Genomic sequencing indicates non‐random mating of Venturia inaequalis in a mixed cultivar orchard

Apple scab is one of the most economically important diseases of apples worldwide. The disease is caused by the haploid ascomycete Venturia inaequalis. Growing apples in cultivar mixtures may reduce disease severity. To determine how the pathogen population structure is affected by host mixtures we studied 24 V. inaequalis isolates sampled from three different apple cultivars (Bramley, Cox, and Worcester) growing in a mixed orchard approximately 50 years old. The isolates were aligned against a reference genome and single nucleotide polymorphisms (SNPs) were called between the isolates. The populations isolated from Bramley and Worcester were distinct, while Cox isolates were an admixture. This supports previous tests of the ability of isolates to cross‐infect hosts, and molecular comparisons using simple sequence repeats (SSRs). Genotype‐specific allele (GSA) loci were not distributed randomly across contigs in proportion to contig length, but were clustered. Clustered GSA loci were observed in almost all contigs. This indicates population differentiation across the whole genome, presumably due to lack of crossing‐over events between Bramley and Worcester isolates. This lack is probably due to physical separation effects: sexual mating is more likely to take place and succeed between isolates from lesions on the same leaf than from contact between independently infected leaves in leaf litter on the orchard floor. This would especially be the case if sexual reproduction is initiated before leaf‐fall

The Vh2 and Vh4 scab resistance genes in two diffferential hosts derived from Russian apple R12740-7A map to the same linkage group of apple

Russian apple R12740-7A is the designation for an accession grown from seed collected in Russia, which was found to be highly resistant to apple scab. The resistance has historically been attributed to a naturally pyramided complex involving three major genes: one race-nonspecific gene, Vr, conditioning resistance to all known races, plus two race-specific genes. The race-nonspecific gene was identified as an independently segregating gene by Dayton and Williams (1968) and is referred to in this paper as Vr-DW. The first researchers to study the scab resistance gene complex in Russian apple never described the phenotype conditioned by the race-nonspecific gene. Later, Aldwinckle et al. (1976) associated the name Vr with a scab resistance gene conditioning distinctive stellate necrotic reactions, which we refer to as Vr-A in order to distinguish it from Vr-DW. We show that the segregation ratios in progenies from the scab differential hosts 2 and 4 that are derived from Russian apple, crossed with susceptible cultivars were consistent with a single gene conditioning resistance in each host. The genes have been named Vh2 and Vh4, respectively. Resistant segregants from host 2 showed stellate necrotic reactions, while those from host 4 showed hypersensitive reactions. Both the phenotypes and the genetic maps for the genes in the respective hosts were very similar to those of the genes previously named Vr-A and Vx, respectively, in an F1 family of Russian apple. We showed that race 2 of V. inaequalis isolated from host 2 was able to infect resistant descendants of the non-differential accession PRI 442-23 as well as host 2. The descendants of PRI 442-23 were expected to carry the race-nonspecific Vr-DW gene, but in fact carry Vr-A. We conclude that the Vh2 gene in host 2 and Vr-A are the same, and that the Vh4 gene in host 4 and Vx are the same. However, a major finding of this study is that the latter gene mapped to linkage group 2 of apple instead of linkage group 10 as suggested from previous research. With the two race-specific genes from Russian apple defined now, we discuss the nature of the race-nonspecific Vr-DW gene in this accession. We also report the identification of a new scab resistance gene, VT57, from either Golden Delicious or Red Dougherty, which conditions chlorotic resistance reactions and is linked to Vh