Genetic Architecture of Fruit Color and Morphology Revealed by Image-Based Phenotyping and Genome-Wide Association Analysis in Octoploid Strawberry

Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid for which the genetic basis of fruit appearance traits has not been comprehensively elucidated. This study investigated the genetic architecture of fruit color and morphological traits using integrated digital phenotyping and genome-wide association analysis of a core collection of diverse strawberry germplasm maintained for Korean breeding programs. A 108-accession core collection was assembled, genotyped, and phenotyped for 12 fruit quality traits. Population structure analysis identified K = 10 genetic clusters, and a Mantel test confirmed significant genotype–phenotype correspondence (r = 0.38, p < 0.001). Genome-wide association studies (GWAS) using BLINK and MLMM identified 15 significant marker–trait associations across six traits. Pleiotropic loci on chromosomes 15 (4C) and 22 (6B) were consistently associated with fruit lightness (L*) and red channel intensity (R) in both models, and the 6B locus explained approximately 18% of the phenotypic variance for each trait. Gene Ontology enrichment implicated transcriptional regulation, SUMOylation, and plastid-to-chromoplast transition, suggesting that the identified loci influenced fruit coloration through cellular regulatory mechanisms rather than direct pigment biosynthesis. These findings provide a genomic foundation for dual-trait marker-assisted selection targeting light and vividly red fruits for strawberry breeding.