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United States Department of Agriculture

Agricultural Research Service


Location: Genetics, Breeding, and Animal Health Research

2010 Annual Report

1a. Objectives (from AD-416)
OBJECTIVE 1. Characterize quantitative and molecular genetic variation between and within breeds for traits that affect life-cycle efficiency of beef cattle. Sub-objective 1A. Characterize direct and maternal breed and heterosis effects among diverse breeds of cattle, and genetic variances and covariances within breeds for calving ease, survival, rate and efficiency of growth, carcass composition, meat quality, age and weight at puberty, reproduction, maternal performance, cow size, and herd life. Sub-objective 1B. Identify and fine map QTL regions that affect quality of beef and efficiency of production. Sub-objective 1C. Determine the efficiency of feed use among mature cows during the production interval from parturition until weaning. Sub-objective 1D. Identify genetic components associated with bovine disease resistance. Sub-objective 1E. Characterize genomic diversity among a broad sample of highly influential germplasm in the U.S. beef industry. OBJECTIVE 2. Examine potential interactions of genetically diverse breeds of cattle with climatic or nutritional environments. OBJECTIVE 3. Evaluate breeds to create an easy-care maternal line of hair sheep for use in low-input production systems. Sub-objective 3A. Evaluate wool and hair breeds in intensive and low-input production systems during traditional fall breeding and for fertility during challenging spring breeding. Sub-objective 3B. Evaluate life-cycle productivity of reciprocal crosses between the Romanov and Rambouillet breeds. Sub-objective 3C. Create an easy-care maternal line of hair sheep. OBJECTIVE 4. Evaluate power of experimental designs to estimate quantitative and molecular genetic parameters. OBJECTIVE 5. Develop statistical theory and computational algorithms to incorporate DNA information and multi-breed comparisons into genetic evaluations of beef cattle.

1b. Approach (from AD-416)
Genetic variation among and within breeds, including allelic variation, provides a foundation for genetic improvement through selection and for management of genetic effects through crossbreeding (or mating) systems. Improvement of production efficiency and sustainability of beef cattle and sheep production systems are dependent on greater knowledge of genetic effects on fundamental traits affecting life-cycle efficiency such as fertility, prolificacy, maternal ability, offspring survival, health, longevity, and adaptation to production environments. Two broad approaches will be pursued: 1) large-scale animal experimentation and 2) development and application of statistical theory and software to support discovery and estimation of genetic effects. The first three objectives use experimental populations to provide genotypic and phenotypic data for traits known to affect life-cycle efficiency and for matching genetic resources with specific marketing and production situations. Large-scale beef cattle and sheep experiments using both quantitative and molecular approaches are planned to provide genotypic and phenotypic data for estimation of genetic effects on fundamental traits. Cattle research will emphasize multi-breed genetic evaluation, estimation of genetic parameters within breed, and structuring of populations to facilitate genomic research leading to development of DNA tests for economically important traits. A population of cattle is being developed for QTL identification that has recent ties to industry genetics, several half-sib families large enough to contribute to identifying QTL through linkage, and many smaller families and several potential origins of QTL allowing fine mapping, association analyses, and marker validation. Potential interactions of temperate and tropically-adapted cattle breeds with temperate and subtropical environments will be investigated through evaluation of F1 cows consistent with commercial production systems in the subtropical environment of Louisiana and the temperate environment of Nebraska. Sheep experimentation will focus on breed evaluation, leading to creation and development of an easy-care maternal line of hair sheep. The animal experiments will be complemented by research to develop and apply statistical technologies required for discovery, estimation, and use of genetic effects, including incorporation of genetic markers into multibreed genetic evaluations for beef cattle. The fourth objective addresses designs of experimental populations for estimation of genetic effects. Various mating plans will be simulated and evaluated for their power to detect QTL effects of various sizes, power of detecting breed-specific heterosis, and for the standard errors of other genetic effects. The final objective focuses on the development and application of statistical theory required for analysis of data and exploitation of genetic effects by livestock industries. Whole genome selection will be investigated as a method to reduce bias and improve accuracy of genetic prediction.

