2008 Annual Report 1a.Objectives (from AD-416) 1: Characterize rumen microbial populations, including cellulolytic microbes, and elucidate dynamics of these populations through the use of metagenomic approaches. 2: Determine rumen microbial and host genetic effects associated with differences in measures of efficiency of heifers developed under divergent planes of nutrition or different diets. 3: Determine phenotypic and genetic relationships of early-in-life measures of feed consumption, growth and body composition, with subsequent reproduction and lifetime productivity. 4: Determine if the level of nutrition in utero and prior to puberty results in epigenetic effects on traits associated with production efficiency at later stages in life. 5: Develop and validate appropriate phenotypes for measuring fertility in cattle in order to determine interactions between variation in cow feed efficiency and reproductive performance. 6: Identify and fine map quantitative trait loci (QTL) affecting feed intake, growth and reproduction. 1b.Approach (from AD-416) Line 1 Hereford, an intercross (CGC) of Charolais (25%), Red Angus (50%) and Tarentaise (25%), and two predominantly Hereford-Angus crossbred herds are used. Line 1 Hereford cattle are ~30% inbred, with consequently reduced fitness, and have close ties to the bovine genome sequence. Two distinct nutritional environments will be imposed on the CGC population to challenge the nutrition-reproduction axis. One Hereford-Angus cowherd provides donor and recipient females for studies using embryo transfer. The other Hereford-Angus cowherd calves in two seasons and thus has differential synchrony between nutritional value of range forage and nutrient requirements of the cows. 1: Identify new species of rumen microbes through whole genome shotgun sequencing of rumen microbial milieu. Compare rumen bacterial species diversity responses to different diets. 2: Evaluate rumen microbial diversity and host animal gene expression in samples of animals expressing extreme differences in feed efficiency. 3: Estimate genetic and phenotypic variances and covariances of longevity, stayability, number of calves produced, and cumulative production of beef cows with early-in-life measures of growth rate, feed consumption, and indicators of body composition. Determine effects of phenotypes measured early-in-life on subsequent fertility of bulls. 4: Determine effects of feed intake prior to puberty and level of supplementation during mid to late gestation on genetic (co)variance and gene expression of the treated animals and their progeny. Determine effects of nutrient intake during gestation on phenotypes of treated animals and their progeny. 5: Determine factors controlling establishment and maintenance of pregnancy in cows induced to ovulate different sized follicles. Establish relationships between previous nutrition, time post-partum, resumption of estrus, and energetic efficiency in young postpartum beef cows. 6: Identify QTL affecting growth and reproduction in an advanced intercross of Red Angus, Charolais, and Tarentaise. Identify QTL with over-dominance effects on fitness. Identify genes expressed in tissues of cattle. 3.Progress Report Reducing cost of production hinges on maintaining high rates of reproductive success while reducing the use of harvested feeds. Genetic selection to make cumulative progress toward this goal in the US beef industry requires selection criteria that simultaneously consider several traits. Traditional heifer development systems attempt to maximize pregnancy rates, but not necessarily optimize profit or sustainability. The fuel requirement to harvest feed and deliver it to cattle creates high energy demands in the traditional development system. Cereal grains, often used as a major energy source in heifer diets, detract from the system’s sustainability due to growing demand for human food and ethanol production. We have found that heifers developed to lower target weights than those traditionally recommended consumed 27% less feed over winter and had improved efficiency throughout the postweaning period and subsequent grazing season. This strategy is estimated to reduce costs of developing each replacement female by more than $31. Healthfulness of beef is determined, in part, by its fatty acid composition. We found a major QTL with additive