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Harnessing rice genetic diversity to accelerate impact

Rice and its wild relatives naturally contain an immense amount of genetic variation, including variants conferring superior yield, enhanced nutritional quality, and improved biotic and abiotic stress tolerances – indeed for all the major targets for achieving impact through developing improved rice varieties. This theme searches for the best sources of genes and genotypes with valuable traits and transfers them to rice breeders in a form that can be easily used to improve the best rice varieties. It focuses on the traits that will have highest impact and have proved the most challenging for breeders to date.

Challenge

Rice has almost 50,000 genes. After sequencing only 3,000 varieties, we have already found an average of 10 functionally distinct variants of each gene, and we know there are many more still to be discovered. Hence, there is an almost unimaginably large number of potential combinations of genes that need to be explored to design and develop the best possible varieties. Determining the agronomic value of each combination is an even more challenging task, because of the low heritability of most traits, their dependence on environment and management, the high cost of measuring them and the specialized equipment and expertise required. Furthermore, for some key traits, we haven’t even found a way to measure the trait effectively. The potential is huge, but the challenge is even more formidable. Using conventional technologies and approaches, breeders have barely begun to tap the potential.

Progress in breeding superior rice is too slow to meet the Sustainable Development Goals; too many rice-dependent people continue to suffer in poverty, hungry and malnourished.

Inadequate advance in rice production is too slow for nations and regions to meet their development targets on poverty, hunger, malnutrition, and climate change.

Contribution

This challenge is being addressed through four main areas of work:

Sustaining the basic operations of the genebank, to secure the diversity of rice and make it available for current and future use.

Simply maintaining the genebank is a sine-qua-non for the theme and for IRRI , and resources must be dedicated to maintaining it. The Global Crop Diversity Trust, an international organization founded by the Food and Agriculture Organization of the UN (FAO) and Bioversity International on behalf of the CGIAR, has signed an agreement with IRRI for permanent funding of the genebank.

Engaging with relevant national and international fora on genetic resources policy, to ensure compliance with relevant regulations and agreements, and hence ensure fair and responsible use of the innovations arising out of the theme.

An enabling policy environment is also a sine-qua-non, as inappropriate policies and associated legislation have the potential to prevent effective use of the genebank. Mechanisms are in place, coordinated across the CGIAR system through the CGIAR Genebank Platform, to engage in relevant fora, and to remain engaged as the policy environment evolves. The major current issues are farmers’ rights, the “dematerialisation” of genetic resources (reflecting the fact that their value lies in the information about them as much as in the material itself), and the need to ensure that a fair share of the benefits arising from the use of genetic resources flows back to the countries that originally provided those resources.

Transforming the operations of the genebank to reduce costs, increase throughput, improve conservation standards, and enhance conservation coverage, through measures such as automating basic operations, replacing infrastructure, and developing a “digital genebank” of DNA data and associated phenotypic data.

Although the genebank is already operated to the highest approved international standards, investment in robotics, genomics and informatics technologies provides a new opportunity for a step change to a next generation genebank that is much more cost effective and able to support far more effective use.  Initial steps have been taken towards redesigning the way the genebank operates, such as managing high-value genetic stocks in addition to traditional accessions, sequencing 3,000 accessions, bar-coded sample tracking, image-based phenotyping of grains, automated seed sorting, automated germination testing, and tablet-assisted data collection. However, major additional investments are required to achieve a thorough transformation.

Using the power of modern technologies in genomics, phenomics and big data to transform how we find and deliver to breeders the material, tools and knowledge that they most need to speed their progress.

This will include developing new approaches to high-precision and high-throughput phenotyping, new approaches to generate novel high-value combinations of genes, new tools to predict the breeding value of accessions based on environment, genotype and phenotype, and new approaches to link data from multiple sources through a Global Information System. Priority traits for this area of work will be set by combining the Variety Product Profiles generated through the theme “shaping future rice value chains and policies” with the breeders’ assessments of their most challenging traits to work with. Inadequate understanding of diversity in rice, as well as inadequate tools to gain the necessary understanding, has been the primary hindrance to more effective use of diversity. Traditional approaches to phenotyping genebank accessions hoping to find useful ones have very limited potential. Applying new technologies for gene discovery and new technologies for predicting breeding value, combined with creating new combinations of genes by hybridizing varieties in ways that have not previously been attempted, brings the power to harness genetic diversity in ways that were previously inconceivable. Initial steps have been taken towards high-throughput and high-precision phenotyping, deep genomic understanding of diversity in the collection and the genetic control of traits, and the creation of novel combinations of genes. However, again major additional investments are needed to scale up capacity to undertake this work.

Impact

As implied by the name of this theme “... to accelerate impact”, the primary outcome of this work is internal to the rice science community, both inside IRRI and outside, enabling others in this community to step up the rate of the impact resulting from their work. As such, the theme is agnostic with respect to any specific sustainable development goal: we can help work towards any goal that relies on the use of genetic diversity.

By conserving diversity and devising novel approaches for fast progress, we not only help others have faster immediate impact, but also provide a pipeline that will indefinitely support rapid adaptation to emerging developmental challenges as they arise, thus ensuring truly sustainable development in the sense of the 1987 Brundtland report on the definition of sustainable.