Understanding and exploiting the genomics and genetic diversity of crop species and their wild relatives is crucial in order to develop the next generation of 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). A. tauschii is diploid and its genome has been recently sequenced [2].
This PhD offers the opportunity to work with two research groups: Dr R Bergero from SRUC and Dr M Hartfield, from the Institute of Evolutionary Biology, University of Edinburgh, with complementary areas of expertise in plant genetics and evolutionary genomics (Dr. Hartfiled, University of Edinburgh).
You will learn how to generate sequencing reads from natural accessions of A. tauschii from the Mazandaran Province, Iran (covering the natural distribution of the sublineage L2E, which represents the closest ancestor of the wheat D genome [3]), map sequencing reads to the reference genome, retrieve polymorphisms, identify non-recombining haplotypes and test for haplotypes underlying plant adaptation and ecotype differentiation.
Linkage disequilibrium analyses coupled with coalescence and phylogenetic analyses will be employed to estimate haplotype size, age and origin 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 natural accessions from Mazandaran Province (Iran). Such knowledge will aid in further characterizing the large and complicated genomes of wheat and will help identify new elite coadapted alleles for developing the next generation of wheat cultivars.
This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.
The project will be supervised by: Dr Roberta Bergero, Dr David Marshall and Dr Matthew Hartfield
[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.
[3] Zhou et al. (2021) Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement. Nat. Plants 7, 774-786.
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