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United States Department of Agriculture

Agricultural Research Service

Research Project: REDUCING COST OF EFFICIENT BEEF PRODUCTION
2010 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 forage and varying percentages of concentrates ; estimate parameters needed for including molecular breeding values in national cattle evaluation; develop new systems of national cattle evaluation for feed intake and sustained reproductive success; determine interaction level of feed input for females with that of their dams; develop evidence that nutritional influences on replacement heifers begins in utero and continue throughout life; and determine explanatory mechanisms for fertilization and early embryonic survival.


4.Accomplishments
1. Genetic evaluation of sustained reproductive success. Genetic improvement of reproductive performance has been hampered by lack of systems to use in conducting national cattle evaluation. In collaboration with the American Hereford Association, ARS scientists at Miles City developed such a system based on ages when females fail to maintain an annual calving interval and using survival analysis techniques. Breeders of Hereford seedstock now have a tool to use for genetic selection to improve reproductive efficiency.

2. Using genomics to enhance national cattle evaluation. Genomic companies produce products that may be predictive of economically relevant traits. When these products are used independent of national cattle evaluation, producers making selection decisions can be misinformed. In collaboration with the American Angus Association, ARS scientists at Miles City developed the necessary information to incorporate genomic information into systems of national cattle evaluation. Breeders of Angus seedstock now have a tool to use for efficient genetic selection to improve carcass merit.

3. Copy number variation among breeds of cattle. Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle including 90 animals from 11 Bos taurus, 3 Bos indicus, and 3 composite breeds. Over 200 candidate CNV regions were identified. Regions with varying copy number span about 400 known genes for specific biological functions, such as immunity, lactation, reproduction, and rumination. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research.

4. Microbial diversity in the bovine rumen. In collaboration with the J Craig Venter Institute, ARS scientists in Miles City, MT, surveyed the diversity of microbial populations in the rumen of cows fed forage diets and established protocols for use in future investigation. This work established guidelines for conducting future research examining the rumen micro-biome. The observed bacterial diversity was between 3181 to 7483 species-level OTUs, the greatest number of OTU ever observed for a ruminant species. This diversity was dominated by Bacteroidales, unknown bacteria, Clostridiales and Bacteroidetes taxa. There was a considerable difference in microbial diversity between cows from which the samples came. The fungal community was sequenced to saturation and also resulted in identification of a novel unknown fungal group. Raw extrusa should be suitable for future studies on rumen microbial diversity.

5. Genes associated with return to estrous. Being late in returning to estrous after calving compromises the ability of a cow getting rebred early in the breeding season after calving. This failure comprises both the chance that she will get rebred at all and the weaning weight of her subsequent calf, if she does get rebred. In a collaboration between scientists at ARS Miles City and Washington State University, gene expression profiles in anterior pituitary glands collected from anestrous and cycling postpartum beef cows were compared. Surprisingly few transcripts identified have been previously associated with reproductive function. Gastrin-releasing peptide exhibited the largest fold increase in expression, and IGFPB-3 was expressed at greater levels in samples from different stages of the estrus cycle than in anestrous cow samples. Expression of versican was decreased in samples from the different stages of the cycle when compared to anestrous cow samples. Results identify numerous genes that may be involved in the transition from anestrous to cycling status, providing novel insight into mechanisms regulating reproductive function.

6. Early embryonic mortality. Fertilization from a single insemination is known to approach 100%. However, subsequent pregnancy rates are only approximately 60%. Working at Miles City, scientists from ARS and University of Missouri used reciprocal embryo transfer to ascertain contributions of oocyte competence and maternal environment to pregnancy success in suckled beef cows. Increased ovulatory follicle size directly increased pregnancy rate by increasing fertilization rate, and indirectly increased pregnancy rate by:.
1)increasing serum E2 concentration at breeding through increased fertilization rate, increased P4 during the early luteal phase, and increased pregnancy establishment, and.
2)increased P4 during the early luteal phase (through increased embryo viability, increased embryonic developmental stage, and increased pregnancy establishment). However, increased follicle size also had direct negative effects on embryonic developmental stage and pregnancy establishment. The negative effects of ovulatory follicle size on pregnancy success appear to be mediated by oocyte competence and positive effects through improved maternal uterine environment. These results aid in understanding the complex interplay of factors ultimately affecting production efficiency through the timely establishment of viable pregnancies.

