Identification and characterization of a key gene controlling purple leaf coloration in non-heading Chinese cabbage (Brassica rapa).

Chalcone isomerase (BraCHI, BraA03g059660.3C) is the candidate gene controlling purple leaf coloration in non-heading Chinese cabbage. A 10-bp deletion in its promoter enhances gene expression in purple plants, likely by disrupting MYB transcription factor binding, leading to anthocyanin accumulation. Leaf color is a critical trait influencing the commercial and nutritional value of leafy vegetables, with purple-leafed varieties prized for their high anthocyanin content. In this study, we investigated the genetic basis of purple leaf coloration in non-heading Chinese cabbage (Brassica rapa). Using a recombinant inbred line (RIL) population derived from a cross between purple-leafed S45P and green-leafed S45G lines, bulked segregant analysis sequencing (BSA-seq) and fine mapping were performed. The analysis identified BraP2, a locus on chromosome A03 associated with purple leaf coloration. Within the 65.31 kb candidate region, BraA03g059660.3C, encoding chalcone isomerase (CHI), was identified as the strongest candidate gene. Quantitative real-time PCR (qRT-PCR) revealed significantly higher expression of BraA03g059660.3C in purple-leafed S45P plants compared to green-leafed S45G plants. Further sequence analysis uncovered a 10-bp deletion in the promoter region of BraA03g059660.3C in S45P plants. This deletion likely disrupts a MYB transcription factor binding site, enhancing gene expression and promoting anthocyanin accumulation. Our findings demonstrate that BraA03g059660.3C plays a pivotal role in controlling purple leaf coloration in non-heading Chinese cabbage. This discovery advances the understanding of anthocyanin biosynthesis regulation and provides valuable genetic resources for breeding Brassica crops with improved esthetic and nutritional qualities.