Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.)

Abstract

Polymorphisms in the grape transcription factor family VvMybA are responsible for variation in anthocyanin content in the berries of cultivated grapevine (Vitis vinifera L. subsp. sativa). Previous study has shown that white grapes arose through the mutation of two adjacent genes: a retroelement insertion in VvMybA1 and a single-nucleotide polymorphism mutation in VvMybA2. The purpose of this study was to understand how these mutations emerged and affected genetic diversity at neighbouring sites and how they structured the genetic diversity of cultivated grapevines. We sequenced a total of 3225 bp of these genes in a core collection of genetic resources, and carried out empirical selection tests, phylogenetic-and coalescence-based demographic analyses. The insertion in the VvMybA1 promoter was shown to have occurred recently, after the mutation of VvMybA2, both mutations followed by a selective sweep. The mutational pattern for these colour genes is consistent with progressively relaxed selection from constrained ancestral coloured haplotypes to light coloured and finally white haplotypes. Dynamics of population size in the VvMybA genes showed an initial exponential growth, followed by population size stabilization. Most ancestral haplotypes are found in cultivars from western region, whereas recent haplotypes are essentially present in table cultivars from eastern regions where intense breeding practices may have replaced the original diversity. Finally, the emergence of the white allele was followed by a recent strong exponential growth, showing a very fast diffusion of the initial white allele.

Role of an esterase in flavor volatile variation within the tomato clade

“…Copia-like retrotransposons are highly abundant in the tomato genome (29), and they were likely an important source of species diversification. Insertion of a retrotransposon in the transcriptional promoter of a gene can have a detrimental effect on its expression as illustrated by the inactivation in some white grape cultivars of a transcription factor controlling the accumulation of red anthocyanin pigments (35). Retrotransposons can also positively affect gene expression as recently demonstrated in blood oranges (36).…”

Ecophysiological, Genetic, and Molecular Causes of Variation in Grape Berry Weight and Composition: A Review

“…Anthocyanin concentration is characterized by a high broad sense heritability (from 0.65 to 0.98), and this heritability is stable in different populations (Liang et al 2009). The analyses of mapping populations have indeed identified a single locus on LG2 responsible for the presence or absence of skin color and total anthocyanin content in the skin (Doligez et al 2002, Fischer et al 2004, Fournier-Level et al 2010, Lijavetzky et al 2006, Salmaso et al 2008). This locus accounts for 48 to 62% of the total variation in anthocyanin concentration in a Syrah x Grenache progeny and colocalizes with a cluster of VvMYB genes (VvMYBA1, VvMYBA2, VvMYB3, and VvMYB4) (Fournier-Level et al 2010).…”

On the identification of human selected loci in grapevines

“…The identification of the genes responsible for agronomically important traits can now give insights into plant phenotypic evolution. The articles published in this issue by Fournier-Level et al (2010) and Pelsy (2010) on grapevines both contribute towards this general aim.…”

“…For instance, most of the variation in grape colour is explained by genetic variation at a single gene cluster of three MYB-type transcription factor genes called VvMybA1, VvMybA2 and VvMybA3 (see Fournier-Level et al, 2010, and references therein, in this issue). In the case of VvMybA1, silencing of the gene is due to the insertion of a gipsy-like retrotransposon (Gret1), whereas a single nucleotide polymorphism (K980) in the VvMybA2 coding sequence leads to protein truncation, and thus, to a non-functional protein.…”