Using QTL analysis of Brachypodium distachyon to understand the genetic basis of grass cell wall saccharification

Second generation biofuels are seen as a sustainable solution to the problem of dwindling fossil fuels stocks. However, the process of converting lignocellulosic biomass to sugars for fermentation is expensive due the recalcitrance of these materials to enzymatic digestion. The identification of quantitative trait loci (QTL) in the model grass species Brachypodium distachyon was undertaken in order to improve our understanding of genes that affect straw digestibility. Initially, the study focused on the analysis of natural accessions to determine if there was variation, in terms of digestibility and cell wall composition, within the species and to identify lines suitable for producing recombinant inbred lines (RILs). This information was successfully used to initiate the production of a RIL population that can be used in future research. I made use of a pre-existing RIL population produced previously from a bi-parental cross between Bd21 and Bd3.1 to study pathogen resistance. This RIL population was screened for straw digestibility using a semi-automated robotic platform. This data together with the genotype data was used to identify QTL linked to digestibility. A single QTL was detected on chromosome 5 together with a further QTL on chromosome 3 that acted in epistasis. A candidate gene for each of the QTLs was identified by reviewing those located within the QTL regions. The chromosome 5 candidate gene encodes a glycosyl hydrolase family 43 family protein likely involved in xylan biosynthesis and the chromosome 3 candidate gene is a cellulose synthase-like subfamily A protein that has a possible glucomannan 4-beta-mannosyltransferase function. Functionality was analysed by studying the cell wall composition of selected RILs and corresponding Arabidopsis thaliana T-DNA lines to determine any differences in the secondary cell wall structure. The results indicated that the differences in digestibility are associated with subtle differences in cell wall composition.