effects on fatty acid composition near the centromere of chromosome 2. Preliminary results suggest this effect may be due to plieotrophic effects of the myostatin locus. Residual feed intake (RFI) is a measure of feed efficiency and therefore an economically relevant trait. We found a putative QTL indicative of a recessive gene(s) with favorable effects on RFI at approximately 58 cM on chromosome 6. Data collection in support of all objectives is ongoing as planned. This work supports National Program 101 Action Plan Component II.c: Component II. Enhancing Animal Adaptation, Well-Being and Efficiency in Diverse Production Systems - Improving Efficiency of Nutrient Utilization and Conversion to Animal Products. 4.Accomplishments 1. Fatty acid composition in beef has received considerable interest in view of its implications for human health and meat quality characteristics. While unsaturated fats are beneficial when consumed in moderation, high levels of saturated fat are associated with increased serum low-density lipoprotein cholesterol concentrations and pose a risk factor for coronary heart disease. In addition, beef with the most desirable flavor has a higher percentage of monounsaturated fatty acids. We have discovered a QTL with large effects on the fatty acid composition of beef and preliminary results suggest the myostatin locus may be causative. The results guide future research to provide a richer understanding of genetic mechanisms controlling palatability and healthfulness of beef and may ultimately lead to tools for producing beef of greater value to consumers. (NP 101 Action Plan: Component I - Understanding, Improving, and Effectively Using Animal Genetic and Genomic Resources, Problem Statement 1B: Identify Functional Genes and Their Interactions) 5.Significant Activities that Support Special Target Populations none 6.Technology Transfer Number of New Germplasm Releases 1 Number of New Commercial Licenses Executed 6 Review Publications Tshipuliso, N., Alexander, L.J., Geary, T.W., Snelling, W.M., Rule, D.C., Koltes, J.E., Mote, B.E., MacNeil, M.D. 2008. Mapping quantitative trait loci for fatty acid composition that segregate between Wagyu and Limousin. South African Journal of Science 38(2):126-130. Spangler, M.L., Sapp, R.L., Bertrand, J.K., MacNeil, M.D., Rekaya, R. 2008. Different Methods of Selecting Animals for Genotyping to Maximize the Amount of Genetic Information Known in the Population. Journal of Animal Science 86:2471-2479. Standley, T., Paterson, J., Skinner, K., Rainey, B., Roberts, A.J., Geary, T.W., Smith, G., White, R. 2008. The Use of an Experimental Vaccine in Gestating Beef Cows to Reduce the Shedding of Escherichia coli O157:H7 in the Newborn Calf. Professional Animal Scientist 24:260-263. Grings, E.E., Roberts, A.J., Geary, T.W., Macneil, M.D. 2008. Milk Yield of Primiparous Beef Cows From Three Calving Systems and Varied Weaning Ages. Journal of Animal Science 86:768-779. Jiang, Z., Michal, J.J., Tobey, D., Wang, Z., MacNeil, M.D., Magnuson, N.S. 2008. Comparative understanding of UTS2 and UTS2R genes for their involvement in type 2 diabetes mellitus. International Journal of Biological Sciences 4(2):96-102. Harris, H.L., Cupp, A.S., Roberts, A.J., Funston, R.N. 2008. Heifers fed soybeans or milling by-products utilization of soybeans or corn milling by-products in beef heifer development diets. Journal of Animal Science 86:476-482. Busch, D.C., Atkins, J.A., Bader, J.F., Shafer, D.J., Patterson, D.J., Geary, T.W., Smith, M.F. 2008. Effect of Ovulatory Folicle Size and Expression of Estrus on Progesterone Secretion in Beef Cows. Journal of Animal Science 86(3):553-563. Alexander, L.J., Macneil, M.D., Geary, T.W., Snelling, W.M., Rule, D.C., Scanga, J.A. 2007. Quantitative trait loci with additive effect on palatability and fatty acid composition of meat in a Wagyu-Limousin F*2 population. Animal Genetics 38:506-513. Alexander, L.J., Juneja, B., Shiroma, D., Nonneman, D.J., Snelling, W.M., Fahrenkrug, S.C. 2007. Comparative and physical mapping of 112 previously reported and 105 new porcine microsatellites. Animal Genetics 38:584-594. MacNeil, M.D., Northcutt, S.L. 2008. National cattle evaluation system for combined analysis of carcass characteristics and indicator traits recorded using ultrasound in Angus cattle. Journal of Animal Science 86: 2518-2524.