R gene triplication confers European fodder turnip with improved clubroot resistance

Abstract

Summary Clubroot is one of the most important diseases for many important cruciferous vegetables and oilseed crops worldwide. Different clubroot resistance (CR) loci have been identified from only limited species in Brassica, making it difficult to compare and utilize these loci. European fodder turnip ECD04 is considered one of the most valuable resources for CR breeding. To explore the genetic and evolutionary basis of CR in ECD04, we sequenced the genome of ECD04 using de novo assembly and identified 978 candidate R genes. Subsequently, the 28 published CR loci were physically mapped to 15 loci in the ECD04 genome, including 62 candidate CR genes. Among them, two CR genes, CRA3.7.1 and CRA8.2.4, were functionally validated. Phylogenetic analysis revealed that CRA3.7.1 and CRA8.2.4 originated from a common ancestor before the whole‐genome triplication (WGT) event. In clubroot susceptible Brassica species, CR‐gene homologues were affected by transposable element (TE) insertion, resulting in the loss of CR function. It can be concluded that the current functional CR genes in Brassica rapa and non‐functional CR genes in other Brassica species were derived from a common ancestral gene before WGT. Finally, a hypothesis for CR gene evolution is proposed for further discussion.

The clubroot pathogen Plasmodiophora brassicae: A profile update

“…Genetic analysis and fine mapping studies have identified major loci, quantitative trait loci (QTLs) and genes from different Brassica species involved in P. brassicae resistance (Hasan, Shaikh, et al, 2021;Lv et al, 2020). Due to the lack of CR genes in B. napus (canola, genome AACC) germplasm, the canola progenitor B. rapa (Chinese cabbage, genome AA) is considered as a major source in CR breeding (Huang et al, 2017;Yang et al, 2022).…”

“…Several candidate CR genes have been identified to encode NLR proteins in B. rapa (Hatakeyama et al, 2017(Hatakeyama et al, , 2022Huang et al, 2017;Matsumoto et al, 2012;Wang et al, 2022;Yang et al, 2022;Zhang et al, 2021). CRa and Crr1a were successfully iso- and CRA8.1b, and those three genes could be responsible for the clubroot resistance, the TIR-NBS-LRRs BraA08g039211E…”

“…Genetic analysis and fine mapping studies have identified major loci, quantitative trait loci (QTLs) and genes from different Brassica species involved in P. brassicae resistance (Hasan, Shaikh, et al, 2021 ; Lv et al, 2020 ). Due to the lack of CR genes in B. napus (canola, genome AACC) germplasm, the canola progenitor B. rapa (Chinese cabbage, genome AA) is considered as a major source in CR breeding (Huang et al, 2017 ; Yang et al, 2022 ). Several candidate CR genes have been identified to encode NLR proteins in B. rapa (Hatakeyama et al, 2017 , 2022 ; Huang et al, 2017 ; Matsumoto et al, 2012 ; Ueno et al, 2012 ; Wang et al, 2022 ; Yang et al, 2022 ; Zhang et al, 2021 ).…”

Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L.

“…Two genes encoding TNL proteins and one candidate gene encoding RLP protein were the most probable candidate genes responsible for clubroot resistance in DingWen (DW). Again, the same locus PbBa8.1 was fine mapped in the ECD04 (most valuable resources for CR breeding) genome and narrowed down into a 1428 Kb region and nine candidate genes were identified in this region [ 103 ]. Functional analysis of one candidate gene, CRA8.2.4 , with NBS-LRR domain revealed that the plants with higher expression of CRA8.2.4 were not infected with clubroot.…”

“…Furthermore, very recently, one candidate gene, named CRA3.7.1 , identical to CRa from B . rapa T136-8 [ 121 ] and CRb _α [ 122 ] was functionally characterized by Yang et al [ 103 ]. B .…”