Developing Rice with Increased Resistance to Salinity and Drought

Lead Research Organisation: University of York
Department Name: Biology


Food production needs to be expanded drastically to feed an ever growing human population. Drought and saline soils are two environmental conditions that greatly depress agricultural production around the globe and it is estimated that around 20-30% of rice yield is lost in areas where these stresses are prevalent. To limit such losses, it is imperative that we develop rice varieties that are more resistant to these stresses, either through breeding or by using engineering.
Both breeding and engineering approaches require knowledge about the genes that contribute to tolerance. Not only will that help us understand the molecular mechanisms that plants use to respond to stress, the accumulation of such 'positive' genes will enhance rice resilience to drought and salinity. In this project we propose to use a technique called GWAS (genome wide association studies) to identify (new) genes and variations in genes (alleles) that are important in rice drought and salt tolerance. In contrast to previous work, we use very specific traits when we carry out GWAS to maximise our confidence that we are targeting the right genes. We will further confirm the relevance of the identified alleles by analysing their function, for example via deletion and subsequent characterisation of the 'knock out' plant. After these stringent 'quality controls' the positive alleles will be introduced into existing, high yielding varieties that are commonly grown in Vietnam and the Philippines. Introduction can be achieved via molecular breeding (crossing plants), a well established but very time consuming process. In parallel, we plan to use state of the art genetic engineering which will greatly accelerate the process which is important because there are many beneficial alleles that need to be transferred. The introduction of these modern engineering, or 'genome editing', techniques is also vital because it avoids the drawbacks of genetically modified organisms which have low public acceptance.

Planned Impact

Food security is a serious and topical issue for both developed and developing nations. This project will implement the latest approaches to produce rice with increased tolerance to salinity and drought stress. We will transfer scientific expertise to partner countries.

Who will benefit:
Researchers in the partner countries will be trained in the UK for state of the art genetic approaches. The germplasm that will be identified and developed will benefit rice breeders and in a later phase, farmers and consumers. Both commercial and state funded breeding institutes will be involved. The project will have societal impacts because the knowledge gained has bearing on important disciplines including crop breeding and agricultural biotechnology. In the short to medium term the research will benefit rice breeders via the identification of rice varieties and molecular markers associated with tolerance and the generation of improved rice by GE. In the longer term, the research will benefit farmers by providing tailor-made, high yielding rice cultivars with improved resistance to salt and drought.

How will they benefit
Research in the partner countries will benefit by sensing researchers to the UK for training and through knowledge exchange via meetings. Researchers will furthermore benefit via dissemination of outcomes and materials through the usual channels (publications, deposit in databases and seed banks). Breeders will have access to improved germplasm and markers for current and future breeding programmes. Farmers will be able to grow rice in areas hitherto unsuitable (because of salinity) and increase yield by growing cultivars with increased tolerance. The public at large will benefit from increased food security and potentially lower prices for staples such as rice.


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Description As part of the very early project outcomes a salinity GWAS (genome wide association study) was conducted which yielded many candidate loci that are involved in salinity tolerance. Among these data a main locus was localised on chromosome 8. We are introgressing this locus into an elite (salt sensitive) rice variety, an approach for which the initial crosses have been made. By using genome editing we have made loss of function (KO) mutants for many of the candidate genes found in the main chr 8 locus and these are now being characterised for a potential role in salt tolerance and thus as a breeding target. In parallel, we have intitated a (molecular) breeding programme to combine salinity and drought tolerance into one elite variety. For this we developed new screening protocols to test simultaneously applied drought and salinity stress in lab and field conditions. Our results of the role of silicon in mitigating salt and water stress in rice will be compiled into 'Technical Bulletins' that are diseminated to farmers to give practical advice and cost benefit analyses regarding the use of silicon fertilisation to improve yield.
Exploitation Route The identified candidate genes that will be identified as playing a role in salinity tolerance can be used in a range of applications as breeding targets and for techniques such as allele swapping to improve salinity and/or drought tolerance.
We are waiting for field trial data after which 'Technical bulletins' will be composed that directly inform farmers regarding the mitigating effects of silicon fertilisation on salt and water stress.
The breeding and introgression parts of the project should lead to varieties that can be released for field trials and subsequently for dissemination among farmer in ~2020 and 2022 respectively. This will require participation of rice breeders and certification authorities.
Sectors Agriculture, Food and Drink

Description A rice Genome Wide Association Study for improved tolerance to the combined stresses of salinity and drought
Amount £27,428 (GBP)
Organisation United Kingdom Research and Innovation 
Department Global Challenges Research Fund
Sector Public
Country United Kingdom
Start 11/2018 
End 07/2019
Description BBSRC-IAA Rice field trials to determine the mitigating potential of silicon on salinity stress
Amount £12,210 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 05/2019 
End 09/2019
Title Rice Screening Protocol for Combined Drought and Salt Tolerance 
Description A soil based protocol was devised to control both soil salinity (6 or 8 dS m-1) and soil moisture content (30%) to apply combined stress to rice seedlings. 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2019 
Provided To Others? No  
Description Field trial collaboration, Canning Town, West Bengal with Dr Sudhanshu, Dr Sarangi and Dr Rajurkar 
Organisation International Rice Research Institute
Department IRRI South Asia Regional Centre (ISARC)
Country India 
Sector Charity/Non Profit 
PI Contribution Contribution by the Maathuis lab (York): detailed lab data on the effect of Si on rice salt tolerance derived from hydroponics and soil based experimentation. Contribution by the Sudhanshu lab: detailed on station and farmers field data on the effect of Si on rice salt tolerance, field trials.
Collaborator Contribution Rice field trails to assess the impact and efficacy of Si fertilisation on rice salt tolerance. This is carried out over two different seasons using several rice cultivars and growth/fertilisation regimes with data collected from both on station and from farmers fields. The first half of exps. has been completed. On the basis of this, a brochure on the recommendation of Si fertiliser for kharif and rabi seasons is being prepared.
Impact Contribution by the Maathuis lab (York): detailed lab data on the effect of Si on rice salt tolerance derived from hydroponics and soil based experimentation. Contribution by the Sudhanshu lab: detailed on station and farmers field data on the effect of Si on rice salt tolerance, field trials. On the basis of this, a brochure on the recommendation of Si fertiliser for kharif and rabi seasons is being prepared.
Start Year 2019
Description IRRI 
Organisation International Rice Research Institute
Country Philippines 
Sector Charity/Non Profit 
PI Contribution The project involves IRRI collaborators and Vietnamese collaborators who are mainly involved in the breeding part of the project
Collaborator Contribution Rice crosses and phenotyping
Impact Rice crosses
Start Year 2015
Description Public lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Public lecture on the role of silicon in crops such as rice, in relation to the development of more resilient crops. International Conference on Agriculture, Environment, and Food Security meeting in Medan, Indonesia, 2020.
Year(s) Of Engagement Activity 2020