National Program 101            Food Animal Production

National Program Annual Report:  FY 2006 

• Introduction
• Reproductive Efficiency
• Conservation, Characterization, and Use of Genetic Resources
• Product Quality
• Genetic Improvement
• Genomic Tools
• Growth and Development
• Nutrient Intake and Utilization
• Integrated Systems
• Animal Well-Being and Stress Control 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 animal well-being, adaptability to production environments, product quality, reduction of feed and energy inputs, enhancements in nutrient retention, and reduction of negative environmental impacts.

During the past year, the structure of the national program changed as a result of the merger of the former national program 105, Animal Well-Being and Stress Control Systems, in to the Food Animal Production program.  This merger added four existing research projects to the portfolio and three new unit locations.

The program had a very good year in 2006.  In total, 113 full-time scientists working at 20 locations across the U.S. were actively engaged in 45 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 fourth year of implementation of these five-year project efforts.

During fiscal year 2006, program increases were appropriated for forage animal pasture research ($108,000 to Lexington, KY), bovine genetics ($270,000 to Beltsville, MD), dairy forage research ($510,000 to Madison, WI), beef cattle feed efficiency genomics ($315,000 to Clay Center, NE), and beef cattle rumen metagenomics ($135,000 to Miles City, MT) bringing the total appropriations in the national program to over $46.5M.  Additionally, funds were appropriated for development of new facilities in the program at Lexington, KY ($4M), Marshfield, WI ($8M), and Bozeman, MT ($4M).

Several new permanent scientists were welcomed to the program including:  Wayne Coblentz (Madison, WI); Michael Flythe (Lexington, KY); Larry Keuhn (Clay Center, NE); Jeremy Miles (Clay Center, NE); Corey Moffett (Dubois, ID); and Michelle Mousel (Dubois, ID).

The ARS animal production research community was saddened by the death of Larry Satter (retired) from the U.S. Dairy Forage Research Center.

Ronnie Green served as the national program leader for the program with 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:

Rick Barb, Athens, GA – Animal Physiology and Endocrinology Award, American Society of Animal Science

Tony Capuco, Beltsville, MD – WestAgro Award, American Dairy Science Association

Jeff Carroll, Lubbock, TX – National Pork Board Innovation Award, Southern Section, American Society of Animal Science

Bill Dozier, Starkville, MS – HyLine International Research Award, Poultry Science Association

Calvin Ferrell, Clay Center, NE – Animal Growth and Development Award, American Society of Animal Science

Mary Beth Hall, Madison, WI – Foundation Scholar Award in Dairy Production, American Dairy Science Association

Mike Looper, Booneville, AR – Outstanding Young Animal Scientist Education Award, Southern Section, American Society of Animal Science

Mike MacNeil, Miles City, MT – Hall of Merit Inductee, American Hereford Association

John Nienaber, Clay Center, NE – Fellow Award, American Society of Agricultural and Biological Engineers

Rex Powell (retired), Beltsville, MD – Distinguished Service Award, Northeast Section, American Dairy Science Association

Vern Pursel (retired), Beltsville, MD – Hall of Fame Inductee, USDA Agricultural Research Service

Dale Van Vleck, Clay Center, NE – International Gamma Sigma Delta Distinguished Achievement in Agriculture Award

George Wiggans, Beltsville, MD – National DHIA Outstanding Service Award

The high quality and impact of research conducted in the program was further evidenced by the fact that scientists delivered 128 invited presentations at international and national symposia during the past year.   During the year, two new CRADAs were established and four new patents were filed by researchers in the program.  Additionally, a total of $2.7M 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 Eduardo Casas (Clay Center, NE), Dan Nonneman (Clay Center, NE), John Ralph (Madison, WI), and David Donovan (Beltsville, MD).

Partnerships with land grant and 1890s universities continued to be very important to the success of the national program in 2006.  These partnerships are greatly appreciated and take on a variety of forms including work with those in the states of Arkansas, Colorado, Connecticut,  Florida, Georgia, Idaho, Illinois, Indiana, Iowa, Kentucky, Maryland, Michigan, Minnesota, Mississippi, Missouri, Montana, Nebraska, New York, Oklahoma, Oregon, South Carolina, Texas, Virginia, West Virginia, and Wisconsin.

