Brassica rapa is one of the world's most diverse crop species, encompassing leafy greens, turnips, and oilseeds. Purple variants exist across the species—from Chinese cabbage to Zicaitai—but the genetic basis of their coloration varies widely. Previous studies identified several candidate genes, including BrMYB2, BrTT8, and BraANS.A03, yet the gene controlling purple leaf color in pak choi specifically had evaded precise mapping for over 20 years. One major obstacle: the target region on chromosome A03 was unusually difficult to resolve through conventional genetic recombination. This suggested something unusual about its structure—perhaps a foreign DNA fragment that resisted normal chromosomal exchange. Based on these challenges, a high-resolution genome assembly was needed to finally pinpoint the causal gene and understand its evolutionary origins.
A team led by researchers at Gannan Normal University, Huazhong Agricultural University, and Masaryk University in the Czech Republic reports (DOI: 10.1093/hr/uhag193) these findings in Horticulture Research. The study, available online, used PacBio HiFi long-read sequencing, Hi-C chromatin conformation capture, and Illumina short reads to assemble a near-telomere-to-telomere genome of the purple pak choi variety ‘ZBC’. This high-quality assembly, totaling 420.97 megabases, enabled the discovery of a previously hidden introgressed fragment carrying the color-regulating gene.
The researchers discovered that an 854.53-kilobase fragment on chromosome A03 in purple pak choi is entirely absent in green varieties. This fragment, they determined, originated from Brassica carinata—an allotetraploid species carrying the B genome—and had been introgressed into pak choi through natural hybridization. Within this fragment, the team identified BraMYB114, a MYB114-like transcription factor that activates anthocyanin biosynthesis by directly binding to the promoters of two downstream genes, BraDFR.A09 and BraANS.A01. When the team overexpressed BraMYB114 in Arabidopsis thaliana, the transgenic plants developed purple cotyledons and hypocotyls, confirming its color-inducing function. Transcriptomic and metabolomic analyses further showed that BraMYB114 expression correlated positively with the accumulation of 13 distinct anthocyanin compounds in purple pak choi leaves. Notably, the introgressed region overlaps with the fine-mapping target interval by 390 kilobases, explaining why conventional recombination-based mapping had stalled for two decades—the introgressed segment resisted chromosomal exchange. The team also developed specific molecular markers linked to BraMYB114 that perfectly co-segregated with the purple trait in breeding populations, offering immediate tools for marker-assisted selection.
“For years, the gene responsible for purple color in pak choi seemed to hide from us,” the authors said. “Our near-complete genome assembly finally revealed why—it sits on a foreign DNA fragment that doesn't recombine like normal chromosomes do. We were surprised to find that the gene came from B. carinata, not from pak choi's own genome. This tells us that natural hybridization has contributed more to vegetable diversity than we previously appreciated, and it opens new ways to breed for anthocyanin-rich crops using the genetic resources stored in wild relatives.”
The findings have immediate practical value. The BraMYB114-linked markers developed in this study enable breeders to rapidly select purple offspring without waiting for plants to mature or relying on visual scoring. More broadly, the study demonstrates that introgressed fragments from wild relatives can be reservoirs of useful traits—color, nutrition, possibly disease resistance—that are invisible in conventional genome assemblies. As telomere-to-telomere genomes become more common, breeders can systematically scan for such hidden introgressions in other crops, unlocking genetic diversity that has been overlooked. For consumers, this means more nutritious, anthocyanin-rich vegetables may soon reach the market faster, backed by precise breeding tools that ensure consistency and quality.
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References
DOI
10.1093/hr/uhag193
Original Source URL
https://doi.org/10.1093/hr/uhag193
Funding information
The research was supported by the Natural Science Foundation of Jiangxi Province (20252BAC220044), the National Natural Science Foundation of China (32160454), and the Key R&D Program of Jiangxi Province (20243BBH81027 and 20252BCF320007). The work was also supported by the project TowArds Next GENeration Crops (CZ.02.01.01/00/ 22_008/0004581) of the ERDF Programme Johannes Amos Comenius.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.