United States 

Department of 

Agriculture

Agricultural

Research

Service

Cooperative

State Research,

Education, and

Extension Service

September 2007

Blueprint for USDA 

Efforts in Agricultural 

Animal Genomics 

2008­–2017

Education & Training

Animal Resource Populations

Databases & Bioinformatics

Genomic Tools

Gene Discovery

Functional Genomics

Host:Pathogen Interactions

Systems Biology

Genome-Enabled Animal Selection

Precision Management Systems

Precision Mating Systems

Animal Identity/Traceability

Discovery Science

Science to Practice

Infrastructure

Blueprint for USDA 

Efforts in Agricultural 

Animal Genomics 

2008–2017

United States 

Department of 

Agriculture

Agricultural

Research

Service

Cooperative

State Research,

Education, and

Extension Service

September 2007

USDA Animal Genomics Strategic Planning 

Task Force
Abstract

USDA Animal Genomics Strategic Planning 

Task Force. 2007. Blueprint for USDA Efforts 

in Agricultural Animal Genomics 2008–2017. 

U.S. Department of Agriculture, Agricultural 

Research Service and Cooperative State 

Research, Education, and Extension Service, 

Washington, DC.

Following the recommendation of the 

National Science and Technology Council’s 

Interagency Working Group on Animal 

Genomics, a task force was established 

in January 2006 to develop a blueprint 

for USDA efforts in agricultural animal 

genomics. This task force of Agricultural 

Research Service (ARS), Cooperative State 

Research, Education, and Extension Service 

(CSREES), and university scientists and 

administrators developed a “Blueprint” for 

future research, education, and extension 

efforts in agricultural animal genomics, 

based on a vast array of stakeholder input. 

The Blueprint is designed as a pyramid, with 

“Science to Practice” at the top, supported by 

fundamental and mission-oriented research in 

“Discovery Science,” and is based on a solid 

foundation of “Infrastructure.” The Blueprint 

will guide activities in this critical area of 

science over the coming decade.

Keywords: animal genomics, animal 

genomes, food animal, animal production, 

animal selection, genome mapping, 

bioinformatics, comparative genomics, 

functional genomics, genetic selection, 

systems biology.

Mention of trade names or commercial 

products in this report is solely for the 

purpose of providing specific information 

and does not imply recommendation or 

endorsement by the U.S. Department of 

Agriculture.

To ensure timely distribution, this report was 

reproduced essentially as supplied by the 

authors. It received no publication editing and 

design.

While supplies last, single copies of this 

publication may be obtained at no cost from 

Ronnie D. Green, USDA-ARS, National 

Program Leader, Animal Production, 5601 

Sunnyside Avenue, Room 4-2104, Beltsville, 

MD 20705-5148; or by e-mail at ronnie.green@

ars.usda.gov.

Copies of this publication may be purchased 

in various formats (microfiche, photocopy, 

CD, print on demand) from the National 

Technical Information Service, 5285 Port 

Royal Road, Springfield, VA 22161, (800) 553-

6847, www.ntis.gov.

The U.S. Department of Agriculture (USDA) 

prohibits discrimination in all its programs 

and activities on the basis of race, color, 

national origin, age, disability, and where 

applicable, sex, marital status, familial status, 

parental status, religion, sexual orientation, 

genetic information, political beliefs, reprisal, 

or because all or part of an individual’s 

income is derived from any public assistance 

program. (Not all prohibited bases apply to 

all programs.) Persons with disabilities who 

require alternative means for communication 

of program information (Braille, large print, 

audiotape, etc.) should contact USDA’s 

TARGET Center at (202) 720-2600 (voice and 

TDD). To file a complaint of discrimination, 

write to USDA, Director, Office of Civil 

Rights, 1400 Independence Avenue, S.W., 

Washington, D.C. 20250-9410, or call (800) 

795-3272 (voice) or (202) 720-6382 (TDD). 

USDA is an equal opportunity provider and 

employer.

September 2007
Contents

Executive Summary........................................................................... 1

Introduction ........................................................................................ 4

Stakeholder Input............................................................................... 5

Science to Practice .............................................................................. 7

Discovery Science............................................................................... 9

Infrastructure .................................................................................... 12

Conclusion ........................................................................................ 14

About the Task Force ....................................................................... 16

References.......................................................................................... 17

Appendix I ........................................................................................ 19

Appendix II....................................................................................... 20
Discovery Science

Science to Practice

Infrastructure

Animal Identity/Traceability

Precision Management Systems

Precision Mating Systems

Genome-Enabled Animal Selection

Systems Biology

Host:Pathogen Interactions

Functional Genomics

Gene Discovery

Education & Training

Animal Resource Populations

Databases & Bioinformatics

Genomic Tools
Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017

Science to Practice

Infrastructure

Discovery Science

Executive Summary

Animal improvement programs have 

greatly increased the ability of animal 

agriculture to provide high quality, low 

cost and safe animal products to the 

American consumer. A large part of this 

change is a result of investments made 

by USDA in quantitative animal genetics 

and animal molecular biology research 

as well as the ability of private industry 

to rapidly adopt these new technologies. 

Investments in genomic technology, from 

gene discovery to sequenced genomes, 

and state-of-the-art technology developed 

by the biomedical research community, 

have animal agriculture poised at the 

threshold of the genomic revolution. 

Although quantitative geneticists have 

made tremendous progress in improving 

the efficiency of meat, milk, and egg 

production, there is still a significant 

need for increased production efficiency. 

For example, if Americans are to fully 

meet the 2005 Dietary Guidelines for 

Americans, U.S. dairy producers will 

need to increase annual production of 

milk and milk products (especially fatfree or low-fat dairy products) by an 

estimated 65% (Buzby et. al., 2006). In 

addition, by 2020-2030 world demand for 

meat and dairy products is expected to 

increase 40-50% (Rosegrant et. al., 2001; 

FAO, 2002), which will stimulate the 

competitiveness of American food animal 

products. Genome-enabled technologies 

will also lead to improvements in product 

quality, including nutrient-fortified lean 

meat, milk, and eggs to satisfy increasing 

demand for healthier food from aging or 

obese consumers. Animal genomics will 

also provide the ability to understand and 

improve genetic traits that were difficult 

to measure with quantitative genetics 

approaches (e.g., disease resistance, 

animal well-being, feed efficiency, and 

product quality) and will lead to enhanced 

functionality and well-being of animals 

in environmentally neutral production 

systems. In the near future, genomeenabled technologies will be used to trace 

animals and animal products throughout 

the food production chain resulting in 

enhanced biosecurity as well as increased 

food safety and consumer confidence. 

