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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"3 Animal Agriculture." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Below is the uncorrected machine-read text of this chapter, intended to provide our own search engines and external engines with highly rich, chapter-representative searchable text of each book. Because it is UNCORRECTED material, please consider the following text as a useful but insufficient proxy for the authoritative book pages.

3 Animal Agriculture 1. INTRODUCTION Animal products are a primary source of protein and key nutrients in American diets (Bentley, 2017). In addition, livestock and poultry production account for approximately $100 billion per year in agricultural cash receipts (USDA-ERS, 2018a). In the United States, most food animal production (meat, fish, milk, eggs) is accomplished through an intensive rearing system that reflects decades of improve- ments in production efficiencies made possible by research and development. Genetic improvement and adoption of optimized nutritional programs, along with innovations to maintain and improve animal health status, have reduced the costs of production, lowered prices for consumers, decreased resources used (resulting in lower greenhouse gas [GHG] emission intensities per unit of production), and increased the competitiveness of American products internationally, benefiting both local and national economies (Havenstein et al., 2003; Capper et al., 2009; Capper, 2011; Gerber et al., 2011; Tokach et al., 2016). For example, the GHG emissions associated with the production of a glass of milk in the United States in 1977 were one-third of what they were in 1944 (Capper et al., 2009); and today, livestock sources (includ- ing enteric fermentation and manure) account for about 3.9 percent of U.S. anthropogenic GHG emissions expressed as carbon dioxide equivalents (EPA, 2016). Over the past 15 years, the U.S. livestock industry has gained greater access to international markets with a growing share of its production destined for for- eign markets. In 2016, exports accounted for 23 percent of pork produced, nearly 20 percent for broiler meat, 14 percent for turkey, and 11 percent for beef (see Figure 3-1). This brings in more than $25 billion annually in export sales (USDA-ERS, 2018b) to the national economy. FIGURE 3-1 U.S. meat exports (beef and veal, pork, and poultry) as a share of domestic production from 1976- 2018. NOTE: 1/ Carcass-weight equivalent. SOURCE: USDA, Foreign Agricultural Service, Production, Supply, and Distribution database. 36 Prepublication Copy

Animal Agriculture 2. CHALLENGES The science that produced advances in animal agricultural productivity and efficiency in the past will need to be accelerated and expanded in scope in the decade ahead. Recent analyses have warned that the agricultural production worldwide will have collective difficulty in meeting global demand for food in 2050 as a consequence of the growing world population, with demands increasing in the range of 59-98 percent (Ingram et al., 2010; Valin et al, 2014; UN, 2015). The production required to meet that demand will occur within the United States and across a global landscape, including places with different envi- ronments, production systems, and animal breeds. As a world leader in efficient animal production, it is in the best interests of the United States to continue research in approaches to efficiently address the world’s demand for animal products. There are several compelling reasons for investing in animal agricultural research to meet this chal- lenge. First, the increasing global demand for animal-source food will impact domestic prices, and there- fore continuing to augment efficiencies is essential to keep food affordable for U.S. consumers. Although it is beyond the scope of this report to comment on the American landscape of chronic diseases related to dietary choices, hunger and hidden hunger remain problematic in the developing world. Cognitive stunt- ing due to lack of micronutrients, which are bioavailable predominantly in animal-source foods, is a ma- jor problem that results in whole generations of children who cannot reach their cerebral potential and consequently a corresponding drop in country gross domestic product potential (Galasso and Wagstaff, 2018). Despite western-centric concerns that overconsumption of meat is detrimental to health in the de- veloped world, the situation is the reverse for the world’s poorest as the underconsumption of animal- source food is detrimental to health (James and Palmer, 2015; Beal et al., 2017). It is this latter population that, once given the economic liberty to choose their foodstuffs, will select more animal-source foods and create a larger global demand. Second, with increasing efficiencies and intensity of production, animals need to be reared in systems that promote animal welfare, minimize GHG emissions and pollution, and decrease the potential of foodborne illness. Third, animal diseases continue to move throughout the world which at a minimum decrease productivity, while transboundary animal diseases (which are high conse- quence contagious animal diseases) can bankrupt animal industries in the United States and globally. 2.1 Increased Demand for Animal Protein Population growth combined with rising incomes in the developing world will result in the need to increase animal production to meet domestic and export market demands. Animal protein production has made impressive advances in the past 50 years, but more will be required to meet the projected demands of a growing global population (Ingram et al., 2010; UN DESA, 2015). On a per capita basis, consump- tion of animal-source foods (defined as meat, eggs, dairy, and fish) has steadily increased in the United States and is projected to continue to increase globally (NOAA, 2015; USDA-ERS, 2018a). As low- income countries become emerging economies, consumption of animal-source foods will increase, and so the “bottom billion” will begin to get a share of nutrients that promotes better health by supplying ade- quate protein and nutrients through animal-source foods. Figure 3-2 shows the levels of animal products produced globally from 1970 to present, with numbers projected to 2030. Predictions are that demand for animal-derived food in 2050 could be 70 percent higher than 2005 levels, with the demand for beef and pork increasing by as much as 66 percent and 43 percent, respectively (Alexandratos and Bruinsma, 2012). The highest growth is expected for poultry meat at 121 percent growth, especially in developing countries, with demand for eggs potentially increasing by 65 percent (Mottet and Tempio, 2017). As a result, livestock numbers are expected to continue to increase significantly, although at lower rates than in past years (Alexandratos and Bruinsma, 2012). Prepublication Copy 37

