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Title: Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

item Labate, Joanne
item Robertson, Larry
item Baldo, Angela

Submitted to: Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/13/2009
Publication Date: 6/25/2009
Citation: Labate, J.A., Robertson, L.D., Baldo, A.M. 2009. Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.). Heredity 103:257-267.

Interpretive Summary: Genetic diversity of crops is important for their continued improvement in quality and response towards environmental challenges. Although tomato is very diverse in appearance it is known to be limited in its variation at the gene level. Identifying sources of new genes within the tomato collection at the USDA-ARS Plant Genetic Resources Unit (PGRU) will be valuable to breeders. We surveyed 50 genes in a set of 30 PGRU tomato populations and one commercial type. Most of the populations were originally collected in Peru, Chile, Ecuador, and neighboring countries. The crop originated in this region and several wild tomato relatives are native to the area. Most of the genes showed variation (mutations). These mutations may be linked to favorable traits and can be used as tools to help fix the traits during breeding. Gene diversity was highest in populations that originated an Chile, Ecuador, and Peru. Diversity decreased with increased distance from this "center of origin". By comparing gene sequences to a wild tomato relative, we also saw evidence of cross breeding between the crop and one or more wild species. Wild tomatoes are currently used extensively by breeders as sources of new genes. The PGRU populations are valuable in that many of the undesirable properties of wild tomatoes (for example small, green fruit) were previously eliminated either naturally or with the aid of humans. Observed patterns of gene diversity discovered in this study will be helpful to geneticists working on improving the crop in the future.

Technical Abstract: Limited genetic variation has been observed within tomato (Solanum lycopersicum L.), although no studies have extensively surveyed single nucleotide polymorphism (SNP) diversity among tomato landraces. We estimated intraspecific DNA sequence variation by analyzing 50 gene fragments (22.9 kb) per plant in a 31 plant diversity panel, and uncovered evidence of natural interspecific hybridization as well as human-aided introgression. Three populations - primary centers of diversity, contiguous countries, and secondary centers, were not genetically differentiated (FST = 0.03). Mean expected heterozygosity decreased (He = 0.254, 0.152, 0.092, respectively) while mean coefficient of inbreeding increased (FIS = 0.793, 0.947, 1.000, respectively), in the populations. The majority of loci (80%) were polymorphic with the minor allele at a frequency of 10% or less for most (141 of 155) SNPs. Mean diversity as estimated by theta and pi was approximately 1.5 SNPs per kb. Significant linkage disequilibrium was observed between 19% of locus pairs, and within-locus population recombination estimates were negligible. We also sequenced 43 gene fragments from wild tomato Solanum arcanum Peralta as an outgroup. Various statistical tests rejected a neutral equilibrium model of molecular evolution at 10 of 50 loci. Interspecific introgression was inferred for at least seven tomato lines and five loci. Introgressed alleles likely originated both from natural hybridization with Solanum pimpinellifolium and from crosses with wild relatives for crop improvement. Extensive introgression and frequent bottlenecks within S. lycopersicum pose a challenge to reconstructing the genetic bases of domestication and selection using methods that rely on patterns of molecular polymorphism.