Research Project: Identifying and Mitigating Factors that Limit Beef Production Efficiency

Location: Livestock and Range Research Laboratory

2023 Annual Report

Objectives
Objective 1. Determine the limiting nutrients for efficient growth of beef calves and reproduction in beef females grazing native forages at different stages of maturity. Sub-objective 1A: Determine effects of autumn/winter utilization (i.e., dormant) rangeland forage utilization on heifer development, and subsequent reproductive performance. Sub-objective 1B: Develop management strategies to improve rangeland cattle production and ecological stability through effective use of rangeland forage and supplementation of young cows. Sub-objective 1C: Identify better strategies for extensive rangeland livestock operations to prepare for seasonal and/or extended droughts through strategic supplementation of mature cows that optimize milk constituents and improve calf gain. Sub-objective 1D: Evaluation of livestock nutrition models for predicting weight gains/losses and body condition for livestock under supplemental and precision feeding. Objective 2. Determine the limitations of efficient embryonic development involving successful placentation and implantation to mitigate embryonic losses that decrease reproductive efficiency in cattle. Sub-objective 2A: Determine the physiological role of estradiol in endometrial function, conceptus growth, and gene expression that contribute to increased pregnancy success in cattle. Sub-objective 2B: Determine specific nutritional impacts on ovum fertility and early embryonic development in beef heifers that contribute to pregnancy success. Sub-objective 2C: Determine the effect of fertilization by suboptimal sperm on embryonic mortality in beef cattle. Objective 3. Optimize selection and assign breeding to maintain genetic variation (limit inbreeding) in Line 1 Hereford population. Sub-objective 3A: Utilize recombination rate to increase genetic variation and mitigate the accumulation of inbreeding. Sub-objective 3B: Evaluate the effects of selection on runs of homozygosity on inbreeding depression and performance of Line 1 Hereford. Objective 4. Determine G x E (genetic/genomic x environmental/management) interactions and the effect of heterozygosity on the composite trait of lifetime production efficiency in order to enable management practices that favor desired outcomes. Sub-objective 4A: Determine effects of dry lot heifer development, and subsequent reproductive performance from dams developed on different nutritional planes and evaluate the genetic variation and the existence and extent of genotype by nutritional environment interaction in heifer development. Sub-objective 4B: Determine differences in respiration gas fluxes throughout a production year from weaning to 3 years of age by cattle from dams developed on different planes of nutrition. Sub-objective 4C: Determine effects of variation among adult cows that experienced in utero nutrient restriction on embryonic survival of genetically similar embryos and their performance as calves.

Approach
Feed consumption, genetic selection and reproductive efficiency, are primary determinants of beef production efficiency. Our overarching goal is to better define these variables and develop strategies and technologies to alleviate their limitations to beef production efficiency. Sufficient nutrient intake resulting in adequate body energy stores are believed essential for reproduction. Thus, producers are challenged to match nutritional environment, which is subject to seasonal and annual variation, and various genotypes to obtain sustainable reproduction and female retention rates. Our approach is, of necessity, multi-disciplinary, involving both basic and applied aspects of genetics, nutrition, and physiology in a semi-arid grazing production system. This plan brings to fruition ongoing research and establishes investigations of genetic by environmental interactions as well as nutritional and physiological mechanisms limiting reproductive success. Four distinct cattle populations (an intercross of Charolaise (25%), Red Angus (50%) and Tarentaise (25%) herd, Line 1 Hereford herd, Precision Livestock Hereford-Angus herd, and Physiology Hereford-Angus herd) will be used to facilitate assessment of genetic, strategic nutritional and physiological factors affecting productivity. Distinct nutritional environments differing in provision of strategic supplements to cattle grazing forage will be tested to challenge the nutrition-reproduction interface to reveal roles of genetic, physiological, and management factors influencing feed utilization and animal productivity. Identification of genetic, nutritional, and physiological mechanisms that limit or contribute to beef production efficiency will facilitate early in life selection and management of replacement animals that are most fit for rangeland environments. This research will result in the establishment of evidence-based selection, development and management protocols that provide producers options for addressing industry needs and dealing with climate and environmental variability.