Science Breakthroughs to Advance Food and Agricultural Research by 2030 FIGURE 3-2 Global milk, fish, broiler, pork, beef, and egg production since 1970 and projected to 2030. SOURCE: Alexandratos and Bruinsma, 2012. With respect to the contribution of fish to 2030 animal protein demands, the capture fisheries supply is unlikely to increase as stocks of key species are already fully harvested, and ocean acidification from cumu- lative GHG emissions over several decades is leading to biodiversity loss and threatening single-cell phyto- plankton—the base of marine food chains that account for more than 50 percent of the photosynthesis and oxygen production on earth. Eutrophication and algal blooms resulting from the widespread use and run-off of nitrogen and phosphorous-based fertilizers into lakes, rivers, and coastal estuaries are further depleting aquatic plant and animal species, many of which provide food for humans (Canfield et al., 2010; Carpenter, 1998). Aquaculture is therefore expected to dominate growth in the fish sector. Fishery production is ex- pected to expand by more than 30 Mt by 2030, 95 percent of which will come from developing countries. China is likely to have a significant influence on global fish markets, accounting for 37 percent of total fish production in 2030. Assumptions suggest that steady improvements in feed and feeding efficiency within the aquaculture sector will contribute to its growth (The World Bank, 2013), and recirculating aq- uaculture systems could contribute to more efficient water and nutrient use (see Chapter 6 for further dis- cussion of Controlled Environments). Food security in future years will surely depend on increasing the food-provisioning capacity of aquatic as well as terrestrial ecosystems. 2.2 Animal Diseases Animal diseases are responsible for an average loss of more than 20 percent of animal production worldwide and can have major economic impacts (OIE, 2018). Export partners can justifiably block im- ports and issue trade sanctions if zoonotic or transboundary animal diseases, such as highly pathogenic avian influenza, occur in the United States. Blocked exports can cause a glut of the commodity for do- mestic consumption, resulting in ripple effects in the economy, from decreased prices for consumers to very negative farm-level impacts in the rural economy. Introduction of foot-and-mouth disease into the United States remains a constant threat, with estimates of the economic burden ranging from $37 billion to $228 billion (Oladosu et al., 2013). Box 3-1 provides two examples in which recent cases of high- consequence animal diseases had major economic impacts. Even endemic diseases, such as bovine respir- atory disease—the leading cause of morbidity and mortality in cattle that is caused by a variety of viruses and bacteria—can greatly hamper an animal’s productivity, may result in death, and is estimated to cost the cattle industry approximately $3 billion annually (Griffin, 1997). 38 Prepublication Copy

Animal Agriculture BOX 3-1 Recent Cases of Animal Diseases and Their Economic Impact Highly pathogenic avian influenza entered the United States through migratory birds and caused an extensive outbreak in the Midwest that extended through mid-2015. USDA undertook the most ag- gressive foreign animal disease control efforts ever by depopulating 7.5 million turkeys and 42 million chickens in an effort that cost U.S. taxpayers $879 million. The decision to eradicate was made be- cause of the costs associated with not controlling the disease, which, through simulations, would have averaged $1.53 billion. Bovine spongiform encephalopathy (BSE) was found in late 2003 in one cow for the first time in the United States. This single case of “mad cow disease” prompted massive closure of major U.S. beef export markets, with 80 percent of exports blocked for the following year, costing the industry between $3.2 billion and $4.7 billion. SOURCES: Coffey et al., 2005; USDA-APHIS, 2016. 2.3 Sustainability in Animal Agriculture There is increased public interest in environmental, economic, and animal welfare sustainability questions related to animal agriculture. Unfortunately, there are no clearly defined objective measures for all of the sustainability questions related to animal agriculture, which in itself represents a notable area for investigation. Sustainability goals are sometimes in conflict, and managing a system for optimal environ- mental stewardship may clash with economic or animal welfare objectives (Llonch et al., 2017). Although extensive systems might appear to be less taxing on the environment in relation to resource use, waste treatment, and GHG emissions, scientific analysis has shown that intensive systems can actually reduce these outputs (Gerber et al., 2011; Capper, 2014). Conversion of animal feed into edible animal products is always an efficiency concern in animal ag- riculture. And this is a particular concern in cases where animal feed may contain human-edible products, or animal feed is grown on land suitable for growing human food (Mottet et al., 2017). Approximately one-third of total cereal production is used to feed animals, and this is expected to rise further by 2030 (Makkar, 2017; Mottet et al., 2017). Currently 86 percent of global livestock feed is made of materials that are not consumed by humans, and ruminants play an important role in this in that they are uniquely able to convert human-inedible forages (e.g., leaves and grass) into high-quality protein and a variety of micronutrients (Mottet et al., 2017). Opportunities exist to increase this human-inedible proportion fur- ther, thereby decreasing the use of food-grade grains in both monogastric and ruminant diets. Sustainability also encompasses animal welfare, and this is also a key component regarding con- sumer concerns. Unfortunately, there are few rigorous assessment criteria in use for scoring of animal welfare (Llonch et al., 2016). One definition states that animal welfare is “[when] animals are healthy and they have what they want” (Dawkins, 2017), while another definition from the World Organisation for Animal Health states that animal welfare is “[When] an animal is in a good state of welfare if (as indicat- ed by scientific evidence) it is healthy, comfortable, well nourished, safe, able to express innate behavior, and if it is not suffering from unpleasant states such as pain, fear, and distress” (Terrestrial Animal Health Code, OIE, Article 7.1.1). The Terrestrial Animal Health Code (the international standard for animal pro- duction) further outlines aspects of animal welfare for all of the major livestock species and includes ob- jective assessments of behavior, morbidity, mortality, and reproductive performance, which can be used for taking into account animal well-being, thereby serving as the “scientific evidence” stated in the defini- tion. However, there are few objective standards to assess many aspects of animal welfare, making quan- titative evaluations problematic. To leave sustainability goal evaluations to the political process or public opinion potentially exposes the process to subjective interpretation and political pressure from special-interest groups. There is a need Prepublication Copy 39

