National Program 101 Food Animal Production
National Program Annual Report: FY 2004
- 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
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 again experienced a high level of productivity and success in 2004. In total, 92 full-time scientists working at 17 locations across the U.S. were actively engaged in 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 second year of implementation of these five-year project efforts.
During the past year, program increases were appropriated for forage animal pasture research ($536,814 to Lexington, KY), bovine genetics ($536,814 to Beltsville, MD), bioinformatics ($223,673 to Clay Center, NE), dairy forage research ($1,252,566 to Madison, WI), beef cattle feed efficiency genomics ($270,000 to Clay Center, NE), and grazing beef systems ($89,469 to Beaver, WV) bringing the total appropriations in the national program to over $39M.
A total of eight new permanent scientists were welcomed to the program during 2004 including: Dr. Lee Alexander (Miles City, MT); Dr. LeAnn Blomberg (Beltsville, MD); Dr. John B. Cole (Beltsville, MD); Dr. Randy Dinkins (Lexington, KY); Dr. Mary Beth Hall (Madison, WI); Dr. Isabelle Kagan (Lexington, KY): Dr. Heathcliffe Riday (Madison, WI); and Dr. Richard Waterman (Miles City, MT).
Ronnie Green served as the national program leader for the program in 2004 with invaluable co-lead responsibilities provided by Lewis Smith. Contributions to the national program were also provided by program team members Evert Byington, Cyril Gay, and Robert Heckert.
Several scientists in the national program were recognized with prominent awards, including:
Curt Van Tassell, Beltsville, MD, Presidential Early Career Award for Scientist and Engineers
Curt Van Tassell, Beltsville, MD, 2004 Outstanding Young Scientist, American Dairy Science Association
Duane Norman, Beltsville, MD, Outstanding Alumni, College of Agricultural Science, Pennsylvania State University
Chad Chase, Brooksville, FL, 2004 Researcher of the Year, Florida Cattlemens Association
Larry Cundiff (as a part of team with Keith Gregory and Bob Koch), Clay Center, NE, Beef Industry Top 40 Award, BEEF Magazine 40th Anniversary
Keith Gregory (retired), Clay Center, NE, USDA/ARS 2004 Hall of Fame Inductee
Tom Jenkins, Clay Center, NE, 2004 Pioneer Award, US Beef Improvement Federation
Steve Kappes, Clay Center, NE, 2004 Continuing Service Award, US Beef Improvement Federation
Mohammad Koohmaraie, Tommy Wheeler, Steven Shackelford, Clay Center, NE, 2004 Technology Transfer Award, USDA/ARS
Dale Van Vleck, Clay Center and Lincoln, NE, 2004 A. B. Chapman Distinguished Lecturer Award, University of Wisconsin, Madison.
Dave Mertens, Madison, WI, 2004 Pioneer Hi-Bred Forage Award, American Dairy Science Association
Ronnie Green, National Program Staff, Brother of the Century Award, 100th Anniversary, National Alpha Gamma Rho Fraternity and 2003 Continuing Service Award, US Beef Improvement Federation
The high quality and impact of research conducted in the program was further evidenced by the fact that scientists delivered 56 invited presentations at international symposia during the past year. During the year, one new CRADA was established and three new patents were filed by researchers in the program. Additionally, a total of $2.4 M in extramural grant award funding was received by scientists in the program, supported in many cases by cooperative research programs with partners at land grant universities. Administrator’s Postdoctoral Awards were granted to Julie Long (Beltsville, MD), Mike MacNeil (Miles City, MT), and Harvey Blackburn and Phil Purdy (Fort Collins, CO).
Partnerships with land grant universities continued to be very important to the success of the national program in 2004. These partnerships are greatly appreciated and take on a variety of forms including work with those in the states of Arkansas, Colorado, Florida, Georgia, Idaho, Illinois, Iowa, Kentucky, Maryland, Michigan, Minnesota, Montana, Nebraska, New York, Virginia, West Virginia, and Wisconsin.
