Development of KASP Markers for the Potato Virus Y Resistance Gene Ry_chc Using Whole-Genome Resequencing Data

Potato virus Y is the most important potato virus worldwide, affecting tuber yield and quality. The resistance gene Ry_chc, derived from the potato wild relative Solanum chacoense, provides broad spectrum and durable resistance to the virus and has been used to develop resistant cultivars. Several DNA markers have been developed and have contributed to the efficient selection of resistant individuals. In this study, we developed Kompetitive Allele Specific PCR markers for Ry_chc using whole-genome resequencing data for a diverse set of 25 PVY susceptible cultivars and a Ry_chc-positive clone. Marker Ry_4099 targets two variants in the 3ʹ-UTR and was able to discriminate all five allele dosages in a tetraploid test population. Marker Ry_3331 targets two variants in Exon 4 and, although it only provides presence/absence information, it discriminates between the two known resistant alleles of Ry_chc. These markers will greatly contribute to efficient development of resistant cultivars.