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Using association mapping to identify Quantitative Trait Loci (QTL) for straw digestibility in rice straw

Nguyen, Duong (2016) Using association mapping to identify Quantitative Trait Loci (QTL) for straw digestibility in rice straw. MSc by research thesis, University of York.

Text (Duong T. Nguyen MSc by research thesis)
Duong T. Nguyen MSc. by research Thesis - June 2016.pdf
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There is an urgent need to reduce our dependency on fossil fuels, and to reduce greenhouse gas (GHG) emissions. In recent years, a conversion of lignocellulosic biomass from agricultural wastes to biofuel has been considered a promising solution to provide sustainable liquid fuels without competing with food production. At present, this is limited by the cost effectiveness of the production process, due to the recalcitrance of lignocellulosic biomass to digestion. One way to tackle this problem is to improve the digestibility of the biomass feedstock itself, which would help to decrease chemical and enzyme treatments necessary for converting biomass to fermentable sugars for bioethanol production. With this objective in mind, the aim of this study is to identify genes that affect the digestibility of rice straw. Rice (Oryza sativa), the third biggest cereal crop in the world, has a small diploid genome, and well-developed molecular genetic tools to underpin the use of Genome Wide Association Studies (GWAS), a powerful tool for identifying quantitative trait loci. The genotypic data of 151 varieties, containing 328,915 Single Nucleotide Polymorphism (SNPs), was analysed together with the phenotypic data from three different cell wall characterisation assays: (1) saccharification, (2) total lignin content, and (3) silica measurement by by X-ray fluorescence. This resulted in the identification of 10 significant QTL for saccharification potential, 3 significant QTL for Silica content, and 8 significant QLTs for total Lignin. The digestibility QTL regions identified include three strong potential candidate genes which determine on digestibility: OsAT10 (Bartley, et al., 2013); OsIRX9 (Chiniquy, et al., 2013); and OsMYB58/63-L (Noda, et al., 2015). A strong correlation between silicon content and digestibility was also identified. A QTL in chromosome 6 occurred in both GWAS for digestibility and silica, and revealed a contrasting bi-allelic effect between the amounts of sugar released and silica content. The OsAT10 gene, located in this common QTL region was validated using the straw from overexpression lines, showing that OsAT10 had large effect on both silica content and digestibility.

Item Type: Thesis (MSc by research)
Academic Units: The University of York > Biology (York)
Depositing User: Mr Duong Nguyen
Date Deposited: 21 Oct 2016 10:22
Last Modified: 30 Apr 2018 00:18
URI: http://etheses.whiterose.ac.uk/id/eprint/15236

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