Using wild ancestor plants to make rice more resilient to increasingly unpredictable water availability

Enabling food production to keep pace with population growth in the face of global climate change is a significant challenge. Both high and low extremes in rainfall increasingly limit food production, particularly for the poorest farmers. Furthermore, droughts and floods are predicted to occur more frequently under climate change, whilst the availability of water for agriculture will decline. The "green revolution" resulted in a doubling of rice yields across much of Asia, but demand for rice now exceeds production and UN FAO predictions suggest rice yields will need to increase by 50% by 2050 to meet population growth. A quarter of global rice production, rising to 45% in India, is in rain-fed environments thus at serious risk from climate change.

New developments in modern plant breeding are allowing scientists to address this problem. The use of DNA based molecular markers that predict how adult plants perform under challenging environments such as drought allow breeding to be speeded up and different phenotypes or traits to be combined and transferred from one variety to another. These molecular tools make the selection process much more efficient so that what previously would have taken six generations can now be done in two. However, the loss of genetic diversity during the hundreds of years of domestication of crops such as rice means that the germplasm associated with modern cultivars offers limited scope for the improvements that are needed to meet the challenges of the 21st Century.

The exciting thing about this project is that we will use new technology platforms developed in one of our laboratories at Cornell University, USA, to access valuable genetic variation from ancestral wild species of rice, introduce this to modern day elite cultivars that are widely grown in India and identify new varieties that have increased yields under drought conditions due to the presence of small segments of DNA from the wild species. Field trialling of hundreds of different lines carrying different segments of DNA from the wild species will be conducted by the Central Rice Research Institute in India and in parallel researchers at the Universities of York and Cornell will carry out a range of different experiments to understand what causes increased drought resistance in specific lines. With this new understanding it will be possible to develop new DNA based molecular markers that allow the genetic variation from the wild species to be efficiently transferred to a wide range of commercial rice cultivars. So the outputs during the four year project will not only be improved rice varieties but also new breeding tools for rapid deployment of drought conferring genetic variation to multiple rice cultivars.

However, the adoption of new rice varieties by local communities is dependent on multiple factors in addition to yield performance with grain quality being one of the most important. Cultural and sociological issues such as the role of gender also play a significant part in determining the success of a new cultivar and in order to address this we will perform a socioeconomic study to assess the likely uptake patterns of any new varieties and their impact on farmers' incomes. The impact of new rice cultivars on yield, per unit cost of production, and total production per specific input (land, labour, fertilizers, seeds) will be evaluated and on-farm testing and participatory evaluation will be an integral component of cultivar field trials.

This project will also model the impact of new varieties to quantify how yields are enhanced in drought-prone landscapes currently and in the future as climate changes. This information along with the outputs from our socio-economic studies will inform policy makers in developing countries about the socio-economic benefits of new varieties and thus improve adoption of the most effective strategies to address food insecurity and poverty.

The loss of genetic diversity during domestication means that the germplasm associated with modern rice cultivars offers limited scope for improvements that are needed to meet the challenges of a growing population and changing environment. To address this issue the McCouch lab have pioneered the use of wild genetic resources of rice to enhance performance of elite cultivars. In this project we will perform comprehensive field trials for drought resistance in rain-fed areas of India using two sets of 96 Chromosome Segment Substitution Lines (CSSLs) both in the elite, O. sativa, indica cv. IR64 background, but containing introgressions from two, genetically diverse accessions of the wild ancestor, O. rufipogon. In parallel we will perform elemental, metabolomic, transcriptomic, physiological and water use efficiency analysis of the same material in York and Cornell. Combining the outputs of the field and laboratory analysis will lead to the selection of elite lines for immediate use and drought conferring CSSLs that can be rapidly introgressed into multiple commercial cultivars. Multiple sociological and agronomic factors dictate uptake of new rice cultivars by local communities and to address this issue the work on development of new cultivars will be fully integrated with a socio-economic study to assess from a farmer perspective what influences their likely uptake pattern, their impact on yield and related cost of production. To further facilitate impact promising material selected from field trials and experimental analysis will undergo on-farm testing and participatory evaluation by year 4 of the project. Modelling the impact of new varieties to quantify how yields are enhanced in drought-prone landscapes currently and in the future as climate changes will feed into the socio-economic study and the outputs will be used to inform policy-makers about the benefits to be gained through investment in developing new, locally adapted drought tolerant rice cultivars.

Who will benefit from this research and how?

We anticipate a number of beneficiaries.

First and foremost people in poverty in rain-fed areas of India who are dependent on rice for survival are expected to benefit directly through the use of improved drought tolerant cultivars of rice that will be produced either during the lifetime of the project or as a direct result of deployment of genetic resources and tools such as drought tolerance conferring CSSLs that are outputs of the project. The integration of socio-economic and modelling components designed to align both current and future rice farmer needs with plant breeding targets and outputs is a particular feature of this research programme that should maximise translation of the research outputs and impact. The availability of new varieties that deliver reliable high yields under drought and flooding conditions will help alleviate hunger and provide sufficient security for farmers to diversify their activities and seek other forms of income to lift themselves out of poverty. The timeframe for expected benefits in this respect are in the years immediately following the end of the 4 year project since the relevant outputs will take at least 4 years to develop.

The investment of approximately 10% of the total budget of this project in capacity building in India, particularly in the education and training of personnel in topics relevant to the work programme will provide long term benefit to the public infrastructure underpinning agricultural development and extension. A concerted effort to train staff to adopt a multidisciplinary approach that encompasses modern molecular breeding of new rice cultivars with socioeconomic studies that address the barriers that often delay or prevent their uptake should result in a culture change in approach that has a long term impact. Workshops in India and the UK in Years 2 and 3 of the project will focus particularly on this aspect.

In terms of capacity building the project will also introduce the use of high throughput single nucleotide polymorphism (SNP) assays developed specifically for rice to CRRI staff and will enable them to do marker assisted selection as part of this research initiative. This will represent a step-change in through-put of marker assisted selection which can then be applied to other traits and crops in India. This exemplar should therefore lead to further investment in this cutting edge technology in India.

Public Sector Policy Makers will also benefit from this work because it will provide them with information on the impact of developing new rice cultivars that is based on robust socio-economic and modelling studies that take into account current end-user preferences and needs and future climate change predictions. This should represent a powerful information pack that can help inform government policy not only in India and the UK but in other countries as well. Although the current programme of work is focussed on India, the outputs could have wider impact since elite cultivars such as IR64 are used widely throughout Asia. Furthermore, the approach we are adopting could serve as a template and exemplar for other R&D programmes that combine cutting edge science with strategic targets in a multidisciplinary approach that addresses both product development and factors affecting delivery from the outset.

Academia will also benefit from this work. The PIs involved have impressive track records in terms of peer review publications and cutting edge interdisciplinary research. The combination of robust datasets from comprehensive experimental and field trial analysis of CSSL populations will produce multiple publication quality datasets. The molecular basis of drought tolerance in higher plants is a hot topic of research and we anticipate this work will contribute to that field in particular through top quality peer reviewed publications and presentations at international meetings.