Uncovering the genetic architecture of pungency, carotenoids, and flavor in <i>Capsicum chinense</i> via TWAS-mGWAS integration and spatial transcriptomics.

ABSTRACT: Capsicum chinense (habanero pepper) exhibits substantial variation in fruit pungency, color, and flavor due to its rich secondary metabolite composition, including capsaicinoids, carotenoids, and volatile organic compounds (VOCs). To dissect the genetic and regulatory basis of these traits, we conducted an integrative analysis across 244 diverse accessions using metabolite profiling, genome-wide association studies (GWAS), and transcriptome-wide association studies (TWAS). GWAS identified 507 SNPs for capsaicinoids, 304 for carotenoids, and 1176 for VOCs, while TWAS linked gene expression to metabolite levels, highlighting biosynthetic and regulatory genes in phenylpropanoid, fatty acid, and terpenoid pathways. Segmental RNA sequencing across fruit tissues of contrasting accessions

SUBMITTER: Reddy UK 

PROVIDER: S-EPMC12701575 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature