A divergent haplotype with a large deletion at the berry color locus causes a white-skinned phenotype in grapevine

Abstract

The current genetic model explaining berry skin color in Vitis vinifera is incomplete and fails to predict berry skin color phenotypes for one allele of VvMybA1, referred to as VvMybA1_SUB. Our study focuses on this specific allele, revealing that the haplotype containing VvMybA1_SUB (haplotype F) represents an ancient lineage of the berry color locus. Within haplotype F, we identified two functional subhaplotypes, HapF1 and HapF2, associated with black-skinned phenotype, and one non-functional subhaplotype, HapF^DEL, responsible for white-skinned phenotype. HapF1 likely originated from wild populations domesticated in the Near East and subsequently spread globally with the expansion of viticulture. In contrast, HapF2 has a more restricted distribution and may have emerged from hybridization events between cultivated grapevines and local wild populations as viticulture migrated to the Italian peninsula. Furthermore, we found that in white-skinned berry cultivar, HapF has undergone a large deletion at the berry color locus, removing the majority of the VvMybA genes. Previous works suggested a single common origin for white-skinned varieties during grapevine domestication. Our results challenge this notion, instead proposing that white-skinned grape cultivars arose at least twice during grapevine domestication history. Alongside the major haplotype A, some white-skinned cultivars, such as cv. ‘Sultanina’ harbor HapF^DEL. Since HapF^DEL is present only in table grape varieties, we suggest that it likely arose from a recent mutational event and dispersed along the ancient Silk Road into East Asia. These findings enhance our understanding of the genetic diversity and evolutionary trajectory of grapevine cultivars, offering insights into their domestication and spread across different geographical regions.

Figure 1

Schematic illustration of different alleles of the VvMybA1 gene. VvMybA1c is the functional allele; VvMybA1a is the non-functional white allele containing Gret1, a transposable element (TE), in the promoter region of the gene. For VvMybA1b, Gret1 is partially excised, and only a portion (soloLTR) remains in the promotor region. The VvMybA1_SUB allele has three small insertions (black triangles: 44 bp, 111 bp, and 33 bp) compared to VvMybA1c.

Figure 2

Genetic relationships between nine black-skinned cultivars from the Alps region according to the literature (if not specified, each arrow corresponds to a parent/offspring relationship according to different sources: Raimondi et al. [22] in yellow, Onofrio et al. [23] in green, Lacombe et al. [24] in red, Cipriani et al. [25] in violet and the dashed line indicates that at least one allele is shared across 9 SSR markers, as referenced on www.vivc.de). All nine cultivars carry the VvMybA1_SUB allele. HS and FS stand for half or full sibling. Flags indicate where each cultivar is grown: Switzerland (Valais) and/or Italy (Aosta Valley).

Figure 3

Representation of the predicted MybA proteins produced from MYB genes at the color locus on chromosome 2, depending on the haplotype. Colored boxes are used to denote similar regions. R2 and R3 refer to repeats in c-Myb. The C-terminal domain (CR) is repeated in VvMybA2_HapC-N and VvMybA2_HapF. The black star in VvMybA2_HapA indicates a non-conservative change (R⁴⁴L), and the red star stands for a dinucleotide deletion introducing a premature stop codon. The protein length is given in amino acids (aa). Haplotype A produces no VvMybA1 protein, given the insertion of a transposable element in the promoter region of the gene. VvMybA3 in haplotypes C-N and A lacks most of the C-terminal domain, due to a 209 bp deletion in the coding region of the gene. VvMybA2 and VvMybA3 encode proteins with a similar structure in both haplotypes F1 and F2. VvMybA1_HapF is present in all three subhaplotypes (F1, F2, and F^DEL; see Table 1) and also exhibits a similar structure.

Figure 4

Organization of the berry color locus (BCL) on chromosome 2 for two haplotypes present in Vitis vinifera. HapA is the canonical non-functional haplotype from PN40024, while haplotype F is the one containing VvMybA1_SUB. a Schematic representation of the cluster of MybA genes (denoted here by A followed by a number) found in both haplotypes. Similar colors denote regions with similarities. The grapevine retrotransposon (Gret1) is shown in the VvMybA1 promoter region of haplotype A. Transposable element insertions specific to haplotype F are shown as gray triangles, and two superfamilies were identified: Copia (RLC) and Gypsy (RLG); b Phylogenetic tree constructed from the different nucleotide sequences of MybA genes identified at BCL for both haplotypes A and F. The sequences are colored according to the haplotypes in which they have been identified (HapA in blue and HapF in green). MybA75 (DQ222406) from Arabidopsis thaliana is used as the outgroup. The scale bar shows the number of substitutions per site.

Figure 5

Organization of the berry color locus (BCL) for haplotype F compared to F^DEL. a Schematic representation of the cluster of MybA genes (denoted here by A followed by a number) fount at the BCL. The deleted region in HapF^DEL compared to HapF is indicated with a dashed line. Insertions specific to haplotype F^DEL are shown as gray triangles (RLG for TE from Gypsy superfamily, for other insertions, size (in kb) is written above each insertion). b Phylogenetic tree constructed from the different nucleotide sequences of MybA genes identified at the BCL from both haplotypes F and F^DEL. The sequences are colored according to the haplotype in which they have been identified (haplotype F in red and haplotype F^DEL in green). MybA75 (DQ222406) from Arabidopsis thaliana is used as the outgroup. The scale bar shows the number of substitutions per site.

Figure 6

Phylogenetic tree constructed from different nucleotide sequences of MybA genes identified at BCL for Vitis vinifera and Muscadinia rotundifolia (H2) (Cochetel et al. [29]). The sequences are colored according to the haplotypes in which they have been identified. Haplotype A in blue and haplotype F in red were identified in Vitis vinifera, whereas haplotype H2 in green originated from Muscadinia rotundifolia. MybA75 (DQ222406) from Arabidopsis thaliana is used as the outgroup. The scale bar shows the number of substitutions per site.