Standing Variation in AvrLm2 and AvrLm4-7 Underlies Virulence of Leptosphaeria maculans on Newly Deployed Rlm2 and Rlm7 Canola in Western Canada

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Abstract
Canola cultivars carrying the blackleg resistance genes Rlm2 and Rlm7 were released in Western Canada in 2022. To determine the origin of virulence on these genes, we phenotyped and sequenced 21 Leptosphaeria maculans isolates collected before deployment (2010–2015) and seven isolates recovered from Rlm2 and Rlm7 plots. Three AvrLm2 variants differed only at residues 133 and 146: 13 of 14 isolates carrying the reference Gly133/Glu146 allele were avirulent on Rlm2, whereas 10 of 14 carrying His133/Gln146, Asn133/Gln146 or an allele inactivated by repeat-induced point mutation (RIP) were virulent or intermediate. Eight isolates carried RIP-inactivated AvrLm4-7 alleles sharing a premature stop at codon 35; seven were virulent or intermediate on Rlm7, and five were avirulent on Rlm3, consistent with masking of AvrLm3 by AvrLm4-7. Virulence alleles at both loci predated deployment: both post-pressure Rlm7 isolates carried an AvrLm4-7 allele identical to that of a 2015 isolate, and the His133/Gln146 allele of two post-pressure Rlm2 isolates occurred in four pre-pressure lineages. A core-genome phylogeny based on 39,012 SNPs placed the post-pressure isolates in at least five lineages of a single regional clade. Rlm2 and Rlm7 deployment is therefore selecting on standing variation that can be monitored before resistance genes are released.

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