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Population Genomic Analysis of Introgression between Outcrossing and Selfing Plant Taxa

Reference	BB/J006580/1
Principal Investigator / Supervisor	Professor Richard Ennos
Co-Investigators / Co-Supervisors
Institution	University of Edinburgh
Department	Sch of Biological Sciences
Funding type	Research
Value (£)	327,374
Status	Completed
Type	Research Grant
Start date	01/06/2012
End date	31/08/2015
Duration	39 months

Abstract

Hybridisation is an important process in both animal and plant evolution with up to 10% of animals and 25% of plants hybridising with at least one other species. If hybrids are fertile, exchange of genes (introgression) may occur between species, which can both increase the adaptive potential of the recipient species, and widen its ecological amplitude. The limited numbers of genetic markers that can be scored using traditional molecular ecological techniques means that, despite its importance, we have few quantitative estimates of the extent of introgression between hybridising species. Application of next generation sequencing technology, in particular the restriction site-associated DNA tags (RAD tags) technique, now means that we can score high densities of genetic markers across the genome in non model organisms lacking genome sequence information. This gives us the potential, for the first time, to accurately quantify genome transfer between hybridising species. In this research we will apply the RAD tag technique to study genome exchange between two plant species, Geum rivale and G. urbanum which hybridise widely throughout Britain. The species differ in their breeding systems, and we predict that genome exchange should occur preferentially from inbreeding G. urbanum to outcrossing G. rivale. To test this prediction we will identify species specific RAD markers in allopatric populations of the two species. We will then score these markers in plants taken from both hybrid zones, and from areas outside hybrid zones. From this we will deduce the extent and direction of genome transfer both in the immediate area of hybridisation, and more widely in the species range. To complement these studies we will use traditional genetic markers to study patterns of matings within hybrid zones to determine whether the observed genome transfer can be accounted for by the pattern of matings between hybrids and parents within the hybrid zone.

Summary

Individuals belonging to different plant species are usually unable to mate with one another to produce fertile seed. In this situation the species remain distinct from one another and do not exchange genetic material. However certain pairs of species (some 20% of all plants), despite being very different in their flower and leaf shapes, are able to mate and produce hybrid offspring which are intermediate in form between their parents. If these hybrids can produce pollen and seed they can in turn mate with their parents. The outcome of this is that genetic material from one species is transferred to the other, with the hybrid acting as a go between. There is sharing of genetic material between the species. The genetic material that is transferred may affect the way the recipient species behaves. For instance it may mean that the recipient can tolerate waterlogging or low temperatures better that before because it has acquired these attributes from the other species. So transfer of genetic material between species may not only break down distinctions between species, it may also be very important in allowing them to adapt to new environmental conditions such as we expect under climate change. At present we know of many pairs of plant species which can mate with one another and produce hybrids. What we don't know is how much genetic material is exchanged between these species and how important this is in evolution. The aim of this research is to find out how much genetic material is exchanged between two common flowering plants, water avens and wood avens, which form hybrids in many places throughout Britain. In order to do this we will look at the genetic material of the two species in populations that have never hybridised. We will find out how the two species differ in their genetic material by comparing the sequences of their DNA. We will then sequence the genetic material of the two species in areas where they have hybridised, and in areas where they grow together but have not apparently formed hybrids. The DNA sequence information will tell us whether genetic material has been exchanged between the species, how much has been exchanged, and in which direction the genetic material is transferred. For our species we think that genes will be transferred from water avens to wood avens, because water avens is more attractive to pollinators and will mate more often with the hybrid than will wood avens. In order to investigate whether this idea is correct we will collect the offspring of hybrids and parents in hybrid zones, and grow them up. By looking at the genetic makeup of the hybrid's offspring we will find out which parent fathered the seed and therefore whether it has preferentially mated with water avens as we predict. The results we obtain will give us for the first time a quantitative idea of the extent of genetic exchange between hybridising species in present day populations. This will tell us the extent to which the hybridising species share their genetic material, and will allow us to assess the importance of present day hybridisation in the evolution and adaptation of plants. It may fundamentally change our ideas about the nature of plant species as discrete and distinct entities, and open our eyes to an important evolutionary process that is happening around us today in the British countryside.

Impact Summary

A centrepiece of this proposal is the application of a novel next generation sequencing technique (RAD markers) for analysing the transfer of genetic material between plant species for which we have no existing genomic information. This is a topic which is of great interest to plant evolutionary biologists, both pure and applied. For example much of the development of crop plants relies on transfer of genomes within and among plant species which in the past has been very difficult to asses in a quantitative fashion. Apart from academic researchers therefore a potential beneficiary of this research is the crop breeding industry interested in the introgression of genes between varieties and species, particularly in minor crops which lack genome information. The first benefits these groups would derive would be the refinement of molecular protocols for RAD analysis in plants, where the problems of repetitive DNA and ancient polyploidy are far more prevalent than in animals. The second benefit for evolutionary biologists and plant breeders would be the development of bioinformatics pipelines for analysis of RAD data coming from plants, where stringent filtering of sequences to avoid problems with repetitive sequences and homeologous loci need to be available. Taken together the wider dissemination of these developments would open up RAD analysis as a powerful techniques that could be used 'off the shelf' with standard protocols to tackle previously intractable monitoring of gene transfer in plants. The second hallmark of this proposal is that it deals with wild plant biodiversity and contemporary evolution which can be observed in the British countryside. A second beneficiary of this research is therefore the general public interested in biodiversity for whom the project provides a showcase for 'everyday evolution' that they can observe within almost all regions of Britain. The plants involved are common, distinct, and form readily identified hybrids. Providing the general public with information on such examples of evolution in action, demonstrating that evolution is a contemporary process, not confined to dinosaurs in prehistoric eras, is of importance for wider public understanding and support for science and a better appreciation of the ubiquity of evolution.

Committee	Research Committee B (Plants, microbes, food & sustainability)
Research Topics	Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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