Our current understanding of the impact of sequence variation on fitness in barley is extremely limited. Recent efforts in human, and latterly also in rice, have modelled fitness consequences of variation by combining conservation data with functional genomic data to infer levels of selection across the entire genome, including intergenic regions.
In barley, we are now in the privileged situation of having a vast collection of public sequence datasets that can be used for this purpose, including high quality chromosome scale genome assemblies of both Hordeum vulgare ssp. vulgare and other species in the same genus. This project will make use of these datasets and apply and extend the approaches used in other species to generate a genome wide fitness map for barley.
The existing approach uses a variety of functional sequence data, including RNA-Seq, miRNA, ChIP-Seq, ATAC-Seq, PRO-Seq and bisulfite sequencing, and combines this with conservation data as input into a model which infers the probability of the observed variants being caused by neutral, positive or negative selection.
The data generated will be of use to both barley breeders and researchers alike and will constitute another important data resource for the wider barley community. Fitness consequence maps can, for example, aid in the identification of deleterious mutations that can be targeted for removal in breeding programs.
This project will be based at the International Barley Hub in Dundee, Scotland, and will be carried out under the supervision of Dr Micha Bayer, Dr Luke Ramsay (both James Hutton Institute) and Dr Sarah McKim (University of Dundee, Dept of Plant Sciences). We will provide training in highly relevant and timely skills in plant bioinformatics. These include sequence analysis, programming, visualization and high performance computing (HPC). The student will also learn about general plant science and barley genetics and evolution. This mix of skills will ensure that the student – while ideally placed to work in plant bioinformatics following their PhD – will also have the opportunity to work in areas outside plant science, e.g. the biomedical sector