CC-NBS-LRR, a set of VvCRP markers, can distinguish cultivars with ripe rot resistance to Colletotrichum pathogens in grapevine

Grape ripe rot is a fungal disease, which is almost inextinguishable particularly before and after harvest in most vineyards. The management of this disease largely depends on the breeding of resistant varieties. Thus, the search for resistant varieties should parallel the molecular analysis of the markers associated with disease resistance. Here, we tested the leaf inoculation assay of Colletotrichum acutatum and C. gloeosporioides by inoculating them into 350 grapevine varieties. As a result of the phenotypes common to both species, 119 varieties (34%) were classified as resistant. Consequently, we discovered the locus with nucleotide-binding sites and carboxyterminal leucine-rich repeat regions (NBS-LRR) associated with grape ripe rot resistance through genotyping-by-sequencing and genome-wide association study. Ultimately, we identified the Vitis vinifera Colletotrichum resistance protein (VvCRP) markers from chromosome 3, which belongs to the CC-NBS-LRR type, as disease-resistant proteins. These markers were verified as the melting peak, and their chromatograms of nucleotide sequences were visualized in each single nucleotide polymorphism (SNP) loci. All the SNP markers differentiated successfully the resistant from the susceptible cultivars. Interestingly, we also found that a resistant cultivar named Bailey Alicante A has a heterozygous genotype, substantiating its potential usefulness for crops such as grapevine with many hybrids. Altogether, our results indicate that VvCRP markers can be utilized to distinguish grape ripe rot-resistant cultivars, particularly in crossbreeding populations.