Science Breakthroughs to Advance Food and Agricultural Research by 2030 to objectively evaluate the full sustainability implications of different agricultural systems. This would give the scientific community an opportunity to develop measures of product- and system-level perfor- mance to assess and compare the ability of different systems to sustainably meet the needs of both human and animal populations (Siegford et al., 2008). Likewise the holistic implications of utilizing mixed popu- lations of animals that feed upon wild grasses need to be objectively compared to the metrics associated with existing US production systems to understand the food safety, environmental, animal health and well-being, worker safety and health, ranch viability, and food affordability tradeoffs associated with these differing production systems. An example of such rigorous assessment is one conducted by the Coalition for Sustainable Egg Supply (CSES), which formed to evaluate the sustainability of several laying-hen housing systems (CSES, 2018). The goal of the CSES is to provide scientifically based information on trade-offs related to varying housing systems by conducting holistic comparative research. CSES members represented vari- ous stakeholders, including food retailer companies, egg suppliers, animal welfare scientists, academic institutions, and government (USDA Agricultural Research Service) and nongovernment organizations. This $6 million study examined “various laying hen housing systems and potential impacts on food safe- ty, the environment, hen health and well-being, worker health and safety and food affordability, providing food system stakeholders with science-based information on sustainability factors to guide informed pro- duction and purchasing decisions” (Mench et al., 2016). The study results demonstrated the complexity of addressing sustainability problems, as there were positive and negative aspects associated with each housing system that resulted in numerous trade-offs. Although the study was largely undertaken due to public pressure for cage-free hens because of animal welfare concerns, the cage-free system actually resulted in the highest rates of hen mortality and the worst indoor air quality, thus creating unexpected risks for both the animals and the workers. Assessing the efficiency of livestock production systems likewise requires a holistic approach (Makkar, 2017). For example, Schader and colleagues (2015) explored the possibility of feeding animals only on human-inedible feedstuffs and found that it decreased the availability of livestock products glob- ally by 53 percent, with a 91 percent decrease in meat from poultry and swine, and a 90 percent decrease in egg production compared with current levels of consumption. This underscores the important role of ruminants as consumers of human-inedible feedstuffs. However, the trade-off associated with removing high-energy concentrate feed from animal diets is that it increases the emission intensity of GHG produc- tion per unit of animal product. Effective science communication of the results and trade-offs revealed in such studies will be essen- tial to provide a factual basis for tackling sustainability issues in animal agriculture. Public opinion is not necessarily formed in response to objective scientific evidence, and especially when the issue involves ethical aspects, such as humane treatment of animals, the issue becomes much more complex, and simply reading or hearing the facts is not enough to sway majority outlook (Croney et al., 2012). 3. RESEARCH OPPORTUNITIES Significant knowledge gaps and research opportunities exist in each of the sections below. Address- ing increased animal protein demand sustainably will require advancing basic knowledge in core disci- plines of animal science and will also entail considerable cross-disciplinary contributions. 3.1 Animal Genetics There are new, hitherto unforeseen opportunities to accelerate genetic improvement of livestock by incorporating genomic information, advanced reproductive technologies, and precision breeding methods into conventional breeding and selection programs. Genomic selection alone has doubled the rate of ge- netic gain in the U.S. dairy industry since its introduction in 2009. The past decade has seen an explosion of genotyping and resequencing data that are currently being used to develop genomically-enhanced 40 Prepublication Copy

Animal Agriculture breeding approaches in several industries (Weller et al., 2017). A large of number of omics datasets (e.g., genomics, proteomics, metabolomics, transcriptomics) have been and are being produced by researchers. The challenge now is to combine and analyze these big data to produce basic and applied knowledge on how best to genetically improve livestock populations for traits of interest. Hickey and colleagues (2017) propose that genomic selection presents a unifying approach to bring plant and animal breeders together to deliver innovative “step changes” to the rate of genetic gain (see Figure 3-3). Sequence data from thousands of phenotyped animals may help uncover important quantitative trait polymorphisms that can be used to improve genomic predictions (VanRaden et al., 2017) or that can be introduced into breeds using genome-editing tools (Proudfoot and Burkard, 2017; Ruan et al., 2017). Us- ing biological information on key single nucleotide polymorphism (SNP) loci obtained from sequencing projects, single base modifications can be precisely introduced into animal genomes to obtain a genotype with desired traits. Novel breeding schemes involving multiple in vitro rounds of genomic selection, gene editing, gam- ete production, and fertilization could reduce by orders of magnitude both the generation interval and the genetic lag between nucleus and commercial populations. Such schemes can be envisioned based on ex- citing developments in embryonic stem cell technologies (Bogliotti et al., 2018) and surrogate sire/dam technology (Park et al., 2017; Taylor et al., 2017). This technology is poised to enable the development of a population of commercial animals that lack their own germline cells, but which carry transplanted goni- al stem cells delivering the genetics from elite donor seedstock animals (Gottardo et al., 2017). FIGURE 3-3 Capturing new opportunities to accelerate the pace of genetic gain based on efficient and targeted ac- cess to genetic diversity, coordinated phenotyping across environments, cost-effective sequencing, genomic predic- tion, and genome editing. NOTE: GEBV = genomic estimated breeding value. SOURCE: Hickey et al., 2017. Prepublication Copy 41

