Table3_Multi-omics analysis provides insights into the mechanism underlying fruit color formation in Capsicum.docx

Fruit color is a crucial attribute of fruit quality in peppers (Capsicum spp.). However, few studies have focused on the mechanism of color formation in immature pepper fruits. In this study, the light-yellow color observed in immature CSJ009 fruits compared to CSJ010 could be attributed to decreased chlorophyll and carotenoid pigments. Through integrated analysis of the transcriptome and metabolome of CSJ009 and CSJ010, we identified 23,930 differentially expressed genes (DEGs) and 345 differentially accumulated metabolites (DAMs). Furthermore, integrated analysis revealed a strong correlation between the HCT-like gene and metabolite MWS0178 (chlorogenic acid). Paraffin section assay revealed that the epidermal cells of immature CSJ010 fruits exhibited a more compact arrangement with significantly greater length than those of CSJ009. Quantitative determination of carotenoids showed that lutein emerged as the predominant carotenoid in immature pepper fruits. Additionally, missense mutation of LCYB2 is likely to lead to a decrease in β-carotene content in immature CSJ009 fruits, whereas CCS may directly catalyze the conversion of lycopene to β-carotene in mature fruits. The null mutation in CCS promoted the biosynthesis of β,ϵ-branch carotenoids leading to lutein being the most abundant carotenoid found in orange CSJ010 fruits. These findings provide important insights into the mechanism underlying color formation in pepper fruits and establish a foundation for the further exploration of color-related genes.

果实颜色是辣椒（Capsicum spp.）果实品质的关键性状。然而，目前针对辣椒未成熟果实色泽形成机制的研究相对较少。本研究中，与CSJ010相比，未成熟CSJ009果实呈现出浅黄色表型，这一差异可归因于其叶绿素与类胡萝卜素色素含量的降低。通过对CSJ009与CSJ010进行转录组与代谢组联合分析，本研究共鉴定得到23930个差异表达基因（differentially expressed genes, DEGs）以及345个差异积累代谢物（differentially accumulated metabolites, DAMs）。此外，联合分析显示，HCT-like基因与代谢物MWS0178（绿原酸）之间存在极强的相关性。石蜡切片实验结果表明，未成熟CSJ010果实的表皮细胞排列更为紧密，且细胞长度显著长于CSJ009的表皮细胞。类胡萝卜素定量检测结果显示，叶黄素是未成熟辣椒果实中占主导的类胡萝卜素组分。此外，LCYB2基因的错义突变可能导致未成熟CSJ009果实中β-胡萝卜素含量下降；而CCS基因可能在成熟果实中直接催化番茄红素转化为β-胡萝卜素。CCS基因的无义突变促进了β,ε-分支类胡萝卜素的生物合成，使得橙色CSJ010果实中叶黄素成为含量最高的类胡萝卜素。本研究结果为解析辣椒果实色泽形成的分子机制提供了重要参考，同时也为后续色泽相关基因的深入研究奠定了基础。