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Sugars are the main drivers of strawberry sweetness, and understanding their genetic control is of critical importance for breeding. Large-scale genome-wide association studies were performed in two populations totaling 3399 individuals evaluated for soluble solids content (SSC) and fruit yield. Two stable quantitative trait loci (QTL) on chromosome 3B and 6A for SSC were identified. Favorable haplotypes at both QTL for SSC decreased yield, though optimal allelic combinations were identified with reduced impacts on yield. Metabolites in the starch and sucrose metabolism pathway were characterized and quantified for 23 contrasting genotypes in leaves, white fruit, and red fruit. Variations in sucrose concentrations/efflux indicated genetic variation underlying sucrose accumulation and transportation during fruit ripening. Integration of genome-wide association studies and expression quantitative locus mapping identified starch synthase 4 (FxaC_10g00830) and sugar transporter 2-like candidate genes (FxaC_21g51570) within the respective QTL intervals. These results will enable immediate applications in genomics-assisted breeding for flavor and further study of candidate genes underlying genetic variation of sugar accumulation in strawberry fruit.

Powdery mildew (PM) caused by Podosphaera aphanisis a major fungal disease of cultivated strawberry. Mildew Resistance Locus O(MLO) is a gene family described for having conserved seven-transmembrane domains. Induced loss-of-function in specific MLOgenes can confer durable and broad resistance against PM pathogens. However, the genomic structure and potential role of MLOgenes for PM resistance have not been characterized yet in the octoploid cultivated strawberry. In the present study, MLOgene families were characterized in four diploid progenitor species (Fragaria vesca, F. iinumae, F. viridis, and F. nipponica) and octoploid cultivated (Fragaria ×ananassa)strawberry, and potential sources of MLO-mediated susceptibility were identified. Twenty MLOsequences were identified in F. vescaand 68 identified in F. ×ananassa. Phylogenetic analysis divided diploid and octoploid strawberry MLOgenes into eight different clades, in which three FveMLO(MLO10, MLO17, and MLO20) and their twelve orthologs of FaMLOwere grouped together with functionally characterized MLOgenes conferring PM susceptibility. Copy number variations revealed differences in MLOcomposition among homoeologous chromosomes, supporting the distinct origin of each subgenome during the evolution of octoploid strawberry. Dissecting genomic sequence and structural variations in candidate FaMLOgenes revealed their potential role associated with genetic controls and functionality in strawberry against PM pathogen. Furthermore, the gene expression profiling and RNAi silencing of putative FaMLOgenes in response to the pathogen indicate the function in PM resistance. These results are a critical first step in understanding the function of strawberry MLOgenes and will facilitate further genetic studies of PM resistance in cultivated strawberry.