Local adaptation for seed banks in wild tomato species

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Seed dormancy for long periods of time promoting so called seed banks is a crucial physiological adaptation which allowed plants to successfully colonize a large number of variable and unpredictable environments. This evolutionary bet hedging consists in decreasing short-term reproductive success in favour of longer-term risk reduction, and is also widely prevalent in bacteria, protozoans (including human parasites), and insects species. Although, seed banking appears to be a ubiquitous mechanism facilitating adaptation to unpredictable environments, the evolutionary, genetic and genomic mechanisms driving the evolution of seed banking are largely unknown. Up to date we do not know 1) how fast such bet hedging strategies evolve in time, or 2) what the genetic underpinnings are. In this project, we use a four-pronged approach to address both questions by combining the development of a population genomics theoretical method with genome sequencing and empirical measures of seed dormancy. We use as a model system, Solanum chilense, a wild tomato species found in various habitats in Southern Peru and Northern Chile, to reveal loci responsible for bet hedging evolution.First, in the theoretical part of the project, we aim to develop a Hidden Markov Model (HMM) statistical method to analyse full genome sequences from plant populations. The HMM method will infer specifically the past evolution of seed banking from variation in polymorphism and recombination rates along genomes.Second, we will quantify the genomic mutation rate for the wild species S. chilense, by sequencing the full genome of 20 F1 progenies from two already sequenced parental plants. This step is crucial for obtaining accurate estimates in our inference method.Third, we will uncover local adaptation for seed banking and infer the speed of adaptation by contrasting six populations of S. chilense chosen in different habitats (North mesic, Southern coastal and Southern high altitudes). Full genomes sequences from 30 plants from these populations will be obtained and studied using our HMM method. We want to test if colonization of new habitats in S. chilense was correlated with changes in seed banking, and importantly reveal novel genes underlying local adaptation to abiotic factors and seed dormancy.Fourth, to complete the evidence for seed bank adaptation, we will perform germination experiments of seeds from the six sequenced S. chilense populations under different temperature and humidity regimes. This project presents a unique combination of statistical population genetics modelling, full genome data analyses, and empirical test of germination to provide the first demonstration of recent local adaptation for seed dormancy in a wild plant species.