Food Animal Production is the ARS national research program that supports scientific needs for delivering a nutritious, high quality, safe and satisfying diet to the American public and people worldwide.  Production efficiency and product quality form the basis for profitability and global competitiveness of the U.S. livestock and poultry industry.  Increasing efficiency of animal production allows food to be produced with fewer inputs and generating less animal wastes. Greater production efficiency will be necessary to meet demands of the increasing world population, especially if food supplies were threatened.  Preserved germplasm enables animal agriculture to respond to changing cultural, regulatory, and ecological environments.

COMPONENTS: 

 Reproductive Efficiency

• Environmental effects
• Fertile gamete production
• Gamete and embryo storage, sexing, cryopreservation, and use
• Embryo, fetal, and neonatal development and survival
• Interactions of endocrine and immune systems

 Conserve, Characterize, and Use of Genetic Resources

• Characterizing genetic resources
• Preserving genetic resources
•  Information systems 

Genetic Improvement

• Develop breeding objectives
• Accelerate selection response
• Improve health and well-Being
• Transgenic livestock and poultry 

Genomic Tools

• Comprehensive maps
• Genotyping systems
• Tools and reagents
• Genomic enhancement systems
• Bioinformatics and statistical analysis tools

Nutrient Intake and Use

• Regulating gene function
•  Interactions affecting reproduction
• Microbial effects
• Minimizing production losses
• Nutrient use and feed evaluation       

 Growth and Development

•  Regulating feed intake
• Tissue growth and development

 Product Quality

• Interactions of genetics and nutrition
• Biological mechanisms controlling variation
• Predicting product quality or defects

 Integrated Systems

• User Information Packages

 

I.  BACKGROUND

Successful and efficient reproduction is essential to food and fiber production from livestock and poultry.  Numerous environmental factors compromise preproductive efficiency and increase unit cost of production.  Periods of diminished gonadal activity reduce efficiency or production through added costs from maintaining reproductively inactive animals.  Inefficiencies in collection, storage, sexing, and use of semen, oocytes, and embryos limit utilization and conservation of valuable germplasm.  Sub-optimal embryonic, fetal, and neonatal development and survival significantly reduce efficiency and profitability.  Complex and poorly understood relationships between endocrine, metabolic, and immune systems hinder development and implementation of improved systems for managing reproduction.

Vision Statement

Produce reproductively efficient domestic livestock and poultry that require fewer resources, produce less waste, and supply animal products that more fully meet consumer expectations.

Mission Statement

We seek to mitigate environmental conditions that reduce reproductive efficiency; enhance production of fertile gametes and survival of embryos, fetuses, and neonates; understand interactions between reproductive and immune systems; and ultimately achieve optimum reproductive rate per breeding female. 

Impact

Decrease overhead and unit cost of production in all farm animal species, resulting in greater profitability for U. S. livestock producers and in lower food costs for consumers.

Linkages

USDA-ARS National Programs: 103 Animal Health; and 105 Animal Well-Being and Stress Control Systems

Other Agencies and Departments:  Other USDA Agencies and Universities:  Howard University, Texas A and M University, Carroll College, Utah State University, University of Georgia, Oregon State University, Alcorn State University, Danbred USA, University of Nebraska.

Private sector:  National Association of Animal Breeders, Monsanto Company, and the U.S. Poultry and Egg Association.

II.  PROBLEMS TO BE ADDRESSED

Environmental Effects

Problem Statement

Reproductive efficiency is affected by numerous environmental factors including temperature, humidity, photoperiod, nutrition, and non-specific stressors.  Environmental factors are detected by higher brain centers which affect the neuro-endocrine system, subsequent pituitary hormone secretion, and secretion of other hormones.  Environmental factors may also directly influence gonadal and uterine function and the conceptus.  Managing the environment for optimum reproductive efficiency requires understanding basic neuro-endocrine regulatory mechanisms, gonadal and uterine function, and conceptus development. These systems may be further altered by other environmental factors including social interactions among animals, handling by humans, housing, and transportation.

 Goals

 1. Elucidate environmental influences on specific components of reproductive performance.

 2. Mitigate environmental effects on critical control points limiting reproductive efficiency.

 Approach

1. Determine how to mitigate the effects of environment on reproductive performance.

2. Determine environmental effects on neuro-endocrine pathways controlling adrenal, thyroid, and gonadal function, and behavior.

3. Determine direct environmental effects on fertilization, implantation, embryo survival, pregnancy, parturition, and egg production.

Outcome

Management techniques and production systems that optimize reproductive efficiency by reducing negative environmental effects.

 ARS Locations

Athens, GA; Beltsville, MD; Brooksville, FL; Clay Center, NE; Dubois, ID; Miles City, MT .

 Fertile Gamete Production

Problem Statement

Prepubertal development, seasonally reduced gamete production, postpartum anestrus, and aging all represent periods of inefficiency in livestock and poultry.  During prepubertal development the hypothalamus and pituitary are highly sensitive to suppressive factors primarily secreted by the gonads.  During seasonal declines in gamete production or extended periods of dietary restriction, the reproductive axis is more sensitive to suppressive factors, many of which are produced in the brain or gonad. Opportunities exist to optimize economic returns by determining how to combine genetic and nutritional resources in a manner that reduces the duration of these periods of diminished gonadal activity that result in reproductive quiescence.

