Genomic Diversity of Four Closely Related Wild Tomato Species As Revealed by Genotyping-by-sequencing

Wild tomato species have been exploited for many decades to develop cultivated tomato varieties that can resist biotic and abiotic stresses.  The highly variable wild tomato species Solanum peruvianum sensu lato (s.l.) has been reclassified into four distinct species - Solanum peruvianum sensu stricto, Solanum corneliomuelleri, Solanum huaylasense, and Solanum arcanum.  However, the genetic relationships within and among the four species are not well understood.  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.  Origins of accessions in Peru, Ecuador and Chile 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 and was relatively more pronounced between interspecific compared to intraspecific pairs.  Eriopersicon and Arcanum species groups were genetically distinct from each other with the exception of 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.  Approximately 12% of the SNPs rejected a genome-wide test of selective neutrality based on differentiation among species.  These are candidates for more comprehensive studies of adaptive divergence within this species complex.  These DNA markers will be valuable for working with these highly similar and closely related species in tomato breeding and conservation of wild populations.