BBSRC EASTBIO PhD Programme: Understanding gene networks influencing straw digestibility for industrial biotechnology

Huge potential exists for using waste plant biomass (straw, grain husks etc) as a renewable and sustainable feedstock for making fuels and chemicals or as animal feed. Using plant biomass for industrial biotechnology in a bio-based economy will displace the use of oil and fossil fuels, thereby reducing carbon dioxide emissions and mitigating climate change. Plant biomass is largely composed of plant cell walls which are naturally recalcitrant to being broken down into components that can be fermented into useful products or used in industrial processes. In order to usefully improve the digestibility of plant cell walls we need to understand more about the complex interplay of genes and enzymes that lead to their production, recognise and protect their role in normal plant health, development and yield, and be able to predict the specific manipulations to cell wall components that would lead to more efficient, less expensive, industrial processing.

We have been investigating how to do this for many years, most recently using Genome Wide Association Studies (GWAS) across a panel of 850 elite barley cultivars to identify the loci and genes that influence straw digestibility, yield, lodging resistance (the ability of stems to stay erect in bad weather), lignin content and other relevant phenotypes. We have identified many exciting candidate genes including some that we have already validated as being important to digestibility. In the process, we have uncovered networks of interacting genes that cooperate to produce plant secondary cell walls and ensure the production of strong stems that support high grain yield. The networks include many genes of unknown function or that are not appreciated to be involved in cell wall development and we want to discover their specific roles and functions. Some are transcription factors of various classes and others are biosynthetic enzymes.

This studentship will help to elucidate how these gene networks function, and to discover the roles of specific genes. We have large datasets at our disposal that will be very powerful in facilitating this work including large populations of cultivars with RNAseq and exome capture data (providing gene expression levels in different tissues plus information on single nucleotide polymorphisms – SNPs), a pseudomolecule assembly of the barley genome, TILLING populations of barley mutants, and the ability to use very efficient transgenesis methods (RNAi and CRISPR). Understanding how these genes interact and how they influence cell wall traits will produce data both of fundament importance to understanding plant biology, and of translational importance in expanding opportunities for targeted improvement of plant biomass by rational ‘designer’ approaches.

This project provides training in a wide range of molecular techniques (mapping, RNAseq analysis, cloning, CHIPseq, promoter analysis, depending on the genes chosen for study), in biochemistry and cell biology (cell wall analysis, saccharification, tissue sectioning etc), in production of gene edited or RNAi transgenic plants and in bioinformatics. The student will be part of the University of Dundee, School of Life Sciences but will be based at the near-by James Hutton Institute and will benefit from the facilities and expertise on both sites.