Genome-wide identification and comparative analysis of NBS-LRR resistance genes in Brassica napus

Abstract

Plant disease-resistance genes play a critical role in providing resistance against pathogens. The largest family of resistance genes are the nucleotide-binding site (NBS) and leucine-rich repeat (LRR) genes. They are classified into two major subfamilies, toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) and coiled-coil (CC)-NBS-LRR (CNL) proteins. We have identified and characterised 641 NBS-LRR genes in Brassica napus, 249 in B. rapa and 443 in B. oleracea. A ratio of 1 : 2 of CNL : TNL genes was found in the three species. Domain structure analysis revealed that 57% of the NBS-LRR genes are typical resistance genes and contain all three domains (TIR/CC, NBS, LRR), whereas the remaining genes are partially deleted or truncated. Of the NBS-LRR genes, 59% were found to be physically clustered, and individual genes involved in clusters were more polymorphic than those not clustered. Of the NBS-LRR genes in B. napus, 50% were identified as duplicates, reflecting a high level of genomic duplication and rearrangement. Comparative analysis between B. napus and its progenitor species indicated that >60% of NBS-LRR genes are conserved in B. napus. This study provides a valuable resource for the identification and characterisation of candidate NBS-LRR genes.

Identification of new QTLs for resistance to Plasmodiophora brassicae in Brassica napus using genome wide association mapping

“…The uneven distribution of TNLs and CNLs is not uncommon in other plant species [30,31,32,33]. The vast majority of TNLs and CNLs appeared in clusters of 2 to 10 TNLs and CNLs, which is similar to the results of previous studies in B. napus [29], Arabidopsis, Medicago truncatula and Solanum tuberosum [30,34,35].…”

“…RNLs are likely derived from the CNL lineage [27,29]. The function of RNLs is yet to be determined, but they have no direct response to the pathogen and may have not the same duplication rates as TNLs and CNLs, which explains their lower abundance in the genome [27,29]. They may have a role in defence-signal transduction [38] or as helpers of other NBS genes [38].…”

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

“…TNLs were found to be more abundant than CNLs. The greater number of TNLs compared with CNLs has been previously reported in B. napus (Alamery, ; Alamery et al ., ), B. rapa , Arabidopsis (Meyers et al ., ; Mun et al ., ; Yu et al ., ) and Linum usitatissimum (linseed) (Kale et al ., ). It has been reported that the TIR domain is an important component of innate immunity across species through self‐association and ligand‐specific protein–protein interactions (Ve et al ., ).…”

“…For example, Alamery et al . () found 641, 443 and 249 NBS‐LRR genes in B. napus , B. oleracea and B. rapa , respectively, while Yu et al . () identified 157, 206 and 167 NBS‐LRR genes in B. oleracea , B. rapa and A. thaliana , respectively, which may be due to using different approaches.…”

“…Sequencing of Brassica genomes has resulted in reference genome sequences for B. napus Chalhoub et al, 2014;Sun et al, 2018), B. rapa (Cai et al, 2017;Wang et al, 2011), B. oleracea Parkin et al, 2014), B. juncea (Yang et al, 2016) and B. nigra (Yang et al, 2016), permitting a comprehensive study of R-genes in these Brassica species. For example, Alamery et al (2017) found 641, 443 and 249 NBS-LRR genes in B. napus, B. oleracea and B. rapa, respectively, while Yu et al (2014) identified 157, 206 and 167 NBS-LRR genes in B. oleracea, B. rapa and A. thaliana, respectively, which may be due to using different approaches. Moreover, a total of 1989 RGA candidates were identified in the B. oleracea pangenome by Bayer et al (2018).…”