New genetic weapon: scientists identify crr5 gene conferring clubroot immunity in brassica rapa
image: Application of Crr5-specific marker in molecular-assisted breeding. (A) Development of the resistant line R16-Crr5 using the Crr5-specific marker-assisted selection. DH40 was used as the donor parent and susceptible R16 was used as the recurrent parent. (B) Validation of the presence of Crr5 in the R16-Crr5 genome by PCR. (C) Clubroot phenotype of R16 and R16-Crr5 after inoculation of PbXY-2 isolate. Gall formation was examined and photographed at 35 days after inoculation. (D, E) Validation of the Crr5-specific marker in (DH40 × DH199)-F2 population (D) and in a natural population (E).
Credit: Horticulture Research
A high-quality genome of a clubroot-resistant Chinese cabbage line has revealed the key resistance gene Crr5, offering vital insights into disease defense in Brassica rapa. The gene, which encodes a nucleotide-binding leucine-rich repeat (NLR) protein, was shown to trigger immune responses and confer resistance to Plasmodiophora brassicae in both cabbage and transgenic Arabidopsis. Its discovery was enabled by a chromosome-level reference genome of the doubled haploid line DH40, assembled using PacBio HiFi and Hi-C technologies. Functional assays confirmed that Crr5 activates cell death and localizes in the nucleus, paving the way for marker-assisted breeding of resistant cabbage varieties.
Clubroot disease, caused by Plasmodiophora brassicae, is a devastating soil-borne pathogen that severely threatens global production of cruciferous crops. It can persist in soil for up to two decades, causing yield losses exceeding 40% in severe outbreaks. Although over 20 clubroot-resistant loci have been reported in Brassica rapa, only two genes—CRa and Crr1a—had been successfully isolated and functionally validated. Moreover, resistance breakdown has frequently occurred in cultivated varieties. Due to these challenges, it is necessary to conduct in-depth genomic and functional research to identify novel resistance genes and develop reliable molecular markers for sustainable clubroot control.
Researchers from the Henan Academy of Agricultural Sciences and Peking University have constructed a chromosome-level reference genome of the doubled haploid line DH40 and identified the clubroot resistance gene Crr5. The study (DOI: 10.1093/hr/uhae338), published on March 1, 2025, in Horticulture Research, provides a new molecular framework for combating P. brassicae infection in Chinese cabbage. By integrating next-generation sequencing, PacBio HiFi, and Hi-C technologies, the team pinpointed Crr5 on chromosome A08 and demonstrated its functional role in both Chinese cabbage and transgenic Arabidopsis thaliana.
The DH40 genome, spanning 420.92 Mb with a contig N50 of 11.97 Mb, represents one of the most complete assemblies for B. rapa. Comparative genomic analysis revealed that DH40 is genetically closer to the Chinese cabbage cultivar ‘Chiifu’ than to the turnip ‘ECD04’. Bulked segregant analysis (BSA) combined with map-based cloning rapidly located the Crr5 locus on chromosome A08. The gene encodes a TIR-NBS-LRR protein localized in the nucleus, with its TIR domain capable of self-activation and cell death induction—key features of plant immune signaling. Expression profiling showed that Crr5 responds to P. brassicae inoculation, with peak expression at 7 days post-infection in resistant lines. Functional validation through transgenic Arabidopsis confirmed that Crr5 alone is sufficient to confer clubroot resistance. To accelerate breeding applications, researchers developed two Crr5-specific Kompetitive Allele-Specific PCR (KASP) markers, enabling efficient marker-assisted selection. Using these markers, a resistant near-isogenic line, R16-Crr5, was successfully developed through backcrossing, showing complete resistance to P. brassicae isolate PbXY-2.
“Crr5 not only represents a novel resistance gene but also a key molecular tool for developing durable clubroot-resistant cultivars,” said corresponding author Dr. Xiaowei Zhang. “By providing a high-quality reference genome, our study enables precise gene discovery and comparative genomic analysis in Brassica rapa. The identification of Crr5 opens new possibilities for stacking multiple resistance loci and designing improved breeding strategies to protect cruciferous crops from one of the most persistent soil-borne pathogens.”
The discovery of Crr5 offers a crucial advancement for breeding clubroot-resistant Chinese cabbage and related Brassica crops. The availability of a high-quality genome sequence for DH40 facilitates rapid gene mapping and provides valuable genomic resources for resistance improvement. The newly developed Crr5-specific molecular markers can be directly applied in marker-assisted selection to produce resistant varieties efficiently. Beyond practical breeding, the functional characterization of Crr5 deepens understanding of plant immune signaling, contributing to future efforts in engineering multi-gene resistance systems and enhancing global crop resilience against clubroot disease.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae338
Funding information
This study was financed by the National Natural Science Foundation of China (grant No. 32 202 485), Zhongyuan Sci-Tech Innovation Leading Talents (grant No. 244 200 510 041), the Key Sci-Tech R&D Project of Joint Foundation in Henan Province (grant No. 232 301 420 024), the Fund for Distinguished Young Scholars from Henan Academy of Agricultural Sciences (grant No. 2024JQ02), and the Taishan Scholars Program and Natural Science Foundation for Distinguished Young Scholars of Shandong Province (grant No. ZR2023JQ010).
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.