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Tomato SNP Discovery by EST Mining and Resequencing

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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.

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  1. USDA, Agricultural Research Service, Plant Genetic Resources Unit, 630 W. North Street, Geneva, NY, 14456, USA

    Joanne Aaron Labate & Angela M. Baldo

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  1. Joanne Aaron Labate
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  2. Angela M. Baldo
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Correspondence to Joanne Aaron Labate.

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Labate, J., Baldo, A.M. Tomato SNP Discovery by EST Mining and Resequencing. Mol Breeding 16, 343–349 (2005). https://doi.org/10.1007/s11032-005-1911-5

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