Developing the Next Animal Genome Blueprint to Address Global Challenges in Animal Agriculture

October 28, 2017

Lakshmi Matukumalli a, Adele Turzillo a, Jeff Vallet b, Caird Rexroad III b
a National Institute of Food Agriculture, USDA
b Agricultural Research Service, USDA

Animal agriculture converts 6 billion tons of dry matter from agricultural waste into nutritious protein and minerals for human consumption annually . Increasing global population coupled with improved economic status of people from several developing nations is leading to higher demand for animal based protein. However, there are many challenges associated with meeting this demand. To increase production in a sustainable manner, animal agriculture must quickly adapt to a multitude of factors including climate change and reducing greenhouse gas emissions; antibiotic resistance and consequent restricted use of antibiotics; and increased focus on animal welfare leading to new housing systems and management systems. Research is urgently needed to address these challenges effectively and meet the rapidly increasing global demand for animal protein.

Genomics has provided new opportunities to improve agricultural animal production by accelerating animal breeding to achieve higher growth rates, reduce feed intake, improve fertility, and improve resistance to diseases. Moving forward, genomics will also enable knowledge of gene structure and function leading to better understanding of the genetic basis of observed phenotypes that can be further improved. The animal genome community has undertaken a momentous task of developing “Genome to Phenome: USDA Blueprint for Animal Genomics 2018 – 2027”, a document that will outline the science priorities to be addressed over the next decade. This effort will build on the successes of the previous report, “Blueprint for USDA Efforts in Agricultural Animal Genomics 2008­–2017”. In that report, community goals were clustered into three categories: (i) Science to Practice (ii) Discovery Science and (iii) Infrastructure. Here we present our perspectives on accomplishments from the previous blueprint, discuss the challenges that remain, and describe early stages of development for the new blueprint.

The animal genome community has met or exceeded the ambitious goals set forth in the Science to Practice category. Notable successes achieved in the past decade for most agricultural animals (including aquaculture species) are the development of high quality genome assemblies, high density SNP marker assays, quantitative genetics software (ssBLUP, Bayes A & B, GenSel), and implementation of genome selection. Genomic prediction and animal selection based on SNP genotyping are now widely practiced in several livestock industries, and genotyping assays have improved accuracy of predictions along with reduced generation intervals compared to using traditional, pedigree based approaches.

The ambitious goals set in the Discovery Science category were only partly realized. Analysis of large-scale genotype data using approaches such as genome-wide association, haplotype, and homozygosity analysis has led to identification of genomic regions associated with Mendelian and complex traits such as feed efficiency, fertility, product quality, fitness and disease resistance. However, further understanding of gene function and identification of causal mutations controlling complex traits will require high-quality genome annotations and extensive functional genomics research. The Functional Annotation of Animal Genomes (FAANG) global consortium is making headway in improving the annotation of agricultural animal genomes. Going forward, genomic predictions based on functional SNPs will be breed independent. New technologies such as automated sensors will enable measurement of more diverse phenotypes, improve accuracy, and facilitate real-time data acquisition at the farm level for uses in decision support systems. To address these and other knowledge gaps in Discovery Science, the primary focus of the new blueprint is on elucidation of the hidden connections between the genome and the phenome.

The challenges outlined in the Infrastructure category of the previous blueprint, such as education and training, resource populations, databases and genomic tools, are on-going. Employers in the livestock industries report a lack of trained quantitative geneticists whose skills are needed to run evaluations on large genotype datasets. Generation of huge amounts of genomics data (from genotyping and sequencing) and phenotyping data (collected in real-time from multiple sensors) has created complex and unprecedented challenges associated with data storage, analysis, curation, transfer, visualization, and information privacy. These big data issues continue to expand rapidly, and solutions are urgently needed. Except for large repositories such as National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI), there are very few databases dedicated to livestock genomics research.

