The genome of Vitis vinifera cv. Mgaloblishvili reveals resistance and susceptibility factors to downy mildew in the Rpv29 and Rpv31 loci

Mgaloblishvili is a grapevine variety from Georgia (Southern Caucasus) with a unique resistance mechanism against downy mildew, based on pathogen recognition, ethylene signaling pathway, and structural and chemical defenses. The resistance mechanism was found to be mediated by the Rpv29, Rpv30 and Rpv31 resistance loci. We sequenced Mgaloblishvili genome using PacBio HiFi. Long reads were assembled into a chromosome-scale diploid genome assembly consisting of about 986 Mb. A total of 58,912 protein-coding genes were predicted on the two sets of phased chromosomes. By comparisons with PN40024 genome, we searched for differences in structure, gene content, gene expression and impact of Structural Variants (SVs) and Single Nucleotide Polymorphisms (SNPs) between loci associated with resistance in Mgaloblishvili, and susceptibility in PN40024. Resistance haplotypes were identified through DNA sequencing of a Mgaloblishvili self-pollinated population. Comparing with PN40024, the Rpv29 locus exhibited reduced gene content, while Rpv31 showed comparable content. Most genes were associated with well-known plant defense pathways. Although genes in both genotypes served similar functions, SVs and SNPs were identified as determinants of structural differences between the genomes. Investigation of the Rpv30 locus was challenging due to ambiguity in defining its region precisely. DNA sequencing facilitated the identification of resistance haplotypes for both Rpv30 and Rpv31 loci, situated on Mgaloblishvili haplotype 2. Decisive information about the Rpv29 locus was lacking. We conclude that the resistance in Mgaloblishvili is the result of numerous small SVs and SNPs, which lead to loss of susceptibility factors and contribute to differential transcriptional regulation of defense-related genes.