A number of meetings and workshops were sponsored by this national program in the past year including: Chicken Genome: Outlook and Applications (Atlanta, GA); USDA/ARS Swine Production Research Workshop (Ames, IA); Beyond the Chicken Genome (Kansas City, MO); American Society of Animal Science Symposium (St. Louis, MO); USDA/ARS Forage Animal Pasture Research Unit Stakeholder Workshop (Lexington, KY); USDA Animal Genomics Workshop (Washington, DC); and ADSA DISCOVER Conference on Animal Germ Plasm (Cheyenne, WY).
This is a particularly exciting time for this research and program area. In 2004, draft genome sequences were released for the chicken (6.3-fold coverage) and the cow (initial 3.3-fold coverage). Success in obtaining the needed funding for sequencing of the swine genome was announced as this report was being written with the formal launch of the project expected to occur in the latter part of 2005. Major long-term efforts are now yielding results in building 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.
In September of 2004, USDA conducted a workshop in Washington, DC focused on needs in animal genomics. Forty-five leading researchers and administrators were invited to the workshop to formulate priority needs for agricultural animal genomics programs in the “post-sequencing” era. ARS was well represented in this group by 15 of the leading scientists from this national program. Input from this workshop is currently being utilized to develop a long-term strategic plan for USDA animal genomics research efforts. The strategic plan development is targeted for completion in the latter half of 2005 and is being lead by Ronnie Green from ARS and Muquarrab Qureshi from CSREES.
The following sections of the report summarize high impact research results addressing the eight objectives in the current national program action plan.
Chicken genome sequence exploited to reveal variation in gene expression in turkeys. The commercial turkey industry relies exclusively on artificial insemination (AI) for production. Due to low success of cryopreservation of semen, these AI procedures rely on the use of fresh semen, which requires costly maintenance of male populations on production farms. A unique aspect of turkeys is that they have the ability to store live sperm in the oviduct of the hen for extended periods of time in sperm storage tubules. Scientists in the ARS Biotechnology and Germ Plasm Lab at Beltsville, MD have exploited the recent release of the chicken genome sequence to apply proteomics techniques to identify 40 proteins that are expressed in the turkey sperm storage tubule epithelium. Four proteins were uniquely expressed when sperm were absent while three additional proteins were only expressed when sperm were present. These results are the first step in identifying novel proteins for maintenance of poultry sperm viability and provide one of the first examples of the power of having whole genome sequence available from the chicken.
Genomics research identifies important genes affecting reproductive capacity in swine and cattle. One of the primary selection criteria in genetic improvement programs in the livestock industry is reproductive rate. By increasing the total production per female in the breeding herd, profitability is enhanced significantly for the individual producer through increased output over static fixed costs. Swine reproduction research over the past 20 years at the US Meat Animal Research Center, Clay Center, NE has been focused on identification of physiological mechanisms contributing to increased male reproductive capacity, and to enhanced litter size and uterine capacity of sows. This past year, this research team validated that a previously identified genetic marker for the pig erythropoieten receptor gene is associated with a 2 to 3 pig difference in ultimate litter size. The frequency of the favorable allele for this marker was also found to be low in the population indicating that selection could be used to make genetic change at this chromosomal location. The research team also identified, for the first time, two quantitative trait loci for male reproductive traits; one QTL for testes size (which is highly related to sperm production and age at puberty) and one QTL for follicle stimulating hormone (FSH). Further research is being conducted by this team to fine map these genes.
Conservation, Characterization, and Use of Genetic Resources
Rapid expansion of national animal germ plasm repository. Breeding populations of livestock have narrowed considerably in their genetic diversity over the past several decades prompting concerns regarding adequate levels of genetic variability and biosecurity. The National Animal Germ Plasm Program, located at Fort Collins, Colorado, was formally established in 1999 to better ensure the protection of American consumers and the US livestock industry. The number of germ plasm and tissue samples in the collection was increased by 114% and the number of breeds represented by 50% in the past year. This growth is far ahead of original plans and expectations. Two breeds of dairy cattle, four lines of chickens, and one line of pigs were increased to a level considered as secure in the collection. Additionally, six important fish species were added to the collection for the first time. This progress provides increased security of farm animal genetic resources and maintenance of animal genetic variation.
