Late blight resistance of Julius Kühn Institute pre-breeding potato clones: a genome-wide association study

Late blight caused by Phytophthora infestans remains one of the most devastating diseases in potato cultivation, and durable resistance requires the combination of multiple resistance loci. The Julius Kühn Institute (JKI) has maintained a late blight resistance breeding program for more than 60 years and has developed extensive pre-breeding material with largely unknown resistance genetics. To characterize the genetic basis of this resistance, field trials were conducted over three years with 200 genotypes, including pre-breeding clones and cultivars. Genotypes were inoculated with P. infestans and assessed for foliage blight by relative area under the disease progress curve (rAUDPC) and maturity-corrected ΔrAUDPC. Detached leaf assays and tuber slice tests were evaluated as additional resistance-related traits.

Genome-wide association studies (GWAS) identified significant marker-trait associations for foliage and tuber blight resistance exclusively on chromosomes 9 and 11. The chromosome 9 locus accounted for up to 28% and the chromosome 11 locus for up to 16% of the marginal variance in phenotypic resistance, depending on the trait analyzed. Of the 200 genotypes, 121 carried the alternative allele on either chromosome and showed markedly reduced disease symptoms compared with non-carriers. Only one genotype carried resistance alleles at both loci, suggesting near-independent segregation and indicating good prospects for marker-assisted pyramiding. On chromosome 11, 52 significant markers spanned an approximately 5.2 Mbp region. The significant markers themselves showed strong linkage disequilibrium (LD), consistent with a shared introgressed LD block harboring five NBS-LRR candidate genes. Two candidates are of particular interest, one located 13.8 kb from the most significant marker and another containing a significant marker within the gene.

The major GWAS signal for late blight resistance in European potato breeding material on chromosome 11, with two structurally divergent NBS-LRR genes emerging as strong positional candidates, further supports this region as a resistance hotspot. Together with the second marker-trait association on chromosome 9, these results provide a useful genetic framework for the targeted pyramiding of resistance loci in potato breeding and support the development of cultivars with more durable late blight resistance.