Science Breakthroughs to Advance Food and Agricultural Research by 2030 The main scientific challenge remains in how best to harmonize, combine, analyze, and utilize phe- notypes, environmental, and omics information in conjunction with gene editing and advanced reproduc- tive technologies. The goal would be a 10-fold increase in the rate of genetic improvement in livestock, poultry, and aquaculture populations by 2030. Additionally, there is a need to develop objective selection criteria to enable the incorporation of important components of sustainability, such as increased fertility, improved feed efficiency, functionality, and decreased susceptibility to disease into breeding objectives and animal breeding programs. 3.2 Animal Nutrition Opportunities for research and progress abound for animal nutrition through the growing field of precision feeding and exploration of the microbiome, as well as through examination and implementation of novel feedstuffs. Precision feeding entails offering feed to each animal that is exactly tailored to the animal’s needs. Currently, rations are formulated to be the least-cost ration that provides essential dietary requirements, which may result in overfeeding certain components such as protein. A recent paper exam- ined the use of precision feeding stations to increase broiler flock uniformity by sequentially feeding chickens according to their individual body weight and needs (Zuidhof et al., 2017). Future innovations might address how feed rations can be more precisely formulated to maximize utilization efficiency and minimize negative environmental impact, and how technology could be used to more precisely deliver feed to animals on an individualized basis (Gerber et al., 2013). Also, the microbiome of animals is just beginning to be explored (O’Callaghan et al., 2016). Nutrient formulations could be combined with more information about the microbiome and its interactions with nutrients. As the human microbiome and as- sociated research reveal connections between microbes and disease susceptibility, similar understandings will undoubtedly emerge concerning animals. Finding novel feedstuffs for livestock could markedly enhance sustainability, as 14 percent of the global feedstock feed ration consists of human-edible feed materials (Mottet et al., 2017). Use of human- inedible resources—such as slaughterhouse and food wastes, by-products of biofuel production, leaf meals, seaweeds, and insect meals—could replace human-edible components of livestock diets (Rumpold and Schlüter, 2013; Makkar, 2017). Diverting food loss and waste to animal feed represents an obvious opportunity to replace grain-based feed with human-inedible resources. Plant breeding could also increase livestock production efficiency by (1) raising the feed crop yield per hectare (e.g., improved drought tol- erance or nitrogen-use efficiency) and (2) improving the rate of feed conversion efficiency of vegetable calories into animal calories (e.g., altered digestibility or crop composition) such as reduced-lignin alfalfa (Van Eenennaam and Young, 2014). This will involve collaborations between plant breeders and animal nutritionists (see Chapter 2). New electronic and digital tools may also enable better management of and feed conversion in ru- minants grazing on grasslands and range. Virtual fences are a new foray into this area and could improve grassland productivity and protect sensitive areas from overgrazing (Umstatter, 2011). 3.3 Animal Health There are multiple knowledge gaps in animal health and thus many research areas in need of explo- ration. Decreased production and death from disease are currently huge inefficiencies in the system, be- cause nutrients and resources put into animal growth and well-being are minimized or completely lost. Vaccine research to date has primarily focused on finding the right protein or engineered surrogate that will prompt a protective immune response when the animal encounters the specific pathogen in the field. Reverse vaccinology offers an exciting opportunity to use advances in genomics to predict good antigens for vaccine development and is currently being investigated by many researchers. For example, researchers have used reverse vaccinology to predict immunoprotective proteins for a tick vaccine (Andreotti et al., 2018) and leptospirosis vaccine candidates (Dellagostin et al., 2017). This approach was also used to identi- fy vaccine candidates for a Campylobacter vaccine for broilers, an important food safety concern (Meunier 42 Prepublication Copy