3. Progress Report
Marker associations for feed intake/efficiency and carcass traits were detected on crossbred steers formed through crosses of F1 sires and dams sired from the 7 beef breeds with the most registrations. Steers were born from 2004 through 2008. Markers tested for associations were from the Illumina BovineSNP50 Beadchip. Fine mapping efforts have begun for both of these suites of traits. Approximately 800 terminal steers and heifers born from F1 sires of the same 7 breeds as well as Brahman were produced and measured for disease resistance phenotypes: vaccination response, treatment and diagnostic records, lung lesions at slaughter, and blood counts upon entering the feedlot. A combined analysis of markers for growth, feed efficiency, carcass, and reproductive traits on genotyped cattle populations at the U.S. Meat Animal Research Center and collaborators in Canada and Australia yielded marker associations that were more significant than any of the individual sources of genotyped animals. Markers with similar effects can be detected across diverse environments and sources of germplasm. Cows continued to be mated to AI sires sampled from the 16 largest beef breed associations with genetic evaluations. Breeds included Angus, Hereford, Simmental, Charolais, Limousin, Red Angus, Gelbvieh, Shorthorn, Brangus, Beefmaster, Maine-Anjou, Brahman, Chiangus, Santa Gertrudis, Salers, and Braunvieh. Backcross progeny of several of these breeds were born in the fall of 2009 and spring of 2010. Over 1,500 F1 calves and almost 500 backcross calves have been produced since these crosses began. Additionally, 29 7/8-blood calves were produced this spring; these were the first calves born as ‘purebreds’, an eventual goal in this project. Steer and heifer progeny from AI matings to these sire breeds were measured for feed intake. Carcass data, including tenderness phenotypes (spring 2009 born), were collected on these steers. Heifers were retained for reproductive performance assessment and to continue producing calves that will contribute to estimation of breed differences, heterosis, and genomic marker effects. Experimental design and analysis methods were developed to detect marker associations for disease traits using phenotypic measures such as lung lesions, treatment records for pneumonia, and bloat treatment records using pooled DNA samples from animals with extreme phenotypes. These procedures, already applied in human case control studies, have the potential to improve marker association testing on large phenotypic databases with minimal costs. We completed research to measure fertility rates during spring breeding on crossbred ewes produced by mating Dorset, Dorper, Katahdin, Rambouillet, and White Dorper rams to Romanov ewes. We evaluated productivity of 4- and 5-year-old Rambouillet-Romanov reciprocal crossbred ewes mated to 2 terminal sire breeds. We produced over 1,500 lambs of an easy-care line of prolific hair sheep (½ Romanov, ¼ White Dorper and ¼ Katahdin) and continued to increase flocks of Katahdin and Polypay sheep as industry standards for easy-care maternal breeds of prolific hair and wool sheep, respectively.

4. Accomplishments
1. High fertility during spring breeding of Romanov crossbred ewes. Most breeds of sheep are far more fertile during fall breeding than spring breeding, resulting in the vast majority of lambs being born in the spring. The seasonal production of lambs adversely affects product availability for consumers and this situation is a major obstacle for the U.S. sheep industry. To deal with this problem, producers have traditionally used crossbred ewes of Dorset, Finnsheep and Rambouillet breeding to achieve fertility rates averaging from 60 to 70% following breeding in the late spring. ARS researchers at Clay Center, Nebraska documented that Romanov crossbred ewes realized fertility rates of 87 to 89% when exposed during May, regardless of the remaining breed composition (Dorper, Dorset, Katahdin, Rambouillet, and White Dorper). Commercial producers can overcome the seasonal constraint of fertility rate by use of Romanov crossbred ewes.

