family glycosyltransferases, 2OG-Fe(II) oxygenase superfamily members, and regulatory transcription factors (MYB, bHLH, NF-Y, and ERF). These findings may provide the first genome-wide genetic framework for flavone diversification in pepper leaves and a foundation for breeding efforts targeting this underexploited source of bioactive compounds.