A pioneering project exploring ancient environmental DNA (eDNA) – genetic material left by plants, animals and microbes in soil sediments, ice and other resources up to two million years old – could help scientists to develop more climate-resilient crops by understanding how ecosystems have adapted to environmental changes in the past.
The Ancient Environmental Genomics Initiative for Sustainability (AEGIS) project has been awarded DKK 585 million ($85 million) over seven years, with the lion’s share ($72 million) coming from the Danish non-profit Novo Nordisk Foundation and the rest from UK charities Wellcome Trust.
By sequencing DNA fragments from samples around the world and comparing them to DNA in modern reference genomes, researchers can better understand past genetic diversity and learn how ancient species adapted to their environment. them, claims the leader of the research, evolutionary geneticist Professor Eske Willerslev from the University. of Copenhagen and the University of Cambridge.
While modern food crops are usually bred for traits such as higher yield or disease resistance, their wild-type ancestors had enormous genetic diversity, developing a wide range of genetic variations that helped them survive in harsh conditions. different and changing, he said.
“Using ecosystem modelling, we can determine which combinations of species led to the most stable ecosystems in the past. This knowledge can serve as a blueprint for creating climate-resilient food systems, improving both the crops we grow and the sustainability of the environments they grow in.”
“We had the human genome project… this is the planetary genome project”
The expectation is that AEGIS will demonstrate proof of concept in major crops such as barley, wheat and rice, say the researchers, who span disciplines including bioinformatics, AI/ML, microbial ecology, plant breeding and environmental genomics.
They will also create a public data portal featuring climate data, time points, sample types, genomic data and reference genomes collected during the project, said Novo Nordisk Foundation SVP Dr. Claus Felby. AgFunderNews.
“There is DNA everywhere. In a teaspoon of soil, you can see fragments of DNA from everything from bacteria and fungi to the largest mammals. So we had the human genome project… this is the planetary genome project; you can map everything to a given ecosystem. Every plant, tree, microorganism, every mammal that was there at a certain point in time and then over time, so you can see how that ecosystem evolved and adapted over time.”
‘I can say the initial results so far are breathtaking’
So how far are researchers looking?
“Anything between 10-50,000 years is very feasible,” Felby said. “And if you’re lucky, you can go back a lot further, I think that’s the record [for collecting usable DNA] it’s about 2.5 million years.”
He added: “I can say that the initial results so far are surprising. For example, we have found how rice adapted to a much wetter climate [in a part of China] about 8000 years ago. And you can see down to the single gene how the whole ecosystem adapted. You can also see how the microbiology of the soil has changed.”
According to Felby: “You can read the climate at the same time [as analyzing DNA fragments from a given period] looking at things like oxygen isotopes because they change with precipitation, temperature, etc. So then you can start designing the two things.
“But we’re not just looking at rice, or any particular plant. We are looking at the entire ecosystem. And if you see changes in everything plants, there is a pattern.”
‘Bioinformatics’
Looking back, he said: “We often speculate about what will happen [to our ecosystems] with climate change. But all these experiments have been done before [if you look back far enough]and now we can read the results, and it’s fascinating.
“But it also enables much more targeting and much faster [plant] breeding if you know where to look. It allows for polygenic traits, not just a single gene, but you see many genes changing at the same time. It’s like suddenly having a spaceship that would allow you to fly from one end of the solar system to the other in two hours.
“And now we have AI and machine learning and superfast computers, we can handle these huge data sets. It’s the big time of bioinformatics. So as part of this project we’re also building one of the supercomputers most powerful in the world here in Denmark with NVIDIA.”
Metagenomics — the study of genetic material recovered directly from environmental samples — has been around for a while, he said, “but this is the first time we’re doing it at the full ecosystem scale. We can map not only the effect of climate and climate change, but also what happens to an ecosystem when people come in, what happens when we develop agriculture, what happens when we start applying fertilizers and pesticides?”
According to the European Bioinformatics Institute of the European Molecular Biology Laboratory, based at the Wellcome Genome Campus near Cambridge, UK:
- Through human cultivation, agricultural plants have lost the genetic diversity that was present in their wild-type ancestors.
- Ancient environmental DNA found in soil may help researchers understand how crop plant ancestors adapted to historical climate changes
- This knowledge can be used to develop new strategies to make modern crops more resilient and provide new solutions as climate change continues to threaten global food security
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