Genomics–Powering Agriculture Breakthroughs:
Reference genome case studies from EBP-affiliated projects
The Earth BioGenome Project (EBP) and EBP-affiliated projects, have been advancing scientific breakthroughs around-the-world by generating an accessible database of Eukaryotic reference genomes across the Tree of Life, today reaching 3,541 assemblies (GoaT Live). Access to these reference genomes has accelerated population genomics studies, advanced research aimed at identifying pathogens and diseases, and opened doors for conservation actions to help stem the tide of biodiversity loss (as we covered in depth during our last issue of EBP Life). Today, we will focus on how our global networks of EBP-affiliated projects–and the genomes they generate–are powering breakthroughs in the agriculture and food industries.
Rice (Oryza sativa) is the most economically important crop in the world. The genus Oryza consists of two domesticated cultivar species, O. sativa and O. glaberrima. However, there are over 22 wild rice varieties, including Wild Red Rice (O. longistaminata), some of which are being considered for independent domestication. The O. longistaminata reference genome was sequenced by EBP-affiliate 10KP.
Agriculture is a critically important global industry, but the roadblocks that must be overcome to feed the growing global population can seem insurmountable. Today, farmers and agricultural experts work to suppress pathogens and diseases that threaten crops, eliminate pests and invasive insects without relying on harmful pesticides, and grow even more food–often with shorter optimal growing seasons. Overcoming these obstacles is daunting, but EBP-affiliated groups are offering a lifeline; by harnessing the power of genomics, scientists can decode the map of these critical global crops and sometimes improve the code to help all humanity.
Decoding Crops to Increase Yields and Breed Disease Resistance
EBP-affiliated 10,000 Plants Project (10KP) has generated hundreds of plant reference genomes, including the widely grown agricultural crop: wild red rice (Oryza longistaminata). The downstream work leveraging the 10KP wild rice reference genome revealed that underground stems are capable of regeneration; the genome helped identify key genes that allowed the plant to regrow annually without requiring replanting (Lian et al., 2024). Identifying these critical regeneration genes enabled “breeders to design crops with increased yields, climate resilience, and perennial traits–slashing labor and environmental impact” costs of rice cultivation (personal communication, Dr. Sahu Sunilkumar). 10KP also assembled a high-quality reference genome for maize, which was recently used to generate a detailed transcriptome map of developing corn ears (Wang et al., 2024). This work resulted in the identification of critical genes, such as ZmMADS8/14, which controls flower formation and increases grain yield (Wang et al., 2024). This work highlights how reference genomes can inform agricultural and breeding breakthroughs that enhance crop yields and benefit the larger agrio-economy. This work is already enabling precision breeding aimed at enhancing the ear size, kernel number, and stress adaptation of corn. “By bridging spatial omics with genomics, these studies decode the molecular blueprints of crop development. This leap in precision farming promises hardier harvests and a greener future for agriculture” (Dr Sahu Sunilkumar). Another 10KP reference genome, this time for the common lettuce crop species, Lactuca sativa, was critical to the downstream research that identified major resistance clusters (MRCs), which confer resistance to the widespread disease: downy mildew (Reyes-Chin-Wo et al. 2017). These findings advanced the targeted breeding for disease-resistant lettuce varieties, improving yields and reducing crop losses (Reyes-Chin-Wo et al. 2017).
Hyacinth Macaw (Anodorhynchus hyacinthinus) is currently found in three main regions of Brazil, is listed as a vulnerable species, and its population size is decreasing according to the IUCN Red List (BirdLife International, 2016). This reference genome was sequenced by the Vertebrate Genomes Project.
