• Introduction
• Reproductive Efficiency
• Conservation, Characterization, and USe of Genetic Resources
• Pre-harvest Product Quality
• Genetic Improvement
• Genomic Tools
• Growth and Development
• Nutrient Intake and Utilization
• Integrated Systems

Introduction   

The food animal production national program is charged with conducting cutting edge research to contribute to increased efficiency and sustainability of production of beef and dairy cattle, poultry, swine, and sheep.  Research efforts in the animal sciences over the past century have had dramatic impacts on animal agriculture both in terms of improved biological and economic efficiency of production and in terms of quantity, quality, and safety of animal products.  Many major challenges remain, however, requiring the dedicated focus of long-term research teams, particularly in the areas of reproductive longevity and well-being, product quality, reduction of feed and energy inputs, enhancements in nutrient retention, and reduction of negative environmental impacts.

The program experienced a high level of productivity and success in 2003.  In total, 92 scientists working at 17 locations across the U.S. were engaged in over 50 research projects in the program.  Research projects in this program area were approved through the ARS Office of Scientific Quality Review in 2002, making this the first year of  implementation of these five-year project efforts.

During the past year, program increases were appropriated for forage animal pasture research ($800,000 to Lexington, KY), bovine genetics ($300,000 to Beltsville, MD), bioinformatics ($350,000 to Beltsville, MD and $250,000 to Clay Center, NE), and dairy forage research ($1,000,000 to Madison, WI), bringing the total appropriations in the national program to over $42M.

A number of new scientists were welcomed to the program during 2003 including Steven Trabue (Ames, IA); Brent Woodward (Dubois, ID); Jim Strickland and Glen Aiken (Lexington, KY); Phil Purdy (Fort Collins, CO); Mark Allan (Clay Center, NE); and Melvin Kuhn (Beltsville, MD). 

USDA/ARS was pleased to name Ronnie Green as the national program leader for food animal production in February of 2003 and looks forward to his leadership.  Special appreciation is extended to a number of individuals who served in detail in this position during the search for a new national program leader including John McMurtry and Curt Van Tassell (Beltsville, MD), Mike MacNeil (Miles City, MT), Chad Chase (Brooksville, FL) and Tom Jenkins (Clay Center, NE). Their contributions, coupled with those of national program leaders Lewis Smith and Evert Byington were invaluable.

Several scientists in the national program were recognized with prominent awards for their research including:

Curt Van Tassell, Beltsville, MD, Herbert L. Rothbart Outstanding Early Career Scientist, USDA/ARS

Curt Van Tassell, Beltsville, MD, 2003 Young Research Scientist of the Year, Northeast Section of the American Dairy Science Association

Eduardo Casas, Clay Center, NE, Early Career Scientist, Northern Plains Area, USDA/ARS

John Klindt, Clay Center, NE, National Pork Board Swine Innovation Award

Cal Ferrell, Clay Center, NE, President, Midwest Section of American Society of Animal Science

Tim Smith, Clay Center, NE, Outstanding Young Scientist, Midwest Section of American Society of Animal Science

Ron Christenson, Clay Center, NE, Animal Physiology and Endocrinology Award, American Society of Animal Science

Brad Freking and Kreg Leymaster, Clay Center, NE, Superior Performance Award, Northern Plains Area, USDA/ARS

Darrell Light, Clay Center, NE, Outstanding Technical Support Award, Northern Plains Area, USDA/ARS

Elaine Grings, Miles City, MT, Outstanding Achievement Award, Society for Range Management

Dave Mertens, Madison, WI, American Feed Industry Association Award, American Dairy Science Association

Brian Kerr, Ames, IA, Superior Performance Award, Midwest Area, USDA/ARS

The high quality and impact of research conducted in the program was further evidenced by the fact that scientists delivered over 90 invited presentations at international symposia during the past year.   Three CRADAs were instituted and two patents were filed by researchers in the program.  Additionally, a number of extramural grant awards were received by scientists in the program, many supported by cooperative research programs with partners at land grant universities.  Administrator’s Postdoctoral Awards were granted to Hans Cheng (East Lansing, MI) and Mark Richards (Beltsville, MD).

A number of meetings and workshops were sponsored by this national program in the past year including Livestock Genomes:  Bioinformatics and Annotation Challenges (Conroe, TX); Chicken Genome:  Outlook and Applications (Atlanta, GA); ARS Swine Production Research Workshop (Ames, IA); ARS Poultry Production Workshop (Orlando, FL); and DISCOVER Conference on Antibiotic Use in Animal Agriculture (Abe Lincoln Lodge, IN).