Thus, with additional USDA-supported 

efforts, new genomic technologies will 

be available to livestock, poultry, and 

aquaculture producers to improve the 

efficiency, sustainability, biosecurity, and 

social acceptance of agricultural animal 

production.

To meet these national needs, a blueprint 

for future research, education, and 

extension efforts in agricultural animal 

genomics has been developed by a task 

force of ARS, CSREES, and university 

scientists and administrators. The 

Blueprint is built on a vast array of 

stakeholder input and is designed as 

a pyramid, with Science to Practice at 

the top supported by fundamental and 

mission oriented research in Discovery 

Science, and is based on a solid foundation 

of Infrastructure. 

The goals and recommendations of 

the Blueprint are consistent with the 

President’s American Competitiveness 

Initiative (2006) which stresses the 

importance of targeting “..investments 
Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017

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Discovery Science

toward the development of deeper 

understanding of complex biological 

systems..”. The Blueprint is consistent 

with the 2005-2010 USDA Strategic 

Plan, including its Goal 1 (Enhance 

International Competitiveness of 

American Agriculture), Goal 2 (Enhance 

the Competitiveness and Sustainability 

of Rural and Farm Economies), Goal 4

(Enhance Protection and Safety of the 

Nation’s Agriculture and Food Supply), 

and Goal 5 (Improve the Nation’s 

Nutrition and Health). Appendix I 

provides additional information regarding 

how the Blueprint aligns with these USDA 

Goals.

Science to Practice Priorities: 

Quantitative genetics has been used 

for many years in selecting animals for 

improved production (e.g., growth, yield, 

efficiency) and has achieved remarkable 

results. The addition of animal genomic 

technology to quantitative genetics 

programs has the potential to lead to more 

accurate and rapid animal improvement, 

especially for phenotypic traits that are 

difficult to measure (e.g. disease resistance, 

animal well-being, feed efficiency, product 

quality). Genomic technologies also offer 

new opportunities to develop precision 

management systems to optimize the 

production environment based on an 

animal’s genotype. In the short-term, 

research, education, and extension efforts 

in animal genomics are expected to deliver 

the following genome-based technologies 

to animal producers:

1) Whole-genome-enabled animal 

selection.

2) Prediction of genetic merit of 

individual animals from genomebased data combined with 

phenotypes.

3) Integration of genomic data into large 

scale genetic evaluation programs 

and the use of genomic information to 

design precision mating systems.

4) Precision management systems to 

optimize animal production, health, 

and well-being. 

5) Genomic capabilities that enable 

parentage and identity verification 

(traceability). 

Discovery Science: Critical gaps in 

our understanding of gene structure 

and function in animals must be filled 

before animal genomics technologies 

can be successfully applied to animal 

industries. Agricultural animals form a 

unique resource to study the fundamental 

underlying biological mechanisms of gene 

structure and function, regulation of gene 

expression, and the genetic contribution 

to phenotypic variation because, unlike 

humans, animals have been artificially 

selected to express or repress specific 

traits. Advances in discovery science will 

require interdisciplinary teams of scientists 

that address complex agricultural issues 

with state-of-the-art equipment and 

approaches that include systems biology 

and comparative genomics. The following 

are priorities in discovery science for 

animal genomics:

1) Identify genes and gene products 

that regulate important traits in 

agricultural animals such as disease 

resistance, animal well-being, feed 

efficiency, and product quality. 
Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017 

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2) Understand mechanisms that regulate 

agriculturally relevant genes in a 

systems biology framework.

3) Define the mechanisms through which 

specific genes and genetic variation 

influence phenotypes and phenotypic 

variation. 

4) Understand the roles and interactions 

of host animal and microbial genomes 

and environmental influences (e.g., 

animal feed, vaccines) for improving 

animal health, well-being, and 

production efficiency. 

Infrastructure: A solid infrastructure is 

needed to support advances in discovery 

science. The priorities for a solid 

infrastructure are:

1) Genomic tools to connect genotype to 

phenotype and elucidate pathways 

of complex traits for all agricultural 

animal species. These genomic 

tools include comprehensive, 

high resolution genome maps and 

assembled and annotated genomic 

sequences.

2) National, comprehensive databases 

and the statistical and bioinformatics 

tools that integrate genomic, 

phenotypic, and experimental 

information for each species. 

3) Genetic resources such as centralized 

animal populations that are deeply 

phenotyped as well as repositories for 

cell lines, DNA and RNA collections, 

and gene expression resources for all 

species. The mission of the National 

Animal Germplasm Program should 

be broadened to become a coordinated 

national repository for genomic 

DNA, appropriate DNA libraries, and 

specialized cell lines. 

4) Education and training of students, 

scientists, and the public on 

genome-enabled animal sciences 

and opportunities that help prepare 

the next generation of scientists. 

Particular emphasis should be placed 

on integrating quantitative genetics, 

genomics, immunology, nutrition, 

physiology, biochemistry, cell biology, 

developmental biology, ecology, 

engineering, physics, mathematics, 

and computer science with 

development of scientists who have a 

keen appreciation for, and knowledge 

of, animal production systems. 

Additional emphasis on extension 

and outreach will enable and facilitate 

effective translation of genomics 

research and resulting technologies 

to the agricultural animal production 

sector and the public.
 Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017

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Introduction

Agricultural animal research has been 

successful in developing technology 

and methodologies that have enhanced 

production efficiency of the beef, dairy, 

swine, poultry, sheep, and aquaculture 

industries. Excellent examples of the 

changes that have taken place over the 

last ~50 years are: 1) The dairy industry’s 

coupling of genetic selection and 

efficacious use of artificial insemination 

has more than doubled the annual milk 

yield per cow while reducing the size of 

the national dairy herd by about 50%; 2)

Genetics, nutrition and other management 

changes resulted in a “modern day” 

broiler that requires approximately 

one-third the time and over a threefold 

decrease in the amount of feed consumed 

to produce a market-age broiler; and 

3) The pounds of feed needed to produce 

a pound of pork is estimated to have been 

halved. While quantitative geneticists have 

been successful in improving production 

traits, genomic technology has potential 

to lead to more accurate and rapid animal 

improvement, especially for phenotypic 

traits that are difficult to measure (such 

as disease resistance, animal well-being, 

feed efficiency, and product quality). 

