A research team led by Professor Eske Willerslev, in collaboration with researchers from the Carlsberg Research Laboratory, Cambridge University in the UK, the Chinese Academy of Sciences and the Beijing Genomics Institute, is mapping the genetic material of ancient domesticated rice varieties and wild rice to uncover the genetic basis of rice resilience to diseases and environmental changes. This knowledge is important to addressing the challenges around food security in a changing world. By Eske Willerslev, professor, Doctor of Science, Section for Geogenetics, University of Copenhagen Rice is a staple food for more than half the world’s population, which makes it one of the most important crops today and for the foreseeable future. The International Rice Research Institute recently estimated that rice production needs to increase by 25% over the next 25 years if the global demand for the grain is to be met. Ongoing climate change, however, is a big challenge to achieving this target. Calculations show that the global rice yield will fall by 3.2% with every 1°C rise in average temperature. Even more concerning is the expected rise in the frequency of extreme weather (drought, flooding) and outbreaks of disease, which could reduce regional rice yields by more than 50%. Genetic modification, i.e. the introduction of new genetic variants into existing varieties, is an important strategy for improving the resilience of rice varieties to climate change and to diseases. While the insertion of genetic variants from wild rice into domesticated varieties used for food production is a well-established practice, the possibility of reinserting “lost” genetic variants from extinct rice varieties has not been explored. Humans have been growing and breeding rice for the past 10,000 years. The purpose of this research project is to identify useful genetic variants from ancient rice populations that have since been lost and, with the aid of advanced gene technology, to reintroduce them in modern rice varieties During the gradual processes of domestication, contemporary rice has lost many genetic variants present in ancient wild and domesticated types, including the variants that may have contributed to the capacity of rice populations to adapt to climatic perturbations and various diseases in earlier times. The purpose of this research project is to identify useful genetic variants from ancient rice populations that have since been lost and, with the aid of advanced gene technology, to reintroduce them in modern rice varieties (see fig. 1). Fig. 1 Schematic illustration of the principles, methods and purpose of the ancient rice project: (A) sample collection and production of data; and (B) bioinformatic analysis of eDNA data and assessment of genetically modified rice plants. Fig.: Mikkel Winther Pedersen Design: Kontrapunkt Use of eDNA to map the genetic material of ancient rice eDNA and pollen DNA Environmental DNA (eDNA) consists of tiny fragments of DNA from modern and ancient organisms that are preserved in various sediments, including lake, cave and marine sediments as well as ice cores. I have previously shown that DNA from higher plants and animals that lived thousands of years ago is preserved in, and can be recovered directly from, sediment samples. The method has since been refined so that all the DNA found in a sample can be recovered. Consequently, many species (plants, animals, fungi, microbes) that lived at the place and time in question can be identified and provide information about the surrounding ecosystem. Besides ‘free’ fragments of DNA attached to sediment particles, sediment samples also harbour a number of microfossils, including pollen, diatoms, and fungal and bacterial spores, which also contain DNA. The benefit of these microfossils is that they allow individual genomes to be reconstructed. The first step in identifying useful genetic variants in ancient rice varieties and wild species is to reconstruct their genomes and track the genetic changes that have taken place in response to various selection pressures over time. The study draws on an important discovery that I made in 2003, namely that DNA from ancient plants and animals can be recovered directly from permafrost and various forms of sediments. DNA recovered from environmental samples is called “environmental DNA” (eDNA), and this study is based on eDNA from lake sediments, including DNA preserved in fossilised pollen grains. Using this approach, we can obtain the genetic material from both ancient rice varieties and wild rice, as well as from the diseases to which these rice plants were subject to, and use it to reconstruct the impact of diseases and climatic changes on ancient rice populations. Lake sediments as a source for locating DNA from ancient rice plants Lake sediments are rich in pollen and eDNA from the surrounding catchment and can also be reliably dated using radiocarbon methods. In collaboration with archaeobotanical specialists and geologists, we have identified a number of lakes in the Yangtze region of China, which covers central areas where rice has been grown for the past 10,000 years. Sediment cores will be collected from these lakes using specialised drilling equipment. Different layers of the lake sediments are collected in metre-long sections using a special drill anchored to a platform and operated by two to four people. The samples are sealed with aluminium foil and placed in plastic containers before transportation to storage facilities, where they are kept at 4°C prior to analysis. Photo: Yucheng Wang Can characteristics of ancient rice be used to improve modern rice varieties? Once we identify genetic variants that have been selected for in response to climatic or disease pressures, a subset of these will be examined to determine which characteristics they influence. The selected genetic variants will be inserted in modern rice varieties by editing the genetic material with the CRISPR/Cas9 technology. The modified plants will then be tested for resilience to diseases and water scarcity, and effect on yield, to identify the genetic variants that ensure improved performance of modern rice varieties. Researching ancient rice genes The results from the study can hopefully offer solutions for increasing the resilience of modern rice varieties to climate change and diseases, and at the same time address the growing demand for higher yields imposed by global population growth. Furthermore, the study will be able to determine whether rice’s own past genetic strategies for combating pests and diseases can help us to reduce our current dependence on pesticides, which often threaten other organisms in the ecosystem, including human consumers. DNA from ancient plants and animals can be recovered directly from permafrost and various forms of sediment The study will also generate a number of new methods for investigating selection processes using eDNA and pollen DNA data; methods that, in principle, are universal and can be used for studies of other plants and animal species. This is a novel approach to preserving and enhancing the genetic diversity of important crops.