Developing rice resources for resilience to climate change and mitigation of carbon emissions

Lead Research Organisation: University of York
Department Name: Biology


Climate change associated with global warming poses a threat to our ability to produce sufficient food, energy and water to meet the demands of the growing human population. Human activity is helping to drive the upward trend in global warming by increasing the levels of warming agents such as greenhouse gases in the atmosphere. Episodes of severe weather, such as drought and flooding, increase as global temperatures rise, and this can lead to losses in crop yield. Rice is one of the main staple crops grown in the world and represents a major source of food and livelihood for many people, particularly in the tropics. Every year more than 700,000 million tons of rice straw is produced in the world and much of this is burned in the field in order to make way for the next season's crop. This releases large amounts s of black carbon and tropospheric ozone into the atmosphere with negative consequences for air quality, human health (respiratory illnesses), crop yield and global warming. One of the main aims of the proposed research is to help move rice straw away from being a waste product and toward its widespread utilisation as a valuable resource. Rice straw is primarily composed of lignocellulosic structural cell walls that provide support to the growing plant. Lignocellulose is a strong and resistant fibre composite material composed of a network of structural polysaccharides (polymers of sugars). These polysaccharides are potentially a rich source of sugars that could serve as nutritious animal feed, or be used as feedstock for fermentation to produce biofuels or other valuable chemicals and polymers that can replace those derived from petroleum. Unfortunately, the polysaccharides in lignocellulose are difficult to digest into sugars for animal nutrition or fermentation partly because they are sealed in a highly resistant polyphenol called lignin, and partly because they are partially crystalline, both of which block access to digestive enzymes. In rice straw, this situation is further exacerbated by the presence of large amounts (up to 10% dry weight) of silica, which makes it unpalatable to most animals and also precludes the use of rice straw in biomass furnaces to make electricity as it causes severe slagging of boilers.
This project brings together the expertise of five world class laboratories to tackle the complex problem of environmental resilience and carbon footprint in a world staple food crop. We will use cutting edge plant genomic approaches to identify the genetic basis of natural variation in straw digestibility, lignocellulose composition and silica content found in large diversity collections of rice collected in the Philippines and Vietnam. We will employ genome wide association scans in these diversity collections to identify associations in the variation of digestibility, composition and silica content with differences in the sequences of DNA in regions of the genomes of these plants. This will identify molecular markers that can serve as proxies for improved straw quality and allow rapid marker assisted breeding approaches to be used. The same methods will also allow us to identify the genes that have strong influence on these traits in rice. We will also identify regions of the genome influencing the ability of rice crops to deal with drought (a major problem resulting from climate change) and produce molecular markers for improved drought tolerance.
Our work will identify existing rice varieties with low silica or highly digestible straw and we will use these to investigate and demonstrate the advantages of using straw with better quality for applications as animal feed and for biofuel production. We will use the results from our research to alert farmers and other stakeholders to the potential benefits of using rice straw in these applications to improve farmer income, local livelihoods and air quality as well as helping mitigate the damaging effects of human activity on global warming.

