Characterization of SNPs from microsatellite flanking regions in vitis

Resumen

Microsatellites are hypervariable regions of the genome, while their flanking regions are assumed to be as conserved as the average of the genome. In this study, the flanking regions of ten microsatellite loci (VVMD5, VVMD7, VVMD28, VVS2, VVS29, VrZAG62, VrZAG67, VrZAG79, VrZAG83, and VrZAG112) were sequenced in different cultivars of Vitis vinifera. For every microsatellite, about eight homozygous cultivars (regarding the allele size) were chosen, to facilitate the sequencing. A total of 91 DNA sequences were analysed to determine the level of sequence variation within the microsatellite flanking regions. Several sequence variations were detected for all the microsatellite flanking regions studied, including single nucleotide polymorphism (SNPs), insertions, and deletions. The number of identified changes varied considerably among the loci, VVS2 being the most polymorphic one. A number of SNPs were selected to design SNP markers, scored by dideoxy single base primer extension and capillary electrophoresis methodology. These SNP markers were analysed in 21 cultivars of Vitis vinifera and four varieties of other Vitis species. The goodness of the markers developed as well as their utility for varietal identification and pedigree studies is discussed.