Two dominant loci determine resistance to Phomopsis cane lesions in F1 families of hybrid grapevines.

Key message: Rapid characterization of novel NB-LRR-associated resistance to Phomopsis cane spot on grapevine using high-throughput sampling and low-coverage sequencing for genotyping, locus mapping and transcriptome analysis provides insights into genetic resistance to a hemibiotrophic fungus.Abstract: Phomopsis cane and leaf spot, caused by the hemibiotrophic fungus <italic>Diaporthe ampelina</italic> (syn = <italic>Phomopsis viticola</italic>), reduces the productivity in grapevines. Host resistance was studied on three F₁ families derived from crosses involving resistant genotypes ‘Horizon’, Illinois 547-1, <italic>Vitis cinerea</italic> B9 and <italic>V. vinifera</italic> ‘Chardonnay’. All families had progeny with extremely susceptible phenotypes, developing lesions on both dormant canes and maturing fruit clusters. Segregation of symptoms was observed under natural levels of inoculum in the field, while phenotypes on green shoots were confirmed under controlled inoculations in greenhouse. High-density genetic maps were used to localize novel qualitative resistance loci named <italic>Rda</italic>1 and <italic>Rda</italic>2 from <italic>V. cinerea</italic> B9 and ‘Horizon’, respectively. Co-linearity between reference genetic and physical maps allowed localization of <italic>Rda</italic>2 locus between 1.5 and 2.4 Mbp on chromosome 7, and <italic>Rda</italic>1 locus between 19.3 and 19.6 Mbp of chromosome 15, which spans a cluster of five NB-LRR genes. Further dissection of this locus was obtained by QTL mapping of gene expression values 14 h after inoculation across a subset of the ‘Chardonnay’ × <italic>V. cinerea</italic> B9 progeny. This provided evidence for the association between transcript levels of two of these NB-LRR genes with <italic>Rda</italic>1, with increased NB-LRR expression among susceptible progeny. In resistant parent <italic>V. cinerea</italic> B9, inoculation with <italic>D. ampelina</italic> was characterized by up-regulation of SA-associated genes and down-regulation of ethylene pathways, suggesting an R-gene-mediated response. With dominant effects associated with disease-free berries and minimal symptoms on canes, <italic>Rda</italic>1 and <italic>Rda</italic>2 are promising loci for grapevine genetic improvement. [ABSTRACT FROM AUTHOR]