Gene Mapping and Molecular Marker Development for Controlling Purple-Leaf Trait in Pakchoi (Brassica rapa subsp....

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.

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.

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.

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.