The potential for future improvements 

in animal production efficiency, quality 

of animal products, animal health and 

animal well-being lies in the elucidation 

and understanding of interactions of the 

various components of animal biology 

in concert with all of the parameters of 

the production environment. To begin 

to fully understand these interactions, a 

redirection of the traditional “reductionist 

science” approach to a “systems biology”

approach is required. It is also clear that 

publicly supported agricultural research 

must be focused on enhancing the nutrient 

composition of meat, milk, and eggs and 

enhancing the functionality and wellbeing of animals in environmentally 

neutral production systems.

In the past two decades, molecular biology 

has changed the face of agricultural 

animal research, primarily in the arena of 

genomics and the relatively new offshoot 

areas of functional genomics, proteomics, 

transcriptomics, metabolomics and 

metagenomics. Recently, the agricultural 

research community has been able to 

capitalize on the infrastructure built by 

the human genome project (Collins et al., 

2003; International HapMap Consortium, 

2005) by sequencing two of the major 

agricultural animal genomes, Gallus 

domesticus (International Chicken Genome 

Consortium, 2004; Wong et al., 2004) and 

Bos taurus (Gibbs et al., 2002). The 2006 

calendar year marked a major milestone 

in the history of agricultural animal 

research since annotated draft genome 

sequences were completed for chickens 

and cattle and sequencing was initiated 

for the porcine and equine genomes. We 

now have in place a powerful toolbox 

for understanding the genetic variation 

underlying economically important and 

complex phenotypes of agricultural 

animals.
Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017 

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Stakeholder Input

The priorities and recommendations 

contained in this Blueprint are based on a 

substantial amount of stakeholder input 

that was provided to USDA National 

Program Staff by scientists, producers, 

animal industry and commodity groups, 

other federal research agencies, and the 

general public.

In 1990, an Allerton Conference entitled 

“Mapping Domestic Animal Genomes: 

Needs and Opportunities” was hosted 

by the University of Illinois while a 

Banbury Conference was held at Cold 

Spring Harbor on “Mapping Genomes 

of Agriculturally Important Animals”. 

Participants at these workshops 

recommended to USDA that genetic maps 

be developed for each of the agriculturally 

important species (cattle, swine, poultry, 

sheep, and fish). 

A second Allerton Conference entitled 

“Genetic Analysis of Economically Important 

Traits in Livestock” was convened in 1996. 

The primary recommendation of the 

workshop was a call for building the 

research infrastructure necessary to enable 

researchers to identify important genes 

that control economically important traits 

and, eventually, gain an understanding of 

the function of individual genes and their 

interactions across the genome (Schook, 

1997). 

In 2002, the National Academy of 

Sciences hosted a public workshop 

entitled “Exploring Horizons for Domestic 

Animal Genomics” (National Academies 

Press, 2002). The workshop participants 

identified the need to produce highcoverage, draft genome sequences of some 

domestic animal species (cattle, chicken, 

swine, dog, and cat) for deposit into the 

public domain databases. Furthermore, it 

was recognized that there would be a need 

to scale up bioinformatics resources to 

make effective use of the information that 

would result from the genome sequencing 

projects. Based upon the experiences of 

the National Plant Genome Initiative, it 

was also discussed that funding for such 

large-scale projects would likely need to 

come from a variety of sources, including 

the U.S. Federal government, private 

industry, and international partners.

In 2002, a third Allerton Conference 

entitled “Beyond Livestock Genomics” was 

conducted to develop an initial plan for 

the full utilization of genomic information 

to promote animal health and productivity. 

The overarching recommendation from 

this workshop was that additional basic 

research was needed to identify genomic 

mechanisms and novel genes/proteins 

in a variety of tissues under a variety of 

environmental conditions (Hamernik 

et al., 2003). Functional genomics was 

recognized as the vehicle for capitalizing 

on the investment of obtaining whole 

genome sequence information. The need 

to increase bioinformatics infrastructure, 

teaching, and outreach efforts in animal 

genomics was recognized also. To further 

define priorities for animal bioinformatics, 

an electronic workshop was conducted 

in 2002. Priorities for animal genome 

database development included: 1) data 

repository, 2) tools for genome analysis, 
 Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017

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3) annotation, 4) practical application 

of genomic data, and 5) a biological 

framework for DNA sequence (Hamernik 

and Adelson, 2003).

 

An Interagency Working Group (IWG) 

on Domestic Animal Genomics was 

chartered in September of 2002 by the 

U.S. National Science and Technology 

Council. The membership of the IWG 

included representatives from the 

Department of Agriculture (USDA), 

Department of Energy (DOE), Food and 

Drug Administration (FDA), National 

Institutes of Health (NIH), National 

Science Foundation (NSF), Office of 

Science and Technology Policy (OSTP), 

Office of Management and Budget (OMB), 

Department of Homeland Security (DHS) 

and the U.S. Agency for International 

Development (USAID). The IWG 

identified the following broad strategic 

goals: 1) Bring into place the programmatic 

elements needed to advance the study 

and understanding of domestic animal 

genomes, including large-scale DNA 

sequencing; functional characterization 

of expressed genes (functional genomics); 

tools for data storage, analysis and 

visualization (bioinformatics); and 

study of similarities among genomes of 

different species (comparative genomics); 

2) Leverage the national infrastructure 

for large-scale DNA sequencing that has 

been established for the Human Genome 

Project and other vertebrate and model 

organism genomes; 3) Advance and utilize 

the enabling tools and infrastructure of 

functional genomics and bioinformatics 

to enhance the understanding not only 

of basic science and disease mechanisms, 

but also to address critical agricultural 

missions, including animal health and 

well-being, food safety, and human 

nutrition; 4) Ensure that genomics data 

are freely available in the public domain 

and genomics reagents and resources are 

available to the public; 5) Increase the 

training opportunities for genomics and 

bioinformatics at all levels of education; 

and 6) Coordinate and encourage 

international cooperation to achieve these 

goals. 

