Ry Confers Extreme Resistance to Potato virus Y in Potato

The Potato virus Y (PVY) is responsible for huge economic losses for the potato industry worldwide and is the fifth most consequential plant virus globally. The main strategies for virus control are to limit aphid vectors, produce virus-free seed potatoes, and breed virus-resistant varieties. The breeding of PVY-resistant varieties is the safest and most effective method in terms of cost and environmental protection. Ry, a gene that confers extreme resistance to PVY, is from S. chacoense, which is a wild diploid potato species that is widely used in many PVY-resistant breeding projects. In this study, Ry was fine mapped and successfully cloned from S. chacoense accession 40-3. We demonstrated that Ry encodes a TIR-NLR protein by stably transforming a diploid susceptible cultivar named AC142 and a tetraploid potato variety named E3. The Ry conferred extreme resistance to PVY^O, PVY^N:O and PVY^NTN in both of the genotypes. To investigate the genetic events occurring during the evolution of the Ry locus, we sequenced 160 Ry homologs from 13 S. chacoense genotypes. Based on the pattern of sequence identities, 160 Ry homologs were divided into 11 families. In Family 11 including Ry, we found evidence for Type I evolutionary patterns with frequent sequence exchanges, obscured orthologous relationships and high non-synonymous to synonymous substitutions (Ka/Ks), which is consistent with rapid diversification and positive selection in response to rapid changes in the PVY genomes. Furthermore, a functional marker named MG64-17 was developed in this study that indicates the phenotype with 100% accuracy and, therefore, can be used for marker-assisted selection in breeding programs that use S. chacoense as a breeding resource.