Exploring the genetic basis of resistance to Neopestalotiopsis species in strawberry

Aggressive strains of Neopestalotiopsis sp. have recently emerged as devastating pathogens of strawberry (Fragaria x ananassa Duchesne ex Rozier), infecting nearly all plant parts and causing severe outbreaks of leaf spot and fruit rot in Florida and globally. The development of host resistance is imperative due to the absence of fungicides that effectively inhibit Neopestalotiopsis sp. growth on an infected strawberry crop. Here, we analyzed 1578 individuals from the University of Florida's (UF) strawberry breeding program to identify and dissect genetic variation for resistance to Neopestalotiopsis sp. and to explore the feasibility of genomic selection. We found that less than 12% of elite UF germplasm exhibited resistance, with narrow-sense heritability estimates ranging from 0.28 to 0.69. Through genome-wide association studies (GWAS), we identified two loci accounting for 7%-16% of phenotypic variance across four trials and 3 years. Several candidate genes encoding pattern recognition receptors, intra-cellular nucleotide-binding leucine-rich repeats, and downstream components of plant defense pathways co-localized with the Neopestalotiopsis sp. resistance loci. Interestingly, favorable alleles at the largest-effect locus were rare in elite UF material and had previously been unintentionally introduced from an exotic cultivar. The array-based markers and candidate genes described herein provide the foundation for targeting this locus through marker-assisted selection. The predictive abilities of genomic selection models, with and without explicitly modeling peak GWAS markers as fixed effects, ranged between 0.25 and 0.59, suggesting that genomic selection holds promise for enhancing resistance to Neopestalotiopsis sp. in strawberry.