Romanov sheep germ plasm improves fertility. Length of seasonal fertility largely determines the effectiveness of accelerated lambing systems and annual systems that breed females in the spring of the year. Efficiency of commercial sheep production could be markedly improved if a line of maternal germ plasm could be identified with enhanced seasonal fertility. Research conducted at the US Meat Animal Research Center, Clay Center, NE has concluded that ewes sired by Romanov rams were 59% more productive than ewes sired by traditional breeds used for out of season breeding, (i.e. Dorset and Finnsheep). Greater use of Romanov-crossbred ewes in maternal roles of terminal crossbreeding systems would contribute to enhanced profitability of sheep production.
Beef cattle germplasm evaluation shows narrowing of between breed variation. The beef cattle industry has widely capitalized upon the characterization of germplasm representing 34 breeds conducted in 8 cycles of the Germ Plasm Evaluation Project at the US Meat Animal Research Center since 1970. Most recently, results from evaluation of Cycle VII of the project provided evidence that the genetic variation observed amongst breeds for growth performance has significantly decreased over the past decade. Using Angus and Hereford as the common base breeds in the project, and through reevaluation of four Continental European breeds evaluated previously in Cycles I, II and IV, the research team was able to show that differences amongst the Continental European and British breeds had narrowed substantially for slaughter weight and final weight. These results are important to beef cattle breeders as they design selection objectives within breeds and crossbreeding systems using multiple breeds to make genetic improvement.
Pre-Harvest Product Quality
Image analysis system validated for prediction of beef carcass fabrication yields and carcass value under commercial processing conditions. One of the targeted areas to increase production efficiency in the beef industry is improved lean retail yield of carcasses. The standard system used to evaluate retail yield of beef carcasses is through the assignment of a visually determined USDA yield grade by a human grader prior to carcass fabrication. Due to the inherent subjectivity of this system, ARS researchers in the Meats Research Unit of the US Meat Animal Research Center at Clay Center, NE, in collaboration with the National Cattlemens Beef Association and Tyson Fresh Meats, have developed an image analysis system for use on-line in commercial packing plants to predict boneless, closely-trimmed sub-primal cutout yields. This past year, this image analysis system was validated under commercial conditions and shown to be an accurate predictor of cutout yields. Two of the four major beef processors have now implemented this system with others considering it for future implementation.
Selection index tools transferred to beef cattle seedstock industry. Genetic improvement programs in the beef cattle industry are complex due to the need to select upon a wide array of performance criteria. Many of these traits are genetically correlated and differ in their relationship to enterprise profitability. The optimal approach to genetic improvement is through the utilization of selection indices where trait breeding values are appropriately weighted according to their economic value, genetic variation, and genetic relationships in to an aggregate “overall” breeding value. ARS scientists at Miles City, MT have been working for a number of years to develop such a framework for application in the beef cattle seedstock industry. In the past year, selection indexes based on this research were made available for breeders of Charolais cattle in the US. Additionally, this research group developed and delivered indexes to the American Hereford Association, American Simmental Association, North American Limousin Foundation, the Angus Sire Alliance, and the South African Agricultural Research Council.
Detection of QTL for fertility in dairy cattle. One of the most critical issues facing the US dairy industry is a decline in fertility that is thought to be associated with a gradual accumulation of inbreeding depression over the past 45 years, largely due to widespread use of genetically superior sires through artificial insemination. Advances in livestock genomics, including the development of highly saturated genetic linkage maps, have allowed scientists to identify a number of chromosomal regions harboring genes affecting a wide array of traits of economic importance (so-called Quantitative Trait Loci (QTL)). ARS researchers at Beltsville, MD, working collaboratively with scientists at the University of Illinois, have recently reported the first QTL detected affecting fertility traits in dairy cattle. This QTL, specifically for the trait of pregnancy rate, was found in a genomic scan of US Holstein germ plasm. Additional QTLs were also detected in this genome scan for somatic cell score, an indicator of mastitis incidence.
