FACCE ERA-NET+ GreenRice

Lead Research Organisation: University of Aberdeen
Department Name: Inst of Biological and Environmental Sci

Abstract

In Europe, rice (467 000 ha) is gown under permanently flooded (PF) conditions using irrigation waters of major rivers. Climate change, which already induces decrease in the river flows, is a major challenge in the production systems used to grow rice that needs also to cope with the increased demand of rice supply (net deficit of 0.86 Mt in Europe). Rice yields under existing production practices are therefore threatened by scarcer water availability and more frequent extreme weather events. In addition, PF rice fields emit greenhouse gases (GHG), mainly methane (CH4), that have a very strong warming potential. Alternative wetting and drying (AWD) is a system in which irrigation is applied to obtain 2 to 5 cm of field water depth. After a certain number of days (normally 2 to 7), when the field reaches a threshold of soil water potential, water is applied again. It is considered that water input can be reduced by 15-30% with no loss in yield and that GHG emissions will be reduced by up to 48 %. AWDS represents therefore an interesting alternative for European rice production. The objective of GreenRice is to test AWDS in three regions of Italy, Spain and France that are representative of the diversity of European rice growing areas. In the deltaic areas (Spain and France), rice and natural wetlands protected through natural regional parks are interdependent. We will evaluate the implications of shifting from a PF to an AWD system on rice environment and productivity. Changes on environmental elements such as water consumption, soil salinity, soil microbial community, GHG emission, soil chemistry, and arbuscular mycorrhizal (AM) colonization will be monitored. We will identify varieties that maintain their productivity under AWDS through whole genome association mapping of a large panel of temperate varieties and will set the bases for marker-aided breeding using genomic selection to predict the values of additional breeding lines. We will investigate traits determining adaptation to AWDS such as root development, AM colonisation, salinity tolerance and resistance to nematodes using the same large panel of European genotypes; AM symbiosis impact on biotic stress (blast) alleviation will be tested. An extensive gene expression study will identify the root types and genes of major importance in transport process and the degree to which they are affected by AWDS. The role of plant traits and the soil microbial community in modulating C, N and GHG cycling will be investigated in controlled environment studies. The results obtained will be disseminated to the local stakeholders (farmers and natural parks and spaces, mainly) and to the scientific community (through web site, database and publications). Scientists specialized in molecular genetics, functional genomics, phytopathology, agronomy, ecology, and bioinformatics from 7 institutions of 4 countries will be involved.

Technical Summary

The effect of a shift from a permanent flooded system to an alternate wetting and drying system (AWDs) on rice environment and productivity will be assessed in Italy, Spain and France over two seasons. Environmental changes such as water consumption, soil salinity, soil microbial community, GHG emission, soil chemistry, and microbial associations will be monitored. Cultivars differences in root development, salinity tolerance, or CH4 emission rates will be assessed by studying the impact of the system on varietal performances as a whole using a set of 10 cultivars. The impacts on grain quality in terms of heavy metals and mycotoxygenic fungi accumulation will be followed.
Varieties maintaining their productivity under such AWDS will be identified. A panel of 300 temperate rice accessions genotyped at high density that represent the genetic diversity of the breeding programs of the three rice growing countries will be selected. The panel will be used to identify accessions best adapted to AWDS and assess the genetic control of adaptation using association mapping. Data from this WP and from WP3 will be used in a genomic selection approach to develop a prediction model which will, then, be validated. The model will be used to predict the genomic estimated breeding value of breeding material genotyped with the same marker density as the panel.
Plant traits determining adaptation to AWDS will be identified. The same panel will be tested under controlled conditions to assess traits linked to adaptation to the major constraints expected in AWDS: root development, AM colonisation, salinity tolerance and resistance to nematodes. AM symbiosis impact on biotic stress alleviation will be tested. The role of plant traits and the soil microbial community in modulating C, N and GHG cycling will be investigated in controlled environment studies. Transciptomics on roots will be linked to transport processes to identify key genes impacted by AWDs.

