Genomic diversity patterns linked to berry color variation

Abstract

Grapevine (Vitis vinifera L.) is one of the most widely cultivated and emblematic crops in the world. Understanding the biology of grapevine, and how plant genetics determines the general performance of a variety is crucial for its optimization and quality monitoring. Advancements in genomic studies have enabled the use of refined technologies to explore the influence of genome-wide variations and evolutionary dynamics. Pool-Seq is a cost-effective genomics strategy that enables the generation of important information on genetic variation within a population. In the present work, we implemented a Pool-Seq strategy to characterize the clonal diversity of 18 ancient varieties. We carried out an extensive characterization of genetic diversity within each variety, assessed genetic differentiation between varieties, and inferred on signatures of selection within the grapevine genome. A particular focus was placed on identifying selection signatures associated with berry color variation, by contrasting red versus white grape varieties. We detected several genes underlying selective sweeps for berry color variation, including the canonical MYB genes that compose the well-established berry color locus. However, the strongest selection signals were present in a downstream genomic tract that included multiple genes of interest, suggesting a more complex relationship between berry color variation, selection, and the aromatic profile of grapes.

Acknowledgements

Funding: Fundação para a Ciência e Tecnologia (FCT/MCTES) for project GrapeVision (PTDC/BIA-FBT/2389/2020).