Validation that genetically-enhanced dairy cattle are more resistant to mastitis. Mastitis costs the dairy industry $2 billion 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, three 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 validated in these transgenic females that lysostaphin is secreted in their milk and does confer resistance to S. aureus infection. They have also shown that slightly more than 1 ug per liter of lysostaphin expression is adequate to completely protect cows against this form of mastitis.
Beef cattle, swine, and sheep genomics toolbox grows larger. 2004 was a milestone year in livestock genomics with the completion of the chicken genome sequence and the release of the first draft of the bovine genome sequence. ARS research has laid much of the path for this development and in the past year has significantly enhanced the information contained in the livestock genetic maps. Researchers at the US Meat Animal Research Center have: 1) added 800 genes to the integrated bovine map via single nucleotide polymorphism (SNP) mapping in introns; 2) increased the number of microsatellite markers in the bovine linkage map from 1,500 to 3,800; 3) deposited 680 sheep, 4,429 cattle, and 5,445 swine SNPs in the public database, GenBank, at NCBI (prior to these submissions no more than 100 SNP had been deposited for any of the species); 3) deposited 13,922 bovine and 65,866 porcine expressed sequence tags (ESTs) in GenBank; 4) developed a set of 14,000 ESTs with unique 3-prime end sequences for use in developing a commercial cattle microarray; and 5) developed and tested a pipeline for identification, complete sequencing, and annotation of full-length cDNA clones for livestock genes through which 500 bovine full length cDNAs were identified.
Bioinformatics software developed for worldwide use. The volume of data being generated from analysis of DNA sequence and downstream applications in functional genomics and proteomics research is growing exponentially as the genomes of the major livestock species are being added to the sequence infrastructure. Bioinformatics applications are sorely needed to facilitate ease of transfer and access to such data by researchers worldwide working across many species. Research conducted in the ARS Bovine Functional Genomics Lab at Beltsville, MD has resulted in the development of bioinformatic software called EST-PAGE which allows researchers to easily process large volumes of data on expressed genes (known as expressed sequence tags (ESTs)) and more importantly, to submit their data to the public databases for worldwide application and use. Over 25 groups around the world have already requested and received the source code for this software.
Marek’s disease causing clone is sequenced. Marek’s disease, a T-cell cancer caused by the Marek’s disease virus is estimated to result in over $160M in economic losses annually in the US poultry industry. Understanding how variation in specific Marek’s disease virus genes influences the immune system is of fundamental importance. ARS researchers in the Avian Disease and Oncology Lab at East Lansing, MI developed and sequenced a disease-causing clone of the Marek’s disease virus genome. This infectious clone, which can be easily manipulated, will enable the group to identify critical virus-host interactions and develop diagnostic reagents. Utilization of the cloned virus will lead to the identification of immunological pathways and genes that promote disease resistance.
Genomics-Derived Tools Critical in U.S. BSE (Mad Cow Disease) Crisis. When the first case of bovine spongiform encephalopathy (BSE), more commonly referred to as “mad cow disease”, was reported in Washington state in December of 2003, little did anyone know that it would become one of the first major cases for the application of genomic technology to providing a valuable and rapid solution in a crisis situation in animal agriculture. Shortly after the identification of the BSE case, records associated with the particular cow in question indicated that she was originally imported from Alberta, Canada, where a similar case of BSE had been identified several months earlier. However, the records did not unequivocally prove her origin. Fortunately, the records identified the sire and other relatives of the BSE index case and their tissues were available for genetic analyses. The availability of these tissue samples permitted rapid pedigree verification, using genomic technology, and thus confirmed the records indicating the Canadian origin of the BSE index cow. ARS scientists at Clay Center, Nebraska had previously identified 32 selected single nucleotide polymorphisms in cattle that provided very accurate identification of individual animals. Using this genotyping test, they were able to provide scientific evidence that the Washington state index cow was one of a group of 81 females that had crossed the US border from Canada several years earlier. This provided the missing link in the traceability of this female to verify that she was born prior to the 1997 implementation of a full ban on animal protein feeding in Canada.
