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United States Department of Agriculture

Agricultural Research Service


Location: Range and Livestock Research

2009 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 undertaken significant efforts to: develop procedures for cataloging species of prokaryotic, eukaryotic, viral and archaeal species in the rumen of cows fed high quality forage; estimate parameters needed for including molecular breeding values in national cattle evaluation; implement analytical methods for genetic analysis of longevity using survival analysis; determine interaction level of feed input for females with that of their dams; develop evidence that nutritional influences on replacement heifers may begin in utero and continue throughout life. Cows ovulating a small dominant follicle have lower pregnancy rates than cows ovulating a large follicle. To determine how this phenomenon affects fertility, cows ovulating follicles of known sizes were used as either embryo donors or embryo recipients in a reciprocal embryo transfer experiment. Approximately 80 more embryo transfers need to be completed. Preliminary results suggest that the ovum from small ovulating cows may be less fertile than that of large ovulating cows.

4. Accomplishments
1. A catalog of cattle genes. As a major step toward understanding the biology and evolution of ruminants, the cattle genome was sequenced to ~7x coverage. Scientists from Fort Keogh provided genomic DNA and RNA from numerous tissues to this effort. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 identifiable equivalents found in seven mammalian species. There are many evolutionary breakpoint regions in chromosomes identified by cross-species analysis, but those that are cattle-specific have a higher density of chromosome segment duplications, several types of repetitive elements, and species-specific variants in genes associated with lactation and immune responsiveness. Genes involved in metabolism were found highly conserved, although five metabolic genes are deleted or extensively diverged from their human counterparts. The cattle genome sequence provides a new resource for mammalian genome annotation and for accelerating genetic improvement for milk and meat production.

2. Healthy lean beef. Healthfulness of beef is determined, in part, by its fatty acid composition. Seventy single nucleotide polymorphism markers (SNPs) were used to scan the centromeric portion of chromosome 2 of 328 F2 progeny in a Wagyu x Limousin cross for straits associated with rib-eye area, lipid deposition, composition and palatability of meat. ARS scientists in Miles City, MT found a major QTL with additive effects on fatty acid composition near the centromere of chromosome 2. Results suggest this effect may be due to plieotrophic effects of the myostatin locus and lead to a greater understanding of the genetic control of composition of beef.

3. Reduced cost heifer development. Developing replacement heifers is the second largest cost of beef production. Current recommendations are based on maximizing the probability of conception at about 14 months of age. ARS scientists in Miles City, MT found 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.

4. Moving genes between populations, naturally. Backcrossing is a breeding strategy to introduce new genetic material into established breeds or lines of livestock and poultry. When coupled with marker or gene assisted selection, a specific gene or chromosomal region can be introduced into a new genetic background. It is often intended that the remainder of the genome remain unaffected when using these technologies. The objective was to assess the genomic structure of cattle produced by backcrossing for loci that are unlinked to a specific locus that was being moved from a donor breed to a recipient breed in when the particular genetic variant was not otherwise present. Genotypes of the two parental populations, their F1 progeny, and two subsequent backcross generations of animals were determined at 34 independent loci. There was little evidence to suggest any systematic genome-wide departure from pedigree derived expectation as a result of the breeding system. These data validate the desired intention of a backcrossing program that progressive generations migrate genotypically toward one of the parental types.

Review Publications
Sprangler, M.L., Robbins, K.R., Bertrand, J.K., MacNeil, M.D., Rekaya, R. 2009. Ant colony optimization as a method for strategic genotype sampling. Animal Genetics 40:308-314.

Elsik, C.G., Gibbs, R., Skow, L., Tellam, R., Weinstock, G., Worley, K., Kappes, S.M., Green, R.D., Alexander, L.J., Bennett, G.L., Carroll, J.A., Chitko Mckown, C.G., Hamernik, D.L., Harhay, G.P., Keele, J.W., Liu, G., Macneil, M.D., Matukumalli, L.K., Rijnkels, M., Roberts, A.J., Smith, T.P., Snelling, W.M., Stone, R.T., Waterman, R.C., White, S.N. 2009. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution. Science. 324:522-528.

Tshipuliso, N.O., Alexander, L.J., Kotze, A., Ehlers, K., Leesburg, V.L., Macneil, M.D. 2008. Structural assessment of backcrossing using microsatellite markers. South African Journal of Science 38(4):290-292.

Roberts, A.J., Geary, T.W., Grings, E.E., Waterman, R.C., MacNeil, M.D. 2009. Reproductive performance of heifers offered ad libitum or restricted access to feed for a 140-d period after weaning. Journal of Animal Science 87:3043-3052.

MacNeil, M.D. 2009. Invited Review: Research contributions from 75 years of breeding Line 1 Hereford cattle at Miles City, Montana. Journal of Animal Science 87:2489-2501.

Jiang, Z., Michal, J.J., Tobey, D.J., Daniels, T.F., Rule, D.C., Macneil, M.D. 2008. Significant associations of stearoyl-CoA desaturase (SCD1) gene with fat deposition and composition in skeletal muscle. International Journal of Biological Sciences 4(6):345-351.

Alexander, L.J., Kuehn, L.A., Smith, T.P., Matukumalli, L.K., Mote, B., Koltes, J.E., Reecy, J., Geary, T.W., Rule, D.C., Macneil, M.D. 2009. A Limousin specific myostatin allele affects longissimus muscle area and fatty acid profiles in a Wagyu-Limousin F*2* population. Journal of Animal Science 87:1576-1581.

Sa Filho, O.G., Vilela, E.R., Geary, T.W., Vasconcelos, J. 2009. Strategies to improve fertility in post partum Bos indicus cows submitted to a fixed-time insemination protocol with GnRH and PGF2a. Journal of Animal Science 87:2806-2814.

Last Modified: 10/16/2017
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