Genetic studies on host and pathogen to inform Phytophthora blight resistance breeding

Abstract

Phytophthora blight, caused by the oomycete pathogen Phytophthora capsici, is a devastating disease of various vegetable crops, including squash (Cucurbita pepo) and pepper (Capsicum annuum). Options for host resistance to Phytophthora blight vary dramatically between these two crops. In squash, no sources of complete resistance have been described, although variation for quantitative disease resistance exists in both commercial and unadapted germplasm. In pepper, on the other hand, landraces demonstrating complete or near-complete disease resistance have been identified and used in breeding. However, varieties with durable resistance to diverse pathogen isolates have not been developed. In order to contribute to genetic solutions for disease control in these two crops, genetic variation in squash associated with quantitative disease resistance as well as genetic variation in P. capsici associated with virulence on distinct pepper genotypes were characterized. In squash, two quantitative trait locus (QTL) mapping approaches were used in a zucchini _ gray zucchini population, resulting in the discovery of six QTL, representing the first reported for Phytophthora blight resistance in C. pepo. In order to identify genetic variants in P. capsici associated with virulence on pepper, a collection of 252 pathogen isolates, predominantly from vegetable production regions of New York state, was genotyped at over 100,000 single-nucleotide polymorphism (SNP) loci using genotyping-by-sequencing. The utility of this isolate collection as a genetic resource was demonstrated by the successful identification of SNPs associated with mating type and sensitivity to the fungicide mefenoxam via a genome-wide association study (GWAS). Inoculation of 117 genetically distinct isolates onto a panel of 16 pepper accessions revealed a significant effect of inter-species genotype-genotype interactions on disease outcomes. However, the only SNP associated with virulence in a GWAS demonstrated an effect that was consistent across pepper genotypes, suggesting that genes involved in host-specific virulence may be of smaller effect and more challenging to map. The results of these genetic experiments – conducted on both pathogen and host – are expected to inform efforts to breed vegetable crops with durable Phytophthora blight resistance.