Genomics-assisted discovery of clubroot resistance gene Crr5 and its application in breeding of Chinese cabbage. Brassica rapa subsp. pekinensis

Here, we presented a high-quality chromosome-level genome sequence of clubroot resistant line DH40, a doubled haploid line derived from the hybrid offspring of a Europe turnip ECD01 and two Chinese cabbage lines. The assembly was 420.92 Mb in length with a contig N50 of 11.97 Mb. 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 showed that the Crr5 conferred clubroot resistance in Arabidopsis and Chinese cabbage, responded with the inoculation of Plasmodiophora brassicae, expressed both in roots and leaves, localized in nucleus, and the TIR domain alone could be autoactivated and elicited cell death. Most importantly, we developed two Crr5-specific KASP markers and successfully applied in breeding of clubroot resistant varieties through marker-assisted selection. Overall, our study provides valuable resource for genetic and genomic studies in B. rapa, and deepens our understanding of molecular mechanism underlying clubroot resistance against to Plasmodiophora brassicae.

本研究报道了抗根肿病株系DH40的高质量染色体级基因组序列。该双单倍体（doubled haploid, DH）株系由欧洲芜菁ECD01与两份大白菜品系的杂交后代经染色体加倍获得。该基因组组装序列总长420.92 Mb，重叠群（contig）N50值为11.97 Mb。DH40基因组为抗根肿病基因Crr5的图位克隆提供了直接参考，极大促进了该基因的图位克隆工作；该基因编码一类核苷酸结合富亮氨酸重复（nucleotide-binding leucine-rich repeat, NLR）蛋白。后续功能分析证实，Crr5可在拟南芥与大白菜中赋予根肿病抗性；该基因在接种芸苔根肿菌（Plasmodiophora brassicae）后会产生响应，在根与叶中均有表达，且定位于细胞核；仅其TIR结构域即可实现自激活并诱导细胞死亡。尤为关键的是，本研究开发了两个Crr5基因特异性KASP标记，并成功通过标记辅助选择（marker-assisted selection, MAS）将其应用于抗根肿病品种的育种工作。综上，本研究为芸苔（Brassica rapa）的遗传与基因组学研究提供了宝贵资源，同时加深了我们对介导芸苔抗芸苔根肿菌侵染的根肿病抗性分子机制的理解。