Nucleotide sequence polymorphism in ancient cultivars of grape (Vitis vinifera L.)

Grape cultivars arise from a single seed resulting from a crossing event between the parents of the cultivar. The cultivars are then vegetatively propagated to preserve important phenotypic traits. Within the somatic lineages of ancient grape cultivars, phenotypic variation of economic value has arisen. This work presents three approaches to the identification of genotypic variation within ancient grape cultivars. In addition to the economic value of identifying such variation, there is important scientific value in the study of these ancient somatic lineages.; The first approach to identifying nucleotide sequence variation within ancient cultivars was the identification of single nucleotide polymorphisms (SNPs) in the flanking sequence of microsatellites and in the genomic sequence amplified from primers based on expressed sequence tag (EST) sequences. Both intron and exon sequences were examined. While some unconfirmed SNPs from different 'Pivot noir' accessions were identified, interesting data also resulted from the haplotype analysis of reproducible polymorphisms found between the alleles of 'Pivot noir'. Physical association of multiple SNPs within a sequence may increase the power of these markers to reveal underlying diversity.; The second portion of this work was the confirmation that variation in simple sequence repeat (SSR) regions was actually due to changes in repeat number. Sequencing of these regions was performed to confirm this. Again, interesting data resulted from the comparative analysis of both alleles of 'Pinot noir'. Sequence structure within the repeat itself, unique to each allele, may make it possible for future studies to identify which predominant allele gave rise to the variant alleles observed in some repeat regions.; The final portion of this work was the isolation and identification of novel copia-like retroelement sequences in the grape genome. The identified sequences were used to design markers for sequence specific amplified polymorphism (S-SAP) analysis for variation within many different cultivars. Data from this portion of the work suggest an interesting model for the ancestry of different Pinot color variants.