In early 2004, as the sequencing goals 

of the IWG appeared to be within 

reach, the IWG charged the USDA with 

evaluating how bioinformatics and 

functional genomics programs should be 

developed further to allow full utilization 

of annotated genome sequences and 

associated tools. An Animal Genomics 

Workshop was convened by USDA 

administrators in ARS and CSREES in 

2004. The workshop resulted in a list of 

priorities in each of these areas for the 

“post-sequencing era” for agricultural 

animal genomics (Green et al., 2007). A 

primary recommendation resulting from 

this workshop was that “USDA should 

expeditiously develop a coordinated longterm strategic plan for efforts in agricultural 

animal genomics”. Thus, in January 2006 

the USDA Undersecretary for Research, 

Education, and Economics appointed an 

Animal Genomics Strategic Planning Task 

Force to develop a Blueprint intended to 

guide future decision making and priority 

setting by the Department and its relevant 

agencies.
Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017

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In 2006, the ARS and CSREES conducted a 

joint stakeholder workshop in the area of 

animal production and well-being where 

previous input was further validated by 

scientists, producers, and representatives 

of animal commodity groups and 

animal industries. A summary of the 

ARS and CSREES stakeholder workshop 

is available at: (http://www.ars.usda.

gov/research/programs/programs.

htm?np_code=101&docid=13166 ). 

Additionally, in July 2006, a US-EC 

Livestock Genomics Symposium was held 

under the auspices of the US-EC Joint Task 

Force on Biotechnology. The priorities 

identified in this session allowed USDA to 

assure that efforts between the European 

Commission and U.S. research programs 

were complementary in achieving impacts 

in agricultural animal genomics and 

also identified areas for transatlantic 

collaboration (Burfening et. al., 2006). 

Input from both of these events was used 

in the formulation of the USDA Blueprint.

Science to Practice

Application of basic science to improve 

animal production practices is the goal 

of animal genomics research. In the 

short-term, the combined use of genomic 

information with existing animal breeding 

and animal management programs will 

provide immediate impacts, such as more 

accurate and accelerated rates of genetic 

improvement of breeding stock (especially 

for traits that have been traditionally 

difficult to measure), animals that are 

more adaptable and better suited to 

various production environments, and 

new genome-based technologies to enable 

parentage and identity verification (i.e., 

traceability). Delivery and adoption of 

new genome-based technologies will 

require integrated activities involving 

basic scientists, educators (classroom 

and extension specialists), animal 

breeding and artificial insemination 

organizations, and producers working 

together to utilize these technologies. In 

the long-term, animal genomics efforts 

will lead to efficient and economical 

production of human pharmaceutical 

proteins in animals, new technologies 

for manipulation of gene expression 

in animals (i.e., RNA interference, 

transgenesis, etc.), and improved methods 

for conserving biodiversity and unique 

animal germplasm. Because of the existing 

widespread use of quantitative genetics 

in animal breeding programs in the U.S. 

and the rapid rate at which genomic 

information is being discovered, the 

initial applications of genomics efforts 

will be the combined use of genomic 

data with quantitative genetics for 

animal improvement, management, 

and biosecurity. Thus, USDA-supported 

research, education, and extension efforts 

in animal genomics are expected to deliver 

the following genome-based technologies 

to livestock producers in the short term: 

1) Whole genome enabled animal 

selection resulting in a significant 

reduction in selection cost and 

generation interval. One of the first 

and most exciting avenues to explore 

is the possibility of using dense single 

nucleotide polymorphism (SNP) maps 

coupled with haplotype information 
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within species to enable “wholegenome selection” for traits important 

in the overall breeding objective. Such 

approaches should accelerate the 

rate of genetic improvement, while 

simultaneously reducing progeny 

testing costs to the animal industries. In 

addition, precise genetic improvement 

will be obtained because SNP markers 

can be used to monitor selection for 

more than one trait throughout the 

entire genome.

2) Prediction of genetic merit from 

genome-based data combined with 

phenotypes. In order to fully harness 

the power of genomic information 

for genetic improvement, a meshing 

together of quantitative genetics 

theory and platforms with genomic 

data will be required. Additionally, 

significant research and software 

development is required to integrate 

all forms of genomic information, 

following validation, into large-scale 

genetic evaluation systems. A critical 

step in the process of moving to 

genome-enabled animal improvement 

is the development of standardized 

systems for recording performance 

phenotypes for complex and difficult 

to measure traits. This is particularly 

true for traits that capture the genetic 

variation of animals for adaptation 

to their production environments 

(stress resistance, behavior, innate 

resistance to disease) and for measures 

of efficiency of nutrient utilization 

(e.g. feed efficiency), amongst others. 

A major effort will be required 

for these traits to be defined and 

parameterized, followed by evaluation 

in genetic resource populations to 

identify genomic control mechanisms 

underpinning observed variation.

3) Integration of genomic data into large 

scale genetic evaluation programs 

and the use of genomic information 

to design precision mating systems. 

Not only will genomic information be 

of use in prediction of genetic values 

for complex traits, the resulting tools 

from such approaches will also allow 

design of precision mating systems. 

More precise information at the 

genomic level can be incorporated into 

mating system design to minimize 

the cumulative effects of inbreeding 

from selection and predict matings 

that will optimize the use of nonadditive genetic variation for traits 

where hybrid vigor is of importance. 

Knowledge of epigenetic effects will 

also be required to fully capture the 

value of this use of genomic data. 

4) Precision management systems to 

optimize animal production. Genomic 

information will also provide the 

basis for development of precision 

management systems. Knowledge of 

an animal’s genotype will allow precise 

sorting of animals into the optimal 

production environment, resulting 

in enhanced animal well-being. For 

example, the genotype of some beef 

and dairy cattle may be more suited 

to pasture-based production systems 

rather than confinement systems. 