Planned Impact

Impacts are expected in several domains:
Agriculture:
The project will bring detailed information on a new system with reduced production costs (water saving, use of the AM symbiosis) but no yield negative impact. The replication of similar experiments in three rice growing regions will enable the adaptation of the system to the specific characteristics of the three areas. If adopted, the system will improve the competitiveness of European rice producers. Rice is the only large-scale grain crop in Europe with underproduction at EU scale (net deficit of 860 000 t in 2012). AWDS can participate in a sustainable intensification of European agriculture to avoid increasing the demand on food production in other world regions and causing significant GHG emissions elsewhere.

Environment:
If AWDS is adopted, water will be saved and GHG emissions reduced, mitigating future problems linked to climate change. A reduction of only 10% in water use would free 1 billion m3 of water. Emission of CH4 can be reduced by up to 48% depending on the drainage management. GreenRice results can provide guidelines on the best management options to save water and reduce GHG emissions while proposing varieties more tolerant to possible negative externalities of AWDS. European rice-growing areas are found in important ecological zones with great biological richness. Well managed AWDS, could permit to decrease the negative effect of rice crops on nearby natural spaces, some of which are protected (Spain, France), by manipulating the quantity of drainage water as well as its quality, which are the object of agreements between farmers and parks.

Knowledge:
The projects intends to go further than the testing of a new system, up to a better understanding of the functional traits contributing to performance under AWDS and the alleviation of stress by the AM symbiosis and provide solutions to the possible increased risk of nematodes. Such understanding will permit the definition of the best ideotypes to develop for AWDS, establishing a road map for breeders. The project will bring a fine understanding of the genetic resources usable in European breeding programs by characterizing the phenotype of a large set of varieties for their adaptation to AWDS and to its various component traits (root system, salinity tolerance, blast resistance, AMF colonisation). Through the results of whole-genome association mapping studies, GreenRice will help to identify markers linked with genes controlling these traits and, in some cases, valuable candidate genes. An allelic profile of each line at these markers can be established. Besides helping breeders in defining the best material for future hybridization by improving complementarity between parents, it will set the bases for introgression of specific alleles through marker-assisted selection. Genomic selection that can bypass phenotyping for a few generations, which is particularly useful in temperate conditions where one can grow only one generation per year, could help speed up the genetic progress in the medium term. A basis for a more efficient breeding system using molecular markers will therefore be established.

Society:
Farmers' and other stakeholders' awareness on advantages/drawbacks of an environmentally friendly system to cope with climate change will be improved, enabling them to make sounder decision on the evolution of the rice cropping systems. GreenRice will also provide a more general public awareness of the progress and potential in changing rice systems to reduce their negative impact while maintaining the ecosystem services rice presently provides (maintenance of irrigation and drainage network; contribution to maintenance of highly diverse natural spaces). Derived results from the project can be provided to policy-makers to contribute to the definitions of new or modified policies encouraging a competitive and sustainable rice system

Publications

10 25 50
 
Description Arbuscular mycorhizal fungi (AMF) colonisation rates measured in a large box can be replicated in pots.
AMF protect plants from the parasitic weed Striga
Alternative wetting and drying appears to increase AMF colonisation
Crosses between nematode resistance rice and Italian cultivars have been made
A single major gene for nematode resistance has been mapped to chromosome 11 in the resistant cultivar LD24 by bulk segregant NG Sequencing
Just started using CRISPR to test candidate genes
Exploitation Route Project is only 3 years old, we have la bit of no-cost extension pulling datasets together. We anticipate the nematode resistance locus will be used by breeders across the world.
Sectors Agriculture, Food and Drink

 
Description I continue a public engagement activity with school children focusing on water and rice and the mapping of a nematode resistance gene on rice chromosome 11 is being used by our Italian partner for new breeding priorities.
First Year Of Impact 2017
Sector Agriculture, Food and Drink,Education
Impact Types Societal,Economic

 
Description FACCE ERA-NET+ GreenRice
Amount £1,200,000 (GBP)
Funding ID BB/M018415/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2015 
End 12/2017
 
Description Newton-India-UK project NEWS-India-UK, held by CEH Edinburgh with two CoIs in Aberdeen including Adam Price on rice genetics
Amount £1,139,000 (GBP)
Funding ID BB/N013492/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2016 
End 12/2018
 