Animal Agriculture et al., 2017). More targeted and individual-specific immune interventions based on multiple omics data may be the next breakthrough. When a pathogen enters the body, there is a suite of upregulated host genes which informs the corre- sponding immune response, in a kind of signature response as part of the innate immune system. In this constellation of cascading cytokines, it is now known that some of these signaling molecules serve to pro- tect the host and others may be triggered specifically by microbial genes to aid the organism’s invasion (Davidson et al., 2015). Knowledge and dissection of this full complement of mediators in the innate im- mune response could serve to effectively inform better vaccine development that would be tailored for each invading agent. Such a schema could allow for earlier abrogation of the invading agent, rather than waiting for the acquired immune response to kick in, such as is induced by conventional vaccines. If an infection cannot be prevented in an animal—in other words, there is no vaccine or it is not economically feasible to vaccinate—the next best tactic is to detect the illness at first blush. In most ani- mal production facilities, animals are viewed every day by farmworkers and/or owners and are only seen by health professionals during periodic checks or when called to a farm for an assessment. When animals become visibly ill, they are already in the disease phase and are actively shedding the culpable microbes to their herd- or flock-mates. It would be ideal to be able to detect animals at first infection when they are in the incubation or prodromic stage (the stage of infection when symptoms begin to emerge but prior to full-blown disease becoming evident). Animals recognized at this stage could be removed from their co- horts and potential transmission drastically reduced. An additional problem with animal health is diagnosing the disease so that appropriate intervention strategies can be introduced. In most cases, this involves first actually realizing that the animal is sick, then perhaps contacting an animal health professional for a visit, taking appropriate samples that will prove useful for diagnosing the specific disease occurring, and then relying on the local laboratory to run the appropriate tests. Current technologies, such as next-generation sequencing and MinION (a hand-held DNA sequencer) are currently expensive and require high levels of expertise. With further research, these technologies could be converted into use at the penside rather than the laboratory. It is now possible to purify DNA from plants, animals, and microbes in under 30 seconds under field conditions (Zou et al., 2017). There is also ongoing work in the use of pen-side sensitive and specific biosensing systems for detecting animal diseases at the earliest moment, even before clinical signs are obvious (Vidic et al., 2017). The possibility of diagnosing a wide array of diseases while standing beside the animal could re- move many time-consuming steps to diagnosis, allowing for much earlier and targeted therapies or con- trol measures, thereby minimizing loses, animal suffering, and therapeutic antibiotic usage. 3.4 Animal Facility Design and Management for Sustainability and Animal Welfare There are major research opportunities to study facility design and management for improving ani- mal welfare and decreasing negative environmental consequences. Landmark studies by Dr. Temple Grandin (2012) provided insight into processing-facility design to reduce animal stress while at the same time improving worker safety. As a result of Grandin’s work, more than half of cattle slaughtered in the United States are processed through a curved, single-file chute, using nonslip flooring and adaptive light- ing, resulting in more relaxed and calmer cattle walking to the slaughter site (Economist, 2015). Opportu- nities exist to improve animal facility design by integrating sensors and electronic monitoring of animal health and well-being. For layer hens, extensive research comparing different housing systems was conducted by CSES (previously described in this chapter). The study examined multiple parameters, including behavior, productivity, food safety, efficiency, and worker safety. This type of large holistic study provides the evi- dence base for system comparisons. Such research can be the impetus for research on how modification of facility design can improve welfare outcomes (Stratmann et al., 2015). Rigorous, objective assessments of animal welfare need to be developed and applied. To date, few studies have examined animals’ stress levels and/or senses of comfort and security. While the OIE has developed a robust set of parameters, most involve subjective behavioral or whole-animal observations. Prepublication Copy 43

Science Breakthroughs to Advance Food and Agricultural Research by 2030 In some parts of the world, there has been progress in measuring internal biomarkers as a proxy for ani- mal well-being. For example, cortisol can be quantitated noninvasively through saliva, milk, or hair (Casal et al., 2017; Tallo-Parra et al., 2017). The use of reliable biomarkers could help determine what types of housing facilities are best suited for the animals; facility design professionals could combine this information with their understanding of efficiency of operations, disinfection procedures, and worker safety and health. Animal waste needs to be handled regardless of the animal housing system. Urine, feces, bedding material, and wash water, are products of animal agriculture and are often destined for the waste stream. Designing programs that utilize or transform the waste into useful products are big opportunities for the research community. Some limited examples of successful research in this field include turning manure into solid paving materials, and it is becoming increasingly frequent to capture methane from manure for generating electricity (Fini et al., 2001; MacDonald et al., 2009). Continuing to find sustainable uses for animal wastes is a huge area of opportunity. 3.5 Precision Livestock Farming Precision livestock farming (PLF) is a novel and growing technology with the aim of enhancing ani- mal health and productivity by applying sensor and remote technologies. The use of PLF can enable indi- vidual-animal-targeted nutrition, health and welfare (Rutter, 2012). Daniel Berckmans states that the objec- tive of PLF is “to create a management system based on continuous automatic real-time monitoring and control of production/reproduction, animal health and welfare, and the environmental impact of livestock production” (Berckmans, 2014, p. 190). It is markedly multidisciplinary, requiring coordination among farmers, animal scientists, veterinarians, molecular biologists, immunologists, bioengineers, data scientists, and information technologists. Monitoring can be done remotely through sounds, sights, animal movements, and estimations of environmental parameters such as temperature, humidity, or air particulates. Recent publications outline how PLF might be used in livestock systems to assess and control many aspects of animal lives (Rutter, 2012; Berckmans, 2014; Bocquier et al., 2014; Mottram, 2016). In the dairy cattle industry, the development of rumen wireless telemetry has enhanced metabolic disorder moni- toring, and mastitis can be detected by combining conductivity and behavioral analysis with somatic cell scores that are predictive of disease (Mottram, 2016). Such technologies might offer an approach to rec- oncile the conflict that sometimes exists between animal welfare and efficiency. Investigation of specific sounds using continuous monitoring has been examined in a preliminary way in two different livestock systems. Recording of sound emitted by broilers at various growth stages allowed for a correlation of sounds with optimal growth. This information could be used to investigate flocks when positive growth sounds are not heard, and also to modify the environment and feed to max- imize the periods of these growth sounds being emitted (Fontana et al., 2015). In the cattle industry, re- cording of sounds in calves and labeling those noises specific for respiratory problems as a trigger for ex- amination allowed for early identification of bovine respiratory disease (Vandermeulen et al., 2016). Biosensors that detect physiological changes—such as increased lactate (indication of developing low milk yield in dairy cattle) or cortisol (indicating stress level)—have been developed that work on sweat, saliva, and tears (Weng et al., 2015). Applied to an animal, biosensors can serve as color-changing biotattoos to readily inform workers of impending problems. Information can be transferred via cell phone to create a timestamp as well as geographic coordinates that could be utilized for more effective local, regional, and national coordination of overall stress or developing disease. Prompt reaction to changes could facilitate isolation of infected animals to prevent spread, increase amount of weight gain, and decrease the number of sick animals that require therapeutic antibiotics. For PLF to reach its full po- tential, additional research into relevant bioresponses is needed. Currently, most of the point-of-care diag- nostic development is focused on detection of specific pathogens (e.g., avian influenza). Although useful in monitoring flocks during outbreak periods, a more robust system would be able to detect early stress in an animal during the prodromic period. This will require intensive examination of the innate immune re- 44 Prepublication Copy

