Exploiting the genetic diversity of cultivated strawberry for genomic dissection of leaf and fruit powdery mildew resistance

Abstract

Powdery mildew (PM) is a major fungal disease of cultivated strawberry, reducing yield through severe damage to foliage and fruit. Increasing restrictions in pesticide use have intensified the need for PM resistant cultivars. Here, we investigated the genetic architecture of PM resistance in strawberry using a large, untapped germplasm composed of two panels: a diversity panel of 223 genotypes (DivPanel) and a connected population (CoPop) panel comprising six selfed families and 12 biparental families derived from six cultivars. Disease symptoms were assessed on leaves and fruits over multiple years, indicating moderate to high heritability in the two organs. Genome-wide association studies identified 21 leaf QTLs, most of which are new; and 10 fruit QTLs. Among these, only one leaf QTL was co-localized with a fruit QTL, revealing that the genetic architecture of PM resistance is different in leaves and fruits. Genomic prediction models were evaluated through cross-validation and external validation, with combined-over-year analyses showing the highest predictive abilities (PAs) for both panels and organs (0.45–0.73). For a given year, optimizing the training population and adding co-factors improved the PAs. External validation also showed intermediate PA values (0.48–0.63), depending on the training population size and optimization. Simulation of resistance levels in 24 753 simulated progenies derived from all possible crosses between the 223 genotypes of the DivPanel demonstrated the strong potential of genomic prediction to guide optimal cross selection. Together, these findings uncover new QTLs for PM resistance in strawberry, including on fruit, and provide validated strategies for breeding disease-resistant cultivars.