Feeding regimens and preventative 

health care programs can also be 
Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017 

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designed to match an animal’s 

genotype and lead to increased 

production efficiency, targeted market 

endpoints, and new opportunities for 

niche markets. The expected amount 

of genomic information will require 

development of decision support 

systems for use in the industries to 

implement and manage such genomeenabled precision management 

systems. The ability to precisely control 

expression of selected genes (such as 

inactivation of the myostatin gene to 

increase lean muscle mass) may also 

lead to increased production efficiency, 

more consistent meat quality, and 

healthier animals.

5) Genomic capabilities that enable 

parentage and identity verification 

(traceability). Development of 

high-throughput genotyping 

systems that allow for individual 

animal identification and parentage 

identification will likely have an 

immediate impact on all animal 

industries. High-throughput SNP 

genotyping systems are affordable and 

will likely be commercially available 

for most agricultural animal species 

in the near future. In today’s world, 

biosecurity is a major issue due to the 

concentration of animal populations 

and widespread movement of animals. 

Genomic techniques and technology 

should be harnessed to provide a 

quick, affordable, and foolproof means 

of animal identification for traceability 

resulting in increased food safety 

and consumer confidence in the food 

supply.

Discovery Science

Critical gaps in our understanding of 

gene structure and function in animals 

must be filled before genome-enabled 

technologies can be successfully applied 

to animal improvement, management, 

and biosecurity programs. Rapid progress 

in discovering new knowledge related 

to animal gene structure and function 

will require interdisciplinary teams 

of scientists, access to state-of-the-art 

equipment, technology, and approaches 

that include systems biology and 

comparative genomics. 

Instead of analyzing individual 

components or aspects of the organism, 

systems biology incorporates all 

biological components and their 

interactions. Systems biology will promote 

identification and determination of the 

function(s) of a complete set of genes and 

regulatory elements and will integrate 

analysis of DNA sequences, transcriptional 

regulation, proteomics, and metabolic 

networks and pathways. The ultimate 

goal is to understand how genotype 

contributes to phenotype and phenotypic 

variation. Animal populations that have 

been selected for specific phenotypes 

and that have been well-characterized at 

the molecular and whole animal levels 

provide a valuable resource for discovery 

research in this area.

Comparative genomics will be an essential 

tool to take advantage of knowledge 

obtained from species with finished 

genome sequences (i.e., human, mouse, 

rat) to advance the knowledge of genomes 
10 Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017

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from agricultural animals. DNA sequences 

that have been highly conserved across 

species are likely to have functional 

significance, either as genes or as 

regulatory elements. Agricultural animals 

will play a significant role in revealing 

the basic biology of how chromosomes 

evolved and how functional elements 

within a genome are organized to produce 

different phenotypes. Comparative 

genomics will also point to specific 

targets for understanding and potentially 

modulating gene expression. Since it is not 

likely that the genomes from all animals of 

agricultural importance will be sequenced 

in the near future, comparative genomics 

will provide an important tool for 

extrapolating genetic information between 

closely related species (such as chickens 

and turkeys or cattle and sheep).

The priorities for advancing discovery 

science in the short-term are:

1) Identify genes and gene products 

that regulate important traits in 

agricultural animals. Previous 

research in agricultural animal 

genomics has identified a substantial 

number of genomic regions harboring 

Quantitative Trait Loci (QTL) for a 

variety of economically important 

traits. Fine-mapping of these QTL 

and identification of many more 

gene and genic interaction effects for 

a wide array of traits of economic 

and societal importance are expected 

in the near future. Comparative 

genomics will be an important tool 

to discover genes that are common 

across species (and thus are thought to 

control important biological processes 

conserved throughout evolution) as 

well as novel genes within a species 

that may give rise to species specificity 

and phenotypic variation. In addition, 

proteomics and metabolomics 

studies will need to be conducted to 

discover novel proteins that regulate 

agriculturally relevant traits in 

agricultural animals.

2) Understand mechanisms that regulate 

agriculturally relevant genes in 

a systems biology framework. 

Although progress has been made in 

understanding the mechanisms that 

regulate individual genes in isolated 

systems (i.e., in isolated cell cultures), 

many of the basic mechanisms that 

regulate gene expression in the context 

of the whole animal still need to be 

determined. Expression profiling of 

large numbers of genes across diverse 

tissues, animal populations, and 

environmental conditions using DNA 

chips, microarrays, or next-generation 

sequencing will identify novel genes 

and characterize spatial and temporal 

expression of these genes. Additional 

technologies to knock out (such as 

RNA-interference; RNAi) or knock-in 

(i.e., transgenesis with opportunities 

for spatial and temporal control of the 

transgene) gene expression will need to 

be optimized for more efficient use in 

animals.
Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017 11

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Infrastructure

Discovery Science

3) Define the mechanisms through which 

specific genes and genetic variation 

influence phenotypes and phenotypic 

variation. Discovery science is also 

needed to unravel the complexities 

of epistatis and the interactions of 

genotype by environment and how 

they affect phenotype. Development 

of clear and standardized descriptions 

or ontologies for defining phenotypes 

(especially for phenotypes that are 

difficult to measure) for animals are 

needed. Efficient, systematic, and 

comprehensive phenotypic screening 

procedures and tools that will permit 

comparison among laboratories are 

also needed. The identification of 

haplotypes within and between breeds 

of animals will enhance the mapping of 

traits and the ultimate identification of 

mutations underlying those traits that 

may give rise to phenotypic variation. 

4) Understand the role of host 

genomes and microbial genomes 

to improve animal health and wellbeing. Despite efforts to control the 

production environment (e.g. housing 

systems, feeding systems, thermal 

environment), animals are not born 

and raised in isolation. The interaction 

of host, beneficial and pathogenic 

microbes, and environment ultimately 

determines whether an animal remains 

healthy or is challenged by disease. 

