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The ¹û¶³Ó°Ôº Research Department of Genetics, Evolution and EnvironmentÌýundertakes a broad range of research into plants, and particularly crops.Ìý

The evolution of plants via natural selection andÌýtheÌýimprovement of crops by artificial selectionÌýrepresentÌýtwoÌýsides of the same coin,Ìýand our researchÌýprogrammesÌýin GEE explore both aspects. We use a combination of empiricalÌýstudies of plant evolution (Jon Bridle), ancientÌýcropÌýplant DNA (HernánÌýBurbanoÌýand Richard Mott) and experimental intercrosses (Richard Mott) to dissect the genetics ofÌýadaptation and domestication and improvement.

This work is particularly relevant given the important challenges induced by climate changeÌýon natural ecosystems and on farming.ÌýÌý

Plant responses to environmental change: investigating the evolution of plant behaviour at ecological margins

How plants respond to changing environments is a fundamental question both in understanding the resilience of ecological communities, and in the maintenance of crop yields in increasingly stressed environments. Our research group, headed by Jon Bridle, uses a combination of genomic, ecological, and quantitative genetic analyses to test limits to theÌýadaptive plasticity of two Senecio ragwort species, which show recent rapid ecological divergence to an elevational gradient.ÌýÌý

We are conducting extensive transplants of genotypes (via cuttings)Ìýand seed families on Mount Etna, Sicily, as part of a NERC funded project in collaboration with the Universities of Oxford, Catania, and Napoli and the kind assistance of Piante Faro (Giarre, Italy).ÌýThese results revealÌýtrade offsÌýbetween fitness at different life stages, and in below and above groundÌýbehaviour, as well asÌýhow easilyÌýwhich new forms of adaptive plasticity can evolve beyondÌýeach species’Ìýexisting ecological margin.ÌýÌý

Analyses of transcriptomes of field transplanting cuttingsÌýalsoÌýallow exploration ofÌýthe genomic architecture of plantÌýbehaviour, both between these species during their recent adaptive divergence, as well as within genotypes acrossÌýtheir native elevational rangeÌýand beyond.ÌýWork is ongoingÌýto relate such shifts in gene networks toÌýchangesÌýin trait correlationsÌýandÌýtrade-offsÌýacrossÌýtheseÌýenvironments,ÌýinÌýorderÌýtoÌýunderstandÌýtheÌýlimitsÌýofÌýnaturalÌýandÌýartificialÌýselectionÌýinÌýeffectingÌýphenotypicÌýandÌý
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My group uses a retrospective approach to address a broad range of questions in the evolution of plants and their pathogens. This approach gains its power from obtaining direct observations from the past through sequencing historical and ancientÌýsamples, andÌýcombining them with present-day genomic information. My group has pioneered the use of herbarium specimens and plant archaeological remains for evolutionary genomics studies. Currently, our research focuses on three main topics:ÌýÌý

1. The dynamics of present and past plant-pathogen epidemics: The study of the dynamics of past epidemics and the co-evolution of plant-pathogen interactions is of major relevance, since the emergence and re-emergence of plant diseases pose a major threat to food security and indirectly to human health. Additionally, the strength of natural and artificial selection experienced by the plant-pathogen system permits observing changes in allele frequencies in short periods of time.
   
   My group has centered on the study of 19th and 20th century outbreaks caused byÌýPhytophthoraÌýinfestans, the causal agent of potato late blight (;)ÌýandÌýby the rice blast fungusÌýMagnaportheÌýoryzaeÌý().Ìý
   

   

2. The identification and timing of key events in crop domestication and the spread of agriculture: Using an approach that combines ancient genomics with quantitative and population genetics, my group started characterizing the spread of maize in North America and its adaptation to a temperate climate. Using techniques borrowed from breeding (genomic selection) we predicted for the first time polygenic quantitative traits on archaeological remains ().
   
   The post-domestication dispersal of crops domesticated in the Americas presents a unique opportunity to study the population history and adaptation of plants. Our group reconstructed inÌýgreat detailÌýthe population history of European potatoes combining present-day and historical genomes. Our work showed how allele frequencies can be used under an admixture graph framework to study the relations between temporally and spatially diverse populations ().Ìý
   

   

3. The colonization of new ecological niches by invasive/introduced species: Our group has explored the colonization of North America by Arabidopsis thaliana using a dense time-series spanning the 19thÌýand 20thÌýcenturies to examine the evolutionary forces that have shaped genetic variation in a recently introduced species. We estimated the long-term nuclear mutation rate and showed that although genetic drift predominates, purifying selection also shapes diversity in this colonizing population ().Ìý

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Richard Mott Group

1. ÌýWe carry out research in . These are panels of recombinant inbred lines descended from multiple inbred founders (MAGIC: Multiparent Advanced Generation Inter Cross). We work on the Arabidopsis, rice and wheat MAGIC populations. We develop statistical methods for mapping quantitative trait loci and for imputing genomes from low-coverage sequencing, and we have sequenced each of these populations. Most of this work has been funded by the BBSRC and GCRF.

(a) The was developed in collaboration with Paula Kover (University of Bath). We sequenced the 19 founders of the population in one of the earliest . We have used low-coverage sequence of the population to show how to .

(b) The DIVERSE Wheat MAGIC was developed in collaboration with James Cockram and colleagues at the National Institute for Agricultural Botany (NIAB), Cambridge. The population was designed to sample the major varieties grown in the UK over the past 70 years. We have sequenced the 16 founders by capture and sequenced over 500 genomes at low coverage and in the population.

(c) The rice HEAT MAGIC was developed at the International Rice Research Institute, Philippines, to identify loci associated with heat tolerance. We have sequenced over 800 lines at low coverage, which have been used to .

2.ÌýWe are collaborating with Rajeev Varshney and colleagues at the International Crop Research institute for the Semi-Arid Tropics (ICRISAT, India) on chickpea population sequencing. We have sequenced 2000 landraces of chickpea at low coverage.

(3) We are interested in ancient crop genomes. In collaboration withÌýMark Thomas,ÌýDorian Fuller and colleagues in ¹û¶³Ó°Ôº Dept of Archaeology and the ¹û¶³Ó°Ôº Museum ofÌýEgyptian Archeology we sequenced aÌý3,000 year oldÌýspecimen ofÌýemmer wheatÌýfrom theÌýRamessidÌýperiodÌýand show that most of theÌýgeneticÌýsignatures ofÌýdomesticationÌý.ÌýIt is geneticallyÌýsimilar toÌýmodern emmer wheats that are grown in India, Oman, and Turkey.

Compared to wild relatives, domesticated wheats have larger grains that germinate readily; the seeds are also strongly attached to the plant (scar circled in picture), where they can be harvested more easily.ÌýÌý

Research on Crops and Plants is funded by:

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