Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies

We have identified and characterized a novel, broad-spectrum resistance to Phytophthora infestans from the wild Mexican species Solanum verrucosum. Diagnostic resistance gene enrichment (dRenSeq) revealed that the resistance is not conferred by previously identified nucleotide-binding, leucine-rich repeat genes. Utilizing the sequenced potato genome as a reference, two complementary enrichment strategies that target resistance genes (RenSeq) and conserved orthologous genes (GenSeq), respectively, were deployed for the rapid, SNP-based mapping of the resistance through bulked-segregant analysis. Both approaches independently positioned the resistance to the distal end of potato chromosome 9. Stringent post-enrichment read filtering identified a total of 64 informative SNPs that corresponded to the expected ratio for significant polymorphisms in the parents as well as the bulks. Of these, 61 SNPs are located on potato Chromosome 9 and reside within 26 individual genes, which in the sequenced potato clone DM locate to positions 44.2MB to 60.9MB. RenSeq and GenSeq-derived SNPs within the target region were converted into allele-specific PCR-based KASP markers and further defined the position of the resistance to a 4.3MB interval at the bottom end of Chromosome 9 between positions 52.62 MB – 56.98 MB.