 Goals

 1. Optimize rate of sexual development and maximize efficiency of gamete production.

 2. Lengthen reproductive longevity and minimize periods of gonadal inactivity.

Approach

1. Identify genes and gene products whose expression is differentially regulated in individual animals that have superior rates of gamete production.

2. Identify genes and gene products that are associated with enhanced gamete production,  sub-optimal photoperiod stimulation, at puberty, following parturition, and at advanced ages.

Outcomes

1. Understand genetic regulation of pubertal development in livestock and poultry.

2. Increase efficiency of gamete production in aging animals.

3. Technologies to hasten and extend gamete production.

ARS Locations

Athens, GA; Beltsville, MD; Brooksville, FL; Clay Center, NE; Dubois, ID; Miles City, MT.

Gamete and Embryo Storage, Sexing, Cryopreservation, and Use

Problem Statement

Artificial insemination and embryo transfer extend longevity and use of superior germplasm many-fold. However, these technologies are labor intensive and in some species inefficient.  New and commercially applicable methods for storage of sperm in liquid or frozen form could greatly enhance reproductive efficiency.  New reproductive technologies can further increase the rate of genetic improvement and reduce costs of livestock and poultry production. New technology is also needed to efficiently mature, fertilize, and culture oocytes/embryos in vitro. Storage of embryos, oocytes, and somatic cells enables preservation of maternal genetic information and facilitates international trade in germ plasm.

Goals

1. Develop new and improved existing methods of cryogenic preservation of sperm, somatic cells, oocytes, and embryos for livestock and poultry, placing emphasis on hard to freeze species, breeds, or lines within breeds.

 2.  Improve methods for sex-preselection of sperm so that it can be used for conventional artificial insemination.

 3. Improve in vitro maturation, fertilization, and culturing of oocytes and in vivo developmental competence of mammalian embryos after cryopreservation and embryo transfer.

Approach

1. Evaluate biological factors that impact sperm, oocyte and embryo survival after cryopreservation.

2. Develop freezing and thawing methods that improve fertility and survival of cryopreserved gametes and embryos.

3. Develop new technologies to improve reproductive efficiency.

Outcomes

1. Reliable methods for cryogenic preservation of sperm, oocytes and embryos.

2. Increased reproductive efficiency that expands use of superior germplasm.

ARS Locations

Beltsville, MD; Brooksville, FL; Fort Collins, CO, Miles City, MT.

Embryo, Fetal, and Neonatal Development and Survival

Problem Statement

Delays in establishing pregnancy increase cost and reduce output of food animal systems. Maximum production efficiency requires every fertilized egg to result in birth of a healthy offspring that survives and grows during the neonatal period. Factors contributing to embryonic and fetal losses and/or inappropriate development in domestic livestock are numerous and interacting. Incidence of embryonic and fetal mortality has been estimated to be 20 to 40% in livestock species and 10 to 14% in poultry.  Others are born with extreme birth weights or other developmental abnormalities that contribute to loss during the neonatal period.

Goals

1. Prevent abnormal and inefficient embryonic, fetal, and neonatal growth and development in livestock and poultry species.

2. Mitigate abnormal development and growth of embryo, fetus, and neonate.

3.  Improve embryonic, fetal, and neonatal survival and health.

Approach

1. Identify physiological mechanisms causing inappropriate development and loss in domestic livestock species during the embryonic, fetal and neonatal periods.

2. Develop methods to control physiological mechanisms resulting in inappropriate development and loss and to assess other consequences of these changes.

3. Modify, as needed, those procedures controlling physiological mechanisms resulting in inappropriate development and loss and disseminate appropriate technologies to the  livestock industry.

Outcomes

1. Enhanced embryonic, fetal, and neonatal development and survival through modification of physiological mechanisms, and genetic selection.

2. Disseminate methodology to improve development of embryos, fetuses, and neonates.

3. Reduce inputs used to obtain healthy offspring.

ARS Locations

Athens, GA; Beltsville, MD; Clay Center, NE; Dubois, ID; Miles City, MT

Interactions of Endocrine and Immune Systems

Problem Statement

Complex interactions between immune and endocrine systems affect many physiological processes, including reproduction.  Resolving basic mechanisms that control the many interactions between immune  and endocrine systems is essential for improving growth and development, reproductive management, and production efficiency.

Goals

1.  Elucidate the role of the immune system in modulating reproductive activity, mammary function, gametic production and  survival, luteal function, pregnancy, uterine involution, and embryonic development in the female reproductive tract.

2.  Improve uterine immune functions to reduce uterine and oviductal infections without using antibiotics.

Approach

1. Determine cellular and molecular mechanisms by which endocrine secretions regulate uterine immune functions allowing the uterus to eliminate or manage bacterial contamination.

2. Define cellular and molecular interactions affecting control of reproductive health and efficiency by endocrine and immune systems to influence the reproductive efficiency of both healthy and immune stressed animals.

3. Determine mechanisms of the immune system that regulate luteal function and gametic development, maturation, and survival in the female reproductive tract

Outcomes

1. New, effective methods for managing reproductive events.

2. Novel methods for preventing or treating uterine infection and bacterial contamination that do not rely on antibiotics.

3. Nutritional, genetic, environmental, and management strategies to promote immune functions that enhance reproductive efficiency

 ARS Locations

 Athens, GA; Beltsville, MD; Brooksville, FL; Clay Center, NE; Dubois, ID

ARS Locations

Beltsville, MD; Brooksville, FL; Clay Center, NE; El Reno, OK; Fort Collins, CO; Miles City, MT; East Lansing, MI.