Data sharing remains a challenge because of industry competition and lack of international support for open access to results of federally funded research. In the case of poultry and swine, most of the genetics currently in production today is owned by only a few companies. To tackle some of the cyberinfrastructure issues, the animal genomics community forged productive partnerships with the iPlant Collaborative (Cyverse). Other challenges related to infrastructure include severe reduction in the number of animal research facilities and genetically unique animal populations maintained by land-grant universities due to funding constraints, and the lack of robust methods for germplasm preservation and reproduction of animals representing diverse and/or unique genetics from stored germplasm in many livestock species.

Successes from the previous animal genome blueprint can be attributed to cooperation and collaborations among both domestic and international scientific communities. Some of these consortia are species specific (e.g., the Goat Genome Consortium) while others span all agricultural animal species (e.g., FAANG). The USDA-supported National Animal Genome Research Program (National Research Support Project or NRSP 8), played a major role in bringing all the communities together. Some of the notable international collaborations include the European Union (EU)-U.S. Animal Biotechnology Task Force, the U.S.-Canada Porcine Reproductive and Respiratory Syndrome (PRRS) Consortium, the 1000 Bull Genomes Consortium Project led by Australian researchers, and the FAANG global consortium.

To develop the new blueprint for animal genomics, we assembled a steering committee and a writing team comprised of eminent animal genome researchers. In the fall of 2017, a workshop was convened at USDA in Beltsville, MD to learn about major developments from allied fields, discuss the latest directions in various components of animal genomics, and to establish tangible goals for the next decade along with the challenges that need to be addressed to meet those goals. Workshop attendees agreed that the new blueprint needs to articulate the vision of the animal genomics community and serve as a tool to communicate this vision to federal agencies to drive science priorities and inform regulations. It also needs to challenge, inspire and attract the next generation of researchers, farmers, and industry leaders to develop novel solutions for animal agriculture. To effectively communicate with this broad diversity of stakeholders, the new animal genome blueprint needs to consider scientific goals in the context of their potential impacts on individual and societal values. Accordingly, the Genome to Phenome: USDA Blueprint for Animal Genomics 2018-2027 has four foundational goals. Goal 1, Providing Nutritious Food to a Growing Human Population, focuses on enabling global food security, improving rural economy and development, and increasing productivity of the U.S. agricultural enterprise to support increased exports of animal products. Goal 2, Increasing Animal Fitness and Improving Animal Welfare, addresses adaptation to local and regional conditions, biotic and abiotic stresses as associated with climate change, resistance to diseases and pests, and the role of the microbiome in fitness and health of animals. Goal 3, Improving Sustainability of Animal Agriculture, addresses ways to achieve environmental sustainability (e.g., reduced land and water usage, balanced use of antibiotics for animal health, and reduced greenhouse gas emissions), economic sustainability (e.g., affordability of animal products and farmer profitability), and sustaining germplasm and genetic diversity. Goal 4, Meeting Consumer Needs and Choices, considers cultural or traditional preferences, healthy choices (e.g., lean meat products), nutritional enhancements, and farming practices that optimize animal welfare while achieving high levels of production. To address these challenges effectively, society and the scientific community need to be mutually engaged with regard to the use of science based analysis of the benefits and risks of transformational technologies such as gene editing and other biotechnologies and be vigilant about misinformation.

The writing team is now in the process of developing the preliminary draft of the Genome to Phenome: USDA Blueprint for Animal Genomics 2018-2027. Topics being considered include precision management/precision selection; characterizing animal populations /germplasm preservation; bioinformatics and computational biology; genomic tools and resources; genome modifications for accelerated breeding; host-pathogen interactions; microbiome and metagenomics; high-throughput phenotyping; big data and cyberinfrastructure; genome annotation; functional genomics; and education and training. The preliminary draft of the new blueprint will be presented at the 2018 Plant and Animal Genome meeting in San Diego, CA. In the spring of 2018, we will be seeking comments from the animal sciences and other communities on this draft blueprint. Please send your comments/suggestions to