Deciphering genetic determinants underlying natural variation in strawberry fruit quality

Abstract

Cultivated strawberry (Fragaria × ananassa) is largely appreciated for its flavor and nutritional quality, although breeding efforts has diminished the genetic and biochemical complexity underlying fruit quality traits. Esters, the largest group of volatile organic compounds (VOCs), are key contributors to fruit flavour and aroma. Using genome-wide association studies (GWAS) in a diverse panel, we identified a ~2 Mb haploblock on chromosome 6A explaining over 35% of the variation in medium-chain esters (MCEs). Bulked RNA-Seq of contrasting lines underscored two strongly upregulated candidates within this region: a cinnamoyl-CoA reductase, FaCCR1(6A), and an organic cation/carnitine transporter, FaOCT4(6A). Transient overexpression of the candidates significantly increased MCE content. Subcellular localization, in vitro enzymatic assays and molecular docking revealed a hitherto unknown activity of FaCCR1(6A) toward MCE precursors, demonstrating its role in MCE biosynthesis. Additional QTLs were found for other VOCs, including terpenoids and short-chain esters. Sweetness, another major determinant of fruit quality, is largely influenced by sugar content. We conducted GWAS for distinct sugar traits identifying 16 QTLs associated with their variation. Candidate genes within major QTLs were selected based on putative function and expression levels in accessions contrasting in sucrose content. Notably, deletion of a vacuolar invertase within a QTL on chromosome 7B was associated with higher sucrose. To accelerate breeding, we developed KASP assays in FaOCT4(6A) for MCE selection, and three KASP markers in chromosomes 5B and 7B for sugar prediction, which were validated in a diverse Californian collection. These tools enable marker-assisted selection (MAS) of elite cultivars with enhanced quality. Carotenoids are underappreciated contributors to the nutritional value of strawberry. We validated the role of CCD4(4B) beyond a biparental population and unveiled additional QTLs which may account for the remaining phenotypic variance, representing valuable sources of genetic variation that can be exploited in breeding programs.