Planning for the next 5-year cycle of the national program was a major focal point during the year.  A retrospective assessment panel was appointed and documentation (www.ars.usda.gov/research/programs/programs.htm?np_code=101&docid=14389) was prepared for their review which was completed in February 2006.  A Joint ARS-CSREES Food Animal Production Stakeholder Workshop was held April 10-12, 2006 in Kansas City, MO.  Input from the 145 participants of this workshop was used to guide the development of the newly published 2007-2012 national program action plan (www.ars.usda.gov/research/programs/programs.htm?np_code=101&docid=13753).  Project teams and objectives were developed during the last part of the fiscal year for 31 new projects to address this action plan.  These new 5-year project plans will undergo peer review prior to scheduled implementation in August of 2007.    

The following sections of the report summarize high impact research results addressing the various components of the current national program action plan.

Reproductive Efficiency

Adipose secretory genes revealed by gene expression studies in swine.  ARS scientists in the Animal Physiology Research Unit at Athens, Georgia used microarray and real time RT-PCR technology to demonstrate, for the first time, the expression of 17 genes that encode secreted proteins in porcine adipose tissue from growing pigs. Furthermore, this is the first report of expression of five of these secretory genes in adipose tissue of any kind. Many of these genes are cytokines and include interleukin- 8, interleukin-1beta, brain derived neurotrophic factor, and Insulin-like Growth Factor Binding Protein-7. Expression of these cytokine secretory factors indicates that adipose tissue may mediate the influence of health and well-being on the onset of puberty. This information is vital to the development of novel methods to promote maximal growth and enhance onset of puberty and subsequent reproductive function in the pig.

Conservation, Characterization, and Use of Genetic Resources

Genetic security of animal germ plasm enhanced.  The security of U.S. animal genetic resources was significantly enhanced in the past year. Samples in the ARS National Germ Plasm collection at Fort Collins, Colorado increased from 229,110 to 296,555, a 29% increase. The collection contains germ plasm and tissue samples from 7,322 animals from 25 livestock, poultry and aquatic species, 119 breeds, and 94 unique within breed lines. In addition to collecting samples the repository released genetic material enabling research in quantitative trait locus discovery, genetic distancing of cattle breeds, and broadening the genetic base of a rare cattle breed.

Product Quality

Development and validation of marbling prediction for the  USMARC Beef Carcass Image Analysis System.  A primary determinant of beef carcass value is USDA quality grade, which is largely a function of the degree of marbling as estimated subjectively by USDA graders.  Because marbling score determination is subjective, the grading system has been widely scrutinized due to perceived variation in application from plant-to-plant and among graders within plants.  Therefore, USDA and the beef industry have sought development of instrumental methods to determine beef carcass marbling scores.  ARS scientists in the Meat Safety and Quality Research Unit at Clay Center, NE, collaborated with an instrument manufacturer to develop accurate methods for marbling score determination as an additional function of the U.S. Meat Animal Research Center (USMARC) beef carcass image analysis system.  In collaboration with USDA Agricultural Marketing Service (AMS) scientists and meat grading coordinators, data was collected to develop standards for AMS approval of instruments for marbling score determination.  Additionally, a series of cooperative studies were conducted to gain AMS approval for use of the USMARC beef carcass image analysis system for marbling determination.  Based on the current level of interest in adoption of this technology, it is expected to have an annual multi-million dollar impact on the beef industry.  This technology should benefit both consumers and all sectors of the beef industry.

Genetic Improvement

Heritability of follicle size and genetic correlation with fertility determined in beef cattle.  Sustained reproductive success is the most important determinant of efficient and profitable beef production. However, a lack of identified highly heritable traits that are closely correlated with fertility limits opportunity for genetic improvement of efficiency and profitability. Previous research has identified size of the ovulatory follicle as being temporally associated with conception and/or establishment of pregnancy. However, there has been no previous attempt to estimate the degree to which genetic effects control variation in follicle size or the magnitude of its relationship with pregnancy rate. ARS scientists at the Fort Keogh Livestock and Range Research Laboratory at Miles City, Montana estimated the heritability of follicle size to assess its usefulness as an indicator trait associated with reproductive success in beef cattle. Results indicated heritability of size of the ovulatory follicle is greater than the heritability of pregnancy rate. However, owing to a very low genetic correlation of follicle size with pregnancy rate, its greatest usefulness in genetic selection is as an ancillary trait.

Identification of quantitative trait loci for infectious bovine keratoconjunctivitis.  Infectious bovine keratoconjunctivitis, also known as pinkeye, is one of the most economically important diseases in cattle.  ARS research at Clay Center, Nebraska has identified two putative quantitative trait loci for this trait, one on bovine chromosome 1 and the other on bovine chromosome 20.  A gene known to be involved in pathogen resistance has been located under the quantitative trait loci on chromosome 1.  These findings should motivate future studies with the objective of identifying the genetic base of pinkeye resistance.

