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United States Department of Agriculture

Agricultural Research Service


Location: Genetics, Breeding, and Animal Health Research

2012 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:
This is the final report for the 5-year-project 5438-31000-085-00D which expired in 2012 and was replaced with a new project 5438-31000-090-00D. Beef cattle populations developed during the project have contributed substantially to our knowledge of within and between breed genetic and genomic variation for a variety of economically relevant traits. Crossbred cows and bulls, progeny of the seven most highly used beef breeds, were mated to produce over 2,000 progeny. In addition, over 3,700 progeny of over 500 industry representative bulls from 18 prominent industry breeds (Angus, Hereford, Simmental, Charolais, Limousin, Red Angus, Gelbvieh, Shorthorn, Brangus, Beefmaster, Maine-Anjou, Brahman, Chiangus, Santa Gertrudis, Salers, Braunvieh, South Devon, and Tarentaise) were produced. The goal was to develop a representative fullblood (7/8 or greater of each breed) and crossbred herd of breeding females. About 300 fullbloods, 990 backcross, and 2,450 F1 calves have been produced toward this goal. These combined populations were intensively phenotyped for weight, fertility, feed intake and efficiency, and carcass quality measures. Cattle have contributed to estimates of current breed differences and across-breed genetic evaluation adjustments published each year for growth and carcass traits. These differences and factors are used by producers to compare the genetic merit of sires from different breeds. Over 6,000 progeny from both populations were genotyped using 50,000 marker genotyping arrays and resulting genome associations for regions affecting production traits were disseminated. These same populations were used to develop genomic prediction equations for the beef cattle industry. Foundation animals from these populations are being sequenced to further improve the detection of causal variation affecting economically relevant traits. Analyses conducted on 2,200 other descendants of these populations suggest that vaccination response to respiratory disease virus antigens may be exhibited in a cell-mediated rather than only a humoral (antibody) response. Animals with higher lymphocyte production were genetically less likely to succumb to bovine respiratory disease in feedlot confinement. Genomic analyses of these data are underway. Genomic pooling of DNA samples from cattle with extreme phenotypes helped to cost-effectively identify genomic variation responsible for differences in fertility and disease resistance. Experimental results provided the basis for creation of an easy-care maternal line of prolific hair sheep. Mature Romanov crossbred ewes excelled for raising triplets on pasture without labor or supplemental feed and for high fertility rates during May, a difficult month for breeding sheep. Breed composition of the maternal line is half Romanov, quarter White Dorper and quarter Katahdin. Rams that are reared as triplets on pasture, shed hair/wool, genetically resistant to scrapie, genetically less susceptible to ovine progressive pneumonia, polled, and white are sought for breeding. The potential impact is increased profitability by marketing more lambs per ewe with less use of labor and harvested feed.

4. Accomplishments
1. Low-cost genotyping method. Cost of genotyping is a primary impediment to the use of genomic prediction in livestock selection and management. A method of genotyping based on next generation sequencing was developed that is low-cost per individual when applied to many individuals simultaneously. The method is being applied commercially by a CRADA partner. Initial customers are DNA testing companies, researchers, and beef cattle breed associations. The method is likely to be used by large cattle feedlots and ranches, and corresponding elements of the breeding and production chain for other agricultural species. The use of this technology should improve livestock quality and health, reduce costs of production, and ultimately benefit the consumer and the environment.

2. Reducing the risk of ovine progressive pneumonia infection in sheep. Ovine progressive pneumonia (OPP) is an incurable, slow-acting, wasting disease that affects sheep in most countries. It is one of the most costly sheep diseases in the United States due to a decrease in litter weaning weights of about 20% and premature culling or death of breeding stock. ARS researchers at Clay Center, Nebraska designed a study to compare infection rates of sheep with two different forms of a gene (alleles) known to affect susceptibility to the OPP virus. Sheep with one or two copies of the dominant allele had three times the infection rate (34%) of sheep without the dominant allele (11%). Producers can use DNA testing to reduce the risk of OPP virus infection and, thus, increase productivity and improve well-being of their sheep.

Review Publications
Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Smith, T.P., Ferrell, C.L., Jenkins, T.G., Freetly, H.C. 2012. Evaluation of polymorphisms within the genes GSHR and SLC2A2 that are within a region on bovine chromosome 1 (BTA1) previously associated with feed intake and weight gain. Animal Genetics. 43(1):112.

Heaton, M.P., Clawson, M.L., Chitko-Mckown, C.G., Leymaster, K.A., Smith, T.P.L., Harhay, G.P., White, S.N., Herrmann-Hoesing, L.M., Mousel, M.R., Lewis, G.S., Kalbfleisch, T.S., Keen, J.E., Laegreid, W.W. 2012. Reduced lentivirus susceptibility in sheep with TMEM154 mutations. PLoS Genetics. 8(1): e1002467. DOI: 10.1371/journal.pgen.1002467.

Pollak, E.J., Bennett, G.L., Snelling, W.M., Thallman, R.M., Kuehn, L.A. 2012. Genomics and the global beef cattle industry. Animal Production Science. 52:92-99.

Lindholm-Perry, A.K., Sexten, A.K., Kuehn, L.A., Smith, T.P., King, D.A., Shackelford, S.D., Wheeler, T.L., Ferrell, C.L., Jenkins, T.G., Snelling, W.M., Freetly, H.C. 2011. Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle. BioMed Central (BMC) Genetics. 12:103.

Lindholm-Perry, A.K., Kuehn, L.A., Rempel, L.A., Smith, T.P., Cushman, R.A., McDaneld, T.G., Wheeler, T.L., Shackelford, S.D., King, D.A., Freetly, H.C. 2012. Evaluation of bovine chemerin (RARRES2) gene variation on beef cattle production traits. Frontiers in Genetics. 3:39.

Last Modified: 06/22/2017
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