Submitted to: HortScience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/10/2005
Publication Date: 11/15/2005
Citation: Baldo, A.M., Robertson, L.D., Labate, J.A. 2005. Highly polymorphic genes in cultivated tomato. Hortscience. 40:999.
Interpretive Summary: Like many economically important crops in the U.S. (e.g. soybean, peanut), tomato is low in genetic diversity. This study targets the fundamental unit of DNA variation, single nucleotide polymorphisms (SNPs), in cultivated tomato. We developed a software tool to efficiently discover potential SNPs in 764 tomato genes using data made publicly available at the National Center for Biotechnology Information (NCBI). In the lab we tested 85 of these genes. Fifty three gave clear results and 21 of those revealed a wealth of genetic diversity. These results will provide more detail in genetic maps of cultivated tomato, enabling breeders to efficiently target existing genetic variation for crop improvement.
Technical Abstract: Cultivated tomato varieties are genetically extremely similar. We identified 764 Unigenes with potential single nucleotide polymorphisms (SNPs) among more than 15 cultivars from public expressed tomato data. By sequencing regions from 53 of these Unigenes in two to three cultivars, we discovered an unexpected wealth of nucleotide polymorphism (62 SNPs and 12 indels in 21 Unigenes). This included a high proportion of predicted nonsynonymous nucleotide (17 of 33 SNPs in exons) and nonconservative amino acid (6 of 16 nonsynonymous SNPs) changes. We hypothesize that five of these 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.