Description Mapping resistance to root-knot nematodes 
Organisation University of Ghent
Country Belgium 
Sector Academic/University 
PI Contribution Based on Aberdeen results screening nematode resistance in rice, Aberdeen made and crosses made of completely resistant cultivars with susceptible ones, and sent F2 seed to Godlieve Gheysen in Ghent. Aberdeen then sequenced bulk DNA from resistant and susceptible pools and are drafting a manuscript of the results. This sequencing was funded by GreenRice project
Collaborator Contribution Before GreenRice, the group in Ghent had confirmed the resistance of two rice cultivars to root-knot nematode. They subsequently assessed 200 F2 plants of two crosses for resistance to the nematode, made pools and extracted DNA from them to send to Aberdeen.
Impact A manuscript is being written. In addition we have been able to send segregating seeds to GreenRice partner in Italy and told them to select for the last 3 Mbp of chromosome 11 as we know that holds a major resistance gene.
Start Year 2016
 
Description Panel Discussion on Sustainability of Food for May Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact A Price sat on a panel for an open discussion on the sustainability of food during the May Festival hosted by the University of Aberdeen every year. The main attraction was Carlo Petrini, founder of the Slow Food movement.
Year(s) Of Engagement Activity 2017
 
Description Poster at International Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Roshi Shrestha presented a poster "Genome wide association mapping of drought recovery in temperate rice" at the International Symposium for Rice Functional Genomics in Montpellier
Year(s) Of Engagement Activity 2016
URL http://isrfg2016.cirad.fr/
 
Description Poster by Vikki Oliver at European Geosciences Union 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster by Vikki Oliver at European Geosciences Union 2016 entitled "Preliminary results on yield and CO2 fluxes when using alternate wetting and drying on different varieties of European rice"
Year(s) Of Engagement Activity 2016
URL http://www.egu2016.eu/
 
Description Price on Rice- a talk to general public in the Cafe Sci programme 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Professor Price will give a talk "Price on Rice" at the Cafe Sci event in central Aberdeen on the 21st February. The Cafe Sci is organised by the Public Engagement with Research Unit of the University of Aberdeen and normally has an audience of about 60 members of the general public
Year(s) Of Engagement Activity 2018
 
Description Talk by Adam Price at the DROPs-EUCARPIA conference on Recent Progress in Drought Tolerance, Montpellier, June 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Participants in your research and patient groups
Results and Impact As a culmination of the EU-FP7 project DROPS and in collaboration with EUCARPIA, a conference on drought was organised 8-9th June 2015 in Montpellier, France. Adam Price delivered a talk titled "Genetics and breeding rice that uses less water". There were something like 250 delegates.

Many interesting discussions
Year(s) Of Engagement Activity 2015
URL https://colloque.inra.fr/drought-tolerant_plants_2015%20
 
Description Talk by Vikki Oliver in European Geophysical Union 2017 conference in Vienna 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk entitled The effect of alternate wetting and drying on methane fluxes on different varieties of European rice (authors V. Oliver, N. Cochrane, S. Monaco, A. Volante, G. Orasen, G. Vale, A. Price, Y. A. Teh) was presented in European Geophysical Union 2017 conference in Vienna. Matthias Kuhnert from Aberdeen University showed interest in modelling our data and discussions have been made since then to provide him with GHG and met data.
Year(s) Of Engagement Activity 2017
URL https://egu2017.eu/home.html
 
Description Targets for gene editing from genetic mapping in rice 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at the 20th Association for Promotion of DNA Fingerprinting and Other DNA Technologies (ADNAT) on Genome Editing in Bhubaneswar, India 16-18th February 2017
Year(s) Of Engagement Activity 2017
URL http://kiitbiotech.ac.in/adnat/
 
Description Workshop on Rice Modelling 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A workshop of rice scientists and modellers (mostly interested in greenhouse gas production) met 5th and 6th Septemeber in Aberdeen to discuss data sets and modelling approaches that could improve the modelling of rice growth and its dependency on water input. There were 13 participants from 2 Italian, 2 Spanish institutions (two are GreenRice partners, 2 are not) plus University of Aberdeen. The main aim was to strengthen methodology and collaboration.
Year(s) Of Engagement Activity 2016