Differential expression ofCCD4(4B)drives natural variation in fruit carotenoid content in strawberry (Fragariaspp.)

Abstract

AbstractPigments, mainly anthocyanins and carotenoids, are important contributors to fruits’ visual appearance and nutritional properties. In strawberry (Fragariaspp.), the genetic and molecular mechanisms regulating fruit carotenoid biosynthesis and its natural variation remain largely unexplored. In this study, we sought to identify genomic loci contributing to variation in yellow flesh pigmentation. A major QTL,qYellow Flesh-4B, accounting for 82% of the total phenotypic variation was identified onF. ×ananassachromosome 4B. Following a candidate gene approach, we determined thatCCD4(4B),a carotenoid cleavage dioxygenase (CCD), was the underlying gene. Specific polymorphisms onCCD4(4B)promoter region were associated with the yellow flesh phenotype and with differential regulation ofCCD4(4B)expression during fruit ripening. Furthermore,CCD4(4B)expression levels were negatively correlated with violaxanthin, lutein, zeaxanthin, β-carotene and total carotenoid content. The role of CCD4(4B) in carotenoid turnover was confirmed by transient overexpression inF.×ananassafruits, which led to a decrease in carotenoid accumulation. Notably, a −35 C>T SNP identified inCCD4(4B)promoter was found to be predictive forCCD4(4B)expression, and carotenoid content in fruits of a diverse germplasm collection, which included different octoploidFragariaspecies. Taken together, these results provide important genetic insights into the natural variation of carotenoid content in strawberry. The High-Resolution Melting (HRM) DNA test here developed offers a fast and reliable method to predict high fruit carotenoid content, representing a useful tool for breeding projects aiming to enhance the nutritional value of this crop.