2013 Annual Report
1a.Objectives (from AD-416):
Objective 1. Improve breeding and management decisions by characterizing current genetic and phenotypic variation within and between predominant beef breeds and crosses using novel genomic and genetic evaluation technologies.
Objective 2. Reduce mortality and morbidity of beef cattle and sheep by identifying genetic factors affecting susceptibility to respiratory diseases and by developing effective selection programs.
Subobjective 2a. Increase resistance and resilience to bovine respiratory disease complex (BRDC) through improved genetic and genomic selection tools.
Subobjective 2b. Reduce the prevalence of ovine progressive pneumonia (OPP) in sheep by developing selection guidelines based on four TMEM154 haplotypes affecting susceptibility to infection.
Objective 3. Enhance the competitiveness, profitability and sustainability of lamb production with reduced labor inputs by developing and evaluating an easy-care maternal line of prolific hair sheep.
Objective 4. Increase effectiveness of beef cattle selection programs focused on carcass merit and reproduction by determining correlated responses in relevant traits to marker based selection.
1b.Approach (from AD-416):
The overall goal is to improve genetic merit of purebred and crossbred beef cattle and sheep by enhancing knowledge of genetic variation affecting efficiency and sustainability of production. The ability to prudently exploit various genetic effects in livestock production is limited because key information is lacking. Beef cattle and sheep producers need to know how much performance differs among influential breeds based on current genetics, as well as the degree of genetic variation within breeds. Discovery and development of genetic markers affecting essential traits, determination of gene action for marker alleles, and knowledge of the net outcome of using markers are limited, yet necessary for improvement of production efficiency and product quality. These genetic effects are the foundation for improvement of breeds by selection and for development of effective purebred and crossbred mating systems. Collectively, we have designed experiments to estimate genetic differences among breeds, heterosis effects, genetic variation within breeds, and effects of genetic markers. As precise estimates of genetic effects are required for efficient implementation, we will use large experimental populations of beef cattle and sheep to collect data on a broad range of traits affecting efficiency and sustainability of life-cycle production. Experimental results will provide information as requested by beef cattle and sheep producers to help address profitability and sustainability concerns. Project scientists will provide leadership to deliver these research products to the beef cattle and sheep industries so that producers can make informed genetic and management decisions.
Beef cattle populations developed during this and previous projects contribute to our knowledge of within and between breed genetic and genomic variation. Since 2007, over 5000 progeny and 7500 grand progeny of over 500 bulls representing 18 prominent breeds were produced. The goal is to develop representative purebred (7/8 or greater of each breed) and crossbred herds of breeding females. To date, approximately 900 purebred, 1300 backcross, and 2800 F1 progeny of these bulls have been produced. These populations were intensively phenotyped for weight, fertility, feed intake, efficiency, end product quality, and other economically relevant traits. Data were used to estimate current breed differences and across-breed genetic evaluation adjustments for growth and carcass traits. Over 7,500 progeny from the Germplasm Evaluation Project were genotyped using 54,000 genetic markers and genome associations for regions affecting production traits were disseminated. These same populations were used to develop genomic prediction equations for the beef cattle industry. Over 250 foundation sires from this population were sequenced to improve the detection of causal variation affecting economically relevant traits.
Genetic susceptibility to bovine respiratory disease complex (BRDC) was studied by recording vaccination responses of over 1000 calves. Serum samples and nasal swabs were taken during the first vaccination and later when the calves were vaccinated 21 days prior to weaning and at weaning. Serum samples were used to measure antibody responses to the vaccines. A total of 600 calves were retained, and allowed to express genetic susceptibility to BRDC by not feeding antibiotics.
Additive and dominance effects of TMEM154 haplotypes 1, 2, and 3 on susceptibility to ovine progressive pneumonia virus were studied by measuring the serological status of breeding ewes naturally exposed to the virus. A second replicate of ewes with haplotypes 2 and 3 was produced in 2013, while the first replicate of ewes with haplotype 4 was born.
A maternal line of prolific hair sheep (Easycare) is being developed for low-input production systems. This line will be compared to prominent breeds of prolific wool (Polypay) and hair sheep (Katahdin). A total of 873 Easycare, 316 Polypay, and 311 Katahdin ewes were bred to produce 2278 lambs in 2013. These lambs will be used to initiate the evaluation of Easycare, Polypay, and Katahdin ewes when bred to produce purebred and crossbred lambs.
Results of analyses are being compiled for cattle populations selected to enhance estimation of genetic effects of certain DNA markers. In one population, a myostatin mutation found primarily in Limousin increases rib muscle area and meat yield, reduces fat thickness and marbling, results in meat with lighter color, and delays heifer puberty but has little effect on carcass weight. Results are largely additive. However, there is some indication that the effects of one copy on muscle area and marbling is somewhat less than half of the effects of two copies. In another population, estimated effects of two DNA markers on meat tenderness were individually and jointly additive.
