Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species

The wild currant tomato Solanum pimpinellifolium inhabits a wide range of
abiotic habitats across its native range of Ecuador and Peru. Although it
has served as a key genetic resource for the improvement of domestic
cultivars, little is known about the genetic basis of traits underlying
local adaptation in this species, nor what abiotic variables are most
important for driving differentiation. Here we use redundancy analysis
(RDA) and other multivariate statistical methods (structural equation
modeling (SEM) and generalized dissimilarity modeling (GDM)) to quantify
the relationship of genomic variation (6,830 single nucleotide
polymorphisms) with climate and geography, among 140 wild accessions. RDA,
SEM, and GDM each identified environment as explaining more genomic
variation than geography, suggesting that local adaptation to
heterogeneous abiotic habitats may be an important source of genetic
diversity in this species. Environmental factors describing temporal
variation in precipitation and evaporative demand explained the most SNP
variation among accessions, indicating that these forces may represent key
selective agents. Lastly, by studying how SNP-environment associations
vary throughout the genome (44,064 SNPs), we mapped the location and
investigated the functions of loci putatively contributing to climatic
adaptations. Together our findings indicate an important role for
selection imposed by the abiotic environment in driving genomic
differentiation between populations.