The Metabolic and Genetic Bases of High Carotenoid Deposition in Orange-Fleshed Potato Tuber

Orange-fleshed (O) potato tubers are rich in nutritionally beneficial carotenoids. However, the metabolic and regulatory mechanisms underlying their accumulation remain incompletely understood. Metabolomic profiling identified 32 carotenoids and showed that the O genotype reached peak carotenoid accumulation at the early swelling stage, with 17 xanthophylls present at higher levels than in a white-fleshed (W) genotype. Transcriptome analysis revealed that five biosynthetic genes, including β-carotene hydroxylase 2 ( BCH2 ), were significantly upregulated in O genotype, whereas zeaxanthin epoxidase ( ZEP ) was more highly expressed in the W genotype. Bulk segregation analysis of a backcross population identified five quantitative trait loci, including StBCH2 and StZEP, as key genetic determinants of carotenoid variation. Integrated coexpression networking and molecular validation indicated that APETALA2.7 and ethylene response factor 5.1 likely regulate StBCH2 and StZEP expression, respectively. Our findings elucidate the metabolic, genetic, and transcriptional mechanisms controlling carotenoid deposition in tubers, providing a foundation for genetic improvement of potato quality.