Genomic Analyses Linking Genes and Gene Networks to Fruit Traits in Wild Strawberry

Fruits represent a key evolutionary innovation for seed dispersal. Fruit traits such as color, flavor, size and shape are thus critical to a plant’s reproductive success as well as to its market appeal for human consumption. Fragaria vesca, the diploid strawberry, is emerging as a better model to investigate gene function than the octoploid garden strawberry due to its diploidy, simpler genome, and the availability of molecular genetic tools. Further, abundant natural variations exist, providing rich genetic materials for novel allele identification. One such natural variation is the fruit color; both yellow and red colored fruits can be found among different wild strawberry accessions. We sequenced and compared the genomes of three F. vesca accessions: Hawaii 4, Yellow Wonder and Rügen. While Hawaii 4 and Yellow Wonder develop yellow fleshy fruit, Rügen develops red fleshy fruit. Genetic analysis indicated that the yellow fruit allele is recessive to the red fruit allele, suggesting that a loss of function mutation likely causes the yellow fruit color. Genome-scale analyses of DNA variants in all three accessions identified shared and distinct SNPs among these three accessions. Through a series of filtering, we identified a candidate SNP (causing W to S missense change) in the FveMYB10 gene. Using a transient expression assay, we functionally tested and confirmed that this single SNP was responsible for the yellow color fruits. Our study is a good example of how a genomic approach can effectively link traits of economic importance to specific genotype.