Characterization of deletions causing berry-color variation in Garnacha and Tempranillo
Gray and white somatic variants that can be the basis of new cultivars occasionally appear in some black-berried grapevine cultivars. Genetic and molecular studies have associated color loss with the presence of deletions at the grape color locus located on chromosome 2. This color loss occurs in heterozygous black-berried cultivars carrying a functional and a null allele. Depending on the size of the deletions, side-effects additional to the loss of pigmentation capability may appear in these variants. In this study, we developed a single-nucleotide polymorphism (SNP)-based chip to evaluate, through loss of heterozygosity along chromosome 2, the extension of hemizygous deletions in grape color variants. These markers were used to characterize white and gray isolates that originated from Garnacha Tinta and Tempranillo Tinto collected along the Ebro valley (northeast Spain). Two deletion types were detected in Garnacha Blanca accessions, which correlated with their geographical origin, while the diversity of deletion types was greater in Tempranillo. Comparative genomics of Garnacha variants after whole-genome re-sequencing was conducted to understand the mutational mechanisms that generate these deletions. The results show that differences between the two deletion types are likely related with genome rearrangements already appeared in different ancestral clonal lines of Garnacha Tinta. These results can be exploited for the selection of grape color variants best suited for the development of new cultivars and can help to detect rearrangement hotspots in the grapevine genome.
Royo, C., Rodríguez-Lorenzo, M., Carbonell-Bejerano, P., Mauri, N., Cibríain, F., Suberviola, J., Sagüés, A., Ibáñez, J. and Martínez-Zapater, J.M. (2019). Characterization of deletions causing berry-color variation in Garnacha and Tempranillo. Acta Hortic. 1248, 463-470
Vitis vinifera, grapevine, berry color, somatic variation, genome rearrangements, hemizygosis, whole-genome sequencing