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EASTBIO Testing for the occurrence of non recombining haplotypes in a wild relative of wheat


PHD Opportunities

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Dr R Bergero , Dr M Hartfield , Prof I Mackay No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

Understanding and exploiting the genomics and genetic diversity is crucial in order to develop the next generation of improved crops. Genomic studies of wild relatives of crop species hold a great promise to recover some or most of the functional diversity lost during domestication and further selection processes. Although recombination is required to create and break allele combinations, recent findings show that plant adaptation requires the maintenance of successful allele combinations in the form of non recombining chromosomal regions extending several megabases [1]. This project aims at testing for the occurrence of blocks of coadapted genes (non recombining haplotypes) in Aegilops tauschii, a wild relative of wheat which contributed to the domestication of the hexaploid modern wheat (D genome of wheat). Aegilops tauschii is diploid and a genome has been recently made available [2]. This project offers the opportunity to work with two research groups from SRUC and the Institute of Evolutionary Biology (University of Edinburgh), with complementary areas of expertise in genomic analyses and plant breeding (Dr. Bergero, Prof. Mackay, SRUC) and coalescent and modelling analyses applied to plant adaptation and mating systems (Dr. Hartfiled, University of Edinburgh). You will learn how to generate sequencing reads from a germ plasm collection of A. tauschii, map sequencing reads to the reference genome, retrieve polymorphisms and test for the occurrence of nonrecombining genomic regions underlying plant adaptation and ecotype differentiation. Coalescence coupled with linkage disequilibrium, phylogenetic and sequence divergence analyses will allow to test for long-term maintenance of the inferred haplotype genomic blocks in A.tauschii populations and to estimate their size and age in genomes of this wild relative of wheat. Functional characterisation of the identified haplotypes will be carried out together with association analyses of the phenotypic diversity of A. tauschii germ plasm. Such knowledge can aid in defining the large and complicated genomes of wheat species and will help identify new elite coadapted alleles for developing the next generation of breeding strategies.


[1] Todesco et al. (2020) Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature 584, 602-607.
[2] Jia et al. (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496, 91-95.

Applicants should download the required forms from http://www.eastscotbiodtp.ac.uk/how-apply-0 and send the following documents to [Email Address Removed]:
a. EASTBIO Application Form
b. EASTBIO DTP Equality Form
c. CV
d. Academic transcripts (a minimum of an upper second class or first class honours degree or equivalent is required for PhD study
e. Two references should be provided by the deadline using the EASTBIO reference form (http://www.eastscotbiodtp.ac.uk/how-apply-0). Please advise your referees to return the reference form to [Email Address Removed].
f. If you are nominated by the supervisor(s) of the EASTBIO PhD project you wish to apply for, they will provide a Supervisor Support Statement.


Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership http://www.eastscotbiodtp.ac.uk/how-apply-0. This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition (Please state if your institution will provide funding to cover the difference in fees). Please refer to UKRI website and Annex B of the UKRI Training Grant Terms and Conditions for full eligibility criteria.

References

Two references should be provided by the deadline using the EASTBIO reference form (http://www.eastscotbiodtp.ac.uk/how-apply-0). Please advise your referees to return the reference form to pg.research@sruc.ac.uk.


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