Ancient rice genomics & global food security | Carlsbergfondet
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Ancient rice genomics & global food security

The Carlsberg Foundation's 'Semper Ardens' Research Project

Figure 1 Rice fields in China, Needpix Photos

In 2003, we discovered that DNA of past plant and animal communities can be retrieved from permafrost and cave sediments spanning 400,000 years. This finding gave birth to the field of ancient environmental DNA, that has since grown to encompass many different research topics, experimental methods and computational tools.
By Eske Willerslev, GLOBE Institute, University of Copenhagen & Department of Zoology, University of Cambridge 

Today, we are looking to apply the ancient environmental DNA approach to uncover the genetic basis of rice resilience to environmental stressors, a key question for addressing food security challenge in a changing world.

Rice is the staple food for more than half of the world’s population1, making it one of the most important crops today and the foreseeable future.  The International Rice Research Institute has recently reported that rice production will need to increase by 25% over the next 25 years to meet global demand for the grain. However, current climate change is posing a major challenge to achieving this target. 

For example, each degree Celsius increase in global mean temperature is projected to reduce global yields of rice by 3.2%. Even more concerning is the projected increase in weather extremes (droughts, floods) and pathogen outbreaks, which can decrease regional rice yields by more than 50%.

Rice is the staple food for more than half of the world’s population, making it one of the most important crops today and the foreseeable future

One important strategy to improve the resilience of rice crops to increasing environmental threats is genetic modification, i.e., introduction of new genetic variants into existing rice breeds. While the introduction of extant wild type variants into domesticates is a well-established practice, the use of ‘lost’ alleles from ancient genotypes remains unexplored. This is a major oversight if we consider that rice is among the first plant species to undergo domestication, dating back at least 10,000 years before present. 

During the process of domestication contemporary rice has lost many genetic variants present in ancient wild and domesticated types2, including the variants that may have contributed to the capacity of rice populations to persist under past climatic perturbations and disease loads.  

The ancient rice project aims to identify these genetic variants using state-of-the-art genomics techniques and re-introduce it into modern rice breeds (see figure 2).

Schematic illustration of the principles, workflow and objectives of the ancient genomic rice project. a, sample collection, and data generation and processing and b, bioinformatic analysis of aDNA data, and rice transformation.

Scarcity of rice macrofossils? Use environmental DNA instead

First step in identifying useful genetic variants in ancient rice breeds and wild types is to reconstruct their genomes, and track their changes in response to varying selection pressures over time3

However, there is a general scarcity of rice macrofossils, especially ones that have not been modified by human activities which compromise DNA survival (e.g. charring, heating, burning). 

Environmental DNA and pollen DNA.

Environmental DNA (eDNA) is DNA preserved in environmental samples, including lake sediment, cave deposits, marine sediments, ice cores etc.4. Our group was first to show that DNA of higher plants and animals can be obtained directly from sediment samples going back tens to hundreds of thousands of years in time5. Recently, this approach has been refined by extracting and sequencing the total DNA present in a sample, enabling taxonomic identification across the entire ecosystems (plants, animals, fungi, microbes)6. In addition to extracellular DNA (eDNA sensu stricto), environmental samples contain a variety of microfossils such as pollen, diatoms, fungal and bacterial spores, that also contain DNA. Advantage of microfossils is that they permit reconstruction of individual genomes (unlike eDNA). Our group is currently developing novel methods of taxonomic identification of plants from pollen DNA.

Instead of rice macrofossils, this project will use environmental DNA (eDNA) retrieved directly from ancient sediments4, and DNA preserved in fossilised pollen grains.  

This approach will allow us to retrieve, along with rice DNA, the DNA of rice pathogens from the same sediment samples and reconstruct their impact on rice populations.

Lake sediments as a source of ancient rice DNA

While eDNA and pollen DNA are common and abundant in a wide range of sedimentary archives, our focus is on lake sediments because they tend to be rich in pollen and eDNA from the surrounding terrestrial environment and provide reliable chronological profiling. 

