Genome-wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits

Strawberries are cherished for their organoleptic properties and nutritional value. However, breeding new cultivars involves the simultaneous selection of many agronomical and fruit quality traits. The strawberry germplasm collection here studied exhibited extensive phenotypic variation in 26 agronomic and fruit quality traits across three consecutive seasons. Phenotypic correlations and Principal Component Analysis (PCA) revealed relationships among traits and accessions, emphasizing the impact of plant breeding. Genetic diversity analysis on 124 accessions using 44,408 markers denoted a population structure divided into six subpopulations that still retain considerable diversity. Genome-wide association studies (GWAS) for the 26 traits unveiled 121 significant marker-trait associations distributed across 95 quantitative trait loci (QTL). Multiple associations were detected for fruit firmness, a key breeding target, including a prominent locus on chromosome 6A. The candidate gene FaPG1, controlling fruit softening, was identified within this QTL region. Differential expression of FaPG1 confirmed its role as the main contributor to natural variation in fruit firmness. A Kompetitive Allele-Specific PCR (KASP) assay based on SNP AX-184242253, associated with the 6A QTL, predicts a substantial increase in fruit firmness, validating its utility for Marker-Assisted Selection (MAS). In essence, this comprehensive study provides insights into the phenotypic and genetic landscape of the strawberry collection and lays a robust foundation for propelling the development of superior strawberry cultivars through precision breeding.