Purple Pak-choi is rich in anthocyanins, which have both ornamental and edible health functions, and has been used more and more widely in facility cultivation. In order to further clarify the molecular mechanism of purple Pak-choi, two Pak-choi inbred lines (‘PQC’ and ‘HYYTC’) were selected for the determination of pigment content and transcriptome analysis, and the key genes controlling the formation of purple character in leaves of Pak-choi were discovered. The results of pigment determination showed that the anthocyanin content of ‘PQC’ was 0.29 mg/g, which was about 100 times than ‘HYYTC’; The chlorophyll content of ‘HYYTC’ was 2.25 mg/g, while ‘PQC’ only contained 1.05 mg/g. A total of 20 structural genes related to anthocyanin biosynthesis and 28 transcriptional regulatory genes were identified by transcriptome analysis. Weighted gene co-expression network analysis (WGCNA) was used to construct the weight network analysis map of 14 genes. The results showed that the cinnamate hydroxylase gene (BraA04002213, BrC4H3), flavanone-3- hydroxylase (BraA09004531, BrF3H1), and chalcone synthetase (BraA10002265, BrCHS1) were the core genes involved in the anthocyanin synthesis pathway of purple Pak-choi. The results identified the key genes controlling the formation of purple leaf traits, which laid a foundation for further analysis of the molecular mechanism of anthocyanin accumulation in purple Pak-choi and provided a theoretical basis for leaf color regulation.

Backgrounds: purple pakchoi (Brassica rapa subsp. chinensis (L.) Hanelt) is rich in anthocyanins, which contribute to its significant edible, ornamental, and potential health-promoting value. Fine mapping of the genes responsible for the purple-leaf trait is essential for establishing molecular marker-assisted breeding and facilitating genetic improvement. Methods: In this study, we used the inbred purple-leaf line ‘PQC’ and green-leaf line ‘HYYTC’ as parents to construct a six-generation genetic segregation population. We analyzed the inheritance pattern of the purple-leaf trait and combined Bulked Segregant Analysis Sequencing (BSA-Seq) with penta-primer amplification refractory mutation system (PARMS) to map the causal gene. Results: the main findings are as follows: the purple-leaf trait is controlled by a single dominant gene. Using BSA-Seq and PARMS, the genes were mapped to a 470 kb region (31.18–31.65 Mb) on chromosome A03. Within this interval, 29 candidate genes were identified, Bra017888 which encoding trehalose phosphate synthase 10 (TPS10), was highlighted as a potential regulator of anthocyanin biosynthesis. A developed molecular marker, SNP31304070, based on the final candidate region, successfully distinguished between purple homozygous and purple heterozygous plants in the F₂ and F₃ populations. Conclusions: the candidate gene controlling purple-leaf trait was finally located to A03 chromosome 31.18–31.65 Mb. The SNP31304070 marker and trait were co-separated, This marker could be applied to molecular-assisted breeding in purple pakchoi.