Near telomere-to-telomere genome assembly enables the discovery of introgressed purple-leaf gene <i>BraMYB114</i> in pak choi ( <i>Brassica rapa</i> subsp. <i>chinensis</i> )

Abstract Pak choi (Brassica rapa subsp. chinensis, AA genome) is a widely cultivated leafy vegetable that comes in green and purple varieties. The enrichment of anthocyanins enhances its nutritional value, making it highly preferred by consumers. However, the genes responsible for the purple phenotype in pak choi remain mostly unknown. Here, we assembled a near-complete T2T genome of the ‘ZBC’ variety using PacBio HiFi, HiC, and Illumina sequencing technologies. The assembled genome is 420.97 Mb and contains 51 387 genes. Through genomic variation and evolutionary analysis, we identified an introgressed fragment of 854.53 kb on chromosome A03, which originates from B. carinata (BBCC). The BSA-seq and fine-mapping of the purple trait revealed that the target region overlaps with the 854.53-kb introgressed fragment by 390 kb. Functional annotation of the 390-kb interval revealed 48 genes, including BraA03G007112, a MYB114-like transcription factor named BraMYB114. It positively regulates anthocyanin biosynthesis by activating BraDFR.A09 and BraANS.A01 genes, as shown by transcriptomic, metabolomic, and qRT-PCR analyses. Our research is the first to demonstrate that the BrMYB114 gene, carried by an introgressed fragment, positively regulates anthocyanin synthesis in B. rapa. These findings advance our understanding of the B. rapa genome, introduce approaches for investigating key trait genes in introgression lines, and provide valuable targets for developing anthocyanin-rich vegetables.