Planned Impact

Rice straw burning and the climate change both have negative consequences for agricultural production and human health in the Philippines and in Vietnam. In particular, increased tropospheric ozone from biomass burning has negative consequences for plant productivity through inhibiting photosynthesis, whilst black carbon emissions cause significant losses in productivity through shading, and both lead to respiratory ailments and premature deaths among the human population. Diverting straw away from burning into animal feed, biofuels and bioenergy will therefore not only benefit the environment, but also has the potential to add value to the income of rice farmers, and generate new enterprises. Ninety nine percent of buffaloes and cattle breeders in the Philippines are small hold farmers and 70% of them utilize small amounts of rice straw as fodder for their animals. If improved varieties of rice are developed by this project, the social impact will be realized almost immediately. Whilst Vietnam and the Philippines have invested into research into straw valorisation, these nations will benefit from collaborating with the UK partners, which bring a greater depth of understanding of the molecular and genetic components of lignocellulose composition and digestibility. The UK has made considerable science investment into research to underpin the cost-effective use of lignocellulosic biomass to serve as a feedstock for biorefining to produce fuels, chemicals and bioenergy trough projects such as BSBEC and HOOCH, and the UK investigators in this project have played significant roles in these projects. Most of the accessions in the rice GWAS panels have been genome re-sequenced and have comprehensive SNP maps available. In addition, there is a greater depth of molecular genetic resources (such as T-DNA insertion mutants) available for rice making it an ideal genetic model for cereals. Unfortunately, the large size of rice plants and requirements for high temperature and light make it less than ideal as a model for growth in the UK. Hence, collaborative research such as that outlined here, between the UK and nations able to grow rice in the field, opens up the opportunity to enhance cereal research in the UK through access to rice with the relative simplicity of transferring information between species as a result of the close syntenic relationships between cereals. Work is in progress in the UK to identify the genes responsible for the variation around biomass recalcitrance QTL in barley. The work with rice in the proposed project will help to accelerate the work in barley. This is because the rice genome is much smaller than that of barley and has been characterised in considerable detail. The major aim of the project are to carry out underpinning research that will lead to a reduction in the volumes of rice straw and husk that are burned every year. This will be achieved by improving the quality of rice straw for use as animal feed, for biofuel production and bioenergy generation. We will also carry out research to identify process routes by which value in biofuel and bioenergy applications for rice straw can be achieved. As well as reducing the harmful consequences of biomass burning, the project has the potential to help to increase the income of rice farmers, reduce the costs of animal feed, and lead to additional environmental benefits by displacing the use of fossil resources for fuel and energy generation. In addition to the potential impacts in the area of mitigating GHG emissions, the work will help in the development of rice varieties with greater resilience to temperature stress resulting from climate change. In terms of scientific impact, the proposed work will have direct benefits in helping in the understanding of the molecular interactions in lignocellulosic that cause its inherent recalcitrance to digestion, thereby increase our understanding of the genetics and molecular mechanisms involved in their biosynthesis.


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Halpin C (2019) Lignin engineering to improve saccharification and digestibility in grasses. in Current opinion in biotechnology

Description We have established a new diversity panel of rice varieties from the Philippines that is suitable for genome wide association studies (GWAS). DNA from the panel has been collected and sent for genotyping by sequencing. Straw ill be collected soon and sent tot the UK for phenotyping for digestibility and compositional analysis to allow GWAS. The vietnam diversity panel has been grown again in the field in Vietnam and sent to the UK for a third cycle of GWAs to strengthen earlier results. Crosses have been made between selected lines representing contrasting phenotypes associated with GWAS haplotypes and these are being selfed to allow us to refine QTLs from earlier analysis. Drought studies are being conducted in the Philippines and Vietnam. Successful consortium meetings have been held in the Philippines and by Skype, and in Hanoi in May 2017. Further funding applications to GCRF were submitted, and one GCRF foundation award on improving rice for animal feed applications obtained. We have hosted three visiting assocates from the Philippines and Vietnam in York as part of the project and a third visitor is expected in 2018. We have made some important new findings regarding the basis of digestibility in rice straw. We have obtained additional GCRF funding for a new Royal Society project on shortening life cycles in elite rice cultivars to improve productivity in the face of increasing extreme weather in Vietnam.
We published one paper on QTLs for straw digestibility from our Vietnam diversity panel. We are working on three manuscripts from our combined studies with the Philippines and Vietnam diversity panels. From our QTL analysis we identified several genes ipotentially involved in adding hydroxycinnamic acids to arabinoxylans and lignin that may impact straw quality. the roles of these have been confirmed using Crispr Cas9 gene editing. Genetic markers for straw digestibility have been shared with our collaborators for use in their breeding projects.
Exploitation Route Our research is underpinning improvements in digestibility and composition in rice straw in order to enable cost-effective biofuel production and better animal feed quality.
Sectors Agriculture

Food and Drink




including Industrial Biotechology

Amount £697,000 (GBP)
Funding ID BB/P022499/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2017 
End 04/2019
Description Newton Bhabha Industrial Waste: Reducing Industrial Waste from Sugarcane Processing in India
Amount £711,828 (GBP)
Funding ID BB/S01196X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 09/2022