| Abstract Detail
Potato Genomics - Afternoon De Koeyer, David [1], Griffiths, Rebecca [2], Eveleigh, Robert [1], Douglass, Katheryn [1], Flinn, Barry [3], Lagüe, Martin [1]. Polymorphism discovery in potato: bioinformatics and lab-based approaches to study genetic diversity. THE identification of polymorphisms in DNA sequences and the development of molecular markers are important steps in the application of genomics to potato improvement. We have established a bioinformatics pipeline to mine EST sequences for single nucleotide polymorphisms (SNPs) and predict the functional consequences of the nucleotide substitutions. To validate these polymorphisms and identify additional diversity in candidate genes, we are utilizing mismatch digestion and other SNP marker assays on DNA from mapping population parents and other germplasm. The SNP discovery pipeline has identified almost 7,000 SNPs in 2,354 contigs from a Canadian Potato Genome Project (www.cpgp.ca) assembly of potato ESTs originating from the tetraploid cultivar, Shepody. This represents a polymorphism rate of one SNP per 1,032 bases and 25.6% of the total contigs. These SNPs have been assessed for their substitution type and location relative to the coding region. The effects on the translated amino acid and substitution scores of non-synonymous changes were also determined. The SNP data was used to construct haplotypes to further assess the sequence diversity within each contig. Approximately 85% of the contigs were comprised of two haplotypes and less than one percent had more than four haplotypes. The polymorphism discovery pipeline combined with lab assays, such as those based on the formation of DNA heteroduplexes at polymorphic sites, will facilitate the exploitation of the natural diversity that exists within potato. These tools will provide a rapid method for placing candidate genes and ESTs onto genetic maps and conducting association genetics studies. Results from the analysis of the potato EST assemblies and preliminary SNP validation will be presented.
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Related Links:
Canadian Potato Genome Project
1 - Agriculture and Agri-Food Canada, Potato Research Centre, P.O. Box 20280, 850 Lincoln Rd, Fredericton, NB, E3B 4Z7, Canada
2 - Genome Atlantic, 921 College Hill Road, Fredericton, NB, E3B 6Z9, Canada
3 - Institute for Sustainable and Renewable Resources, 150 Slayton Ave, Danville, VA, 24540, USA
Keywords:
Potato
Single Nucleotide Polymorphism
Bioinformatics
diversity
Haplotype.
Session: SAT09-11
Location: Hall of Ideas Room I/Monona Terrace
Date: Wednesday, July 26th, 2006
Time: 5:00 PM
Abstract ID:295 |