Animal Agriculture sponse and examination into which biomarkers are the most reliable for detection in blood, saliva, tears, or sweat. It will be necessary to detect specific algorithms and intervention points. Phenotypes from sensors and PLF will also be important inputs to global efforts for collecting phe- notypic and genomic data for breeding and genomic discovery programs. Combining large-scale sequence and varying phenotypic information from sensors into databases will be requisite to enable biology to in- form breeding and feeding programs. The biggest obstacle for PLF is the data science challenge of transforming multiple types of data from various sensors and sources into knowledge. This knowledge could then be used to accurately pre- dict a genetically superior animal, an animal in distress or presenting disease symptoms, or an abnormal state that requires farmer intervention. There are two hurdles in this regard: (1) the data science problem associated with developing data-driven methods (e.g., deep learning) that can create predictions based on a variety of measurements coming from different sources, and (2) a translational issue of interpreting the data-driven predictions to produce prescriptive levels of understanding (see Chapter 6). This might range from developing a breeding value of an animal through to how and when a famer should be notified that the intervention is required. Developing farmer-friendly, cost-effective plug-and-play PLF applications will require collaboration among animal scientists, agricultural engineers, and data scientists focused on a shared vision of animal-centered care. 3.6 Systems Analysis In examining various production systems, or even animal-source foods versus plant-based or syn- thetic alternatives, it will be important to conduct comprehensive life-cycle analysis (LCA) of advantages, disadvantages, and trade-offs. For instance, numerous studies have examined organic versus conventional production systems, but none have looked simultaneously at all relevant parameters involving an LCA to include environmental impact, animal welfare, and public health. To date, the most thorough studies in this arena have shown that there are evidently distinct advantages and disadvantages to each in the various categories of carbon footprint, water usage, and nutrient efficiency (van Wagenberg et al., 2017). For in- stance, although many consumers might choose grass-fed beef over cattle receiving conventional feed because of environmental concerns about the efficiencies of feeding grain to ruminants, the carbon foot- print per unit of grass-fed beef can actually be considerably higher than cattle that are finished on concen- trates (Capper, 2012). There is a need to objectively evaluate the sustainability implications of different animal agricultural systems and protein source alternatives using a holistic evidence-based research approach. There are many questions that have been posed that deserve rigorous scientific analysis. Such questions include: “What are LCA and nutritional implications of meat substitutes such as edible biomass grown from ani- mal stem cells in culture, or plant-based meat imitation products?” Reducing animal agriculture may re- duce GHG, but there are other direct and indirect impacts on other aspects of the food and agricultural system. A recent paper analyzed the environmental and nutritional implications of removing animals from U.S. agriculture and found a minimal overall reduction in GHG (2.6 percent), but significant potential impacts to human health through essential nutrient deficiencies (White and Hall, 2017). Insects have been suggested as a future source of protein (Payne and Van Itterbeeck, 2017; Williams and Williams, 2017), and it will be worthwhile to explore the possibilities and implications of this protein source. A recent review by van Huis and Oonincx (2017) examined the LCA and environmental impacts of insect farming compared to livestock production. That study concluded that (1) less land and water is required, (2) GHG emissions are lower, (3) insects have high feed conversion efficiencies, (4) insects can transform low-value organic by-products into high-quality food or feed, and (5) certain insect species can be used as animal feed or aqua feed (van Huis and Oonincx, 2017). For instance, insects might be able to partially replace fish meal feed, which is becoming increasingly scarce and expensive and is important because of projected increases in aquaculture production (Williams and Williams, 2017). Prepublication Copy 45

