Wild tomato species in South-America
In addition to building theory, we also are developing environmental genomics studies which includes a large-scale comparison of genetic diversity in plant populations from various habitats, under various parasite selective pressures and at different host developmental stages. We are using as a model system two wild tomato species: Solanum peruvianum and S. chilense. The objective is to develop theoretical coevolutionary models or coalescent models for seed banks to perform population genetics analysis of DNA sequence data using new statistical methods of inference (such as the Approximate Bayesian Computation, ABC). Examples of our recent application of coalescent theory to data analysis include:
- Tellier et al. PNAS 2011: for application of ABC to infer teh existence of seed banks and metapopulation structure,
- Tellier et al. Heredity 2011: for the study of fitness effect in closely related wild tomato species (S. peruvianum, S. chilense, S. habrochaites and S. arcanum),
- Hörger et al. PLoS Genet 2012: for using ABC to infer the gene conversion rate between copies of genes under balancing selection.
Genome and next-generation sequence data are becoming available in several species of the Solanum clade, and specifically in wild tomatoes.
1) The study of speciation and adaptive gene flow between S. chilense and S. peruvianum assuming the presence of seed banks (using ABC).
2) The study of local adaptation to abiotic conditions in S. chilense at the phenotypic and genomic levels. We assess the phenotypes associated with tolerance to biotic and abiotic stresses of the various S. chilense populations growing in our glasshouses.
3) The analysis of genetic diversity within and between S. chilense populations via full genome sequencing (using NGS data).
We have published a first version of the Solanum chilense genome (Stam et al. 2019) which led us to sequenced a set of resistance genes (NLRs) to search for footprints of selection (Stam et al. 2019).