This is a particularly exciting time for this research and program area.  In the coming year, draft genome sequences will be released for the chicken and the cow.  Efforts are now underway to do the same for the swine genome in 2005.  Major efforts are being put in to place to build infrastructure in the agency for bioinformatics, functional genomics, and proteomics.  These efforts have required creative approaches to funding and the leveraging of resources across federal agencies, international governments, and private industry. These developments open a new frontier for research in food animal production and coincidentally have elevated the expectations of the future impact of this program.

The following sections of the report summarize high impact research results addressing the eight objectives in the current national program action plan.

Reproductive Efficiency

Serial Analysis of Gene Expression (SAGE) reveals differential gene expression in swine embryos.  Swine exhibit high rates (>30%) of early embryonic mortality, primarily between days 11 and 12 of gestation.  ARS scientists at Beltsville, Maryland have revealed differences in the expression of over 430 genes between day 11 and day 12 embryos using SAGE techniques.  This effort is the first step in identifying genes and their function that are likely critical for porcine embryo development and establishes a new paradigm for functional genomics research in agricultural livestock species.

Selection for twinning rate in cattle highly successful.  Long-term genetic selection utilizing estimated breeding values calculated from repeated measures of ovulation rate in yearling heifers and of twinning rate in adulthood, has resulted in an annual increase in ovulation rate and twinning rate of 5 and 3%, respectively in research conducted at the U.S. Meat Animal Research Center, Clay Center, Nebraska.  The twinning rate in this herd is now in excess of 55% annually with a 48% increase in total weaning weight per cow calving.  This research clearly shows that alteration of reproductive rate, the most limiting factor affecting efficiency of beef production, is possible.

Conservation, Characterization, and Use of Genetic Resources

Significant progress in securing animal germ plasm.  Breeding populations of livestock have narrowed considerably in their genetic diversity over the past several decades prompting concern regarding adequate levels of genetic variability.  The National Animal Germ Plasm Program was formally established in 1999 to better ensure the protection of American consumers and the U.S. livestock industry.  In 2003, the total number of breeds in the repository increased to 42 (a 147% increase) in addition to 40 lines of chickens, the total number of units of semen increased by 337% (from 16,000 to 70,000), and the number of cattle and sheep embryos stored increased to 689.  Several economically important breeds, including the Holstein, are now considered secure.  This progress provides increased security of farm animal genetic resources and maintenance of animal genetic variation.

Improved cryopreservation of poultry semen.  Glycerol is the most effective cryoprotectant for poultry semen, but unfortunately is contraceptive in the hen.  Researchers at Beltsville, Maryland and East Lansing, Michigan have developed a novel method for removing glycerol from frozen-thawed chicken semen.  This development is significant in that it allows the immediate banking of semen from at-risk genetically valuable and/or unique chicken lines.

Pre-Harvest Product Quality

Gene variation affecting tenderness in beef cattle identified.  Tenderness of beef has consistently been identified by all sectors of the beef industry as the highest priority issue for enhancing the value of beef products, estimating that approximately 25% of steaks are less tender than desired.  Researchers at the U.S. Meat Animal Research Center, Clay Center, Nebraska have recently identified two DNA markers in the u-calpain gene that are associated with differences in tenderness of product.  ARS has assisted in the successful validation of these markers by cattle producers in two large-scale tests.  This finding suggests that these genetic markers can be used to select against the negative impacts of u-calpain on tenderness.   

On-line tenderness testing system recommended for beef industry use.  Profitability of the U.S. beef industry is limited by the inability to consistently produce lean, highly tender products.  ARS meat scientists at Clay Center, Nebraska were asked by the National Cattlemens Beef Association to compare a system developed in their lab (the MARC Beef Classification System) to two non-invasive systems for identifying beef that could be guaranteed tender on-line in beef processing plants.  The MARC Beef Classification System was identified as the only system accurate for industry use and has been subsequently recommended to companies for implementation by the National Cattlemens Beef Association.    

Genetic Improvement

New genetic evaluation of fertility implemented for U.S. dairy industry.  The dairy industry has identified decreased cow fertility as a major economic concern in recent years.  ARS scientists in the Animal Improvement Programs Laboratory at Beltsville, Maryland developed methodology to allow genetic evaluation of fertility in young females and for calving ease in cows and have recently implemented new genetic evaluations for both traits.  This advancement will allow dairy breeders to make genetic improvement in reproductive efficiency of the nation’s dairy herd.

Brahman sires genetically evaluated for meat quality.  Brahman-based cattle are well suited for use in the subtropical U.S. because of their adaptation to adverse conditions; however, this is at least partially negated by lower market value for these cattle due to lowered meat quality associated with decreased tenderness.  ARS researchers in Brooksville, Florida have completed several years of intensive data collection allowing characterization of tenderness in Brahman sire lines.  In cooperation with scientists at Louisiana State University, these results have been used to produce the first sire genetic evaluation for carcass traits in this economically important breed in the southern U.S..  This development will allow selection for improved carcass quality in subtropically-adapted germ plasm.