Identification of a genomic marker linked with pre- and post-natal growth in beef cattle.  A single nucleotide polymorphism in the osteopontin gene on bovine chromosome 6 was found to be associated with birth weight, weaning weight, and yearling weight, but not twinning or ovulation rate, in a large multi-generation, cross-bred cattle population at the U.S. Meat Animal Research Center at Clay Center, Nebraska.   Frequency of the minor allele in this cattle population was estimated to be 5.2%, and the estimated phenotypic difference between alleles was 1.14 kg for birth weight and 5.16 kg for 205-day weaning weight.  This polymorphism is a probable functional mutation candidate that successfully tracks functional alleles affecting growth.  Marker-assisted selection for the favorable genotype could have a beneficial effect on growth in cattle.

Slick hair gene localized to bovine chromosome 20.  The slick hair coat phenotype has been observed in tropical breeds of Bos taurus cattle and has been found to be beneficial for heat tolerance with body temperatures often 0.5 degrees Celsius lower for slick-haired animals compared to their normal-haired half-sibs during hot summer days. ARS researchers at Brooksville, Florida conducted a genome scan to map the slick hair gene in Senepol-derived cattle. The gene was localized with high certainty to a specific region of bovine chromosome 20 bound by two very tightly linked microsatellite markers. The mapping of the slick hair locus is the first step towards the eventual identification of the causative mutation that would constitute the definitive test for the slick hair coat phenotype.  The results will facilitate efforts towards introgression of this gene into important temperate Bos taurus breeds (such as Angus and Charolais) to enhance their adaptation to tropical environments.

Genomic Tools

Bovine genome tools being used to develop whole genome selection methods and further genome annotation in dairy and beef cattle.  A research consortium including two ARS labs at Beltsville, Maryland, an industry biotech company, a dairy industry organization representing all AI studs, and an industry pharmaceutical company has been formed to investigate the utility of genome selection in improving genetic gain, reducing costs of genetic testing in dairy cattle, and detecting quantitative trait loci (QTL).  Resources were assembled to develop a 60,000 single nucleotide polymorphism (SNP) "chip" for genotyping and material to extract DNA from over 600 Angus, 2,500 Holstein, 250 Brown Swiss and 750 Jersey cattle.  This project was only made possible because of the new availability of genome sequence information that quickly allowed identification of new SNP markers on a dense and genome-wide scale.  In a second project, ARS scientists at Beltsville, Maryland; Clay Center, Nebraska; and Miles City, Montana are developing a “gene atlas” of the bovine genome.  Total RNA from 98 tissues derived from the cow used to develop the bovine genome sequence and one of her offspring has been isolated.  Ultimately, this project will generate 100 million tags of sequence data that will be mapped back to the genome assembly.  This information will assist in annotating most of the bovine transcriptome and will provide a robust framework of gene expression similarities and differences between various bovine tissues to help guide annotation.

Integrated genetic map developed to aid in assembly and annotation of the bovine genome sequence.    Through an internationally funded effort, the Baylor College of Medicine Human Genome Sequencing Center led the effort in generating sequences and assembling the bovine genome sequence into contigs.  ARS scientists at the U.S. Meat Animal Research Center at Clay Center, Nebraska constructed an integrated genetic map comprised of approximately 17,000 markers from several genetic linkage and radiation hybrid maps from around the world.  This integrated map was used in the bovine genome sequencing project to serve as the scaffold for assigning sequence contigs to chromosomal positions.  In addition, over 1,500 full-length cDNA sequences were generated and annotated, which are the gold standards for annotating genes on a genome.  These accomplishments will greatly accelerate the discovery of DNA markers suitable for marker-assisted selection and fine mapping of genes for economically important traits in cattle.

Chicken genome sequence enables DNA fingerprinting of commercial and experimental chicken lines. The availability of the chicken genome sequence offers many opportunities to understand complex biological questions such as how genetic variation influences economically important traits. As a prelude to this advancement, researchers in the Avian Disease and Oncology Laboratory at East Lansing, MI evaluated a large number of chicken lines including birds from 36 elite commercial lines. By scoring 3,072 SNP markers on 2,580 different chickens, it was possible to screen the genome for unique or common alleles among the various chicken lines. This result is relevant to scientists and poultry breeding companies as it helps determine what genes are under genetic selection for economically important traits in industry broiler and layer lines. In addition, it is now possible to “trace back” poultry products to individual companies and lines through DNA fingerprinting using these markers. Additional aspects of this project are developing a linkage disequilibrium map of the chicken genome (i.e. haplotype map) to allow evaluation of whole-genome selection methodology.  This is the first comprehensive genetic profile of virtually an entire commodity group. This research provides substantial contributions to poultry breeding and food safety.

