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The main objective of this research was the evaluation of the variability present in a segregating wine grape population derived from a cross between Graciano × Tempranillo, two Spanish varieties, in order to select improved genotypes with potential for producing high-quality wines in a climate change scenario. For that purpose, the phenotypic segregation of 16 agronomic traits related to production and phenology and 11 enological traits related to technical and phenolic maturity was studied in the progeny for three consecutive years. All traits presented transgressive segregation and continuous variation. Year effect was significant for all traits except total, extractable and skin anthocyanins content. However, a high level of genotype consistency for enological traits was revealed by repeatabilities and correlations between years. Significant correlations among traits were observed but most associations were weak. Furthermore, the CAPS (Cleaved Amplified Polymorphic Sequence) marker for the VvmybA genotype was tested to determine whether it would be useful in indirect selection for berry anthocyanins content. The results showed that the number of homozygous and heterozygous genotypes for the functional colour allele adjusted to a 1:1 segregation ratio, and that homozygous genotypes had significantly higher anthocyanins content. Principal component analysis found eight variables that contributed up to 80 % of the phenotypic variability present in the population. Seven groups of hybrids were distinguished based on ripening time, cluster weight, berry weight and anthocyanins content by cluster analysis; and fourteen genotypes were pre-selected for further research. © 2013 Springer Science+Business Media Dordrecht., This research was funded by the Government of La Rioja through the FOMENTA 04/2008 research project. Shiren Song was initially supported by a fellowship from the Chinese Research Council and for the last 3 years by a MAE-AECID fellowship from the Spanish Government.