Production of genetically-enhanced dairy cattle resistant to mastitis.  Mastitis costs the dairy industry $2B annually with the most deadly form of the disease caused by S. aureus infections.  ARS scientists at Beltsville, Maryland have successfully produced, by nuclear transfer, genetically-enhanced cattle carrying the gene encoding lysostaphin, a potent killer of mastitis-causing bacteria.  Working collaboratively with scientists at the University of Vermont, the research team has confirmed in the first lactating genetically-enhanced cow that lysostaphin is produced in her milk and does confer resistance to S. aureus infection.

Sheep germ plasm evaluation.  Comparison of sheep breeds provides critical information to guide the appropriate use of breeds in commercial crossbreeding systems.  Five sheep breeds were compared at the U.S. Meat Animal Research Center, Clay Center, Nebraska.  Superior productivity of the Romanov breed was documented, due primarily to greater conception rate, prolificacy, and longevity compared to Finnsheep, Dorset, Texel, and Montadale breeds.  Broader use of crossbred ewes incorporating Romanov germplasm would greatly increase the efficiency of commercial sheep production.

Study of host-pathogen resistance addresses Marek’s Disease in chickens.  With Marek’s Disease costing the poultry industry over $160 M per year, developing methods that augment current vaccinal control methods is a high priority.  The USDA-ARS Avian Disease and Oncology Laboratory, East Lansing, Michigan, has screened numerous Marek’s Disease virus proteins for their ability to interact with chicken proteins and has revealed viral proteins that evade the immune response as well as chicken genes that promote disease resistance.  This approach of integrating protein-protein interactions with mapping offers promise to rapidly identify disease resistance genes to quickly transfer to the poultry industry as well as pathogenicity promoting viral genes as vaccine targets to address this important problem.

Genomic Tools

Development of a bovine bacterial artificial chromosome (BAC) map.  Development of a BAC map dramatically reduces the time and expense necessary for identifying genes affecting important traits, improves the effectiveness of marker-assisted selection, and anchors assembled genomic sequence to chromosomes.  ARS scientists at Clay Center, Nebraska and Beltsville, Maryland have worked collaboratively with the International Bovine BAC Mapping Consortium (includes labs in US, Canada, UK, NZ, Australia, Brazil and France) and the Michael Smith Genome Science Centre, Vancouver, BC, to fingerprint over 300,000 BAC clones and 75,000 BAC-end sequences.  This physical map is being used as the scaffold for the sequencing of the bovine genome at Baylor College of Medicine and by ARS scientists in linking the physical, radiation hybrid (in collaboration with Roslin Institute) and USDA linkage maps.

Swine and cattle genetic maps enhanced for fine mapping of genes.  USDA produced the first genetic linkage maps for swine and cattle in 1994 that have since been widely used to identify a number of chromosomal regions containing genes affecting economically important traits.  ARS scientists at Clay Center, Nebraska and Beltsville, Maryland have successfully enhanced these maps to include over 1,000 expressed sequence tags (genetic markers within expressed genes) for both cattle and swine.  The availability of a “gene-based” map allows the integration of all available linkage, radiation hybrid, and physical map information into consensus maps for identification of genes and their function in previously identified important chromosomal regions.  Additionally, comparative approaches between swine, cattle, and human genome information can now be fully utilized.

Comparative maps of two swine chromosomes developed to identify genes associated with reproductive traits.  Previous research at the U.S. Meat Animal Research Center, Clay Center, Nebraska has identified swine chromosomes 10 and 14 to harbor important quantitative trait loci affecting ovulation rate, nipple number, plasma FSH, and age at puberty.  Comparative maps of these two chromosomes were developed to allow identification of positional candidate genes in these QTL regions.  The candidate genes are now being sequenced to determine variation and markers are being developed to study association with phenotypic performance for these traits in MARC resource populations.

Statistical methodology developed for incorporating DNA marker data in to genetic evaluation.  Statistical software was developed by researchers at Clay Center, Nebraska that has been successfully used to identify three genomic regions affecting ovulation rate and twinning rate in cattle and furthermore to incorporate DNA marker genotype information in to breeding value estimation for these traits.  The program allows the use of incomplete marker data in pedigreed populations by estimation of marker allele inheritance probabilities.  The development of such bioinformatics tools will be instrumental in the implementation of marker-assisted selection programs in the livestock industries.