Consequently, understanding the 

variation in how an animal responds 

to various microbes and environments 

can have profound influences on the 

outcome of the interactions. Current 

efforts of most scientists are directed 

toward understanding the genetics 

or physiology of the host, finding 

pathogenicity genes in viruses or 

other pathogens, and examining how 

animal feeds and environmental 

parameters influence the composition 

of the microbial community in 

the digestive tract. While these 

approaches have been successful, 

further advances in animal health 

and well-being will require a systems 

biology approach by interdisciplinary 

teams of scientists. State-of-the-art 

metagenomics technologies can 

be used to understand the genetic 

composition of poorly characterized 

microbial communities in the rumen 

and gastrointestinal tract of animals. 

Functional genomics efforts will define 

the microbial response in the rumen or 

gastrointestinal tract to different hosts 

or changes in environmental conditions 

such as nutrition, management, or 

therapeutics. Future genomics efforts 

will allow selection of animals for 

superior disease resistance, vaccine 

response, or adaptability to various 

production environments. In addition, 

improved vaccines, diagnostics 

and therapeutics can be developed; 

producers can devise better precision 

feeding systems to improve efficiency 

of nutrient utilization and enhance 

animal well-being; and use of antimicrobials and pesticides can be 

reduced in agricultural animal 

production.
12 Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017

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Infrastructure

Discovery Science

Infrastructure

A solid infrastructure is needed to 

facilitate advances in discovery science 

in animal genomics in a time and costeffective manner. Infrastructure refers 

to state-of-the-art genomic tools and 

resources that are available to the scientific 

community as well as a highly trained 

and skilled workforce. The infrastructure 

needed to advance animal genomics 

efforts does not require additional bricks 

and mortar. The priorities for a solid 

infrastructure in animal genomics are:

1) Genomic tools to connect genotype to 

phenotype and elucidate pathways of 

complex traits for all animal species 

important to agriculture. These 

genomic tools include: comprehensive, 

high resolution genome maps and 

assembled and annotated genomic 

sequences. 

Genome Maps: Genetic maps are 

the basis for identifying genome 

regions that affect genes of economic 

importance in agricultural animals. 

Genetic linkage maps are needed for all 

agricultural animal species so that each 

species can utilize the most current 

selection practices. Linkage maps 

for all species must be of sufficient 

density so that genomes can be 

scanned effectively and efficiently for 

economically important loci. Physical 

maps are needed so that researchers 

can characterize specific regions of the 

genome. Maps based on segregation of 

markers in irradiated hybrid cell lines 

provide the resolution needed to order 

markers and genes in very narrow 

regions of the genome (less than 

100,000 bases apart) and are excellent 

resources for developing comparative 

maps between species. Whole genome 

physical maps are composed of 

ordered BAC clones, which contain 

large segments of cloned DNA 

(100,000-200,000 bases) necessary to 

develop markers for use in commercial 

animal populations. 

Assembled and Annotated Genomic Sequences:

An assembled genome sequence is a 

compilation of all of the available DNA 

sequence into long contiguous (contigs) 

stretches of DNA and assignment of 

DNA contigs to specific chromosomes. 

Assembled genome sequences provide 

insight into the evolutionary processes that 

occurred during development of a species; 

allow basic studies on the architecture of a 

genome; allow characterization of genetic 

variation that underlies traits; and provide 

information regarding organization of 

genes and their impact on expression of 

genes in different tissues. An annotated 

genome sequence contains information 

regarding the gene name, gene structure, 

function of the gene product, cellular 

location of the gene product, as well as 

how this knowledge was determined (i.e., 

literature citation). A finished, annotated 

genome sequence should be available for 

the most economically important species 

(currently these species include: cattle, 

chicken, and swine). The target for these 

species should be a 10-fold or greater 

coverage of the genome. The next tier 

of economic importance (for example: 

catfish, equine (currently at 6.8X), salmon, 
Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017 13

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Infrastructure

Discovery Science

sheep, tilapia and turkey) should have 

a high quality draft genome sequence 

(approximately 6X). This level of genome 

sequence quality is necessary for accurate 

functional genomic studies as well as 

comparative analyses. Additional species 

(for example: goat, oyster, shrimp, and 

trout) should have a low quality draft 

genome sequence (approximately 2X). 

This level of coverage, coupled with 

genetic and physical maps, would advance 

the basic biology of these species as well as 

allow for limited comparative analyses. 

2) National, comprehensive databases 

and the statistical and bioinformatics 

tools that integrate genomic, 

phenotypic, and experimental 

information for each species. To 

effectively use the resources being 

generated from efforts in animal 

genomics, there is a need to design, 

construct and maintain large 

comprehensive databases and the 

statistical and bioinformatic tools 

that integrate information from these 

databases for a variety of applications. 

As annotated sequence data, haplotype 

maps, SNP maps, expression profiling 

data, and other genomic data become 

available, these data will need to 

be integrated with phenotypic, 

pedigree, and experimental data 

into a common, national database. 

These databases will require a 

standardized ontology of genotypes 

and phenotypes and mechanisms to 

encourage centralization of producergenerated phenotypic data. The 

National Center for Biotechnology 

Information (NCBI) at the NIH is 

currently the warehouse for genome 

sequence information. However, NCBI 

does not have adequate resources 

to continue to maintain and curate 

all genome sequence databases. In 

addition, agricultural animal species 

have unique population characteristics 

(such as inbreeding or crossbreeding 

that are not present in other species) 

and require unique statistical tools for 

appropriate analyses. 

3) Centralized animal genetic resource 

populations that are deeply 

phenotyped and available to the 

research community. A centralized 

facility with sufficient technical 

expertise to preserve unique 

experimental animal populations, 

collect genotypic and phenotypic 

information on these animals, and 

make the populations available to the 

agricultural and biomedical research 

communities (i.e., the Jackson labs 

model) is needed. The emphasis in 

these animal populations should be on 

the development of rich phenotypic 

measures for common traits of interest 

as well as complex and difficult to 

measure traits such as feed efficiency, 

disease resistance, animal well-being, 

product quality, and environmental 

adaptability. Resource populations of 

animals with divergent responses to 

microbes, vaccines and therapeutics 

are also needed. Repositories for cell 

lines, DNA and RNA collections, 

and gene expression resources for 

all species should also be developed, 

maintained and made readily 

accessible to the scientific community. 
14 Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017

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Discovery Science

The mission of the National Animal 

Germplasm Program should be 

broadened to become a coordinated 

national repository for genomic DNA, 

appropriate DNA libraries, tissues 

and specialized cell lines for access by 

publicly-funded, U.S. scientists.

