Ribosomal DNA variation in multi-locus systems

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The ribosomal DNA (rDNA) evolves under a balance of heterogeneity-inducing point mutations acting against homogeneity-inducing concerted evolutionary processes. This balance is now known to be imperfect, leading to intra- and inter-organism variation in rDNA copy number and unit sequence. This situation is made even more complex by the presence, in many organisms, of multiple rDNA loci that are believed to be homogenised by processes such as gene conversion. Evidence is growing rapidly that rDNA variation is tightly linked to phenotype. Furthermore, the rDNA has now been implicated in vital biological phenomena such as genome integrity and ageing. We therefore urgently need to discover how rDNA variation is organised within a genome, how it is expressed and how it underpins the functionality of an organism.

We have developed VariantLister, a software tool that enables us to systematically characterise rDNA variation in organisms with a single rDNA locus. However, to date we have been unable to attribute rDNA variants to a specific locus in organisms with multiple rDNA loci. Through analysis of single chromosome datasets and further VariantLister development, we will carry out such an analysis for the first time, in yeast and wheat. We will also carefully assess whether clustering of rDNA variants called from whole genome sequence datasets can be accurately ascribed to distinct loci for organisms with multiple rDNA loci. Finally, by analysis of transcriptome datasets, we will discover which of the identified rDNA variants are expressed and how a variant's expression fate depends on its locus and the environment.

The results of these tasks will provide vital new knowledge on the organisation and expression of rDNA variants in two key eukaryotes, which will underpin future investigations of rDNA function and ultimately species improvement programs. Finally we will disseminate all project software and data on a dedicated project website.

This project has considerable promise to impact on the UK society and economy, the general public and the project participants. While economic and societal impact will be derived in the long-term, benefits to the general public and project participants are expected to be realised both during and following the project.

1) The UK society and economy
Our society is currently facing significant challenges stemming from threats ranging from climate change to a growing and ageing population. We have an urgent need to secure and optimise future food production while also utilising food and agricultural waste in the replacement of petroleum as sustainable sources of key chemicals. This project will impact on both of these needs, to the benefit of our society and economy.

a) Crop breeders/Agri-food industry
Wheat is the UK's most important cereal crop, yielding 16.68 million tonnes in 2015, and a vital component of the UK diet. New knowledge of rDNA variation and expression in bread wheat will be communicated to crop breeders and the agri-food industry, to be used for the development of new varieties of wheat tailored to specific environmental conditions. In particular, analysis of RNA-Seq datasets will kick-start the identification of rDNA variants that are preferentially expressed under stress, including conditions of high temperature and low water. Dr Davey's position in the wheat community, including the BBSRC Wheat ISP, will be key to effective knowledge dissemination in the pursuit of continued food security.

b) Industrial biotechnology/Biopharma
The vast quantities of wheat straw left over from food production (e.g. 6.3 million tonnes in 2007), in particular in the East of England close to the project's location, is a key target substrate for secondary biorefining in the UK. Here, sugars released from the straw are fermented by yeast to produce a wide spectrum of platform chemicals and fuels. Harnessing the vast biodiversity of yeast is a fast emerging area of interest to a wide range of UK companies and NCYC has recently developed a new collaboration on yeast natural products with Croda, a FTSE 250 company. Yeast rDNA variants and expression profiles discovered in this project are expected to lead to the development of new strains that efficiently produce optimal quantities of a required chemical product. Consortia such as Sc2.0 and existing relationships with key companies such as Croda will ensure broad communication of our results.

2) The general public
There is a growing public appetite for scientific knowledge, with a wide recognition of the enormous impact that science has on our prosperity and continued well-being. The project team are highly committed to public scientific outreach, each tending to focus on a different part of this broad sector. Within this project, we will engage directly with members of the public, from schoolchildren to our society's most senior members, to educate them in its most important aspects. In particular, we will use our existing contacts within local organisations such as the SAW Trust and BBC Look East to introduce concepts such as genetic variation, synthetic biology and industrial biotechnology, to explain why we are carrying out this project and what benefits we anticipate it will bring to the local population and to the wider UK community.

3) The project participants
The three project investigators are all highly skilled in the training of new members of their field, and combined they have passed on a wide range of scientific and transferable skills to dozens of scientists in the UK and beyond, many of them now holding senior scientific positions of their own. Within this project, the post-doctoral research assistant will benefit from this expertise, gaining excellent inter-disciplinary training, with the project focus ensuring they possess the skill sets essential to the next generation of UK scientists.