Information Systems

Problem Statement

Genetic composition and performance must be integrated to fully understand the status and potential use of genetic populations.  As germplasm collections increase, a critical need exists to develop databases capable of monitoring inventory (within and across locations), germplasm viability tests, and key genetic and phenotypic parameters associated with germplasm stored in the repository system. 

Goals

1. Inventory of preserved germplasm and breed populations in the U. S. electronically linked to international information.

2. Evaluate genetic resources using information on breed performance related to production systems.

3.  Develop software to assist in evaluating economic worth of genetic resources, determining genetic relationships among animals, and planning mating strategies.

Approach

1. Develop decision support tools coupling genetic and economic methodology that enables industry and scientists to assess risk of losing genetic resources and to manage genetic diversity within a breed.

2. Develop databases to combine inventories of cryopreserved germplasm, scientific information on breeds and inventories of breed populations.

3. Develop information systems capable of evaluating changes in population demographics, differences in production systems and genetic by environmental interactions.

Outcomes

1. A database capable of determining the status of germplasm stored in repositories and linked to breed demographics.

2. A decision support tool for industry and genetic resource managers to use to evaluate the status of a population and to make decisions concerning maintenance or enhancement of genetic diversity.

3. An information system for tracking breed population trends over time and environments to interface with environmental and production variables.

ARS Locations

Fort Collins, CO; Clay Center, NE; Beltsville, MD

 

I. INTRODUCTION

Background

Livestock and poultry production provide consistently uniform and nutritious foods to the consumer. However, as consumer demands change and production systems evolve to meet those demands, high product quality must be maintained.  As consumers demand lower fat foods, animal production systems respond with changes in breeding, nutrition, and management to decrease fat content.  Consumers have many choices of food products, so competition among foods is very high.  Factors create challenges to maintaining high sensory quality and satisfied consumers.  New information is continually needed to provide food animal producers with the tools to continue to develop innovative products that meet processor and consumer needs.

Vision Statement

 Livestock and poultry products of consistently superior quality.

 Mission Statement

 We seek to optimize product quality by controlling all sources of variation within geographic and economic constraints and by eliminating defective or substandard products from the marketplace.

Impact

Increased consumer satisfaction and demand for livestock and poultry products.

Linkages

USDA-ARS National Programs: 107 Human Nutrition; 108 Food Safety (animal and plant products); 205 Rangeland, Pastures, and Forages; 207 Integrated Agricultural Systems; and 306 New Uses, Quality, and Marketability of Plant and Animal Products

Other Agencies and Departments: Universities, Foreign Agriculture Service, USDA 

Private Sector: Prairie View A&M College, Arkansas Land and Farm Development Corp.

 

II.  PROBLEMS TO BE ADDRESSED

Interactions of Genetics and Nutrition

Problem Statement

Altering dietary vitamin, mineral, energy, and protein levels affect product quality.  However, incomplete understanding of mechanisms controlling product quality has resulted in variable responses to attempts to improve product quality through nutritional supplementation.  Advances in genomic research provide new insight into mechanisms controlling phenotypic expression.  In addition to facilitating efforts to genetically select for improved product quality, these advances increase the possibility of modifying product quality through nutritional supplementation.  Some alleles may have antagonistic effects on production efficiency and product quality.  Thus, a desirable goal may be to select for alleles that maximize production efficiency and offset any antagonistic effects on product quality through nutritional supplementation. 

Goals

1. Optimize product quality through nutritional and metabolic modification of targeted biochemical pathways.

2. Nutritional regimes that optimize product quality in genetic strains that have been selected for improved production efficiency.

Approaches

1. Identify feeding/management strategies through altered dietary vitamin, mineral, energy, and/or protein levels to improve product quality.

2. Determine effects of novel and/or genetically-modified feeds on product quality. 

3. Quantify interaction effects of animal genetics and nutrition on product quality.

Outcome

1. Enhanced sensory qualities and wholesomeness of livestock and poultry products.

ARS Locations

 Beltsville, MD; Clay Center, NE; Dubois, ID; El Reno, OK; Miles City, MT.

 

Biological Mechanisms Controlling Variation

Problem Statement

Sensory attributes are important drivers of demand for livestock and poultry products. Lack of understanding of biological factors regulating variation in product quality limits efforts to devise methods to ensure consistent high quality products.  Often biochemical pathways or specific enzyme systems involved that affect certain product quality traits are known, but their regulation and control are not known.

Goal

1. Methods to manipulate biological processes that will result in consistently high quality products.  

Approach

1. Determine regulatory steps in biological pathways controlling variation in specific quality traits.

2. Assess strategies to regulate biological pathways controlling variation in specific quality traits.

Outcome

1. Enhanced product quality enabling production for specific markets.

ARS Locations

Athens, GA; Beltsville, MD; Clay Center, NE.

 

Predicting Product Quality or Defects

Problem Statement

Miss-matched genetics and production practices leads to considerable variation in the quality of animal food products.  Many defects in quality are only noticed by the consumer, when it is too late to take corrective action.  Processors need non-invasive, non-destructive testing procedures to identify defects and measure product characteristics. Objective measures of determining value characteristics should allow processors to more effectively communicate differences to producers and give producers greater incentive to improve product quality.

Goals

1. Objective automated systems to evaluate quality of livestock and poultry products.

Approach

1. Assess the efficacy of state-of-the-art instrumentation to measure and/or predict product quality and to identify qualitative defects.

