Hidden grape ancestry reveals a second origin of white-skinned varieties
image: A proposed working model on the role of MdWRKY9 in JA-mediated salt tolerance in apple.
Credit: Horticulture Research
White-skinned grapes were long believed to originate from a single mutation event, but new genomic evidence overturns this assumption. Researchers identified a divergent haplotype at the berry color locus that includes a large chromosomal deletion removing most VvMybA genes responsible for regulating anthocyanin biosynthesis. This nonfunctional subhaplotype, termed HapFDEL, independently produces a white phenotype separate from the classic HapA lineage. The study reconstructs three subhaplotypes within haplotype F—two functional and one nonfunctional—and shows that HapFDEL is responsible for white berries in several table grape cultivars. These findings significantly revise the evolutionary model of grape domestication, demonstrating at least two distinct origins of white-skinned grapes.
Berry skin color in Vitis vinifera is primarily determined by the presence or absence of anthocyanins, pigments produced through the flavonoid biosynthesis pathway. This pathway is activated by R2R3-MYB transcription factors encoded by VvMybA genes located at the berry color locus (BCL) on chromosome 2. Most white cultivars lose pigmentation due to mutations associated with HapA, commonly caused by the retrotransposon Gret1 inserted into the VvMybA1 promoter. However, several reported white-skinned cultivars do not fit this model and instead carry the lesser-known allele VvMybA1_SUB. The evolutionary origin, structure, and function of this allele have remained unclear. Based on these challenges, further in-depth investigation of this locus is required.
A research team from Agroscope (Switzerland), INRAE and Institut Agro (France), Hepia (Switzerland), and the University of Neuchâtel (Switzerland) published (DOI: 10.1093/hr/uhaf069) new findings on March 6, 2025, in Horticulture Research, revealing a previously unrecognized genetic mechanism responsible for white-skinned grape varieties. Using long-read sequencing, genome reconstruction, and transcriptomic profiling, the authors showed that the haplotype containing VvMybA1_SUB diverges into multiple subhaplotypes, including HapFDEL—a form carrying a large deletion that removes most VvMybA genes. This discovery revises long-standing assumptions about grape color evolution and domestication history.
The researchers reconstructed the full structure of the berry color locus for haplotype F and revealed clear genetic divergence among its subhaplotypes. Functional forms HapF1 and HapF2 contain intact VvMybA1, VvMybA2, and VvMybA3 genes, enabling anthocyanin activation. In contrast, the nonfunctional HapFDEL exhibits a ~76-kb deletion that eliminates six VvMybA genes—including VvMybA2 and VvMybA3. This deletion directly disrupts pigment biosynthesis and causes the white-skinned phenotype. Surveying over 500 accessions, the study found HapF1 broadly distributed from the Near East to Central Asia, while HapF2 is restricted to black-skinned alpine cultivars from the Swiss–Italian region. HapFDEL, however, appears exclusively in table grape cultivars from Asia, such as ‘Sultanina’, ‘Khusaine Belyi’, and ‘Otcha Bala’.
Transcriptomic analysis showed that VvMybA1_SUB is expressed at low levels in both white- and black-skinned cultivars. The low expression is insufficient to activate UFGT, a key enzyme required for anthocyanin accumulation, explaining why cultivars carrying HapFDEL fail to develop pigmentation. Evolutionary evidence revealed that HapF1 is ancient and present in Vitis vinifera subsp. sylvestris populations from the Transcaucasus and Israel, whereas HapFDEL likely represents a recent mutation disseminated along the ancient Silk Road. These findings collectively confirm at least two independent origins of white grapes.
The lead authors emphasize that this work fundamentally reshapes the understanding of grape evolution. The discovery of HapFDEL as a second, independent source of white-skinned grapes challenges the long-standing assumption of a single ancestral mutation. They note that the berry color locus is a genomic hotspot characterized by duplications, deletions, and transposable element insertions, which promote phenotypic innovation. This structural plasticity likely facilitated both ancient domestication and human-driven selection for diverse berry colors across regions.
The findings provide valuable genetic markers for breeding programs seeking to optimize berry pigmentation traits. By clearly distinguishing functional and nonfunctional VvMybA haplotypes, breeders can more accurately predict color inheritance patterns and strategically select parent lines for wine or table grape improvement. The identification of multiple independent origins of white-skinned grapes deepens the reconstruction of domestication routes and may help trace ancient cultivar movements across Eurasia. More broadly, the study demonstrates how structural genomic variations drive phenotypic diversity, offering insights relevant to other perennial crops with complex domestication histories.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhaf069
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.