4) Education and training of students, 

scientists, and the public on 

genome-enabled animal science 

and opportunities that help prepare 

the next generation of researchers 

to work in interdisciplinary teams.

Particular emphasis should be placed 

on integrating quantitative genetics, 

genomics, immunology, nutrition, 

physiology, biochemistry, cell biology, 

developmental biology, ecology, 

engineering, physics, mathematics, and 

computer science with development 

of scientists who have a keen 

appreciation for and knowledge of 

animal production. There is a dearth 

of qualified candidates for scientific 

and technical support positions in 

the animal industry. The critical mass 

of expertise in animal genomics at 

colleges and universities across the 

globe that train these scientists is 

diminishing at a rapid pace. The U.S. 

faces the very real possibility of losing 

our ability to train new scientists in 

the integrated fields of quantitative 

genetics, statistics, and computational 

biology for animals unless this 

trend is reversed. Undergraduate 

animal sciences and related curricula 

should contain sufficient exposure to 

“omics” concepts and technologies, 

as well as the social science aspects of 

consumer acceptance of the application 

of genome-enabled technologies 

to animal production systems. In 

addition, faculty development, student 

recruitment and services, curriculum 

development, instructional materials, 

and innovative teaching methodologies 

in agricultural animal genomics are 

needed. A national animal genomics 

commodity-specific model for 

extension and outreach (based on 

“regional” extension specialists) 

will enable and facilitate effective 

translation of genomics research and 

resulting technologies to the animal 

production sector and the public.

Conclusion

Quantitative animal genetics and 

animal improvement programs have 

led to tremendous improvements in 

the efficiency of agricultural animal 

production during the last 50 years. 

Investments in genomic technology 

from gene discovery to sequenced 

genomes, as well as state-of-the-art 

technology developed by the biomedical 

research community, have animal 

agriculture poised at the threshold of 

the genomic revolution. Application of 

new genomic technologies to animal 

producers will improve the efficiency, 

sustainability, biosecurity, and social 

acceptance of animal production. This 

Blueprint describes future research, 

education, and extension efforts needed 

to develop and deliver animal genomeenabled technologies to the animal 

industry. The Blueprint contains specific 
Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017 15

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Discovery Science

recommendations for Infrastructure, 

Discovery Science, and Science to Practice. 

A summary of these recommendations is 

provided in Appendix II.
16 Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017

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Discovery Science

Ronnie D. Green (Chair)

National Program Leader

Animal Production

USDA-ARS

Muquarrab A. Qureshi (Co-Chair)

National Program Leader

Animal Genetics

USDA-CSREES

Peter C. Burfening

National Program Leader

Animal Genome Programs

USDA-CSREES 

Hans H. Cheng

Research Geneticist

USDA-ARS

Avian Disease and Oncology Lab

East Lansing, Michigan

Noelle E. Cockett

Dean

College of Agriculture

Utah State University

Logan, Utah

Deb Hamernik

National Program Leader

Animal Physiology

USDA-CSREES

Steven Kappes (Ex-Officio)

Deputy Administrator

Animal Production & Protection

USDA-ARS

Mark A. Mirando

National Program Leader

Animal Reproduction, Growth, and

 Nutrient Utilization Programs

USDA-CSREES

Anna C. Palmisano (Ex-Officio)

Deputy Administrator

Competitive Programs Unit

USDA-CSREES

Daniel L. Pomp

Professor

Departments of Nutrition and

 Cell and Molecular Physiology

University of North Carolina

Chapel Hill, North Carolina

Gary A. Rohrer

Research Geneticist

USDA-ARS

U.S. Meat Animal Research Center

Clay Center, Nebraska

Curt Van Tassell

Research Geneticist

USDA-ARS

Bovine Functional Genomics and

 Animal Improvement Programs Labs

Beltsville, Maryland

James Womack

Distinguished Professor

Department of Pathobiology

College of Veterinary Medicine and

 Biomedical Sciences

Texas A&M University

College Station, Texas

A word about the USDA Animal Genomics Strategic Planning Task Force:

Following the recommendation of the Interagency Working Group on Animal Genomics, a task force was 

established in January 2006 by USDA’s Under Secretary for Research, Education and Economics, Joseph Jen. 

This task force was charged with developing a Blueprint for USDA efforts in agricultural animal genomics. 

Members include:
Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017 17

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REFERENCES

American Competitiveness Initiative 

Leading the World in Innovation. 

Domestic Policy Council. Office of 

Science and Technology Policy. February 

2006. http://www.whitehouse.gov/

stateoftheunion/2006/aci/

Buzby, J.C., Wells, H.F., and Vocke, G. 

2006. Possible Implications for U.S. 

Agriculture from Adoption of Select 

Dietary Guidelines. http://www.ers.usda.

gov/Publications/ERR31/

Burfening, P., Claxton, J., Green, R., and 

Warkup, C. 2006. The Future of Livestock 

Genomics. Report on a Workshop Held 

in Brussels 17-18 July 2006 Under the 

Auspices of the US-EC Task Force on 

Biotechnology Research. www.ec.europa.

eu/research/biotechnology/ec-us/docs/

ec-us_workshop_animal_genomics_july_

2006_en.pdf

Collins, F.S., Green, E.D., Guttmacher, 

A.E., and Guyer, M.S. 2003. A Vision for 

the Future of Genomics Research. Nature

422:835-47.

Coordination of Programs on Domestic 

Animal Genomics: A Federal Framework. 

National Science and Technology Council. 

Committee on Science. Interagency 

Working Group on Domestic Animal 

Genomics. September 2003. www.ostp.

gov/nstc/html/Animal_Genome~WEB.

pdf

Food and Agriculture Organization of the 

United Nations. 2002. World Agriculture: 

Towards 2015/2030 Summary Report. 

http://www.fao.org/docrep/004/

y3557e/y3557e00.htm 

Gibbs, R.A., Weinstock, G., Kappes, S.M., 

Schook, L.B., Skow, L., and Womack, 

J. 2002. Bovine Genomic Sequencing 

Initiative: De-Humanizing the Cattle 

Genome. http://www.genome.

gov/Pages/Research/Sequencing/

SeqProposals/BovineSEQ.pdf 

Green, R.D., Qureshi, M.A., Long, J.A., 

Burfening, P.J., and Hamernik, D.L. 2007. 