2. Develop integrated control systems for instrumentation to measure and/or predict product quality and to identify qualitative defects.

Outcomes

1. Effective communication of value between producers and processors.

 2. Fewer defective products presented to consumers.

ARS Locations

Athens, GA; Beltsville, MD; Clay Center, NE; Wyndmoor, PA; and University Park, PA.

I. INTRODUCTION

Genetic improvement of livestock and poultry populations is key to increasing production of high quality food efficiently and in an ethically responsible manner.  The rate of improvement is compromised by lack of objective goals for improvement, inadequate understanding of quantitative and molecular genetic controls of component traits and interrelationships among traits, less than optimal methods for evaluating candidates for selection, and inefficient strategies to incorporate quantitative trait loci (QTL) in breeding programs including the ability to move novel forms (alleles) of genes from one population to another.

Vision Statement

 Genetically efficient and humane production of food from livestock and poultry.

 Mission Statement

We seek to accelerate genetic improvement toward more efficient and profitable production of healthy, nutritious and palatable livestock and poultry products; and to improve health and well-being of livestock and poultry species.

Impact

Reduced cost of production and globally competitive animals and food products produced from livestock and poultry.

Linkages

USDA-ARS National Programs: 103 Animal Health; 105 Animal Well_Being and Stress Control Systems; 107 Human Nutrition; 205 Rangeland, Pastures, and Forages; and 207 Integrated Agricultural Systems

Other Agencies and Departments: University of Arkansas, University of Nebraska, and Alcorn State University, and University of Vermont.

Private Sector: National Association of Animal Breeders, cattle breed associations, PIC, USA, Metamorphix, Inc., Anigerics, Beef Improvement Federation, and National Dairy Herd Improvement Association.

II. PROBLEMS TO BE ADDRESSED

Develop Breeding Objectives

Problem Statement

Improving biological efficiency and profitability of livestock and poultry depends on changing several component traits in harmonious concert. These tradeoffs are not well established. Development of appropriate strategies is complicated by  diversity of geographic, climatic, and economic environments in which production occurs and temporal variation within environments.

Goal

 Develop objective goals for genetic improvement for livestock and poultry species.

Approach

1. Systems analysis of a farm-level production to gain new insight into selection goals for genetic improvement of biological efficiency and profitability of livestock and poultry.

2. Experimental validation of proposed objectives.

3. Incorporate new breeding objectives into genetic evaluation systems that can be used across breeds, strains, and lines.

Outcomes

1. Relative economic values for components of life-cycle efficiency linked with macro- and micro-systems for genetic evaluation.

2. Refined systems for local, national, and international genetic evaluations of livestock and poultry.

3. Genetic improvement technologies delivered to livestock and poultry producers.

ARS Locations

Beltsville, MD; Clay Center, NE; Dubois, ID; East Lansing, MI; Miles City, MT;
El Reno, OK.

Accelerate Selection Response

Problem Statement

Cumulative and sustainable change in populations is achieved through selection.  Rate of response to selection is compromised by sub-optimal systems of genetic evaluation, incomplete genetic characterization, interactions of genotype with environment, and genetic antagonisms among traits.  Knowledge of genes affecting production traits and how these genes interact with the rest of the genome and the environment, will enable breeders to make selection decisions that expedite genetic progress and target specific traits limiting efficiency. 

Goals

1. Enhanced systems for genetic evaluation of livestock and poultry.

2. Improved understanding of genetic architecture controlling expression of traits influencing biological efficiency and profitability.

3. Increase biological efficiency and profit for livestock and poultry producers through more optimal selection decisions.

Approach

1. Upgrade systems of genetic evaluation, incorporate QTL information, and evaluate selection response to marker assisted selection.

2.  Develop statistical methods for QTL detection and characterization in complex livestock pedigrees.

3. Partition phenotypic variance into causal components, identify QTL for traits in  breeding objectives (fertility, fitness, growth, composition, nutrient density, etc.), and establish quantitative and molecular genetic relationships among traits.

4. Identify impacts of diverse production environments on estimated genetic parameters and breeding objectives.

5. Assess direct and correlated responses to selection.

Outcomes

1. Identification of significant genetic antagonisms between components of life-cycle production efficiency in livestock and poultry.

2. Deliver technologies for accelerating genetic improvement in efficiency and profitability to livestock and poultry producers.

ARS Locations

Beltsville, MD; Clay Center, NE; Dubois, ID; East Lansing, MI; Miles City, MT

Improve Health and Well-Being

Problem Statement

Disease compromises both health and productivity of livestock and poultry.  Populations vary in resistance to specific pathogens and genetic variation may exist within populations.  Inbreeding is an unavoidable consequence of directional selection.  Due to natural genetic load within populations, inbreeding usually results in reduced reproduction, vigor, fitness, and physiological efficiency.

Goals

1. Reduce disease and use of pharmaceuticals in livestock and poultry production.

2. Enhance fitness and well-being of livestock and poultry.

Approach

1. Identify genes or closely linked markers related to production and disease traits.

2.  Identify genes with joint effects on disease and production.

3. Assess effects of inbreeding concurrent with accelerated genetic improvement.

4. Develop strategies to maintain fitness and allelic diversity in populations of livestock and poultry under directional selection.

