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

Giardini Naxos, Italy - 18/21 September, 2002

ISBN 88-900622-3-1

Oral Communication Abstract - S4h

GENOME DIVERSITY IN GRAPEVINE AS REVEALED BY SNPs

SALMASO M.^#, FAES G.^#, SEGALA C., VELASCO R.

# this two authors equally contributed to the present work

Istituto Agrario San Michele all’Adige, San Michele a/A (TN), Italy

grapevine, SNPs, SSCP, sequencing

Grapevine is a perennial crop that shows an important genetic diversity among cultivars, wild species or hybrids. Grapevine (Vitis sp) has been a species recalcitrant to classical genetic analysis for long time. Nowadays, genomics offers the possibility to overcome traditional scepticism on breeding of perennial plants supplying powerful techniques to marker assisted selection. Our interest is focused on three direction: 1) development of a solid set of new generation markers (SNPs), 2) selection of interesting segregating populations, 3) validation of SSCP techniques for SNPs detection.

We are currently scavenging the grape genome by an ESTs-SNPs approach. 1920 sequences have been produced from cDNA-library of Regent (a newly –bred multiply fungus- resistant cultivar of Vitis vinifera) and 960 from a cDNA library of Pinot noir (Vitis vinifera cv) and classified based on their sequence homology by BLAST search. Seven parental of four inter or intra-specific crosses have been used to evaluate the degree of polymorphism in Vitis vinifera, intra-specific crosses and Vitis riparia. Sub-set of two populations, segregating for resistance to pathogens and for berry quality traits, are used to test the distribution of SSCPs identified from gene sequences of parental plants. To date 72 SNPs have been developed from the first few hundreds sequences (ESTs) selected from four sub-groups: 1) pathogen-related, 2) anthocyanin metabolism, 3) sugar metabolism and 4) cell signalling.

Based on EST sequences, fragments of 30 genes have been amplified and sequenced in all 7 parentals. We calculate a different rate of single nucleotide polymorphisms in the coding and non-coding regions. So we compared the efficiency of SSCP with a 100% approach as re-sequencing.

The use of these results will supply powerful tools in phylogenetic studies, germoplasm classification and characterisation, gene expression analysis as well as bridges between molecular and physical mapping.