Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

Abstract

Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.

Local extirpation is pervasive among populations of Galápagos endemic tomatoes

“…The most striking instance was in Puerto Ayora, Santa Cruz where we were unable to locate endemic plants at any of the six collection sites visited. Such cases of local extinction can result in the irreversible loss of locally-unique trait variation, because genetic and phenotypic diversity is typically high between populations of endemic tomatoes in spite of low within-population variation due to high rates of selfing (Darwin, 2009; Pailles et al, 2017; Rick, 1983; Rick & Fobes, 1975). This loss is additionally troubling as, unlike many Galápagos plants, the endemic tomatoes have historically been an important source of traits for crop improvement (e.g., jointless pedicles in Puerto Ayora populations [Rick, 1967], high beta-carotene [Mackinney et al, 1954; Stommel, 1994], sugar content [Poysa, 1993], drought tolerance [Rush & Epstein, 1981], and insect resistance [Firdaus et al, 2013]; Rick, 1979; Nuez, 1995).…”

“…Past observational and genetic evidence for hybridization between tomato species on the Galápagos is mixed—with evidence both for (Darwin, 2009; Pailles et al, 2017) and against (Nuez et al, 2004) intercrossing. Nonetheless, several biological factors suggest that the potential for gene flow between sympatric species is high.…”

A diversity of traits contributes to salinity tolerance of wild Galapagos tomatoes seedlings

“…A collection of 67 Galapagos tomato accessions (Pailles et al , 2017) was characterized and screened for salinity tolerance, of which 39 are S. cheesmaniae and 28 are S. galapagense . Two commercial S. lycopersicum varieties were also used for comparison: Heinz 1706 and Moneymaker.…”

People and plants: The unbreakable bond

“…In an attempt to tackle problems of over-irrigation and increasing soil salinity in many dry parts of the world, plant breeders have turned to wild relatives to identify genes that could be bred into crops to facilitate their growth in saline soils. This could be achieved in tomato using the genetic diversity of the Galápagos tomato, which grows in coastal regions and is tolerant of salinity (Pailles et al, 2017). To improve nutrition, scientists at Oregon State University crossed a Chilean species of tomato (S. chilense) with S. cheesmaniae to develop the Indigo Rose tomato variety, which is purple and has high levels of antioxidant anthocyanins in the skin and outer flesh.…”