Outcomes

1. Increased resistance of livestock and poultry to disease and infection.

 2. Maintain allelic diversity and improve fitness  in livestock and poultry populations.

3. Delivery of genetic technologies to improve animal fitness, health and well-being in a variety of systems being used by livestock and poultry producers.

ARS Locations

 Beltsville, MD; Clay Center, NE; Dubios, ID; East Lansing, MI; Miles City, MT

 Produce and Evaluate Transgenic Livestock and Poultry

Problem Statement      

During the past 15 years procedures have been developed to introduce transgenes into genomes of livestock and poultry.  This technology provides the opportunity to introduce new traits or modify existing traits that cannot be accomplished by genetic selection.

Goal

Introduce transgenes into livestock and poultry that have potential to impact immunity or resistance to disease, increase product quality or safety, and increase efficiency of animal production.

Approach

1.  Produce and evaluate transgenic animals and birds that contain modified native, foreign, or synthetic genes.

2.  Determine the impact of the introduced phenotype on efficacy, safety, and animal well-being.

Outcomes

Provide producers with livestock and poultry with improved product quality or safety, increased resistance to disease, and enhanced production efficiency.

E.  ARS Location

Beltsville, MD; Clay Center, NE.

I. INTRODUCTION

Background

Knowledge of the genome and its interactions with environmental factors are required to fully understand biological basis of all animal science disciplines.  Acquiring new knowledge pertaining to reproductive efficiency, genetic improvement, nutrient intake and use, and growth and development will be slow and inefficient without appropriate genomic tools.  Both public and private laboratories will develop these tools.  Public involvement in the construction of these resources is critical to ensure development of economically feasible management tools for livestock producers and to provide all researchers access to these tools and technologies.

Vision Statement

 Provide a comprehensive set of genomic tools for food animal production research.

Mission Statement

We seek to develop genomic and proteomic tools and information to facilitate research in livestock and poultry species.

Impact

Rapid progress in elucidating the structure and function of genes.

Linkages

USDA-ARS National Programs: 103 Animal Health; 104 Arthropod Pests of Animals and Humans; 105 Animal Well_Being and Stress Control Systems; 106 Aquaculture; 108 Food Safety (animal and plant products)

Other Agencies and Departments: University of Minnesota, Cornell University, North Carolina A and T, Cold Spring Harbor Laboratory, University of California, University of Delaware, Hebrew University of Jerusalem, NAAB, EMBRAPA, INRA, Institute for Genomic Research, Duke University, NIDDK, and NRI-grant.

Private Sector: Sequenoms, Inc., Metamorphic, Inc., and Chapman Bonsmaras.

II. PROBLEMS TO BE ADDRESSED

Comprehensive Maps 

Problem Statement

Genetic and physical maps for a few livestock species exist today, but more comprehensive genomic maps for livestock and poultry still need to be developed.  Comparative maps that tie to the mouse and human maps are also needed.  These maps need to possess types of markers that facilitate use of high-throughput genotyping platforms.  High-resolution maps would greatly expedite sequencing of the entire genome of food animal species, yielding the ultimate physical maps.  Sequenced genomes have revolutionized investigations into comparative biology, genomics, genetic marker development, and gene identification experiments.

Goals

1. Develop dense genetic linkage maps and comprehensive physical maps for livestock and poultry.

2. Sequence the complete genomes of livestock and poultry species.

Approach

1. Develop and map microsatellite and single nucleotide polymorphisms in well characterized reference populations.

2. Develop bacterial artificial chromosome (physical) maps for agricultural species and link these maps to genetic and physical maps of livestock and other species.

3. Sequence approximately 3 billion bases of genomic DNA per livestock species and 1 billion bases in chickens. 

4. Compare sequence information among species, including mouse and human.

Outcomes

1. Linkage maps and physical maps with sufficient marker densities that will be useful in a wide range of populations.

2. Relatively complete physical (BAC) maps for food animal genomes. 

3. Complete sequence coverage for livestock and poultry genomes.

ARS Locations

Beltsville, MD; Clay Center, NE; East Lansing, MI

Genotyping Systems

Problem Statement

Commercial populations of livestock and poultry have genes affecting economically important traits.  However, labor and other cost constraints limit the ability to collect the necessary genotypes.  High throughput genotyping systems need to be developed to permit the collection of genotypic data for loci spanning the genome.

Goal

Reduced cost and increased rate of genotyping.

Approach

Evaluate and develop genetic marker analysis systems that are highly automated and produce reliable results for single nucleotide polymorphisms and microsatellites.

Outcome

Genotyping systems that can be used  to collect large numbers of genotypes per animal in a timely and economical manner.

  ARS Locations 

Beltsville, MD; Clay Center, NE

Tools and Reagents

Problem Statement

Genomic sequencing provides information needed to obtain rapid gains in agricultural productivity essential to feeding an ever-increasing population. This information, coupled with understanding of gene expression, leads to further understanding biological processes of food production. Nucleotide sequences from normalized cDNA libraries can be used to generate complete profiles of expressed genes for specific tissues and species.  Microarrays of genes (cDNA clones) provide a means to study expression of thousands of genes simultaneously, elucidate the function of unknown genes, and  identify important regulatory genes. 

Goals

1. Construct and sequence normalized cDNA libraries of expressed genes from various tissues and different developmental time points.

2. Develop cDNA microarray technologies, to provide reliable gene expression profiling.

Approach

1. Construct and normalize cDNA libraries from a multitude of tissues and developmental time-points.

2. For each library, sequence clones from both the 5' and 3' ends until the level of redundancy inhibits the usefulness of further sequencing.

