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ARS Home » Northeast Area » Geneva, New York » Plant Genetic Resources Unit (PGRU) » Research » Publications at this Location » Publication #176181
Title: HIGH-THROUGHPUT SNP PREDICTION IN TOMATOES BASED ON ESTS

Author
item BALDO, ANGELA
item HUNTLEY, DEREK - CENTER FOR BIOINFORMATICS
item ROBERTSON, LARRY
item LABATE, JOANNE

Submitted to: Tomato Breeders Roundtable Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 4/1/2005
Publication Date: 7/1/2005
Citation: Baldo, A.M., Huntley, D., Robertson, L.D., Labate, J.A. 2005. High-throughput snp prediction in tomatoes based on ests. Tomato Breeders Roundtable Proceedings. p. 7 In Final Abstracts Guide, Plant and Animal Genome XIII, San Diego, Ca.

Interpretive Summary:

Technical Abstract: Cultivated tomato is extremely low in genetic diversity. Only one nucleotide polymorphism was observed in more than 7 kb in four modern cultivars (Nesbitt and Tanksley, 2002). This monomorphism is a result of microevolutionary processes such as founder events, genetic bottlenecks, and intense selection, and creates a challenge for characterizing germplasm collections. A computational approach to predicting single nucleotide polymorphisms (SNPs) is a powerful way to discover rare polymorphic regions. 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 (Picoult-Newberg et. al. 1999). 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 have verified 62 SNPs within 21 unigenes by DNA sequencing two or three cultivars. Based on our results, the verified SNPs have been found 21 times more frequently (approximately three SNPs) per kb in two to three cultivars) than we'd expect with random sequencing. We have virtually mapped some of the markers by BLASTing the unigenes against published DNA sequences of mapped markers.