Transcriptomic and Targeted Carotenoid Metabolomic Dissection of Pod Color Difference Between Wild Type and an EMS-Induced Stable pcm Mutant in Snap Bean (Phaseolus vulgaris L.).

Pod color is an essential economic trait of snap bean (Phaseolus vulgaris L.), and golden-yellow pods are more commercially popular than light-yellow varieties. Exploring the molecular regulatory mechanism underlying deep-yellow pod formation is essential for snap bean quality improvement. In this study, the wild-type cultivar Jinguan and the EMS-derived deep-yellow pod mutant pcm were used as materials. Integrative analyses of photosynthetic pigment quantification, genetic analysis, transcriptome sequencing, and targeted carotenoid metabolomics were performed to identify key genes and metabolic pathways governing pod color variation. Genetic analysis revealed that the deep-yellow pod trait of the pcm is stably inherited and controlled by a nuclear recessive gene. Transcriptome screening identified three differentially expressed key genes, PSY (Phvul.006G024100g), CCD4 (Phvul.002G120600g), and CYP707A (Phvul.002G122200g), whose expression patterns were strongly correlated with carotenoid accumulation. Metabolomic results demonstrated that the pcm presented reduced upstream β-carotene content, while the synthesis and accumulation of downstream chromogenic carotenoids, including zeaxanthin and capsorubin, were significantly enhanced, resulting in elevated total carotenoid content. Collectively, the differential expression of these genes remodels carotenoid metabolism and ultimately contributes to the deep-yellow pod phenotype. This study explores the regulatory mechanism of carotenoid metabolism in pod color formation, providing valuable theoretical support and genetic resources for quality breeding of snap beans.