Selection against susceptibility to bovine respiratory disease complex. Bovine respiratory disease complex costs the beef cattle industry over $700 million of lost revenue annually. Unfortunately, because subclinical animals are not detected and exposure is not consistent year to year, traditional methods to reduce incidence via genetic selection are not effective. Traits such as immune responses to vaccination provide a mechanism to select for less susceptibility to respiratory disease. ARS researchers at Clay Center, Nebraska measured the change in levels of several white blood cell counts in response to booster vaccines for pathogens causing respiratory disease and determined that increases in lymphocyte levels were genetically correlated to decreased clinical incidence of respiratory disease. Measurement of lymphocyte levels will improve the accuracy of selection for less susceptibility to respiratory disease and allow producers to decrease the overall incidence while reducing dependence on antibiotics in feedlot cattle.
Selection against susceptibility to ovine progressive pneumonia virus. Ovine progressive pneumonia is an incurable, slow-acting, wasting disease that affects sheep production in many countries. It is one of the most costly sheep diseases in the United States due to a 20% decrease in production and premature removal of infected sheep from flocks. A gene that affects susceptibility to progressive pneumonia infection was studied by ARS researchers at Clay Center, Nebraska. Sheep with either one or two copies of an unfavorable form of the gene had infection rates of 33% at nine months of age compared to 9% for other sheep. Sheep producers are using this DNA technology to make their flocks genetically less susceptible to this disease. Eradication of the disease will improve health of sheep and increase profits for producers.
Improved selection of beef cattle through genomics. Traditional methods of improving beef cattle by selection, based on measuring performance, might be improved by use of DNA information. ARS researchers at Clay Center, Nebraska have made critical contributions over many years to improve national selection programs. A key contribution was gathering information on over 2,000 influential bulls of 16 breeds for 50,000 genetic markers. This resource provided the genomic framework for breed associations to develop customized selection procedures. Several breeds currently use genomic information to select cattle with greater accuracy, while other breeds are actively pursuing this opportunity. As a result of this research, cattle breeders are now able to make more rapid genetic progress with less risk of selecting genetically inferior parents.
Weber, K.L., Thallman, R.M., Keele, J.W., Snelling, W.M., Bennett, G.L., Smith, T.P., McDaneld, T.G., Allan, M.F., Van Eenennaam, A.L., Kuehn, L.A. 2012. Accuracy of genomic breeding values in multibreed beef cattle populations derived from deregressed breeding values and phenotypes. Journal of Animal Science. 90(12):4177-4190.
Weber, K.L., Drake, D.J., Taylor, J.F., Garrick, D.J., Kuehn, L.A., Thallman, R.M., Schnabel, R.D., Snelling, W.M., Pollak, E.J., Van Eenennaam, A.L. 2012. The accuracies of DNA-based estimates of genetic merit derived from Angus or multibreed beef cattle training populations. Journal of Animal Science. 90(12):4191-4202.
White, S.N., Mousel, M.R., Herrmann-Hoesing, L.M., Reynolds, J.O., Leymaster, K.A., Neibergs, H.L., Lewis, G.S., Knowles Jr, D.P. 2012. Genome-Wide association identifies multiple genomic regions associated with susceptibility to and control of ovine lentivirus. PLoSOne 7(10):e47829.
Bennett, G.L., Shackelford, S.D., Wheeler, T.L., King, D.A., Casas, E., Smith, T.P. 2013. Selection for genetic markers in beef cattle reveals complex associations of thyroglobulin and casein1-S1 with carcass and meat traits. Journal of Animal Science. 91(2):565-571.
Schmidt, J.W., Griffin, D., Kuehn, L.A., Harhay, D.M. 2013. Influence of therapeutic ceftiofur treatments of feedlot cattle on fecal and hide prevalences of commensal Escherichia coli resistant to expanded-spectrum cephalosporins, and molecular characterization of resistant isolates. Applied and Environmental Microbiology. 79(7):2273-2283.
Peters, S.O., Kizilkaya, K., Garrick, D.J., Fernando, R.L., Pollak, E.J., De Donato, M., Hussain, T., Imumorin, I.G. 2013. Application of multivariate heavy-tailed distributions to residuals in the estimation of genetic parameters of growth traits in beef cattle. Journal of Animal Science. 91(4):1552-1561.
Leeds, T.D., Notter, D.R., Leymaster, K.A., Mousel, M.R., Lewis, G.S. 2012. Evaluation of Columbia, USMARC-Composite, Suffolk, and Texel rams as terminal sires in an extensive rangeland production system: I. Ewe productivity and crossbred lamb survival and preweaning growth. Journal of Animal Science. DOI:10.2527/jas.2011-4640.
Shackelford, S.D., Leymaster, K.A., Wheeler, T.L., Koohmaraie, M. 2012. Effects of breed of sire on carcass composition and sensory traits of lamb. Journal of Animal Science. 90:4131-4139.
Leach, R.J., Chitko-McKown, C.G., Bennett, G.L., Jones, S.A., Kachman, S.D., Keele, J.W., Leymaster, K.A., Thallman, R.M., Kuehn, L.A. 2013. The change in differing leukocyte populations during vaccination to bovine respiratory disease and their correlations with lung scores, health records, and average daily gain. Journal of Animal Science. 91(8):3564-3573.