Articles
GENOMICS TOOLS FOR MARKER ASSISTED SELECTION IN GRAPEVINE
Article number
603_67
Pages
511 – 517
Language
English
Abstract
EST (express sequence tags) sequencing, SNP (single nucleotide polymorphisms) development, haplotypes and subhaplotypes definition constitute extreme powerful tools to sustain marker assisted selection.
We are currently scavenging the grape genome by an EST-SNP approach. 2.880 sequences have been produced at the moment (to the final goal of 20.000 ESTs) and classified based on their sequence homology by BLAST search.
Among them, a few hundred belonging to metabolic pathways of interest have been selected for further studies.
Seven parental types of 4 inter- or intra-specific crosses have been used to evaluate the degree of polymorphism between Vitis vinifera, intra-specific crosses and Vitis riparia, measured by nucleotide diversity,
with = K/L and K defined as number of differences per nucleotide site and L being the sequence length in bp.
Based on cDNA sequences of three libraries (leaf, cv.
Pinot noir; inflorescence, shoot tips, cv.
Regent), primer pairs have been deduced and used to amplify the corresponding genomic sequences.
Most of the times introns were also amplified, supplying a further element of comparison between coding and non-coding regions.
Two approaches have been essentially used: SSCP (single sequence conformational polymorphism) and re-sequencing.
The efficiency of SSCP in comparison with an 100% approach as re-sequencing has also been considered.
Re-sequencing supplied further element of discussion on haplotypes and sub-haplotypes definition in grapevine.
We are currently scavenging the grape genome by an EST-SNP approach. 2.880 sequences have been produced at the moment (to the final goal of 20.000 ESTs) and classified based on their sequence homology by BLAST search.
Among them, a few hundred belonging to metabolic pathways of interest have been selected for further studies.
Seven parental types of 4 inter- or intra-specific crosses have been used to evaluate the degree of polymorphism between Vitis vinifera, intra-specific crosses and Vitis riparia, measured by nucleotide diversity,
with = K/L and K defined as number of differences per nucleotide site and L being the sequence length in bp.Based on cDNA sequences of three libraries (leaf, cv.
Pinot noir; inflorescence, shoot tips, cv.
Regent), primer pairs have been deduced and used to amplify the corresponding genomic sequences.
Most of the times introns were also amplified, supplying a further element of comparison between coding and non-coding regions.
Two approaches have been essentially used: SSCP (single sequence conformational polymorphism) and re-sequencing.
The efficiency of SSCP in comparison with an 100% approach as re-sequencing has also been considered.
Re-sequencing supplied further element of discussion on haplotypes and sub-haplotypes definition in grapevine.
Authors
G. Faes, M. Salmaso, C. Segala, C. Moser, M. Stefanini, I. Salakhutdinov, E. Zyprian, R. Töpfer, M.S. Grando
Keywords
grape ESTs, SNPs development, SSCP and re-sequencing, haplotypes
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