Brassica rapa includes a variety of important vegetable and oilseed crops, yet it is significantly challenged by clubroot disease. Notably, the majority of genotypes of B. rapa with published genomes exhibit high susceptibility to clubroot disease. The present study presents a high-quality chromosome-level sequence of the genome of the DH40 clubroot-resistant (CR) line, a doubled haploid line derived from the hybrid progeny of a European turnip (ECD01) and two lines of Chinese cabbage. The assembled genome spans 420.92 Mb, with a contig N50 size of 11.97 Mb. Comparative genomics studies revealed that the DH40 line is more closely related to the Chinese cabbage Chiifu than to the turnip ECD04. The DH40 genome provided direct reference and greatly facilitate the map-based cloning of the clubroot resistance gene Crr5, encoding a nucleotide-binding leucine-rich repeat (NLR) protein. Further functional analysis demonstrated that Crr5 confers clubroot resistance in both Chinese cabbage and transgenic Arabidopsis. It responds to inoculation with Plasmodiophora brassicae and is expressed in both roots and leaves. Subcellular localization shows that Crr5 is present in the nucleus. Notably, the TIR domain of Crr5 can autoactivate and trigger cell death. In addition, we developed two Crr5-specific KASP markers and showcased their successful application in breeding CR Chinese cabbage through marker-assisted selection. Overall, our research offers valuable resources for genetic and genomic studies in B. rapa and deepens our understanding of the molecular mechanisms underlying clubroot resistance against Plasmodiophora brassicae.

中文翻译：

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染色体水平的参考基因组有助于在大白菜中发现根状根抗性基因 Crr5


甘蓝菜包括各种重要的蔬菜和油籽作物，但它受到根瘤病的严重挑战。值得注意的是，大多数已发表基因组的 B. rapa 基因型对 clubroot 病表现出高度易感性。本研究提出了 DH40 根状体抗性 （CR） 系基因组的高质量染色体水平序列，DH40 根瘤抗性 （CR） 系，一种源自欧洲萝卜杂交后代的双单倍体系 （ECD01） 和两个大白菜系。组装的基因组跨度为 420.92 Mb，重叠群 N50 大小为 11.97 Mb。比较基因组学研究表明，DH40 系与大白菜 Chiifu 的亲缘关系比与萝卜 ECD04 的亲缘关系更密切。DH40 基因组提供了直接参考，并极大地促进了基于定位的根抗性基因 Crr5 的克隆，该基因编码核苷酸结合亮氨酸富集重复序列 （NLR） 蛋白。进一步的功能分析表明，Crr5 在大白菜和转基因拟南芥中均具有根抗性。它对 Plasmodiophora brassicae 的接种有反应，并在根和叶中表达。亚细胞定位显示 Crr5 存在于细胞核中。值得注意的是，Crr5 的 TIR 结构域可以自动激活并触发细胞死亡。此外，我们开发了两个 Crr5 特异性 KASP 标记，并通过标记辅助选择展示了它们在 CR 大白菜育种中的成功应用。总体而言，我们的研究为 B. rapa 的遗传和基因组研究提供了宝贵的资源，并加深了我们对 Plasmodiophora brassicae 的根瘤抗性的分子机制的理解。