Characterisation of novel berry colour mutants originating in South Africa

Abstract

Grapevine (Vitis vinifera) is considered as one of the most economically important crops worldwide. Throughout the course of its domestication history, grapevine growers have routinely relied on vegetative propagation and the subsequent natural accumulation of somatic mutations as a valuable source of phenotypic diversity. These mutations influence important agricultural traits, driving the development of new cultivars. Specifically, somatic mutations affecting berry skin colouration represent one of the major contributors of diversity in cultivated grapevine. Genetic studies have linked berry colour variation to mutations at the berry colour locus on chromosome 2, particularly in the VvMYBA1 and VvMYAB2 genes, which are the main determinants of berry pigmentation. Within the South African context, Sémillon and Cinsaut, and their colour mutants (Sémillon gris; Cinsaut gris and Cinsaut blanc) represent unique viticultural and genetic resources.

Notably, white-skinned Sémillon gave rise to the pink-skinned Sémillon gris. Similarly, purple-skinned Cinsaut has mutated to yield both the white-skinned Cinsaut blanc and the grey-pigmented Cinsaut gris mutant. However, the molecular basis underpinning the colour-related changes in these cultivars have not been elucidated. In this study, Pac-Bio HiFi long read whole genome sequencing was employed, followed by confirmatory molecular, chemical and histological analyses. Anovel layer (L1/L2) specific deletion of over 4 Mb was found to be responsible for the Cinsaut mutants. This deletion included the entire berry colour locus as well as approximately 100 additional genes, and was identified in the supepidermal (L2) cell layer of Cinsaut gris, resulting in a triallelic profile of the berry colour locus for this cultivar. Moreover, the exact same deletion is evident in both cell layers of Cinsaut blanc, leading to only one non-functional copy of VvMYBA1, and indicative of a sequential mutation event, where Cinsaut blanc arose from the displacement of the deletion from the L2 layer of Cinsaut gris to its outer L1 epidermis. In the case of Sémillon gris it was found that colour formation is due to the partial excision of the retrotransposon Gret1, retaining a solo-LTR (long terminal repeat) upstream of VvMYBA1, and leading to the recovery of VvMYBA1 expression. Significantly, while Gret1 excision is considered a rare event across grapevine cultivars in general, it has occurred independently multiple times in Sémillon gris. The discovery and analysis of these unique colour mutants could help shed light on the mechanisms underlying somatic mutations, and their phenotypic implications in vegetatively propagated crops.