Genetic and Transcriptomic Analyses of the Purple Coloration Trait in the Inbred Line 7A01 of Brassica rapa

Anthocyanins are highly valued water-soluble pigments that play pleiotropic roles in plant growth and development, contributing to various physiological and ecological functions. Although multiple Brassica rapa varieties have been reported to accumulate anthocyanins in different tissues, the genes controlling this trait remain largely elusive. In this study, we characterized the B. rapa inbred line 7A01, which exhibits purple coloration in leaf veins, petioles, and flowering stalks, a trait later confirmed to be associated with high anthocyanin content. Genetic analysis indicates that this trait behaves as a monogenic trait, possibly controlled by a single incompletely dominant nuclear locus, which was mapped to a 5.1 cM region on chromosome A10 using a Brassica 50K SNP array combined with bulked segregant analysis. Five simple sequence repeat markers linked to the purple coloration trait were developed. Transcriptome profiling of shoot apices and flowering stalks identified 3953 and 5922 differentially expressed genes (DEGs) involved in anthocyanin biosynthesis, respectively. These DEGs included both structural genes and transcription factors, and their expression was validated by RT-qPCR. Our findings provide a genetic and molecular framework for the purple coloration trait in B. rapa and offer candidate genes for future breeding efforts.