Proceedings of the XLVII Italian Society of Agricultural Genetics - SIGA Annual Congress

Verona, Italy - 24/27 September, 2003

ISBN 88-900622-4-X

Poster Abstract - 2.13

NUCLEOTIDE AND HAPLOTYPE DIVERSITY IN WINE CULTIVARS OF GRAPE (VITIS VINIFERA L.)

G. PRETE, F. CATTONARO, M. MORGANTE

Dipartimento di Produzione Vegetale e Tecnologie Agrarie, Università degli Studi di Udine, via delle Scienze 208, 33100 Udine

grape, SNP, variation, haplotypes, bottleneck

Developments in sequencing technology made it possible to detect DNA polimorphisms at the single nucleotide level. SNPs (Single Nucleotide Polimorphism) and haplotypes derived from them are both a tool to investigate the evolutionary history of genes and species as well as a novel tool to genetically map traits through association approaches that rely on linkage disequilibrium and existing populations.

Pursuing this aim, 13 genes in 16 cultivars of grape used for wine production have been examined. The 13 loci have been chosen from GenBank sequences and primers for PCR have been designed targeting whenever available UTRs and introns. SNPs and Indels have been identified by comparing sequences (chromatograms and text format) from all individuals by using Phred/Phrap/Consed (Ewing et al. 1998). As grapevine is an outcrossing and heterozygous species, the exact sequence of haplotypes at each locus was ambiguous whenever an individual was heterozygous at any locus. To resolve these ambiguities, amplicons from some individuals at each locus have been cloned and the haplotype data coming from cloned loci and homozygous loci have been exploited to infer the remaining haplotypes by using the Haplotyper software (Niu et al. 2003).

All loci investigated were polymorphic. The observed frequency of nucleotide changes is high, on average 1 SNP every 69 bp in coding regions and 1 every 48 bp in non- coding regions; frequency of Indels, found only in non- coding region, is 1 every 714 bp. A mean of 7 haplotypes per gene has been found in the sample of 32 chromosomes we analysed. Linkage disequilibrium as measured by both D’ and r² did not decay within 700 bp distances.

The analysis of sequence diversity by means of the Tajima’s D test shows a significant deficiency of rare variants and an excess of common ones across most loci. This is an indication of a recent bottleneck which may be the result of the breeding and selection process. The high levels of SNP variation we detected in transcribed regions of elite material as well as the presence of significant LD levels at least within short distances make association mapping approaches very attractive for wine grape, especially when the biological difficulties related to the creation of segregating populations are considered.