Ecological and Evolutionary Genomics in the Wild Tomatoes (Solanum Sect. Lycopersicon)

Abstract

The plant group Solanum section Lycopersicon (the clade containing the domesticated tomato and its wild relatives) is ideal for integrating genomic tools and approaches into ecological and evolutionary research. Wild species within Lycopersicon span broad morphological, physiological, life history, mating system, and biochemical variation, and are separated by substantial, but incomplete postmating reproductive barriers, making this an ideal system for genetic analyses of these traits. This ecological and evolutionary diversity is matched by many logistical advantages, including extensive historical occurrence records for all species in the group, publicly available germplasm for hundreds of known wild accessions, demonstrated experimental tractability, and extensive genetic, genomic, and functional tools and information from the tomato research community. Here I introduce the numerous advantages of this system for Ecological and Evolutionary Functional Genomics (EEFG), and outline several ecological and evolutionary phenotypes and questions that can be fruitfully tackled in this system. These include biotic and abiotic adaptation, reproductive trait evolution, and the genetic basis of speciation. With the modest enhancement of some research strengths, this system is poised to join the best of our currently available model EEFG systems. K E Y W O R D S :Abiotic, adaptation, natural selection, reproductive isolation, speciation, tomato. Feder and Mitchell-Olds 2003) aims to provide a detailed mechanistic understanding of the genetic basis of natural biological diversity, and the evolutionary processes responsible for the creation and maintenance of this diversity. To do this requires both an understanding of the mechanistic basis of phenotypic variation (i.e., an ability to connect genotype to phenotype), and an understanding of the mechanistic basis of adaptation (i.e., an ability to connect natural phenotypic variation with fitness consequences in the wild). In this sense, EEFG encompasses many of the aims of classical "ecological and evolutionary genetics" (e.g., Stebbins 1950; Dobzhansky 1970) albeit with more explicitly molecular, and correspondingly more ambitious, goals. The use of genomic tools to address ecological and evolutionary questions is already attracting accelerating interest (e.g., Ecological and Evolutionary Functional Genomics (EEFG-

MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity

“…Inferring how whole assemblages of species react to putative geographical barriers is central to obtaining these larger goals and MTML-msBayes will become an important bioinformatics tool for such inference given multi-level models with large amounts of complexity. Phylogeographic data sets with multiple codistributed taxon-pairs with genetic data collected from multiple loci are rapidly emerging [64-67], and here we demonstrate that correct inference of simultaneous divergence is somewhat robust against violations in assumptions about among locus rate heterogeneity although incomplete isolation with post-divergence migration can make inference of simultaneous divergence difficult. Furthermore, it is likely that other demographic complexities such as pre-isolation subdivision, diminishing/accelerating levels of post-isolation migration, and recombination are likely to affect inference [68].…”

Functional gametophytic self-incompatibility in a peripheral population of Solanum peruvianum (Solanaceae)

“…Despite our finding of strong SI in this population of Solanum peruvianum, these data provide an important comparison for species with mating system polymorphism. The wild tomatoes continue to be a model system for understanding the evolution of mating systems (Igic et al, 2006;Moyle, 2008;Städler et al, 2008), and molecular evolutionary studies of species with documented polymorphism in mating system can shed light on the evolutionary fate of the high sequence diversity typical for SI populations. In addition, our work facilitates future efforts directed at studying Solanum and related genera, as allele-specific primers will reduce the cost and effort of identifying S-RNase alleles in additional species and populations.…”

eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato

“…Cultivated tomatoes, along with their wild relatives, harbor broad genetic diversity and large phenotypic variability (Moyle, 2008;Ranjan et al, 2012). Wide interspecific crosses bring together divergent genomes, and hybridization of such diverse genotypes leads to extensive gene expression alterations compared to either parent.…”