A major QTL region associated with powdery mildew resistance in leaves and fruits of the reconstructed garden strawberry

Attiq ur Rehman, Jahn Davik, Petteri Karisto, Janne Kaseva, Saila Karhu, Marja Rantanen, Ismo Strandén, Timo Hytönen, Alan H. Schulman & Tuuli Haikonen

Theoretical and Applied Genetics; April 7 2025; vol.138; article 93

Key message

Multiple QTLs for powdery mildew resistance were identified in a pre-breeding population derived from the octoploid progenitor species of garden strawberry, including a stable major novel factor on chromosome 3B.

Abstract

Powdery mildew (PM), caused by the biotrophic fungal pathogen Podosphaera aphanis, poses an increasing threat to garden strawberry (Fragaria × ananassa) production worldwide. While a few commercial cultivars exhibit partial resistance, fungicide application remains essential for managing PM outbreaks. However, breeding offers a more sustainable approach for controlling PM. A better understanding of the genetics of resistance is required for informed breeding strategies, e.g. through identifying novel resistance factors derived from the progenitor species of garden strawberry, F. chiloensis and F. virginiana. We conducted genome-wide association (GWA) and multivariate analyses in a reconstructed (ReC) strawberry population to investigate PM resistance under natural infection. Leveraging multi-year field trial data and 20,779 single-nucleotide polymorphism markers, we identified a novel major quantitative trait locus (QTL) on chromosome 3B, designated as q.LPM.Rec-3B.2, that was consistently associated with high PM resistance in both leaves and fruits. Greenhouse validation with a subset of the ReC population confirmed that this QTL region was stable across field and greenhouse environments. Promising candidate genes for resistance, including two for MLO and one for EXO70, were identified within this major QTL. In addition, multi-locus GWA models and non-additive GWA revealed additional resistance QTLs on multiple chromosomes. Despite previous challenges in breeding for robust PM resistance due to its quantitative nature and complex genetic control, our results provide valuable insights into resistance-contributing QTL regions already existing in strawberry, novel wild-derived resistance QTLs not previously known, candidate genes, and pre-breeding germplasm carrying resistance traits as resources for future genome-informed breeding efforts.

See https://link.springer.com/article/10.1007/s00122-025-04871-6

Fig. 6: Chromosomal locations of SNP markers associated with leaf powdery mildew resistance (a, b) and allelic effects of selected SNPs detected within a major QTL in 3B (c). The significant MTAs are shown as a Miami plot for AUDPS using BLINK (upper) and MLM (lower) models (a), a chromosome 3B Manhattan plot highlighting significant MTAs for q.LPM.Rec-3B.2 by MLM (b), and as phenotype–genotype association box plots for its selected SNPs (c). Red lines in both a and b indicate the FDR threshold at − log10(p) = 5.61. SNPs passing the Bonferroni threshold and exhibiting the highest GVE (%) values are highlighted in a and coloured in b based on the respective SNP effects from the MLM model. Names of the major candidate genes are indicated by their relative physical positions in the blue shaded area in panel b. SNP effect box plots for the highlighted SNPs have their respective GVE (%) in parenthesis while the asterisks on box plots indicate significant differences between different allelic classes (Tukey’s HSD; p < 0.0001 = ****, p < 0.01 = ***, and p > 0.05 = ns) (c)