Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

Genetic Diversity In Tomato: SNPs From Various Sources Show Similar Amounts Of Polymorphism And Bottlenecking Due To Domestication.

Angela M Baldo^1,2 , Larry D Robertson^1,2 , Susan M Sheffer¹ , Warren F Lamboy¹ , Joanne A Labate^1,2

¹  USDA-ARS Plant Genetic Resources Unit 630 W. North St. Geneva, NY 14456

²  Cornell University Dept. of Horticultural Sciences 630 W. North St. Geneva, NY 14456

Because cultivated tomato (Solanum lycopersicum syn. Lycopersion esculentum) 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 51 genes in a diverse set of 31 tomato lines. The majority of sampled tomato accessions represented the primary center of diversity (Peru, Chile, and Ecuador), and countries contiguous with the primary center, collected between 1932 and 1976. These are the same accessions studied by Villand et. al. (1998) using RAPDS. Three classes of markers were sampled: i) 26 expressed-sequence tag (EST), ii) 14 Conserved Ortholog Set II (COSII) or unigene, and iii) 11 published genes, 10 of which are related to fruit quality. The latter two types contained mostly noncoding DNA. Totals of 156 SNPs and 35 indels were found in 24 kb. The distributions of nucleotide diversity estimates among marker types were not significantly different from each other. Evidence of historical introgression and the population-level distribution of genetic variation reveal relationships between tomato landraces. There is the most genetic diversity among the samples collected in the primary center of domestication and the least from secondary centers of domestication.