Chromosome-level reference genome of <i>Vitis piasezkii</i> var. <i>pagnucii</i> provides insights into a new locus of resistance to grapevine powdery mildew

Grapevine powdery mildew (GPM), caused by <i>Erysiphe necator</i>, poses a significant threat to all green grapevine tissues, leading to substantial economic losses in viticulture. Traditional grapevine cultivars derived from <i>Vitis vinifera</i> are highly susceptible to GPM, whereas the wild Chinese accession Baishui-40 (BS-40) of <i>V. piasezkii</i> var. <i>pagnucii</i> exhibits robust resistance. To illuminate the genetic basis of resistance, we sequenced and assembled the chromosome-level genome of 'BS-40', achieving a total mapped length of 578.6 Mb distributed across nineteen chromosomes. A comprehensive annotation identified 897 nucleotide-binding leucine-rich repeat (NLR) genes in the 'BS-40' genome, which exhibited high sequence similarity across <i>Vitis</i> genomes. 284 of these NLR genes were differentially expressed upon GPM infection. A hybrid population of 'BS-40' and <i>V. vinifera</i> was constructed and 195 progenies were whole-genome re-sequenced. A new GPM-resistant locus, designated <i>Ren17</i>, located within the 0.74-1.23 Mb region on chromosome 1 was identified using genome-wide association study, population selection, and QTL analysis. Recombinant events indicated that an NLR gene cluster between 1 045 489 and 1 089 719 bp on chromosome 1 is possibly the key contributor to GPM resistance in 'BS-40'. Based on an SNP within this region, a dCAPS marker was developed that can predict the GPM resistance in 'BS-40'-derived materials with 99.4% accuracy in the progenies of 'BS-40' and <i>V. vinifera</i>. This chromosome-level genome assembly of <i>V. piasezkii</i> var. <i>pagnucii</i> provides a valuable resource not only for grapevine evolution, genetic analysis, and pan-genome studies but also a new locus <i>Ren17</i> as a promising target for GPM-resistant breeding in grapevine.