Identifying candidate genes/loci influencing barley secondary cell wall properties

  • Amy Learmonth

Student thesis: Doctoral ThesisDoctor of Philosophy


The structure and composition of the secondary plant cell wall determine its digestibility and therefore on the efficiency of conversion of plant biomass for biofuel production. Bioethanol, a form of biofuel, refers to ethanol generated by fermentation of sugars extracted from plants. Second generation lignocellulosic biofuel is produced from the sugars sequestered in the secondary plant cell wall as cellulose polysaccharides. In grasses, these cellulose molecules are embedded in a matrix of lignin and xylans polymers which form cross-links through cell wall bound ferulic acid; this matrix influences the efficiency of enzymatic breakdown of the cell wall. Changes in lignin content, lignin composition and phenolic acid content have been shown to affect saccharification (sugar release from cell walls).

The second generation biofuels are produced from non-food biomass unlike first generation production which uses parts of the plant normally used as food (e.g. grain and corn kernels). This means that second generation production can co-exist with food production, reducing the amount of waste produced and increasing the net energy gain from the crop and inputs. Currently, commercial adoption is low as the production costs of second generation biofuels are higher than first generation, reducing their economic viability. Most of the extra cost is due to the difficulties in saccharifiying caused by inefficiency in the breakdown of the secondary cell wall. Therefore identifying genes which can be targeted for breeding plants with higher saccharification yields to improve their suitability as biofuel feedstocks could increase the efficiency and lower the cost of second generation production systems.

The work undertaken in this project found regions across the barley genome that are associated with differences in saccharification from straw of a population of elite two-row spring barley cultivars. They were identified through genome wide association studies (GWAS) carried out for saccharification from which interesting quantitative trait loci (QTL) were highlighted. The genes underlying the QTLs were evaluated on annotation/function, presence of polymorphisms and expression levels, based on the evaluation of the data available candidate genes were selected. Differences in cell wall bound ferulic (FA) and p-coumaric (p-CA) acid in mature grains from elite barley cultivars were also analysed using the GWAS method. The same work flow was used as in the straw project: identification of QTLs, evaluation of genes under lying the peaks and selection of candidate genes.

From the results for straw saccharification several candidate genes were distinguished from two QTL on separate chromosomes. Some of these genes were potentially involved in regulating lignin biosynthesis. Under both QTL, numerous cell wall related genes came up in the GWAS or showed differences in expression related to differences in saccharification suggesting an underlying network of genes correlated with cell wall biosynthesis. In the grain hydroxycinnamic acid content results, a strong causal mutation candidate was discovered in a gene involved in incorporating p-coumaric acid into the cell wall. Furthermore, the difference in p-coumaric acid content appears to cause the difference in ferulic acid content in part of the population of cultivars. These data illustrate the value of GWAS for identifying candidate genes for manipulation by breeding or transgenesis to improve straw digestibility for biofuel, biorefinery and animal feed applications.
Date of Award2019
Original languageEnglish
SponsorsEASTBIO Doctoral Training Partnership & Biotechnology and Biological Sciences Research Council
SupervisorClaire Halpin (Supervisor)

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