Reference Genomes to inform breeding programs
Other EBP-affiliated projects have had similar success at coupling conservation genomics with population management in order to identify individuals most likely to enhance the gene pool of threatened populations. Habitat fragmentation, primarily due to the bisecting of habitats with cities or freeways, can be one major hurdle that wild populations need to overcome in order to maintain sufficient genetic diversity throughout the population. The Vertebrate Genomes Project is an EBP-affiliated project that has been working tirelessly to generate high-quality reference genomes for hundreds of vertebrate species (Rhie et al., 2021), including the Hyacinth Macaw (Anodorhynchus hyacinthinus) (pictured). The macaw reference genome was then used by another EBP-affiliated project–the Genomics of the Brazilian Biodiversity–for a population study, where researchers provided a first characterization of population structure, diversity, inbreeding, and gene flow of the remaining macaw population (Vilaça, et al., 2024). The project leaders hope that population studies like this one will inform ex-situ breeding programs to benefit the long-term survival of the species (personal communication, Alexandre Aleixo). A similar effort is also underway for the neotropic Harpy Eagle (Harpia harpyja), which is listed as a vulnerable population with notedly low genetic diversity (Banhos et al., 2016). The Genomics of Brazilian Biodiversity is currently working on a large-scale population genomics study, leveraging another high-quality reference genome–sequenced by the Vertebrate Genomes Project–into an invaluable resource informing captive breeding programs that are focused on increasing the genetic diversity of the remaining Harpy Eagle population (Canesin et al., 2024).
Vancouver Island marmot (Marmota vancouverensis) is a critically endangered species (Roach, 2017) and the only known wild populations are found on Vancouver Island British Columbia, Canada. This reference genome was sequenced by the Canadian BioGenome Project in collaboration with CanSeq150.
Reference Genomes to delay the Threat of Extinction
Around the globe, the human decimation of populations of plants and animals, to the point of near extinction, is a recurring theme. Today, conservation genomics groups are targeting some of these species for human intervention. The critically endangered Black Abalone (Haliotis cracherodii) was threatened by a combination of overhunting, pollution in the intertidal zones, and the onset of a highly virulent bacterial disease (Wooldridge et al., 2024). Now, groups such as the California Conservation Genomics Project are utilizing genomic insights to assess the genetic diversity of the remaining population and investigate the connectivity between these Abalone populations to propose a comprehensive management plan for the Black Abalone (Fiedler et al., 2022; Wooldridge et al., 2024).
Detailed genomes can provide valuable insights into the stability of very small populations; and they can identify signs of poor genetic health in species that might more accurately predict species extinction (Paez et al., 2024). For example, in 2003 fewer than 30 wild Vancouver Island marmots (Marmota vancouverensis) were found (pictured) and the species was then classified as critically endangered by IUCN, first in 2008, then subsequently in 2013, and again in 2017 (Nagorsen et al., 2008 and 2013; Roach, 2017). Today, after extensive initial conservation efforts, the Vancouver Island marmot population has started to demonstrate significant recovery with the wild population reaching a record of 381 marmots in 2024 (MRFAR, 2024; Brougham, 2025). However ongoing genomics research has indicated that the marmot population has very low genetic diversity (Barrett et al. 2022), which can make it challenging to identify unique genetic fingerprints among individuals. The future goal of this research is to use the newly assembled (soon to be released)—chromosome level reference genome—produced by Canadian BioGenome Project, in collaboration with CanSeq150, to compare DNA from marmots and select mating pairs based on genetic dissimilarity to protect the remaining genetic diversity of the Vancouver Island marmot population. Without such efforts, the population risks being unable to cope with future threats such as emerging diseases and climate change.
Southern Corroboree Frog (Pseudophryne corroboree) has wild populations currently found only in Kosciuszko National Park in New South Wales, Australia. It is listed as a critically endangered species and its population size is decreasing according to the IUCN Red List (IUCN SSC Amphibian Specialist Group, 2022). This reference genome was sequenced by the Vertebrate Genomes Project.
