Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/5/2008
Publication Date: 4/15/2009
Citation: Labate, J.A., Robertson, L.D., Wu, F., Tanksley, S.D., Baldo, A.M. 2009. EST, COSII, and arbitrary gene markers give similar estimates of nucleotide diversity in cultivated tomato (Solanum lycopersicum). Journal of Theoretical and Applied Genetics. 118:1005-1014.
Interpretive Summary: DNA diversity is known to be low in the tomato crop. This has severely limited the use of DNA-based tools for crop improvement within the 'cultivated tomato' gene pool. We studied 50 genes in 30 diverse tomato lines conserved at the USDA-ARS Plant Genetic Resources Unit (PGRU). We discovered 188 total mutations in the genes. These mutations can serve as the basis for molecular tags for use in gene mapping and gene selection during crop improvement. The mutations also illustrate that conserved PGRU tomato populations can contribute to increased diversity of the tomato crop. New sources of diversity are important for continued crop improvement and protection against novel diseases, pests or environmental challenges.
Technical Abstract: Because cultivated tomato (Solanum lycopersicum L.) is low in genetic diversity, public, verified single nucleotide polymorphisms (SNP) markers within the species are in demand. To promote marker development we resequenced fragments of 50 genes in a diverse set of 31 tomato lines including TA496. Three classes of markers were sampled: i) 26 expressed-sequence tag (EST), all of which were predicted to be polymorphic based on TA496, ii) 14 Conserved Ortholog Set II (COSII) or unigene, and iii) 10 published genes, nine of which influence fruit quality. The latter two types contained mostly noncoding DNA. Totals of 154 SNPs and 34 indels were found in 23 kb. The distributions of nucleotide diversity estimates among marker types were not significantly different from each other. Ascertainment bias of SNPs was evaluated for the EST markers. Despite the fact that the EST markers were developed using SNP prediction within a sample consisting of only one TA496 allele and one additional allele, the majority of polymorphisms in the 26 EST markers were represented among the other 30 tomato lines. Fifteen EST markers with published SNPs were more closely examined for bias. Mean SNP diversity observations were not significantly different between the original discovery sample of two lines (53 SNPs) and the 31 line diversity panel (56 SNPs). Furthermore, TA496 shared its haplotype with at least one other line at 11 of the 15 markers. These data demonstrate that public EST databases and noncoding regions are a valuable source of unbiased SNP markers in tomato.