In collaboration with archaeobotanical specialist and geologists, we have identified a set of lakes within the Yangtze river region of China, covering key areas of rice domestication during the past 10,000 years. Sediment sequences will be collected from the selected lake sites using specialised drilling equipment (see Box 3).

The contribution of candidate variants to phenotypic traits and yield components will be assessed by genome editing in modern rice varieties using CRISPR/Cas9 technology.

Editing of modern rice genomes

Once genetic variants and loci under strong selection are identified, a selected set of these will be investigated functionally. The contribution of candidate variants to phenotypic traits and yield components will be assessed by genome editing in modern rice varieties using CRISPR/Cas9 technology.  

Finally, the performance of the resulting rice ‘transformants’ will be evaluated (e.g. grain number and size in different environmental conditions, disease resistance) to confirm that variant candidates are indeed contributing to rice resilience.

Scientific social responsibility

Figure 3 Lake coring: Sedimentary sequences are collected from lakes as 3-meter-long segments using Uwitec piston corer from an anchored platform by a team of 2-4 people. The sediments are sealed in aluminium foil and protective plastic containers, shipped to appropriate sampling facility and stored at 4°C.

This study is posed to generate new knowledge about when, how, and why different genetic traits in rice underwent positive selection which is crucial for understanding the natural selection and domestication process leading to the different breeds of rice found today. 

The project will also deliver a suite of novel methods for studying past plant selection from eDNA and pollen DNA data, and while its application will be exemplified by rice, it will be in principle directly applicable to other plant species and, in the case of eDNA, even animal species.

The outcomes of this project will inform strategies for boosting the resilience of rice crops on our rapidly changing planet and meeting the increasing yield demands of the global human population. Both of these results are essential contributions to the UN 2015 Sustainable Development Goal number 2, to “End hunger, achieve food security and improved nutrition, and promote sustainable agriculture.” 

The findings of this project should facilitate the resurrection and use of rice’s own past genetic strategies for combating pests and pathogens rather than via pesticides that often threaten other organisms in the ecosystem, including human consumers. This represents an entirely new approach to preserving and enhancing the genetic diversity of cultivated plants.  

References

1. Gross, B.L., Zhao, Z., 2014. Archaeological and genetic insights into the origins of domesticated rice. Proc. Natl. Acad. Sci. 111, 6190–6197. https://doi.org/10.1073/pnas.1308942110

2. Fuller, D., Weisskopf, A., Castillo, C., 2016. Pathways of Rice Diversification across Asia. Archaeol. Int. 19, 84–96. https://doi.org/10.5334/ai.1915

3. Sweeney, M., McCouch, S., 2007. The Complex History of the Domestication of Rice. Ann. Bot. 100, 951–957. https://doi.org/10.1093/aob/mcm128

4. Pedersen, M.W., Overballe-Petersen, S., Ermini, L., Sarkissian, C.D., Haile, J., Hellstrom, M., Spens, J., Thomsen, P.F., Bohmann, K., Cappellini, E., Schnell, I.B., Wales, N.A., Caroe, C., Campos, P.F., Schmidt, A.M.Z., Gilbert, M.T.P., Hansen, A.J., Orlando, L., Willerslev, E., 2014. Ancient and modern environmental DNA. Philos. Trans. R. Soc. B Biol. Sci. 370, 20130383–20130383. https://doi.org/10.1098/rstb.2013.0383

5. Willerslev, E., Hansen, A.J., Binladen, J., Brand, T.B., Gilbert, M.T.P., Shapiro, B., Bunce, M., Wiuf, C., Gilichinsky, D.A., Cooper, A., 2003. Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments. Science 300, 791–795. https://doi.org/10.1126/science.1084114

6. Pedersen, M.W., Ruter, A., Schweger, C., Friebe, H., Staff, R.A., Kjeldsen, K.K., Mendoza, M.L.Z., Beaudoin, A.B., Zutter, C., Larsen, N.K., Potter, B.A., Nielsen, R., Rainville, R.A., Orlando, L., Meltzer, D.J., Kjær, K.H., Willerslev, E., 2016. Postglacial viability and colonization in North America’s ice-free corridor. Nature 537, 45. https://doi.org/10.1038/nature19085