Reference Genomes to Assess Susceptibility and Resistance to Diseases
Another aspect of conservation genomics is focused on identifying the genetic factors controlling the degree of susceptibility or resistance to diseases of members of a given population. For example, Chytridiomycosis is an infectious disease that poses a significant extinction threat to many amphibians, including the critically endangered Southern Corroboree Frog (Pseudophryne corroboree) (pictured). The Corroboree Frog reference genome, generated by the Vertebrate Genomes Project, was later used by the Amphibian Genomics Consortium to advance downstream population genomics studies (Kosch et al., 2024). This study identified subsets of the Southern Corroboree Frog population with increased genetic resistance to the disease (Davidson et al., 2024). These findings can directly inform selective breeding to improve genetic resilience to disease in vulnerable populations (Davidson et al., 2024) and provide a framework for similar conservation attempts in other threatened amphibian groups. The continued efforts by the Amphibian Genomics Consortium will be instrumental in translating the Corroboree Frog genome into actionable conservation strategies, such as targeted genetic interventions, selective breeding, and genetic engineering for chytrid resistance (Kosch et al., 2022). Similarly, the Bat1K group has been working hard to sequence several threatened bat species, among them the Greater mouse-eared bat (Myotis myotis) (Jebb et al., 2020), which is a species threatened by a fungal infection called the white-nose syndrome (Twort et al., 2024). In this case, researchers have been able to utilize the Bat1K reference genome to embark on population studies to tease apart the factors contributing to susceptibility or resistance to this fungal infection at a genomic level (Twort et al., 2024). Moving forward, the Bat1K working groups are putting strong efforts into informing conservation strategies by prioritizing vulnerable or threatened species for full genome sequencing, laying down a strong genomic foundation for conservation work to come.
Whale Shark (Rhincodon typus) has a circumtropical distribution, is listed as an endangered species, and its population size is decreasing according to the IUCN Red List (Pierce and Norman, 2016). This reference genome was sequenced by Squalomix.
Conservation Genomics Framework–paving the way forward
As EBP-affiliated projects continue to generate new genomes the clear benefit to conservation genomics efforts will deepen. Groups such as EBP-Norway have released genomes from difficult-to-sample Arctic species like the Snowy Owl (Bubo scandiacus) and Atlantic Puffin (Fratercula arctica). Hopefully, conservation work around these vulnerable and decreasing bird populations will be strengthened in the future by the strong genomic foundation these reference genomes provide.
Squalomix and Darwin Tree of Life have sequenced the Whale Shark (pictured) and the Basking Shark, respectively, both of which are endangered and decreasing according to their IUCN Red List abundance and distributions (IUCN, 2024). In Brazil, the endangered Pink river dolphin or Boutu (Inia geoffrensis), was sequenced by the Cetaceans Genome Project and is currently in the process of informing better conservation efforts around this threatened dolphin species. In Europe, the White-Tailed Sea Eagle (Haliaeetus albicilla), the U.K.’s largest bird of prey, was recently sequenced during a collaboration between Darwin Tree of Life and European Reference Genome Atlas (Pálsson et al., 2024). This reference genome will enable scientists to monitor reintroductions of this iconic species and better track their migration range (Pálsson et al., 2024). Ongoing work throughout Africa by the African BioGenome Project and others, will continue to promote the conservation of at-risk African biodiversity, and we eagerly look forward to more conservation insights from the African BioGenome Project as the framework for genomics in Africa by African experts continues to gain traction (Sharaf et al., 2024).
Today, we are facing a global crisis in terms of biodiversity loss in what scientists agree is the 6th global extinction event. However, as EBP scientists around the globe continue to demonstrate, we can more rapidly bridge the gap between genomics and conservation actions when working together as a global community. Together we have the ability to advance technologies allowing for more affordable and widespread full genome sequencing advantages. And together the scientific community can inform and potentially direct conservation policies to better protect our global diversity. As EBP-affiliated projects continue genome sequencing species across the Tree of Life, we expect to see many more examples of how these high-quality reference genomes can directly benefit and inform conservation genomics.
Written by: Anna Bramucci (Earth BioGenome Project: Genomic Insights Coordinator)
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