Growth and Development
Thyroxine binding globulin gene variant reduces swine testes size. Mature testes size is directly related to the number of sperm cells that a boar produces in a day. Research work conducted in the Breeding and Genetics Unit at the US Meat Animal Research Center, Clay Center, NE, has determined that variation in the thyroxine binding globulin gene causes a 30 to 40% reduction in the size of the mature testes with a concomitant reduction in average backfat thickness. This discovery is important as it has identified a new biochemical pathway regulating male reproduction through testes size in swine. Since the swine industry relies heavily upon artificial insemination, maximizing the number of sperm cells produced daily by a boar will minimize the number of boars required in boar studs.
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. Microarray, proteomic, and conventional technology has been used to demonstrate the expression of many secretory genes and proteins in neonatal pig adipose tissue. Over 30 genes that code secreted proteins were reported for the first time in pig adipose tissue including agouti, nerve growth factor, several interleukins, brain derived neurotrophic factor and IFNA2. This information will provide a better understanding of the molecular mechanisms controlling fat tissue secretory function.
Critical control point identification in the progression of oxidative stress in cattle. Chronic low-level disease stress and infection add costs to cattle production by diverting needed nutrients from productive purposes resulting in suboptimal performance and increased management difficulty. In the Growth Biology Lab at Beltsville, MD, research on the animal to animal variability in response to low-level immune challenge was expanded with a series of experiments demonstrating that the oxidative conditions associated with a low level disease stress, as modeled by endotoxin challenge, could efficiently nitrate specific regulatory sites of signal transduction kinases and negate the activation of the kinase, thus blocking initiation of downstream gene actions. Five specific critical control points, all hormonally regulated, were identified in the biochemical pathway between the substrate for the generation of nitric oxide and arginine entering the cell and the point at which vitamin E was shown to be effective in mitigating the generation of the reactive nitrogen product peroxynitrite. Each critical control point constitutes a site at which potential beneficial intervention strategies could be targeted to reduce the severity of host response to immune challenge. Exploiting regulation of these critical control points will lead to effectively decreasing management costs for cattle responding to disease stress.
Nutrient Intake and Utilization
Cloning and sequencing of the chicken proglucagon gene. Development of a more complete understanding of the biological mechanisms regulating feed intake in poultry and livestock is needed in order to better tailor production systems to available genetic lines to improve production efficiency. Ongoing work in the Growth Biology Laboratory at Beltsville, MD has been involved in the study of the chicken proglucagon gene. This gene produces five different peptide hormones, including glucagon-like peptide 1, that function in tissue growth, gastrointestinal function, regulation of insulin and blood glucose levels, and appetite control. This work has recently led to the cloning and sequencing of the chicken proglucagon gene and to the identification of four distinct messenger RNA species produced by this one gene through alternative splicing and alternate promoter usage. The types and levels of specific proglucagon mRNAs were determined in pancreatic, intestinal and brain tissues collected from chickens that had been deprived of feed and/or refed to induce changes in energy status. This work provides new information necessary to understand how these peptide hormones are produced and what impact changes in the expression of this gene might have on glucose metabolism and appetite regulation in poultry.
Demethylation of pectin during plant growth causes decreased digestibility of fiber carbohydrates from forages. Inefficiencies of feed utilization constitute the single largest cost of large ruminant livestock production. One of the key target areas being researched to address this problem is the lignification of fiber from forages, as lignin is highly indigestible. ARS scientists at the US Dairy Forage Research Center in Madison, WI have shown that the normal demethylation of pectin (a cell wall carbohydrate in forages) during plant growth results in greater cross-linking of pectin to lignin, and, ultimately reduces digestibility of fiber. This finding has led to efforts by this research group to identify ways to reduce this cross-linking by manipulation of the demethylation process.
