Identification and functional validation of a grapevine downy mildew resistant NLR gene through biparental graph-based forward genetics

Abstract

Grape downy mildew, caused by the oomycete Plasmopara viticola, is one of the major diseases threatening the viticulture industry. Discovery and functional characterization of resistance genes are key factors for enhancing DM resistance in grapevine. In this study, F1 and BC1 crossing populations were generated by crossing V. vinifera ‘Cabernet Sauvignon’ and V. amurensis Shanghong”. Resistant/susceptible individuals were observed and scored among the BC1 population. In the mean time, we assembled the haplotype-resolved genomes of the parents for the mapping population. Genome-wide synteny analysis revealed extensive SNVs and SVs between haplotypes, highlighting the high heterozygosity and structural complexity of Vitis genomes. In addition, BiPG provides a more comprehensive representation of genomic variation between V. vinifera and V. amurensis, enabling finer mapping resolution. As a result, a DM resistant QTL was mapped on chromosome 7, and a group of resistant candidate genes were identified in this locus. Using bioinformatic analysis and gene mining strategy, a canonical CC-type NLR gene was, designated as Rpv-vnf1 was identified and isolated in the putative DM locus region. Functional analysis revealed that this gene can confer grapevine resistance to downy mildew. This research provides an efficient framework for high-resolution genotyping and gene mining in the complex grape genome. Identification, isolation and characterization of Rpv-vnf1 provides a valuable target of grapevine resistance breeding and basis for elucidating effector-triggered immunity (ETI) mechanisms.