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ARS Home » Northeast Area » Geneva, New York » Plant Genetic Resources Unit (PGRU) » Research » Publications at this Location » Publication #189352
Title: TOMATO SNP DISCOVERY BY EST MINING AND RESEQUENCING

Author
item Labate, Joanne
item Baldo, Angela

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/5/2005
Publication Date: 12/6/2005
Citation: Labate, J.A., Baldo, A.M. 2005. Tomato snp discovery by est mining and resequencing. Molecular Breeding. 16:343-349.

Interpretive Summary: Like many economically important crops in the U.S. (e.g. soybean, peanut), tomato is low in genetic diversity. Because of this lack of variation, many tomato breeders make crosses with wild tomato relatives to improve cultivated forms. Recently there has been a wealth of tomato DNA data made publicly available at the National Center for Biotechnology Information (NCBI). We developed a software tool to efficiently discover potential variation in 764 tomato genes. In the lab we tested 85 of these genes. Fifty three genes gave clear results and 21 of those revealed a wealth of genetic diversity. Based on our work so far, we expect to confirm between 600 and 1,000 variations within the 679 genes remaining to be tested. Our results will enable breeders to efficiently target available genetic variation in cultivated tomato. Unlike other commonly used markers, our predicted gene-based markers are likely to be associated with functional variation. They will also be useful in providing more detail in genetic maps of cultivated tomato. Results also aid the National Plant Germplasm System (NPGS) in conserving a broad range of functional variation potentially responsible for agronomic traits. This paper supports NP301 vision statement “Furnishing genetic and bioinformatic tools, genomic information, and genetic raw materials to enhance American agricultural productivity to ensure a high quality, safe supply of food, fiber, feed, ornamentals, and industrial products."

Technical Abstract: Many economically important crop species are relatively depauparate in genetic diversity (e.g. soybean, peanut, tomato). DNA polymorphism within cultivated tomato has been estimated to be low based on molecular markers. Through mining of more than 148,000 public tomato expressed sequence tags (ESTs) and full-length cDNAs, we identified 764 EST clusters with potential single nucleotide polymorphisms (SNPs) among more than 15 tomato lines. By sequencing regions from 53 of these clusters in two to three lines, we discovered a wealth of nucleotide polymorphism (62 SNPs and 12 indels in 21 Unigenes), resulting in a verification rate of 27.2% (28 of 103 SNPs predicted in EST clusters were verified). We hypothesize that five regions with 1.6-13-fold more diversity relative to other tested regions are associated with introgressions from wild relatives. Identifying polymorphic, expressed genes in the tomato genome will be useful for both tomato improvement and germplasm conservation.