Genome-wide association studies reveal a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogenCercospora beticola

Abstract

SummaryThe major resistance geneBvCR4recently bred into sugar beets provides a high level of resistance to Cercospora leaf spot caused by the fungal pathogenCercospora beticola. The occurrence of pathogen strains virulent toBvCR4was studied using field trials in Switzerland. Virulence of a subset of these strains was evaluated in a field trial conducted under elevated artificial disease pressure. We created a newC. bet colareference genome and mapped whole genome sequences of 256 field-collected isolates. These were combined with virulence phenotypes to conduct three separate GWAS to identify candidate avirulence genes. We identified a locus associated with avirulence containing a single candidate avirulence effector gene namedAvrCR4. All virulent isolates either lackedAvrCR4or had non-synonymous mutations within the gene.AvrCR4was present in all 74 isolates from non-BvCR4hybrids, whereas 33 of 89 isolates fromBvCR4hybrids carried a deletion. We also mapped genomic data from 190 publicly available U.S. isolates to our new reference genome. TheAvrCR4deletion was found in only one of 95 unique isolates from non-BvCR4hybrids in the U.S.AvrCR4presents a unique example of an avirulence effector in which virulent alleles have only recently emerged. Most likely these were selected out of standing genetic variation after deployment ofBvCR4. Identification ofAvrCR4will enable real-time screening ofC. beticolapopulations for the emergence and spread of virulent isolates.