Ancient environmental DNA provides solutions for global food security challenges
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Researchers explore genetic diversity found in ancient environmental DNA to help modern agricultural practices
Summary
- Through human cultivation, crop plants have lost the genetic diversity that was present in their wild-type ancestors
- Ancient environmental DNA found in the soil can help researchers understand how the ancestors of crop plants adapted to historical climate change
- These insights can be used to develop new strategies to make modern crops more resilient and provide novel solutions as climate change continues to threaten global food security
Climate change is creating global challenges for agriculture, affecting crop yields and food security worldwide. Rising temperatures and increased frequency of extreme weather events like droughts and floods are making it harder for crops to grow.
In response to these challenges, researchers are looking to ancient environmental DNA (eDNA) to gain insights into how we can develop more resilient crops. By understanding how ancient plants adapted to past climate change, scientists can develop strategies to create modern crops that can better withstand adverse climate conditions. This could help ensure a stable food supply for the future.
What is ancient environmental DNA (eDNA)?
Ancient eDNA is genetic material extracted from natural sources such as soil, ice, and water, offering a window into the ecosystems of the past. Scientists collect samples that can be thousands or millions of years old and isolate DNA fragments left by ancient plants and animals. By sequencing these fragments and comparing them to the DNA in modern reference genomes, researchers can better understand past genetic diversity and learn how ancient species adapted to their environments.
A new research programme, Ancient Environmental Genomics Initiative for Sustainability (AEGIS), has been awarded £66 million over seven years by the Novo Nordisk Foundation and Wellcome. AEGIS aims to gain insights from ancient eDNA to understand ancient genetic diversity in plants, identify past climate adaptations, and apply these findings to modern crop breeding, including barley, wheat, and rice.
“Agricultural systems and the foods we grow have changed over millennia,” said John-Arne Røttingen, CEO, Wellcome. “We currently know very little about past ecosystems and what changes in biodiversity might have occurred as the environment changed. AEGIS hopes to build the evidence base needed to strengthen the resilience of food systems across the world in the face of future environmental changes.”
Led by evolutionary geneticist Eske Willerslev, AEGIS will bring together expertise from researchers at EMBL’s European Bioinformatics Institute (EMBL-EBI), University of Copenhagen, University of Cambridge, the Wellcome Sanger Institute, and other collaborators.
Ancient genetic diversity
The wild-type ancestors of crop plants boasted far greater genetic diversity compared to their modern day equivalents. This is because ancient plants evolved naturally over thousands of years, adapting to their environments without human interference. Unlike today’s crops, which are selectively bred for specific traits like higher yield or disease resistance, ancient plants developed a wide range of genetic variations that helped them survive in diverse and changing conditions.
“By employing ecosystem modelling, we can pinpoint which combinations of species led to the most durable ecosystems in the past,” said Eske Willerslev, Professor at the University of Copenhagen and 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.”
Data and bioinformatics tools for food security
The AEGIS programme will use advanced DNA sequencing and bioinformatics tools to analyse ancient eDNA. Tools and data generated as part of the project will be made publicly available to help crop breeders, ecologists, and conservation biologists around the world to improve food security.
“Making both the ancient environmental DNA data and modern-day reference genomes publicly available is one of the core principles of this project,” said Fergal Martin, Eukaryotic Annotation Team Leader at EMBL-EBI. “The knowledge we gain from studying ancient environmental DNA can be applied to helping develop more resilient crops and sustainable agricultural practices in the face of climate change.”
EMBL-EBI plays a multifaceted role in AEGIS by acting as both a repository and outlet for the data generated. Our scientists will also play a key role in analysing and processing these data.
- Raw genomic data will be stored and made openly available in the European Nucleotide Archive (ENA). The team will also develop new metadata standards for working with ancient eDNA.
- EMBL-EBI colleagues managing the Ensembl genome browser will work on annotating reference genomes to help identify what species the ancient eDNA samples correspond to.
- MGnify, EMBL-EBI’s database for metagenomics and microbiomes, will support the project by helping construct ancient metagenomes from the various environmental samples collected.
“In order for us to understand what is present in the samples collected from this work, we need to compare these data generated to modern reference genomes,” said Leanne Haggerty, Ensembl Genome Annotation Project Leader at EMBL-EBI. “To ensure we get a complete picture and extract as much information as possible from the environmental DNA samples, the Genome Annotation team at EMBL-EBI will be creating new annotations for genomes relevant to the project that will accelerate downstream data analysis and translational approaches.”
Additionally, EMBL-EBI researchers will create a public data portal to aid the visualisation and accessibility of the various data types collected from the project, including climate data, time points, sample types, genomic data, and reference genomes.
Find out more in the Novo Nordisk Foundation press release.
Funding
AEGIS is funded by the Novo Nordisk Foundation and Wellcome.