3. Evaluate microarraying systems to determine the most useful and economical systems available.

Outcomes

1. Identification of clones and cDNA sequences for genes expressed in food animal species.

2. Microarrays that can be used for gene expression experiments.

ARS Locations

Ames, IA; Athens, GA; Beltsville, MD; Clay Center, NE; East Lansing, MI

Genomic Enhancement Systems

Problem Statement

Developing effective and efficient methods to make precise genome modification is essential for improving productivity, health, and welfare of food animal species beyond levels that can be obtained by selection and increasing genetic diversity.  Methods include inactivation, modification or replacement of native genes, geneclusters or chromosomes and addition of native, foreign or synthetic genes to the genome of food animals.

Goals 

Develop methods to extend the life of food animal somatic cells during in vitro culture.

Develop effective somatic cell nuclear transfer technology for food animals.

Develop alternative homologous recombination procedures for food animals.

Approach

Develop methods to effectively incorporate recombinant DNA into the genome of food animal cells, which can then be used for cloning of live offspring.

Outcome

Techniques for precise gene insertion that can be routinely used to study the function of genes.

ARS Locations

Beltsville, MD; East Lansing, MI                           

Bioinformatics and Statistical Analysis Tools

Problem Statement

Developments of bioinformatic tools has lagged behind development of genomic laboratory procedures.  Current genomic tools can generate data much faster than can be analyzed despite faster computer processors.  Software needs to be developed that is capable of searching the available genome databases for comparative information. Efficient data processing will provide investigators with rapid results, which permit rapid formulation of hypothesis for the next set of experiments to hasten scientific progress.  Statistical analysis software needs to be developed to interpret results from genomic and proteomic experiments and the collective results from many different types of data.

Goals

1. Databases of genomic and proteomic information.

2. Computer software for efficient manipulation and analysis of genomic and proteomic data.

Approach

1. Develop database algorithms for storing genomic data. 

2. Develop software to search and retrieve data from public databases via the internet. 

3. Improve analysis to summarize genomic sequence, linkage, gene expression, and other related data. 

Outcome

Publicly available and highly interactive data management and manipulation tools to expedite genomic research.

ARS Locations

Ames, IA; Beltsville, MD; Clay Center, NE; East Lansing, MI.

I.  INTRODUCTION

Background

Growth and development impact all components of meat and milk production. Feed consumption is a primary regulator of growth and development.  Tissues and biological systems must undergo coordinated developmental changes to form a mature end-product. Growth and development of the fetus and early neonatal animal have lasting effects on health, performance, and productivity.  The manner in which muscle and mammary tissue grows and develops dictates the quantity and quality of meat production, as well as the efficiency of how  feed energy is converted to a final food product.  Growth and development of adipose tissue impact carcass composition, meat quality, and mammary development.  Turnover of mammary epitholium during lactation impacts persistency of lactation.

Vision Statement

Optimize growth and development to enhanced production efficiency and product quality.

Mission Statement

We seek to improve conversion of feeds to animal products; increase rate of production of animal products; and improve composition of animal products.

Impact

Livestock and poultry management systems that promote efficient production and products that promote human satisfaction, health, and well-being.

Linkages

USDA-ARS National Programs: 103 Animal Health; 105 Animal Well_Being and Stress Control Systems; 107 Human Nutrition; and 207 Integrated Agricultural Systems.

Other Agencies and Departments: NADDK, Brigham Young University, Purdue University, University of Maryland, and University of Wyoming.

Private Sector:  US-Israel Binational Agriculture Research and Development Fund, Finn Feads, Fund for Rural America, NRI-Grant, Pfizer Animal Health, Alpharma, Inc., and GroPep, Inc.

II. PROBLEMS TO BE ADDRESSED

Regulating feed intake

Problem of Statement

A major controlling factor of growth across species is feed intake.  Feed costs represent the primary economic input into livestock production systems.  Metabolic and sensory factors affect short-term feeding behavior.  Long-term feeding behavior is controlled by the animal in its attempt to achieve a defined equilibrium within its environment.  Understanding mechanisms involved in regulating feeding behavior and appetite may lead to more efficient production of livestock and poultry.

Goals

 1. Regulate intake to optimize use of feed resources

 2. Improve energy balance of neonatal livestock and poultry

Approaches

1. Elucidate roles of nutritional metabolites and hormones in regulating feed intake.

2. Identify hypothalamic factors that control systems regulating feed intake.

3. Identify physiological processes controlling neonatal feed intake and their interactions with stressors.

 Outcomes

1. Improved efficiency of feed use by livestock and poultry.

2. Increased neonatal survival rates.

ARS Locations

Clay Center, NE; Athens, GA; Beltsville, MD; Dubois, ID; East Lansing, MI.

Tissue growth and development

Problem Statement

Rapid and efficient growth is important for profitable animal production.  Under market conditions with small profit margins for livestock and poultry producers, improved growth and efficiency is critical for economic survival of many producers.  Optimum growth, performance, and efficiency have limited value if product quality is not acceptable to consumers.  The impact of tissue development and growth on meat tenderness and composition is not understood.  Knowledge of genetic factors and nutrition that control development and growth of muscle, fat, and mammary tissue is needed to develop practical methods for improving meat quality and composition and milk production.  

Goals

1. Alleviate physiological and environmental conditions to enhance expression of growth potential by livestock and poultry.