2. A statistical method for estimating the degree to which DNA tests are able to predict economically important traits was developed. The method estimates the proportion of genetic variation in economically important traits accounted for by the DNA test, which in turn determines the degree to which a DNA test can improve the accuracy of evaluations of genetic merit. Previous approaches to estimating this proportion were widely recognized as overstating the effect of the test and, consequently, were not widely used. The method developed by ARS scientists at Clay Center, Nebraska provides accurate estimates and is able to use DNA tests results in the form that DNA testing companies are currently providing them – molecular breeding values. The estimator can be computed using software that is commonly used by animal breeders. This method provides a basis for potential customers of DNA tests to evaluate the utility of DNA testing technology and compare alternative DNA testing products.

3. Breed differences in cow productivity traits were evaluated in two very different environments. ARS scientists at Clay Center, Nebraska and scientists at Louisiana State University compared maternal and reproductive traits of F1 cows sired by breeds adapted to subtropical environments in both Louisiana (subtropical environment) and Nebraska (temperate environment). The breeds evaluated were Beefmaster, Brangus, Bonsmara, and Romosinuano. Estimates of differences among these breeds in different environments help cattle producers choose breeds that will be most productive in their environments.

4. Whole genome single nucleotide polymorphism associations with meat quality and composition traits of beef cattle. A recently developed tool for cattle genomics is a beadchip that can quickly assay 52,156 genetic markers. The associations of these markers with traits important to cattle production are mostly unknown. The associations potentially can be used to aid selection by cattle breeders or management decisions by ranchers and feeders. ARS scientists at Clay Center, Nebraska used the beadchip on 1,800 crossbred cattle measured for meat tenderness, marbling, body composition, and carcass weight. Hundreds of strong associations between markers and growth were estimated with a high degree of confidence, and these markers were often located on chromosomes previously identified as affecting growth. Thousands of weaker associations between markers and growth were identified with less confidence. These results will be useful in developing additional tools that can be widely used by the cattle industry.

Review Publications
King, D.A., Shackelford, S.D., Kuehn, L.A., Kemp, C.M., Rodriguez, A.B., Thallman, R.M., Wheeler, T.L. 2010. Contribution of Genetic Influences to Animal-to-Animal Variation in Myoglobin Content and Beef Lean Color Stability. Journal of Animal Science. 88:1160-1167.

Cushman, R.A., Allan, M.F., Kuehn, L.A., Snelling, W.M., Cupp, A.S., Freetly, H.C. 2009. Evaluation of Antral Follicle Count and Ovarian Morphology in Crossbred Beef Cows: Investigation of Influence of Stage of the Estrous Cycle, Age, and Birth Weight. Journal of Animal Science. 87(6):1971-1980.

Garcia, M.D., Thallman, R.M., Wheeler, T.L., Shackelford, S.D., Casas, E. 2010. Effect of Bovine Respiratory Disease and Overall Pathogenic Disease Incidence on Carcass Traits. Journal of Animal Science. 88(2):491-496.

Hsu, W.L., Johnson, R.K., Van Vleck, L.D. 2010. Effect of Pen Mates on Growth, Backfat Depth, and Longissimus Muscle Area of Swine. Journal of Animal Science. 88(3):895-902.

Cooper, A.J., Ferrell, C.L., Cundiff, L.V., Van Vleck, L.D. 2010. Prediction of Genetic Values for Feed Intake from Individual Body Weight Gain and Total Feed Intake of the Pen. Journal of Animal Science. 88(6):1967-1972.

Heaton, M.P., Leymaster, K.A., Kalbfleisch, T.S., Freking, B.A., Smith, T.P., Clawson, M.L., Laegreid, W.W. 2010. Ovine Reference Materials and Assays for Prion Genetic Testing. BioMed Central (BMC) Veterinary Research [serial online]. 6:23. Available:

Casas, E., Thallman, R.M., Kuehn, L.A., Cundiff, L.V. 2010. Postweaning Growth and Carcass Traits in Crossbred Cattle from Hereford, Angus, Brangus, Beefmaster, Bonsmara, and Romosinuano Maternal Grandsires. Journal of Animal Science. 88(1):102-108.

Last Modified: 05/27/2017
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