Role of Ry chc gene diversity in the resistance of wild potato relative Solanum chacoense to potato virus Y

Abstract Potato virus Y (PVY) is one of the most significant pathogens in the production of cultivated potato Solanum tuberosum worldwide. The most efficient way to combat viral diseases is the use of resistant varieties. The Ry chc gene was discovered in the tuber-bearing wild potato relative Solanum chacoense. This gene is able to confer extreme resistance to PVY by rapidly halting virus multiplication in plants without the development of visible symptoms. Two molecular markers were developed to predict the presence of the Ry chc gene and PVY resistance with 100% accuracy. In this study, the diversity of the Ry chc gene and its relationship with resistance to PVY were investigated in genotypes from the Russian potato genbank. A collection of 60 genotypes originating from different populations was examined for PVY resistance and for the presence of Ry chc using molecular markers. The observed phenotypes ranged from susceptibility to hypersensitive reaction and extreme resistance to PVY. Irrespective of the type of resistance, all the PVY-resistant plants carried the Ry chc gene, indicating the prevalence of this resistance mechanism in S. chacoense. Unexpectedly, two S. chacoense individuals with the Ry chc gene were found to be completely susceptible to PVY. Ry chc sequences were evaluated via long-read targeted sequencing in all Ry chc -positive genotypes. Despite the low overall sequence variation observed in Ry chc gene, identical polymorphisms were found in Ry chc alleles from susceptible S. chachoense genotypes, demonstrating the existence of nonfunctional Ry chc allele unable to confer PVY resistance.