Identification of candidate genes for LepR1 resistance against Leptosphaeria maculans in Brassica napus

Abstract

Utilising resistance (R) genes, such as LepR1, against Leptosphaeria maculans, the causal agent of blackleg in canola (Brassica napus), could help manage the disease in the field and increase crop yield. Here we present a genome wide association study (GWAS) in B. napus to identify LepR1 candidate genes. Disease phenotyping of 104 B. napus genotypes revealed 30 resistant and 74 susceptible lines. Whole genome re-sequencing of these cultivars yielded over 3 million high quality single nucleotide polymorphisms (SNPs). GWAS in mixed linear model (MLM) revealed a total of 2,166 significant SNPs associated with LepR1 resistance. Of these SNPs, 2108 (97%) were found on chromosome A02 of B. napus cv. Darmor bzh v9 with a delineated LepR1_mlm1 QTL at 15.11-26.08 Mb. In LepR1_mlm1, there are 30 resistance gene analogs (RGAs) (13 nucleotide-binding site-leucine rich repeats (NLRs), 12 receptor-like kinases (RLKs), and 5 transmembrane-coiled-coil (TM-CCs)). Sequence analysis of alleles in resistant and susceptible lines was undertaken to identify candidate genes. This research provides insights into blackleg resistance in B. napus and assists identification of the functional LepR1 blackleg resistance gene.

In silico prediction and analysis of transmembrane‐coiled‐coil resistance gene analogues in 27Brassicaceaespecies

“…The presence of TM‐CCs (this study) and their consideration as candidate genes against blackleg disease in B . napus (other studies) (Cantila et al, 2021, 2023; Neik, 2019) indicates the possible functional involvement of the TM‐CCs in disease resistance. So far, RPW8 .…”

“…Abbreviations: Bju, Brassica juncea; BL, blackleg; BT, black rot; Bna, Brassica napus; Bni, Brassica nigra; Bol, Brassica oleracea; CR, clubroot; HR, hypocotyl rot; SSR, Sclerotinia stem rot; WR, white rust. a 1, Stotz et al (2018); 2, Inturrisi et al (2022); 3, Lee et al (2015); 4, Ferdous, Hossain, Park, Kim, et al (2020); 5, Hossain et al (2020); 6, Ferdous, Hossain, Park, Robin, et al (2020); 7, Ferdous et al (2019); 8, Chang et al (2019); 9, Yang et al (2021); 10, Raman et al (2021).TA B L E 2 (Continued)candidate genes against blackleg disease in B. napus (other studies)(Cantila et al, 2021(Cantila et al, , 2023Neik, 2019) indicates the possible functional involvement of the TM-CCs in disease resistance. So far, RPW8.1, RPW8.2 and HR4 are the only genes with both TM…”