Abstract
BackgroundDomestication and selection of Vitis vinifera L. for table and wine grapes has led to a large level of berry size diversity in current grapevine cultivars. Identifying the genetic basis for this natural variation is paramount both for breeding programs and for elucidating which genes contributed to crop evolution during domestication and selection processes. The gene VvNAC26, which encodes a NAC domain-containing transcription factor, has been related to the early development of grapevine flowers and berries. It was selected as candidate gene for an association study to elucidate its possible participation in the natural variation of reproductive traits in cultivated grapevine.MethodsA grapevine collection of 114 varieties was characterized during three consecutive seasons for different berry and bunch traits. The promoter and coding regions of VvNAC26 gene (VIT_01s0026g02710) were sequenced in all the varieties of the collection, and the existing polymorphisms (SNP and INDEL) were detected. The corresponding haplotypes were inferred and used for a phylogenetic analysis. The possible associations between genotypic and phenotypic data were analyzed independently for each season data, using different models and significance thresholds.ResultsA total of 30 non-rare polymorphisms were detected in the VvNAC26 sequence, and 26 different haplotypes were inferred. Phylogenetic analysis revealed their clustering in two major haplogroups with marked phenotypic differences in berry size between varieties harboring haplogroup-specific alleles. After correcting the statistical models for the effect of the population genetic stratification, we found a set of polymorphisms associated with berry size explaining between 8.4 and 21.7 % (R2) of trait variance, including those generating the differentiation between both haplogroups. Haplotypes built from only three polymorphisms (minihaplotypes) were also associated with this trait (R2: 17.5 – 26.6 %), supporting the involvement of this gene in the natural variation for berry size.ConclusionsOur results suggest the participation of VvNAC26 in the determination of the grape berry final size. Different VvNAC26 polymorphisms and their combination showed to be associated with different features of the fruit. The phylogenetic relationships between the VvNAC26 haplotypes and the association results indicate that this nucleotide variation may have contributed to the differentiation between table and wine grapes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0622-2) contains supplementary material, which is available to authorized users.
Highlights
Domestication and selection of Vitis vinifera L. for table and wine grapes has led to a large level of berry size diversity in current grapevine cultivars
VvNAC26 was chosen as a candidate gene that has been sequenced in a set of varieties to determine the existing nucleotide variation, and to identify its possible contribution to the natural variation observed for several reproductive traits in grapevine
The analysis of the nucleotide sequence variation at the grapevine VvNAC26 gene and its association with grapevine reproductive traits has allowed the detection of polymorphisms recurrently associated with berry size
Summary
Domestication and selection of Vitis vinifera L. for table and wine grapes has led to a large level of berry size diversity in current grapevine cultivars. The gene VvNAC26, which encodes a NAC domain-containing transcription factor, has been related to the early development of grapevine flowers and berries. It was selected as candidate gene for an association study to elucidate its possible participation in the natural variation of reproductive traits in cultivated grapevine. Archeological findings suggest that primary domestication events could have taken place between the seventh and fourth millennia BC in the Near East region located between the Black and Caspian seas [4,5,6] Those initial cultivars would had been spread by human civilizations in different directions [4]. Current cultivated grapevine shows important modifications compared to its wild relative, including the radical change in the sexual form of the plant - from dioecy to hermaphroditism-, and the increase in the number of berries per bunch and their individual size [4, 5, 9,10,11]
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