Mechanistic and evolutionary analysis of the natural variation in Arabidopsis vernalization response

A full understanding of how climate change will influence plants requires an understanding of how mechanisms used to monitor environmental cues have changed as plants have adapted to different habitats. Regulation of flowering in many plants in temperate and arctic environments includes a requirement for a period of exposure to cold, known as vernalization. In this proposal we want to fully characterize the molecular basis of natural variation in vernalization. A major regulator of this process is FLC, a floral repressor. The gene encoding FLC needs to be silenced for flowering to proceed and the speed this happens differs in Arabidopsis collected from different habitats. We will analyse FLC regulation and how it has evolved in response to adaptation to different climates. 'Mix-and-match' versions of FLC genes from the different natural variants will be analysed in transgenic plants to uncover which of the different nucleotide changes contributes to the altered vernalization response. In collaboration with Dr Magnus Nordborg, a population geneticist, we will then analyse FLC in a worldwide set of Arabidopsis accessions and relate sequence variation to vernalization response. We will also undertake experiments analysing the fitness benefits of this variation and compare these data to field-derived phenotypic data generated in two parallel studies. This will reveal whether variation in vernalization is important for adaptation.

Our aim will be to understand how molecular variation in the gene encoding the floral repressor, FLC, perturbs the chromatin silencing mechanism underlying vernalization in Arabidopsis natural variants collected from diverse habitats. Mix and match versions of the floral repressor gene FLC will be analysed to identify the causative polymorphism and molecular basis of the altered silencing. At first we will focus on the FLC allele from a N. Swedish accession Lov-1, which is particularly insensitive to 4 weeks cold. We will then analyse FLC alleles from two S. Swedish accessions Ull-2-5 and Var-2-6 in order to explore whether they evolved independently. To extend this analysis even further we will use an association analysis. FLC genomic sequence will be compared with FLC expression dynamics in cold and post-cold conditions in a well-characterized and genotyped, world-wide set of Arabidopsis accessions. Polymorphism likely to be contributing major effects to the variation will be tested through a site-directed mutagenesis strategy aiming to recreate the phenotypic behaviour of the different alleles in transgenic plants. Knowledge of the different causative polymorphism and the overall genetic architecture of FLC will shed light on the evolutionary history of FLC. Lastly, we will undertake controlled environment room reciprocal transplant experiments to ask if the variation in vernalization and FLC contributes to adaptation of these accessions. This analysis will complement two field studies funded from elsewhere.

The research in this proposal will have impact in three quite different areas. Firstly, it should add to our overall understanding of the evolutionary processes underpinning natural diversity. For a given trait what are the constraints of the type of variation that has been successful in nature? How many times has similar phenotypic variation evolved? To date there are still few examples where the molecular basis of diversity has been fully defined. As many more genomic sequences become available it will be increasingly important to have studies linking genotypic and phenotypic variation. This will not only be true for plant genomes but also for human biology field where we are entering the period of 'personal genomes'. Understanding evolutionary processes, and the connection of genotype and phenotype, have never been more important. Secondly, this work has an emphasis on variation in response to changes in temperature. It is clear that our world is warming so information from this research will be highly relevant for improving knowledge on the likely changes in plant phenology - plant timing mechanisms - as our climate changes. Modelling the effects of global warming has so far not included effects on plant populations - will plant populations adapt quickly enough to remain in their present locations? Will timing of flowering change - if so will it become out of sync with the pollinators - this could have global effects on plant biodiversity and a major impact on crop yield. Lastly, it addresses time to flowering, a key trait in breeding of many crops. Our focus is the molecular basis of natural variation in vernalization - a key process in the breeding and production of many winter-grown vegetable crops, broccoli, cauliflower, parsnips and carrots. Varieties of these vegetables are bred to ensure year round supply but the vagaries of winter temperatures tends to lead to gluts or shortages in production. Development of varieties less influenced by temperature but still producing in different seasons of the year would considerably reduce waste, potentially open up new production areas and increase efficiency of delivery. We have ongoing collaborations with breeding companies aiming to translate this understanding into practical benefits.