Discovery of microRNA expression in cattle and swine.  MicroRNA genes are a recently discovered form of genetic regulation with enormous impact on a variety of traits including growth, development, and tissue homeostasis.  ARS scientists at the U.S. Meat Animal Research Center performed the first survey of microRNA in cattle and swine muscle, and identified similarities and differences between reports from human and mouse muscle microRNA expression profiles.  The small RNA fraction containing putative microRNAs was isolated, cloned and sequenced to identify regulatory molecules.  The first experimentally verified cattle microRNA sequences were deposited in the public database, and comparisons with published data from other species were made to identify potential ruminant-specific molecules.  These results have significant impact on understanding the biology of ruminant muscle and address the general problem of annotation and subsequent analysis of the bovine genome sequence.

Growth and Development

Selection for body weight in chickens affects genes controlling growth and metabolism.  Increased body size in commercial chicken and turkey lines has been accompanied by unintended changes in correlated traits such as increases in voluntary food intake and energy storage.  Poultry breeders have intensively selected meat-type birds over many generations with specific emphasis on increasing growth rate (body weight) and meat production.  A study was conducted by ARS scientists in the Growth Biology Laboratory at Beltsville, Maryland, in conjunction with scientists at Virginia Tech, to determine the levels of expression for genes involved in the regulation of fat metabolism, growth, and energy balance.  Significant differences were observed for the expression of genes encoding lipogenic enzymes, AMP-activated protein kinase subunits and IGF system components in liver, brain and breast muscle tissue.  These results indicate some of the potential impact of genetic selection for body weight on genes regulating growth and metabolism in chickens and this information will be useful for developing genetic selection strategies for commercial lines of poultry.

Nutrient Intake and Utilization

Coumarate-3-hydroxylase (C3H) down-regulation dramatically alters lignin composition and improves forage digestibility.  The lignin component of the plant cell wall limits the utilization of polysaccharides by dairy and beef cattle. Down-regulation of the gene for C3H in alfalfa results in lignin that is derived from 65% of a lignin monomer, p-coumaryl alcohol, that is normally only minor (~1-2%). The compositional and structural changes result in improved digestibility of the plant cell wall. In collaboration with the Noble Foundation who produced transgenic plants, ARS scientists at the Dairy Forage Research Center at Madison, Wisconsin performed detailed structural and compositional analysis, and involved the industry in field trials for digestibility. C3H-down-regulation provides a new approach to improving digestibility of forages. A 10% improvement in cell-wall digestibility of forages by dairy cows in the U.S. is estimated to annually produce $350 million in increased milk sales and meat production concomitantly with 2.8 million tons less manure solids and 2 million tons less in grain supplements.

Animal Well-Being and Stress Control Systems

Lairage shown to be beneficial to pigs during transport.  Research conducted at the Livestock Behavior Research Unit at West Lafayette, Indiana showed that use of a clean lairage environment and maintained social structure for a period of 8 hours was beneficial to pigs during transport.  Lairage (temporary housing) in a known clean environment had benefits of diminished stress and immune stimulation, even 2 weeks after transport.  Measures of behavior on the truck, during the lairage, and after the transport showed effects of increased transport stress in continuously transported pigs.  Rehydration during the lairage was beneficial and access to feed improved intestinal microbial population stability, potentially altering the ability of the pig to use the nutrients that it eats.  These results will aid producers and scientists in managing transported swine more efficiently while simultaneously decreasing losses due to animal stress.

Respiration rate used as an indicator to determine heat stress in feedlot cattle.  ARS researchers at Clay Center, Nebraska used respiration rate as an indicator to determine risk factors for heat stress in feedlot heifers.  It was determined that at temperatures above 25ºC, dark-hided animals were 25% more stressed than light-colored animals; a history of pneumonia increased stress level by 10.5%; each level of fatness increased stress level by approximately 10%; and excitable animals had a 3.2% higher stress level than calm animals.  Not only did the stress level increase with these risk factors, but average daily gain was reduced.  The results of this study have not only revealed heat-stress risk factors of breed (color), condition score (fatness), temperament, and health history (treated or not treated for pneumonia), but also have shown the effectiveness of using respiration rate as an indicator of heat stress.