7. Cost effective relationships between genotype and phenotype. ARS scientists at Miles City, MT, working with a visiting scientist from North Carolina State University conducted studies examining accuracy of imputed genotypes, changes in allele frequency resulting from selection, and conducted a genome-wide scan for regions having greater than expected heterozygosity. Using an appropriate segment of the Line 1 Hereford population genotyped with a high density (high cost) single nucleotide polymorphism (SNP) chip, genotypes of the remainder of the Line 1 population can be imputed from a low density (low cost) SNP chip with greater than 80% accuracy. The close pedigree relationship among members of the Line 1 population make this a more stringent test of imputation than using a pedigreed population that is less closely interrelated. Using a novel approach based on selection applied, four quantitative trait loci affecting growth to a year of age were identified. It also appears there are specific regions of the genome where heterozygosity is maintained in Line 1 in excess of levels expected except under an over-dominance model of inheritance.


Review Publications
Geary, T.W., Ansotegui, R.P., MacNeil, M.D., Roberts, A.J., Waterman, R.C. 2010. Effects of flunixin meglumine on pregnancy establishment in beef cattle. Journal of Animal Science. 88:943-949.

Atkins, J.A., Smith, M.F., Wells, K.J., Geary, T.W. 2010. Factors affecting pre-ovulatory follicle diameter and ovulation rate to GnRH in postpartum beef cows. Part I: Cycling cows. Journal of Animal Science. 88:2300-2310.

Atkins, J.A., Smith, M.F., Wells, K.J., Geary, T.W. 2010. Factors affecting pre-ovulatory follicle diameter and ovulation rate following GnRH in postpartum beef cows. Part II: Anestrous cows. Journal of Animal Science. 88:2311-2320.

Macneil, M.D., Nkrumah, J.D., Woodward, B.W., and Northcutt, S. 2010. Genetic evaluation of Angus cattle for carcass marbling using ultrasound and genomic indicators. Journal of Animal Science. 88:517-522.

Marquez, G.C., Enns, R.M., Grosz, M.D., Alexander, L.J., MacNeil, M.D. 2009. Quantitative trait loci with effects on feed efficiency traits in Hereford x composite double backcross populations. Animal Genetics. 40:986-988.

Jiang, Z., Michal, J.J., Chen, J., Daniels, T.F., Kunej, T., Garcia, M.D., Gaskins, C.T., Busboom, J.R., Alexander, L.J., Wright, R.W., Macneil, M.D. 2009. Discovery of novel genetic networks associated with 19 economically important traits in beef cattle. International Journal of Biological Sciences. 5: 528-542.

Chitko Mckown, C.G., Macneil, M.D. 2010. Development of Fibroblast Cell Lines From the Cow Used to Sequence the Bovine Genome. Animal Genetics. 41(4):445.

Liu, G., Hou, Y., Zhu, B., Cardone, M.F., Jiang, L., Cellamare, A., Mitra, A., Alexander, L.J., Coutinho, L.L., Gasbarre, L.C., Heaton, M.P., Li, R.W., Matukumalli, L.K., Nonneman, D.J., De A Regitano, L.C., Smith, T.P., Song, J., Sonstegard, T.S., Van Tassell, C.P., Eichler, E.E., Mcdaneld, T.G., Keele, J.W. 2010. Analysis of copy number variations among cattle breeds. Genome Research. 20:693-703.

Last Modified: 12/24/2014
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