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Title: Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex

Author
item Labate, Joanne
item Robertson, Larry
item STRICKLER, SUSAN - Boyce Thompson Institute
item MUELLER, LUKAS - Boyce Thompson Institute

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/4/2014
Publication Date: 5/5/2014
Citation: Labate, J.A., Robertson, L.D., Strickler, S., Mueller, L. 2014. Genetic structure of the four wil tomato species in the Solanum peruvianum s.l. species complex. Genome. 57:169-180.

Interpretive Summary: Wild relatives of crop species are valuable sources of certain genes. For example, because wild populations live in stressful environments, they often carry genes that help them to survive drought or heat. Wild tomato species have been extensively used in breeding new commercial tomato varieties that can survive environmental and disease stresses. The most variable wild tomato species Solanum peruvianum sensu lato (s.l.) has been re-grouped into four separate species. However, the genetic relationships within and among the four species are not well known. We used DNA sequencing across whole genomes to analyze genetic relationships within and among these four wild tomato species. Geographical origins of the sampled plants in Peru, Ecuador and Chile were mapped. We now understand genetic properties of the four species based on how plants were related to each other within the context of their geographic origins. Many thousands of DNA markers were identified that could potentially be used to distinguish among the four species by using simple lab tests. These DNA markers will be valuable for working with these highly similar and closely related species in tomato breeding and conservation of wild populations.

Technical Abstract: The most diverse wild tomato species Solanum peruvianum sensu lato (s.l.) has been reclassified into four separate species. However, reproductive barriers among the species are incomplete and this can lead to discrepancies regarding genetic identity of germplasm. We used genotyping by sequencing (GBS) to develop tens of thousands of mapped single nucleotide polymorphisms (SNPs) in order to analyze genetic relationships within and among species. The data set was condensed to 14,043 SNPs with no missing data across 46 sampled plants. Origins of accessions were mapped using geographical information systems (GIS). Isolation by distance, pairwise genetic distances and number of clusters were estimated using population genetics approaches. Isolation by distance was strongly supported, especially between interspecific pairs. Eriopersicon and Arcanum species groups were genetically distinct except for S. huaylasense which showed 50% membership proportions in each group. S. peruvianum and S. corneliomuelleri were not significantly differentiated from each other. Many thousands of SNP markers were identified that could potentially be used to distinguish pairs of species, including S. peruvianum versus S. corneliomuelleri, if they are verified on larger numbers of samples. Diagnostic markers will be valuable for delimiting morphologically similar and interfertile species in germplasm management.