2. Alter characteristics of meat products from livestock and poultry to improve palatability and nutritional value.

3.  Determine the genetic and physiological basis for replication and differentiation of adipocyte precursor cells, muscle satellite cells, and mammary epithelical stem cells.

4.  Identify tissue specific bioregulatory mechanisms for adipose, bone, muscle, and mammary tissue growth, and function.

Approaches

1. Investigate neural, endocrine, and immune mechanisms affecting growth and composition at animal and tissue levels.

2. Use whole-animal and in vitro models to understand and control developmental processes as they affect productivity and product quality.

3. Characterize growth- and immune- related endocrine function during tissue wasting that accompany parasitism and endotoxemia.

4. Manipulate differentiation of fat cells from fetal stromal vascular cells.

Outcome

1. Increased growth rate and reduced length of production cycles in the livestock and poultry industries.

2. Livestock and poultry products with sensory attributes and nutrient composition desired by consumers.

3.  Increased lactational persistency and efficiency of milk production in dairy cattle.

ARS Locations

Clay Center, NE; Athens, GA; Beltsville, MD; Dubois, ID; East Lansing, MI.

ARS Locations

Athens, GA; Beltsville MD; Brooksville FL; Clay Center, NE; Dubois, ID; El Reno, OK;  Miles City, MT

 

Microbial Effects

Problem Statement

Ruminants rely on diverse microflora to digest feeds.  Monogastric animals also host microbial populations in their gut that can influence efficiency of nutrient use. Regional differences in types and availability of dedicated and byproduct feeds and release of new varieties of traditional crop species with improved nutritional properties have increased options for formulating rations to improve production. There is a paucity of information on interactions of these feeds in the upper and lower digestive tract of ruminants and  the gastrointestinal tract of  monogastric species.  Understanding how these interactions affect digestibility, digestion kinetics, and nutrient absorption is important for efficient use of feedstuffs.

Goals

1. Determine if there is a genetic component to the interaction of an animal with its stable microflora and develop strategies to optimize populations of specific microbial species.

2. Elucidate roles of genetics and environment in determining composition of species of the GI tract or rumen, products of rumen fermentation, and growth efficiency of rumen or GI microorganisms.

3. Determine interactions among rumen microbes and different feeds, particularly byproduct feeds and new genotypes of forage and grain species.

4. Determine efficiency of substrate utilization and microbial protein yield from various feed components under different rumen environmental conditions.

Approach 

1. Characterize interactions among rumen microbes fermentation characteristics and efficiencies associated with varying production conditions.

2.  Identify gut and rumen microbial species, competitions, and symbioses in animals of varying production levels.

3. Identify individual microbial species instrumental in degradation of  recalcitrant plant tissues and in facilitating nutrient passage from the gut.

4. Characterize rumen microflora of high producing dairy and beef cattle and sheep and gut microbes of nonruminant species through successive generations and with different diets.

5.  Determine the impact the existing gut microflora on nutrient excretion and how modification of the existing microflora affects nutrient utilization, nutrient excretion, and odors.

6. Develop site-specific models of feed quality incorporating agronomic and animal data.

Outcome

Nutritional systems to enhance and maximize efficiency of nutrient use through optimization of relationships between endogenous gut or rumen microflora and diet.

ARS Locations

Beltsville MD; Clay Center, NE; El Reno, OK; Madison, WI; Ithaca, NY; and Ames, IA.

Minimizing Production Losses

Problem Statement

Under-feeding, over-feeding, or imbalanced nutrition will reduce production efficiency and may make livestock and poultry susceptible to infectious pathogens.  Changing genetic potential for production or body composition also may result in imbalanced nutrition and modify the capacity of the immune system to recruit nutrients needed for good health.  Animals harboring overt of subclincal disease use a portion of daily intake to combat the disease resulting in inefficient feed conversion to growth, reproduction, milk production, or egg production.  With current concerns about antibiotic resistance and chmical residues in food, nutritional modulation of the immune system may be a way to maintain animal health, and maintain a competent immune system through improved nutritional or nutrient-based intervention strategies that lead to specific actions during immune challenge.

Goals

1. Strategies that appropriately differentiate between feeding for short-term performance and feeding for life-cycle efficiency.

2. Limits and expectations of benefit for specific nutrient-diet modifications in recommending requirements for nutrients to improve animal health and well-being.

3. Establish nutrient requirements and impact of altered nutrition on periodic production processes as related to interactions with neuroendocrine and endocrine immune axes.

4. Discover effects of specific nutrients on immune gene expression, pro- and anti-inflammatory cytokine status, antimicrobial peptide production, and ability to rapidly return to healthful status.

Approach

1. Develop species-specific immune cytokines, cytokine antibodies, and cytokine gene probes and assays.

2. Elucidate mechanisms by which nutrients affect immune function and effects of immune response on short- and long-term production.

3. Determine whether genetic selection for increased performance and leanness may adversely alter innate immune defenses.

4. Develop nutritional strategies for gastrointestinal stabilization to prevent emergence of zoonotic pathogens due to perturbed gut ecology.

5.   Develop nutrient-based strategies to limit consequences of immune system processes resulting in modification of regulatory proteins and DNA damage.

Outcomes

1. Nutritional systems that modify immune response and improve animal health.

2. Reduced risk of pathogenic contamination of animal products.

3. Improved nutritional management of livestock and poultry.

ARS Locations

Beltsville MD; Clay Center, NE; Ames, IA.

