Current Status and Challenges in Identifying Disease Resistance Genes in Brassica napus

Abstract

Brassica napus is an economically important crop across different continents including temperate and subtropical regions in Europe, Canada, South Asia, China and Australia. Its widespread cultivation also brings setbacks as it plays host to fungal, oomycete and chytrid pathogens that can lead to serious yield loss. For sustainable crop production, identification of resistance (R) genes in B. napus has become of critical importance. In this review, we discuss four key pathogens affecting Brassica crops: Clubroot (Plasmodiophora brassicae), Blackleg (Leptosphaeria maculans and L. biglobosa), Sclerotinia Stem Rot (Sclerotinia sclerotiorum), and Downy Mildew (Hyaloperonospora parasitica). We first review current studies covering prevalence of these pathogens on Brassica crops and highlight the R genes and QTL that have been identified from Brassica species against these pathogens. Insights into the relationships between the pathogen and its Brassica host, the unique host resistance mechanisms and how these affect resistance outcomes is also presented. We discuss challenges in identification and deployment of R genes in B. napus in relation to highly specific genetic interactions between host subpopulations and pathogen pathotypes and emphasize the need for common or shared techniques and research materials or tighter collaboration between researchers to reconcile the inconsistencies in the research outcomes. Using current genomics tools, we provide examples of how characterization and cloning of R genes in B. napus can be carried out more effectively. Lastly, we put forward strategies to breed resistant cultivars through introgressions supported by genomic approaches and suggest prospects that can be implemented in the future for a better, pathogen-resistant B. napus.

Keywords: Brassica napus; R gene; genomics; host-pathogen interaction; pathotype; qualitative resistance.

Figure 1

R genes/QTL mapped on B. rapa (A), B. oleracea (B), and B. napus (C). Each vertical rectangular is a chromosome, with the chromosome name followed by chromosome number at the bottom. Black font denotes R genes/QTL mapped for S. sclerotiorum, blue font L. maculans, red font P. brassicae and bold black font H. parasitica. Boxed R gene is cloned. Where genetic distance applies, the chromosome position is stated in parentheses at the end of the locus. ^*1, Independent minor loci, homologous to A. thaliana chromosome 3; ^*2, Crr3 is independent of Crr1 and Crr2; ^*3, Syntenic with A. thaliana chromosome 4. Crr1 and Crr2 also share the same syntenic region; ^*4, Close to CRa and CRb, also known as Rcr1 (Chu et al., 2014), predicted as TIR-NBS-LRR (Yu F. et al., 2016); ^*5, Independent of Crr1, Crr2, and Crr3; ^*6, Two genes, Crr1a and Crr1b were identified at originally single Crr1 locus; ^*7, All at the same locus and are identical to major QTL BraDM (Yu et al., 2009); ^*8, Candidate gene, Bra016457, is serine/threonine (S/T) kinase. The major QTL in ^*7 and ^*8 lie between 17.6 and 17.8 Mb on chromosome R8; ^*9, Syntenic with CRc on chromosome R2; ^*10, Strong collinearity with chromosome A2 in B. rapa where CRc gene is located. Also overlap with pb-Bo(Anju)1; ^*11, Identified by Voorrips et al. (1997) but mapped on chromosome O3 by Nagaoka et al. (2010); ^*12, CRQTL-GN_2 (15.5–24.3 cM) and CRQTL_YC (8.5–38.1 cM) have similar location. Syntenic regions for these two QTL are on chromosome R3 (Crr3, CRk, CRa, and CRb), R8 (Crr1); ^*13, Same linkage group with QTL-LG1 (Moriguchi et al., 1999); ^*14, May be the same locus; ^*15, Closely linked to CRb, homologous to chromosome R3; ^*16, Adult resistance; ^*17, Field resistance for L. maculans. Candidate gene is cysteine rich RLK; ^*18, LepR3 and Rlm2 are allelic variants.

Figure 2

Identification of R genes in B. napus using next generation sequencing methods.