Science Breakthroughs to Advance Food and Agricultural Research by 2030 Perhaps as important is communication of these findings to the broader public. The sustainability trade-offs associated with agricultural production systems are often not obvious. Marketers may focus on a single sustainability component of a production system without holistically addressing the trade-offs accompanying issues such as food safety and affordability, animal health and well-being, worker safety and health, and the environment. In the United States, the Morrill Act of 1862 provided the basis for strong land-grant university re- search programs, and the subsequent Smith Lever Act of 1917 formed the extension infrastructure that would extend those research breakthroughs to farmers (Tokach et al., 2016). Extension programs could be better engaged in communicating agricultural sustainability research information to the general public as their target audience, using the findings of social scientists on the science of effective science communi- cation, given the importance of the public being able to appreciate the nuances and trade-offs associated with different systems to sustainably meet the needs of both human and animal populations. 4. GAPS There are scientific knowledge gaps that remain that have prevented us from meeting the challenges so far and would need to be addressed in order to realize the opportunities. These are stated as defined basic or applied research questions below and address the areas of animal genetics, animal nutrition, ani- mal health, animal facility design and management for sustainability and animal welfare, precision live- stock farming, and systems analysis. For animal genetics, research questions include (1) Can genetic and reproductive technologies be advanced and successfully combined to result in breeding schemes that achieve a 10-fold increase in the rate of genetic improvement in livestock, poultry, and aquaculture populations by 2030? (2) How can col- laborative work with researchers in various fields (e.g., genetics, animal science, animal health) help to develop reliable, objective selection criteria to enable genetic improvement in sustainability traits such as fertility, improved feed efficiency, welfare, and decreased susceptibility to disease in animal breeding programs? For animal nutrition, research questions include (1) How can precision nutrition be utilized to ensure that each animal gets exactly what it needs? Would it be possible to combine nutrient information with growing data about animals’ microbiomes to further the incorporation of exactness and efficiency? (2) Through collaborations between animal nutritionists and plant/food scientists, would it be possible to dis- cover novel, nutritious, and suitable feedstuffs that are not human-consumable in order to decrease animal agriculture’s resource footprint? For animal health, research questions include (1) What can be done to induce or amplify an animal’s innate immune response to pathogens? What novel prevention and intervention therapeutics can be devel- oped to interfere with the initial encounter and manipulate the innate response so that earlier protection is developed? Would it be possible to breed animals that are themselves resistant to specific pathogens? (2) What methods can be developed to more easily detect an infected animal prior to visual onset of clinical disease? What would be the role of biosensors and “wearable” technologies as inexpensive indicators? (3) To facilitate rapid response and containment, what penside tests can be developed to decrease the lag time between sample collection and laboratory diagnosis for transboundary animal diseases? For animal facility design and management for sustainability and animal welfare, research questions include (1) How can animal housing and management be examined in a multidisciplinary way that would allow for high efficiency and productivity, combined with animal welfare and worker safety, while mini- mizing negative environmental impacts? (2) To assist in objective assessments of animal welfare, what parameters should be used to address welfare concerns in animal production systems? What are the ap- propriate objective modalities for measurement that can be incorporated (e.g., sound, sight, and move- ment) to help explore this area, particularly indicators of animals’ subjective states? How can the social sciences help inform and translate scientific findings for consumers to make informed decisions? 46 Prepublication Copy

Animal Agriculture For precision livestock farming, research questions include: (1) How can sensors and data be used to transform the traditional systems of livestock farming into one that is more closely tailored to each ani- mal’s specific needs? (2) How should a “pilot farm” be designed to demonstrate the utility and efficiency of such a system that would provide continuous automatic real-time monitoring of production, animal health, welfare, and environmental impacts? For systems analysis with regard to animal agriculture, research questions include: (1) As the nation evaluates new systems to improve the efficiency of food production, how can life cycle assessments be used to holistically examine and compare the trade-offs of proposed changes? Parameters for sustainabil- ity and acceptability should include food safety and nutrient composition, nutritional, environmental, an- imal health and well-being, worker safety and health, and affordability. 5. EXAMPLES Some possible applications of combining various breakthrough strategies to provide a systems ap- proach are detailed below in futuristic examples. 5.1 Beef Cattle Biotattoo A farmer raising beef cattle has a new group of calves. Cattle are housed together, and a monitoring system allows the farmer to visually detect, via a biotattoo in the ear, if the animal has ingested colostrum from the dam. A visual inspection shows the farmer that all the biotattoos are pink, indicating that this important antibody-laden milk has been successfully consumed, helping to protect the animal for the first few weeks of life. A biotattoo in the other ear indicates stress level, and a certain color indicates fever and/or production of acute-phase proteins, such as would be generated early in an infection. The farmer notes that two of the calves have a faint blue tinge to the biotattoo, so those calves and dams are brought in to an area for closer observation. Before heading back to the house, the farmer activates the sound monitoring system, which records all sounds made by this group of calves and dams, and there are certain algorithms incorporated that will alert the farmer to the first coughs experienced in bovine respiratory disease and/or maternal distress. Any relevant sound algorithm that is activated alerts the farmer on a cell phone and, even in the middle of the night, the farmer is able to administer the appropriate remedy to the affected animals, saving lives and minimizing antibiotic use. 5.2 “Smart” Hog Facility A state-of-the-art facility in the Midwest specializes in feeder hogs. Recently weaned pigs are brought in and given a thorough assessment by the consulting veterinarian. Sensors in all the animal rooms are tied to the air handling and lighting systems to ensure optimal temperature, humidity, and am- bient light. A small number of workers monitor the animals remotely and are attuned to behavioral cues that the animals need to exert innate behaviors such as rooting or chewing; the workers can insert the req- uisite materials and/or activate access to an outdoor yard so that the animals can be fulfilled. Weight gain and back fat are also measured remotely, and environmental parameters are modified to maximize lean muscle development. Fecal samples are periodically tested using inexpensive rapid assays for Salmonella. Because the microbiome of each pig is known, any carrier pig can quickly be identified, removed, and treated. Removal of sewage is conducted by robotics, and the manure is deposited in a me- thane transfer device that converts the energy and powers the entire facility. Transport to the slaughter plant is achieved through chutes and into trucks that mimic the pigs’ environment for all of their senses. Prepublication Copy 47

