Integrated Metabolomic and Transcriptomic Analysis Revealed the Capsanthin Biosynthesis and Sequestration in Processing Type Red Pepper ( <i>Capsicum annuum</i> var. conoides)

ABSTRACT Fruit color in red peppers is a key determinant of processing adaptability, yet its metabolic and genetic mechanisms in typical Yanjiao cultivars remain poorly understood. Here, we integrated chromatic phenotyping, targeted carotenoid metabolomics, and comparative transcriptomics across 10 Yanjiao cultivars. Colorimetric analysis identified three phenotypic groups, with the yellow‐blue indices showing the greatest variation. Metabolomics classified cultivars into four metabolic types: high‐efficiency capsanthin synthesizer with coordinated precursor flux and extensive esterification; precursor‐accumulating genotypes with bottlenecks in red pigment formation; esterification‐specialized cultivars stabilizing pigments through laurate/myristate esterification; and synthesis‐inhibited cultivars accumulating atypical metabolites. Multivariate analyses linked redness mainly to capsanthin and zeaxanthin, whereas yellowness was associated with zeaxanthin ester pools. Comparative transcriptomes of representative cultivars (Yj425, Yj485, Yj518, and Yj666) identified 34 carotenoid metabolism‐related differentially expressed genes. High‑pigment cultivars exhibited coordinated upregulation of PSY paralogs and GGPPS , while branch‐specific regulation involved CYP97C expression gradients. Fruit color variation in Yanjiao peppers arose from two synergistic mechanisms: capsanthin biosynthesis efficiency and acyl‑transferase‑mediated sequestration stabilizing chromophores. These findings provide mechanistic targets for marker‑assisted breeding, metabolic engineering, and postharvest improvement of color stability and nutraceutical value in red pepper.