Ancient DNA Secrets to Boost Crop Resilience Unlocked by AEGIS

A pioneering project exploring ancient environmental DNA (eDNA) could revolutionize the development of climate-resilient crops by uncovering how ecosystems adapted to past environmental changes. The Ancient Environmental Genomics Initiative for Sustainability (AEGIS) has been awarded DKK585 million ($85 million) over seven years. The bulk of this funding, $72 million, comes from the Danish nonprofit Novo Nordisk Foundation, with the remainder from the UK charity Wellcome Trust.

The initiative aims to sequence DNA fragments from soil sediment, ice, and other sources up to two million years old. By comparing these ancient DNA sequences to modern reference genomes, researchers hope to understand past genetic diversity and the adaptations that allowed ancient species to thrive in changing environments. This knowledge could then be applied to modern crop breeding, enhancing the resilience of crops such as barley, wheat, and rice.

“By employing ecosystem modeling, we can pinpoint which combinations of species led to the most durable ecosystems in the past,” said Professor Eske Willerslev, an evolutionary geneticist at the University of Copenhagen and the University of Cambridge. “This knowledge could serve as a blueprint for creating climate-resilient food systems, enhancing both the crops we grow and the sustainability of the environments they grow in.”

The AEGIS project is a multidisciplinary effort, incorporating expertise in bioinformatics, AI/ML, microbial ecology, plant breeding, and environmental genomics. One of its key goals is to demonstrate proof-of-concept in key crops like barley, wheat, and rice. The project will also create a public data portal featuring climate data, time points, sample types, genomic data, and reference genomes collected during the research.

Dr. Claus Felby, Senior Vice President at Novo Nordisk Foundation, likened the project to the Human Genome Project but on a planetary scale. “There’s DNA everywhere. In a teaspoon of soil, you can see DNA fragments from everything from bacteria and fungi up to the biggest mammal. This is the planetary genome project; you can map everything in a given ecosystem.”

Initial results from the project are already proving to be groundbreaking. For instance, researchers have discovered how rice adapted to a much wetter climate in a part of China about 8,000 years ago. This level of detail, down to the single gene and the entire ecosystem, is unprecedented.

In addition to analyzing DNA fragments, researchers are also reading climate data from the same periods by examining oxygen isotopes, which change according to precipitation and temperature. This dual analysis allows scientists to map the evolution of ecosystems in response to climate changes over millennia.

The implications of this research are profound. By understanding how ancient species adapted to past climate changes, scientists can develop more targeted and faster plant breeding strategies. This could include polygenic traits, where multiple genes change simultaneously, offering a more comprehensive approach to breeding climate-resilient crops.

The project also includes building one of the world’s most powerful supercomputers in Denmark, in collaboration with NVIDIA, to handle the vast datasets generated by this research. This computational power will enable the detailed analysis of entire ecosystems, not just individual species, offering insights into how human activities, such as agriculture and the use of fertilizers and pesticides, have impacted ecosystems over time.

According to the European Molecular Biology Laboratory’s European Bioinformatics Institute, crop plants have lost much of the genetic diversity present in their wild-type ancestors due to human cultivation. Ancient eDNA can help researchers understand how these ancestors adapted to historical climate changes, providing novel solutions for making modern crops more resilient as climate change continues to threaten global food security.

The AEGIS project represents a significant step forward in our understanding of genetic diversity and ecosystem resilience, offering hope for more sustainable and climate-resilient agricultural practices in the future.

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