Science Breakthroughs to Advance Food and Agricultural Research by 2030 5.3 Aquaponics in Elementary School Elementary schools throughout a poor urban area, where fewer than 1 percent of children have ever been to a farm, are each equipped with an aquaponics unit, which sustainably combines fish production and vegetable growth, that has been incorporated into the science curriculum. Students are selected, on a rotating basis, to attend to the fish and the vegetables, and through their science classes learn about sus- tainable agriculture and the value of recycling. The fish and vegetables are periodically harvested and served in the school lunch program, with students helping in the preparation. After 2 years of this pro- gram, there is a noticeable increase in student interest in food science as a career, and several of the hous- ing projects nearby have requested similar aquaponics units. 6. BARRIERS TO SUCCESS Breakthroughs can only be accomplished if various governmental, societal, and funding concerns are also addressed, as currently there are obstacles to achieving what is envisioned through this report. 1. Public research funding levels have remained stagnant for many years, and are disproportionate to the economic contributions of animal agriculture. The National Research Council report Critical Role of Animal Science Research in Food Security and Sustainability (NRC, 2015) recognized the underfunding of animal sciences and called for increased investments. Funding initiatives often omit research on food animals, focusing solely on the genetic improvement of agricultural crops. The National Association of State Departments of Agriculture has noted that “[t]his imbalance in support for animal science puts U.S. animal agriculture at a major disadvantage at a critical time when livestock, fish, and poultry producers are striving to improve sustainability and address glob- al animal protein demands” (NASDA, 2014). Recent disease outbreaks such as porcine reproduc- tive and respiratory syndrome and avian influenza in the United States underscore the need to de- velop science-based tools to prevent and mitigate the impacts of such outbreaks. 2. Big datasets are currently not stored or shared in a way that is useful for research or data scientists. 3. Many novel technologies are too expensive for commercial livestock producers and lack a user- friendly interface to facilitate their adoption. 4. There is little consumer understanding of the trade-offs associated with different production sys- tems and agricultural innovations. 5. There is insufficient focus in current funding calls on bringing together the disparate disciplines needed to address complex problems using data science. 7. RECOMMENDATIONS FOR NEXT STEPS Emerging technologies (such as genomics, genome editing, and biosensors) have transformative po- tential to advance knowledge in animal genetics, animal nutrition, and animal health. Funding mecha- nisms must entice and encourage data scientists, engineers, computer scientists, synthetic biologists, so- cial scientists, and other nonagricultural disciplines to apply this biological knowledge to focus on developing innovative solutions to animal agriculture’s pressing problems in a way that comports with societal expectations. A research strategy to enable the implementation of precision livestock farming using these technologies will require incentivizing the convergence of these disparate disciplines. Some high-priority research areas include: 1. Enable better disease detection and management using a data-driven approach through the devel- opment and use of sensing technologies and predictive algorithms. 2. Accelerate genetic improvement in sustainability traits (such as fertility, improved feed efficien- cy, welfare, and disease resistance) in livestock, poultry, and aquaculture populations through the use of big genotypic and sequence datasets linked to field phenotypes and combined with ge- 48 Prepublication Copy

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For nearly a century, scientific advances have fueled progress in U.S. agriculture to enable American producers to deliver safe and abundant food domestically and provide a trade surplus in bulk and high-value agricultural commodities and foods. Today, the U.S. food and agricultural enterprise faces formidable challenges that will test its long-term sustainability, competitiveness, and resilience. On its current path, future productivity in the U.S. agricultural system is likely to come with trade-offs. The success of agriculture is tied to natural systems, and these systems are showing signs of stress, even more so with the change in climate.

More than a third of the food produced is unconsumed, an unacceptable loss of food and nutrients at a time of heightened global food demand. Increased food animal production to meet greater demand will generate more greenhouse gas emissions and excess animal waste. The U.S. food supply is generally secure, but is not immune to the costly and deadly shocks of continuing outbreaks of food-borne illness or to the constant threat of pests and pathogens to crops, livestock, and poultry. U.S. farmers and producers are at the front lines and will need more tools to manage the pressures they face.

Science Breakthroughs to Advance Food and Agricultural Research by 2030 identifies innovative, emerging scientific advances for making the U.S. food and agricultural system more efficient, resilient, and sustainable. This report explores the availability of relatively new scientific developments across all disciplines that could accelerate progress toward these goals. It identifies the most promising scientific breakthroughs that could have the greatest positive impact on food and agriculture, and that are possible to achieve in the next decade (by 2030).

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