Identifying the Future Needs for LongTerm USDA Efforts in Agricultural Animal 

Genomics. Int J Biol Sci 3:185-191.

Hamernik, D.L. and Adelson, D.L. 

2003. USDA Stakeholder Workshop on 

Animal Bioinformatics: Summary and 

Recommendations. Comp Funct Genom

4:271-274.

Hamernik, D.L., Lewin, H.A., and Schook, 

L.B. 2003 Allerton III. Beyond Livestock 

Genomics. Animal Biotechnology 14:77-82.

International Chicken Genome 

Consortium. 2004. Sequence and 

Comparative Analysis of the Chicken 

Genome Provide Unique Perspectives on 

Vertebrate Evolution. Nature 432:695-716.

International HapMap Consortium. 2005. 

A Haplotype Map of the Human Genome. 

Nature 437:1299-1320.
18 Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017

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National Academy of Sciences. 2002. 

Exploring Horizons for Domestic Animal 

Genomics: Workshop Summary. (Ed. Pool R 

and K Waddell). National Academy Press, 

Washington, DC (42 pp).

Rosegrant, M.W., Paisner, M.S., Meijer, 

S., Witcover, J. 2001. 2020 Global Food 

Outlook: Trends, Alternatives, and 

Choices. International Food Policy 

Research Institute, Washington, D.C. 

http://www.ifpri.org/pubs/fpr/fpr30.

pdf

Schook, L.B. (ed) 1997. Proceedings of 

the Allerton III Conference on Genetic 

Analysis of Economically Important Traits 

in Livestock. Animal Biotechnology 8:1-150.

United States Department of Agriculture 

Strategic Plan for 2005-2010. June 2006. 

http://www.ocfo.usda.gov/usdasp/

usdasp.htm

Wong, G.K. et al. International Chicken 

Polymorphism Consortium. 2004. A 

Genetic Variation Map for Chicken 

with 2.8 Million Single-Nucleotide 

Polymorphisms. Nature 432:717-22.
Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017 19

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Appendix I

Alignment of Blueprint Priorities With National Issues and USDA Strategic Goals

Competitiveness Animal

of American Production Health & Product Food

products* Efficiency** Well-Being*** Biosecurity*** Quality  Safety** * Traceability*** Sustainability**

Science to PracticeWhole Genome Selection

X

X

X

X

X

X

Prediction of Genetic Merit

X

X

X

X

X

Precision Mating

X

X

X

X

X

X

Precision Management

X

X

X

X

X

Genome-Based Traceability

X

X

X

X

X

X

Discovery ScienceGene Discovery

X

X

X

X

X

X

X

X

Systems Biology & Gene

 Mechanisms

X

X

X

X

X

X

X

Genetic Basis of Phenotypic

 Variation

X

X

X

X

X

X

X

Animal Health & Well-Being

X

X

X

X

X

X

X

InfrastructureGenomic Tools

X

X

X

X

X

X

X

X

Databases

X

X

X

X

X

X

X

X

Genetic Resources

X

X

X

X

X

X

X

X

Education and Outreach

X

X

X

X

X

X

X

X

*	 Relates to USDA Goal 1 (Enhance International Competitiveness of American Agriculture)

**	 Relates to USDA Goal

2 (Enhance the Competitiveness and Sustainability of Rural and Farm Economies)

***	 Relates to USDA Goal

4 (Enhance Protection and Safety of the Nation’s Agriculture and Food Supply)

****	Relates to USDA Goal

2 (Enhance the Competitiveness and Sustainability of Rural and Farm Economies) and Goal

5

(Improve the Nation’s Nutrition and Health)
20 Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017

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Infrastructure

Discovery Science Appendix II

Summary of the Animal Genomics Blueprint Priorities

Science to Practice:

1. Whole genome enabled animal selection.

2. Prediction of genetic merit of individual animals from genome-based data 

combined with phenotypes.

3. Integration of genomic data into large scale genetic evaluation programs and the 

use of genomic information to design precision mating systems.

4. Precision management systems to optimize animal production, health, and 

well-being. 

5. Genomic capabilities that enable parentage and identity verification (traceability).

Discovery Science:

1. Identify genes and gene products that regulate important traits in agricultural 

animals such as disease resistance, animal well-being, feed efficiency, and product 

quality.

2. Understand mechanisms that regulate agriculturally relevant genes in a systems 

biology framework.

3. Define the mechanisms through which specific genes and genetic variation 

influence phenotypes and phenotypic variation.

4. Understand the roles and interactions of host animal and microbial genomes and 

environmental influences (e.g., animal feed, vaccines) for improving animal health, 

well-being, and production efficiency.

Infrastructure:

1. Genomic tools to connect genotype to phenotype and elucidate pathways of 

complex traits for all agricultural animal species. These genomic tools include 

comprehensive, high resolution genome maps and assembled and annotated 

genomic sequences.

2. National, comprehensive databases and the statistical and bioinformatics tools that 

integrate genomic, phenotypic, and experimental information for each species. 

3. Genetic resources such as centralized animal populations that are deeply 

phenotyped as well as repositories for cell lines, DNA and RNA collections, and 

gene expression resources for all species. The mission of the National Animal 

Germplasm Program should be broadened to become a coordinated national 

repository for genomic DNA, appropriate DNA libraries, and specialized cell lines. 

4. Education and training of students, scientists, and the public on genome-enabled 

animal sciences and opportunities that help prepare the next generation of 

scientists. Particular emphasis should be placed on integrating quantitative 

genetics, genomics, immunology, nutrition, physiology, biochemistry, cell biology, 

developmental biology, ecology, engineering, physics, mathematics, and computer 

science with development of scientists who have a keen appreciation for and 

knowledge of animal production systems. Additional emphasis on extension and 

outreach will enable and facilitate effective translation of genomics research and 

resulting technologies to the agricultural animal production sector and the public.