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Volume 16
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10.3390/genes16101184
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Article

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

by
Bo Song
1,†,
Qinyu Yang
1,†,
Wenqi Zhang
1,
Xiao Yang
1,
Li Zhang
1,
Lin Ouyang
1,
Limei He
1,
Longzheng Chen
2,
Zange Jing
3,
Tao Huang
1,*,
Hai Xu
2,*,
Yuejian Li
1 and
Qichang Yang
1
1
Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China
2
Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
3
College of Agriculture and Life Science, Kunming University, Kunming 650214, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Genes 2025, 16(10), 1184; https://doi.org/10.3390/genes16101184 (registering DOI)
Submission received: 7 August 2025 / Revised: 7 October 2025 / Accepted: 9 October 2025 / Published: 12 October 2025
(This article belongs to the Section Plant Genetics and Genomics)
Versions Notes

Abstract

Purple pakchoi (Brassica rapa subsp. chinensis (L.) Hanelt) is rich in anthocyanins, which contribute to its significant edible, ornamental, and potential health-promoting value. The previous research on the purple-leaf trait of pakchoi was rather insufficient, key gene controlling the purple-leaf trait remains to be further elucidated. 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, showing complete co-segregation with the trait. The marker could be applied to molecular-assisted breeding in purple pakchoi.
Keywords: anthocyanin; BSA-seq; Gene mapping; PARMS; marker-assisted selection anthocyanin; BSA-seq; Gene mapping; PARMS; marker-assisted selection

Share and Cite

MDPI and ACS Style

Song, B.; Yang, Q.; Zhang, W.; Yang, X.; Zhang, L.; Ouyang, L.; He, L.; Chen, L.; Jing, Z.; Huang, T.; et al. Gene Mapping and Molecular Marker Development for Controlling Purple-Leaf Trait in Pakchoi (Brassica rapa subsp. chinensis (L.) Hanelt). Genes 2025, 16, 1184. https://doi.org/10.3390/genes16101184

AMA Style

Song B, Yang Q, Zhang W, Yang X, Zhang L, Ouyang L, He L, Chen L, Jing Z, Huang T, et al. Gene Mapping and Molecular Marker Development for Controlling Purple-Leaf Trait in Pakchoi (Brassica rapa subsp. chinensis (L.) Hanelt). Genes. 2025; 16(10):1184. https://doi.org/10.3390/genes16101184

Chicago/Turabian Style

Song, Bo, Qinyu Yang, Wenqi Zhang, Xiao Yang, Li Zhang, Lin Ouyang, Limei He, Longzheng Chen, Zange Jing, Tao Huang, and et al. 2025. "Gene Mapping and Molecular Marker Development for Controlling Purple-Leaf Trait in Pakchoi (Brassica rapa subsp. chinensis (L.) Hanelt)" Genes 16, no. 10: 1184. https://doi.org/10.3390/genes16101184

APA Style

Song, B., Yang, Q., Zhang, W., Yang, X., Zhang, L., Ouyang, L., He, L., Chen, L., Jing, Z., Huang, T., Xu, H., Li, Y., & Yang, Q. (2025). Gene Mapping and Molecular Marker Development for Controlling Purple-Leaf Trait in Pakchoi (Brassica rapa subsp. chinensis (L.) Hanelt). Genes, 16(10), 1184. https://doi.org/10.3390/genes16101184

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