Activity of bacteriocin is shown to be high under ensiling conditions. The dairy industry relies heavily upon the use of silage as a feedstuff, but silage preservation is often inadequate to insure quality. One of the critical control points impacting silage quality is the control of detrimental amino acid degrading bacteria during the ensiling process. Previous work by ARS researchers at Ithaca, NY has shown that Clostridium sporogenes, the detrimental bacteria, could be inhibited by the bacteriocin bovicin HC5 that is produced by the ruminal bacterium S. bovis. Inclusion of S. bovis as a silage inoculant has been proposed as an alternative to commonly used Lactobacilli to take advantage of its faster growth rate and ability to cause a more rapid pH decline. The research team has now shown that the activity of bovicin HC5 is at least 10-fold higher at pH of 5.0 as compared to 6.7. These results suggest that the bacteriocin-producing bacteria has potential to improve silage quality.
Resource developed to facilitate functional genomics research on factors affecting metabolism of ruminants. The production of meat, milk, and wool products is considered to be relatively inefficient due to the fact that upwards of two-thirds of the input costs are expended for feed energy required for maintenance of body tissues. This is largely attributable to energy expended by the visceral tissues (liver and gut). Research work conducted in the Bovine Functional Genomics Lab at Beltsville, MD has resulted in the development of a cDNA library resource to facilitate the search for specific metabolic pathways, transporters, growth factor receptors, and growth factors that have profound effects on ruminant visceral energy and protein metabolism. A new normalized cDNA library has been synthesized from lactating dairy cow and calf intestinal tissue to facilitate gene discovery in this area. The library, called 8BOV, has been synthesized, sequenced, and characterized, and is having a direct impact as evidenced by the 19,110 new expressed sequence tag (EST) sequences which have now been deposited in GenBank. A total of 1,123 sequence elements from the ESTs represent genes encoding proteins in other animal systems that can now be exploited in the bovine.
Perennial cool-season grass systems offer lower risk for stocker cattle production systems. Many beef producers in the southern Great Plains region of the US rely on winter wheat pastures for grazing in fall, winter, and early spring months, but forage production by this annual crop is often not sufficient in the fall due to slow establishment and growth. Research conducted at the Grazinglands Research Lab, El Reno, OK, demonstrated that producers can substitute perennial cool-season grasses for wheat, or use a combination of these grasses with wheat, to buffer highly variable wheat forage production and simultaneously meet the nutritional demands of stocker calves. These farm-scale studies of stocker calf weight gains indicate that a variety of grasses can be grazed a full month later in the spring than wheat pasture, extending the marketing date of stocker calves past the seasonal lows in beef prices associated with the end of the wheat pasture grazing season. These findings allow livestock producers to more consistently meet the forage needs of stocker calves and reduce the economic losses associated with livestock production in the southern Great Plains.
Losses from bag silos can be reduced with monitoring. Bag silos are an increasingly common means of ensiling on dairy farms in the US, but relatively little is known about the densities and losses that can be expected from them. ARS researchers at the US Dairy Forage Research Center, Madison, WI, in collaboration with the University of Wisconsin, surveyed the filling and emptying of bag silos made at three research farms. Densities ranged from 10 to 18 lbs of dry matter per cubic foot and were influenced primarily by moisture content, how finely the forage was chopped, and the operator. Losses of dry matter ranged from 0 to 40% (averaging 14.6%) and were most significantly affected by air temperature at the time of emptying the bag, porosity of the silage, moisture content, and how quickly holes in the plastic bags were patched. Consistent losses of less than 15% are possible if bags are routinely monitored and patched. These results will help dairy farmers already using bag silos to obtain the best results and will be useful to those contemplating the use of bag silos in estimating their true costs.