2011 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
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
5: Develop and validate appropriate phenotypes for measuring fertility in cattle in
order to determine interactions between variation in cow feed efficiency and
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
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.
Data analysis and drafting of publications to assess diversity of the rumen microbial community and changes in it are proceeding, albeit at a slow rate than originally planned. Collection of phenotypic data from CGC and Line 1 Hereford populations has proceeded as planned.
Extensive analyses of data pertaining to factors controlling establishment and maintenance of pregnancy in cows were completed and a manuscript is in the final stages of preparation. Relationships among factors affecting the response variables of primary interest are numerous and both direct and mediated through other intermediate factors. No single variable controlled a preponderance of the variation in any of the primary response variables. Understanding factors affecting the primary response variables requires simultaneous consideration of several causative variables. Much of the biology underlying establishment and maintenance of pregnancy remains to be elucidated. Initial studies on the role of estradiol in maintenance of pregnancy form day 7 to day 27 are proceeding as planned.
Analyses of data pertaining to imputation of genotypes from 3K SNP to 50K SNP are proceeding. In Line 1, the imputation appears quite successful with over 85% of 50K SNP genotypes accurately imputed from 3K SNP. Similar efforts to impute from 3K to 50K in CGC are complicated by a lack of correspondence between genes and or scores on the two SNP genotyping platforms. This delays QTL discovery in CGC. Genome-wide heterozygosity in Line 1 Hereford was found to have significant effects on growth to one year of age. Analyses to identify specific loci where heterozygosity is maintained in excess of expectation and where effects of greatest magnitude are ongoing.
In addition, two scientists assigned to this project had lead roles in organizing and host national/regional scientific meetings that were held in Miles City (Western Section American Society of Animal Science) and Bozeman (Beef Improvement Federation).
Gene atlas for cattle. Comprehensive surveys of gene expression levels among body tissues, often referred to as gene atlases, are relatively few, but provide novel and detailed insights into the biology of an organism. ARS researchers in Miles City, MT, comprehensively sampled gene expression in tissues from animals related to the Hereford cow whose genome was sequenced. They identified 1.59 million unique DNA sequence fragments. Filtering these fragments yielded 87,764 sequences that unambiguously mapped to 16,517 annotated protein-coding loci. The gene atlas is the deepest and broadest survey of global patterns of gene expression of any livestock genome to date. The atlas is useful to scientists examining relationships between gene sequence, gene expression, tissue, and gene function.
Gene expression in cycling and anestrous cows. A major limitation to successful reproduction is the failure of cows to resume estrus after parturition. Oligonucleotide microarrays were used to evaluate gene expression in anterior pituitary glands collected from 4 anestrous and 4 cycling postpartum beef cows. To provide greater detail on the influence that stage of the estrous cycle on gene expression, quantitative real-time PCR was used to compare gene expression in anterior pituitaries of anestrous cows with an additional independent set of anterior pituitary glands collected at 4 stages of the estrous cycle. The majority of genes identified have not previously been associated with regulation of reproductive function, or represented currently uncharacterized genes. Results undoubtedly indicate the existence of novel mechanisms involved in regulating reproduction.
Immunocastration as alternative to surgical castration. The idea of active immunization against LHRH, or immunocastration, began with the demonstration that anti-LHRH antibodies can neutralize the reproductive axis. In this study, LHRH immunization effectively suppressed reproductive function, decreased synthesis and storage of LH, and decreased storage, but not synthesis of FSH in bulls. Increased synthesis of LH and FSH in nonimmunized steers, but not in LHRH immunized steers, suggests castration removes the negative feedback on gonadotropin synthesis. However, LHRH is still needed for release of these hormones. This technology has some potential as an alternative to surgical castration, but more work is required prior to practical application.
Prototype systems for national cattle evaluation. National cattle evaluation provides information for use in making genetic improvement in efficiency of beef production. To date, there have been essentially no systems for evaluation of sustained reproductive success, and feed intake and feed efficiency. ARS researchers in Miles City, MT, developed prototype systems as components of the national cattle evaluation systems for Hereford and Angus cattle. Tens of thousands of cattle producers will use these systems to evaluate hundreds of thousands of animals. This technology provides the opportunity for permanent and cumulative improvement in the evaluated traits potentially leading to reduced cost of production and environmental impact.
Waterman, R.C., Richardson, K.D., Lodge-Ivey, S.L. 2011. Effects of Euphorbia Esula L. (Leafy Spurge) on Cattle and Sheep in Vitro Fermentation and Gas Production. Journal of the Science of Food and Agriculture. 91:2053-2060.
Roberts, A.J., Mclean, D.J. 2011. Differential gene expression in anterior pituitary glands from anestrous and cycling postpartum beef cows. Journal of Animal Science. 89:1035-1041.
Jiang, Z., Michal, J., Wu, X., Pan, Z., MacNeil, M.D. 2011. The Heparan and Heparin Metabolism Pathway is Involved in Regulation of Fatty Acid Composition. International Journal of Biological Sciences. 7(5):659-663.
Geary, T.W., Wells, K.J., Deavila, D.M., Deavila, J., Conforti, V.A., Mclean, D.J., Roberts, A.J., Waterman, R.C., Reeves, J.J. 2011. Effects of immunization against LHRH and treatment with trenbolone acetate on reproductive function of beef bulls and steers. Journal of Animal Science. 89:2086-2095.
Daniels, T.F., Wu, X., Pan, Z., Michal, J.J., Wright, R.W., Killinger, K.M., MacNeil, M.D., Jiang, Z. 2010. The reverse cholesterol transport pathway improves understanding of genetic networks for fat deposition and muscle growth in beef cattle. PLoS One 5(12): e15203. doi:10.1371/journal.pone.0015203.
Tang, G., Stewart-Smith, J., Plastow, G., Moore, S., Basarab, J., MacNeil, M.D., Wang, Z. 2011. Opitmizing a Beef Production System Using Specialized Sire and Dam Lines. Canadian Journal of Animal Science. 91:353-361.
Underwood, K.R., Tong, J.F., Price, P.L., Roberts, A.J., Grings, E.E., Hess, B.W., Means, W.J., and Du, M. 2010. Nutrition during mid to late gestation affects growth, adipose tissue deposition, and tenderness in cross-bred beef steers. Meat Science. 86:588-593.
Waterman, R.C., Roberts, A.J., Geary, T.W., Grings, E.E., Alexander, L.J., MacNeil, M.D. 2011. Effect of reduced heifer nutrition during in utero and post-weaning development on glucose and acetate kinetics. British Journal of Nutrition. 106:1702-1712.
Mulliniks, J.T., Kemp, M.E., Cox, S.H., Hawkins, D.E., Cibils, A.F., Petersen, M.K. 2011. The Effect of Increasing Amount of Glucogenic Precursors on Reproductive Performance in Young Postpartum Range Cows. Journal of Animal Science 89(9):2932-2943.
Harhay, G.P., Smith, T.P.L., Alexander, L.J., Haudenschild, C.D., Keele, J.W., Matukumalli, L.K., Schroeder, S.G., Van Tassell, C.P., Gresham, C.R., Bridges, S.M., Burgess, S.C., Sonstegard, T.S. 2010. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biology [online serial]. 11:R102.
MacNeil, M.D., Vukasinovic, N. 2011. A prototype national cattle evaluation for sustained reproductive success in Hereford cattle. Journal of Animal Science. 89:1712-1718.