ARS | Publication request: PREDICTION OF SINGLE NUCLEOTIDE POLYMORPHISMS IN DOMESTIC TOMATO: HOW USEFUL IS EST SEQUENCE DIVERSITY?

Submitted to: Meeting Abstract
Publication Type: Proceedings
Publication Acceptance Date: August 4, 2004
Publication Date: August 4, 2004
Citation: Baldo, A.M., Labate, J.A., Robertson, L.D., 2004. Prediction of single nucleotide polymorphisms in domestic tomato: how useful is EST sequence diversity?. 12th International Conference on Intelligent Systems for Molecular Biology (ISMB 2004)

Technical Abstract: Cultivated tomato is known to be relatively low in genetic diversity. This is a result of microevolutionary processes such as founder events, genetic bottlenecks, and intense selection. For these reasons, a computational approach to predicting single nucleotide polymorphisms (SNPs) is valuable to direct laboratory efforts toward regions more likely to yield results. We have developed a method to screen an entire NCBI Unigene set for potential SNPs using the SEAN SNP Prediction Program(Huntley, 2003). Predictions are based on established criteria: A window on either side of the predicted SNP must be identical for all sequences in the alignment, at least two sequences agreeing on each of a minimum of two polymorphisms, etc. Polymorphisms were further examined in the context of the cultivars and clones in which they were identified. Using this method, we discovered 2,527 potential SNPs among 764 clusters from the unigene set. We are in the process of verifying these polymorphisms in the laboratory, and comparing the results with sequence derived from randomly chosen introns, and diversity in the region of published, mapped markers.