Growth and Development

Expression of genes controlling lipid accretion influenced by dietary protein levels in broiler chickens.  Although changes in dietary protein levels change metabolism during the starter to grower periods in broiler chickens, there is little information concerning the time and course of the process to adaptation.  Research in the Growth Biology Laboratory at Beltsville, Maryland has shown that expression of the genes encoding fatty acid synthase and acetyl coenzyme A in the liver is altered when young broilers are switched from a high protein to lower protein grower diet.  Regulating these genes by diet has the potential to selectively alter fat accretion in market weight birds.

Dual-energy X-ray absorptiometry (DEXA) reveals effects of myostatin gene in genetically enhanced mice.  Genetic disruption in the myostatin gene is thought to interfere with myostatin function resulting in promotion of muscle growth.  DEXA was utilized in research at the Beltsville Agricultural Research Center, Beltsville, Maryland, to determine that an increase in lean mass was initiated between 27 and 34 days of age in genetically enhanced mice expressing the myostatin gene disruption.  The lean mass was accompanied by a small decrease in fat mass and small increases in bone content and bone density.  This work further elucidated the effect of myostatin gene disruption on tissue composition and demonstrated the remarkable effectiveness of DEXA for in vivo measurement of body composition.

Proteomics work identifies 86 proteins involved in adipose tissue development in swine.  Research conducted by ARS scientists at Athens, Georgia is seeking to understand the functional relationships between the numerous proteins associated with the growth and development of fat tissue in pigs.  New techniques in protein analysis were used to identify coincident patterns of secreted proteins by fat tissue and isolated fat cells.  To date, 86 secreted proteins are associated with fat development and include growth factors, enzymes, and structural proteins.   This protein mapping work will be used to reveal critical steps in pathways controlling adipose tissue development and function that can be subsequently manipulated through growth and reproduction.

Nutrient Intake and Utilization

Feed intake gene identified in poultry.  Feed costs are the single most important cost in meat animal production, approaching 75% of total costs in poultry production.  Researchers in the ARS Growth Biology Laboratory at Beltsville, Maryland have successfully identified and cloned portions of the ghrelin gene in both chickens and turkeys.  This gene, shown to have a high degree of similarity to its mammalian counterpart, was expressed in stomach tissue of chickens during periods of feed deprivation and re-feeding, suggesting a functional role for the ghrelin gene in regulating feed intake in poultry.

Plasma urea nitrogen concentration has potential as genetic marker to minimize nutrient excretion in swine production.  Swine diets are over-formulated with nitrogen crude protein to insure no deficiencies and to accommodate genetic variation in crude protein requirement and utilization.  ARS researchers in the Nutrition Research Unit at Clay Center, Nebraska measured plasma urea nitrogen concentrations, a quantitative assessment of inefficient crude protein utilization, and determined that this trait was moderately heritable and not genetically correlated to growth.  Plasma urea nitrogen concentrations may be an exploitable quantitative trait to develop animals with greater ability to efficiently utilize dietary crude protein and minimize nutrient excretion.

Identification of the dietary rumen degraded protein requirement in dairy cattle offers potential for reduction in nitrogen excretion.  Feeding rumen-degraded protein in excess of the amount needed by rumen microbes leads to excess urinary nitrogen excretion, contributing to pollution of water and air.  Research conducted at the U.S. Dairy Forage Research Center at Madison, Wisconsin has found that reducing the amount of dietary rumen-degraded protein from 13.7 to 9.5% did not affect milk or protein yield but did result in a 12% decrease in urinary N excretion.  Rumen microbial protein production did decline in a stepwise fashion, which is being further studied to determine if the 10% dietary requirement level in this study can be recommended for industry use as a means of reducing nutrient load to the environment.

Improved understanding of cross-linking structures in plant cell walls for dairy forage applications.  Using biotechnology to increase the availability of carbohydrates in grass forages for milk production by dairy cattle requires accurate information in how and when the limits to fiber digestion develop during plant maturation.  Research conducted at St. Paul, Minnesota studied the cross-linking chemical structures in fiber that limit digestion in maturing grass stems using a group of corn hybrids.  The results showed that these cross-linking structures are deposited throughout development of corn stems and in both early and late stages of corn fiber development, contrary to earlier conclusions.  This knowledge can be used by biotechnologists to target genetic enhancement of cross-linking to all stages of grass fiber development, rather than in only a limited interval, to ultimately improve forage digestion in dairy production systems.

Integrated Systems

Changing calving season offers potential improvements for rangeland-based beef production systems.  Previous research has identified that overall efficiency of beef production systems can be improved by changing the calving season from spring to summer, thereby allowing better matching of seasonal forage production to animal needs.  Research conducted by ARS scientists at the Fort Keogh Livestock and Range Research Laboratory, Miles City, Montana, is evaluating the full spectrum of animal phenotypic and economic performance under such a system as well as effects on rangeland health and productivity.  Results of this long-term research will allow definition of integrated rangeland-based beef production systems that are more economically and environmentally sustainable.