Nutrient Use and Feed Evaluation

Problem Statement

Animal feeding strategies are limited by a lack of understanding of mechanisms involved in plant cell wall lignification that limits fiber digestion, knowledge of nutritional strategies to increase the utilization of nitrogen and carbon and limit the output of excess nitrogen and carbon, and methodology to accurately measure nutrient digestion kinetics and bioavailability. Chemical and biochemical research is needed to understand intrinsic characteristics of fiber limiting digestion and processes plants use to synthesize indigestible compounds.  Adverse environmental impacts of nitrogenous wastes emphasizes the need to optimize levels of protein fed to livestock.

Goals

1. Develop strategies that alleviate intrinsic limitations to digestion of feeds, especially fibrous plant cell walls.

2. Develop new methods to determine nutrient bioavailability and protein degradability.

3. Develop dynamic systems for site-specific feed evaluations and feeding recommendations.

4. Develop methods to reduce protein breakdown to nonprotein nitrogen in grazed forages and silages.

5. Optimize nutrient utilization in conversion of feed nutrients into food products while balancing costs of production with environmental impact.

Approach

1.  Determine the minimum nutrient requirements to support optimum production while minimizing nutrient losses for modern domestic livestock species under different production systems.

2.  Determine how the deposition and structure of ligmin  in the cell walls of forages restrict the potential digestibility of the cell-wall polysaccharides by ruminants.

3.   Develop models incorporating feed intake, and digestion and passage kinetics that improve prediction of feed digestibility.

4.  Develop systems to measure digestion kinetics more accurately and test and calibrate current and new feed evaluation systems.

5.  Develop strategies for improving nitrogen use by synchronizing carbohydrate degradation and protein degradation in the rumen.

6.  Develop strategies for improving carbon use by increasing digestibility and utilization of structural and non-structural carbohydrates, and conserving protein in stored forages.

7.  Determine how nutrient requirements and excretion can be manipulated through changes in animal physiological processes, diet formulation, environment, and feeding strategies.

8.  Develop procedures for use of dietary enzymes, microbial extracts, supplements, and metabolic modifiers to improve nutrient utilization and decrease nutrient excretion.

9.  Develop simple, inexpensive, rapid and reliable tests to reliably determine the bioavailability of nutrients in feeds.

Outcomes

1. More efficient use of forages in ruminant livestock production.

2.  Development of nutrient management systems optimizing food production with minimal effect on the environment.

ARS Locations

Madison, WI; Beltsville, MD; Clay Center, NE; El Reno, OK; Brooksville, FL; Miles City, MT; and St. Paul, MN; Ames, IA.

1. INTRODUCTION 

Background

Effective resource allocation is key to improving efficiency of production of livestock and poultry.  Managerial and biological processes involved in the conversion of resources to a product by domestic animals are inherent components of a system.  Traditional analytical approaches identify technologies to improve domestic animal production efficiency, but emphasize individual components of the system.  Interactions among the components make typical domestic animal production systems complex and inconsistencies between experimental results and system performance may result. Integrating scientific knowledge using computer-based technologies facilitates improving production efficiency through understanding of entire production systems.

Vision Statement

 Improved production efficiency through integration of knowledge.

Mission Statement

We seek to provide customers with decision aids which synthesize existing knowledge related to conversion of resources to end products and to environmental impacts of livestock and poultry production.

Impact

Objective and effective decision making by policy makers, production managers, consultants, and scientists in evaluating effects of policy, management alternatives, and in identifying needed research.

Linkages

Other National Programs: 205 Rangeland, Pasture, and Forages; 206 Manure and Byproduct Utilization, 207 Integrated Agricultural Systems.

Other Agencies and Departments: Universities.

Private Sector: National Cattlemen’s Beef Association.

II. PROBLEM TO BE ADDRESSED

User Information Packages

Problem Statement

Producers want access to knowledge allowing them to improve efficiency of producing  livestock and poultry.  Discipline specific research has created a large body of information describing biological processes in components of production systems. Transfer of this information will be enhanced through use of computer models.  Models that describe growth and production responses for crops and domestic animals, predict production environment characteristics, and whole farm models are available.  These models were developed to address specific questions and are not structured for management decisions.  Producers and other stakeholders may not have the resources necessary to apply these components to decision making.  Decision support systems are one approach to overcome these limitations.

Goals

1. Integrate information pertaining to crop growth environment, harvesting methods, storage conditions, and ration characteristics into feed evaluation systems.

2. Evaluate whole farm management options, including feed production strategies, to reduce nitrogen in fertilizer and manure.

3. Determine combinations of production inputs that optimize product quality within economic and biological constraints.

4. Improved decision making by producers of livestock and poultry products.

Approach

1. Engage producers in identifying needed user information packages. 

2. Survey existing knowledge bases to obtain software modules that characterize biological process(es); identify biological processes where existing modules are deficient or non-existent; and when necessary reformulate predictive functions.

3.  Use existing databases to test and evaluate new modules.

4. Develop user-friendly information packages linking discipline oriented biological process modules into integrated components and structured models of production systems.

5. Deliver information packages to producers for evaluation and acceptance

Outcomes

1. User-friendly decision-support software that accurately predicts outcomes of biological processes involved in domestic animal production.

2. More efficient use of resources in production systems.

3. Reduced environmental impact from livestock and poultry production systems.

ARS Locations

Brooksville, FL; Clay Center, NE; Madison, WI