Progress Report
This is the first annual report for this project, 3030-31000-019-000D, “Identifying and Mitigating Factors that Limit Beef Production Efficiency”, which expires in October 2027. Objective 1, Sub-objective 1A: Progress included collection of growth and reproductive success among heifers receiving strategic supplement of key amino acids during development. Objective 1, Sub-objective 1B: Data has been collected from cows that were traditionally managed or whose performance was continually measured using precision measurement technologies for management decisions. Objective 1, Sub-objective 1C: Milk constituents and calf growth data has been collected from cows receiving strategic supplementation before and after calving to determine the ability to improve performance. Objective 1, Sub-objective 1D: Scripting and data aggregation schemes for climate and sensor data were prepared and database development for nutrition models was initiated. Objective 2, Sub-objective 2A: Collection of tissues to complete this sub-objective has not been possible, but will be completed this fall, when cows are routinely available to apply treatments. The exact timing of tissue collection is anticipated both before and after the start of FY2024 but before the start of the 2024 calendar year. Objective 2, Sub-objective 2B: Embryo and uterine secretions have been collected from heifers that received limiting or abundant energy and protein after fertilization to understand the effects of reduced nutrition on early embryo development and pregnancy success. When energy was limited in heifer diets, we observed altered conceptus gene expression and uterine metabolites available for embryo development and the alterations among uterine metabolites were not related to those present in the blood of heifers indicating that simple blood tests are not predictive of uterine capacity for pregnancy. Objective 2, Sub-objective 2C: Laboratory analyses of bovine sperm biomarkers has been completed and has identified three lectins for inclusion in our methods to remove subfertile sperm from samples before packaging for artificial insemination. In a related project, specific biomarkers on bull sperm associated with field fertility were identified. Objective 3, Sub-objective 3A: A computer program has been developed to estimate the recombination rate of genes associated with important production traits in cattle. Additional data still needs to be collected to be added to the model. Objective 3, Sub-objective 3B: The effects of runs of homozygosity (ROH; genetic repeats) have been characterized related to the effects of inbreeding depression in the Line 1 Hereford cattle breed. Related to this objective, researchers at Miles City, Montana developed a statistical model to strengthen our ability to make livestock selection decisions based on lowly heritable traits. In addition, these researchers demonstrated that genomic selection can be improved by including genomic sequence data, gene copy number variations or causative variants in genomic prediction. Objective 4, Sub-objective 4A: Growth and performance data has not been collected from heifers that were born to nutrient restricted or nutrient abundant cows during in-utero development because insufficient heifers were available from this herd for completion of both sub-objectives 4A and 4B. Sub-objective 4A will begin next spring using heifers born this year. Objective 4, Sub-objective 4B: Data related to respiration and production efficiency has been collected from heifers with different epigenetic inputs. Objective 4, Sub-objective 4C: Embryos have been produced for transfer into cows that had experience in-utero nutrient restriction or abundance to evaluate the effects of such in-utero treatments on their ability to establish and maintain pregnancies.

Accomplishments
1. Genetic selection model for enhanced contribution of lowly heritable traits. Genetic selection model for enhanced contribution of lowly heritable traits. Genomic selection is currently accepted in most livestock industries including beef cattle. This powerful method allows producers to make accurate selection of breeding candidates and improve the overall genetic gain and herd profitability. However, genomic selection is still not optimal for lowly heritable traits, like reproduction. ARS researchers at Miles City, Montana, studied the accuracy of genomic selection for traits with low heritability. A Bayesian statistical model to predict genomic estimated breeding values was developed by combining correlated high and low heritability traits. Results suggest that multiple trait predictions using conventional BLUP (Best Linear Unbiased Prediction) and Bayesian mixture models are feasible for genomic selection in beef cattle. Our findings indicated that the proposed method outperforms the current methods and the low-heritability traits showed reliable prediction accuracy. These results enhance scientists’ ability to provide selection tools for lowly heritable traits that should improve livestock profitability.

2. Addition of specific genomic characteristics to models improves accuracy of genomic selection. Addition of specific genomic characteristics to models improves accuracy of genomic selection. Measures such as EPDs (expected progeny differences) are used by producers to compare the genetic and economic value for selection of seedstock. Previous studies have demonstrated that EPDs can be enhanced by addition of genomic data. The accuracy of genomic selection can be improved by including other sources of information such as sequence data, copy number variations, or causative variants. In this study, several scenarios were simulated to test the accuracy of genomic selection when directly including and adjusting for causative variants. ARS researchers at Miles City, Montana, evaluated uniform, quadratic, and nonlinear weights for the causative variants. The addition of these variants into the model led to significant accuracy gains. Furthermore, adjusting for causative variants helped explain the trait architecture features based on changes in the genomic prediction accuracy. The results of this study have been published in the Journal of Animal Breeding and Genetics and provide methods to enhance selection of more desirable seedstock animals by livestock producers.

3. Timing of pregnancy loss in beef cows is impacted by estrus and estradiol supplementation at time of artificial insemination. Early pregnancy loss in beef and dairy cattle often exceeds 30 to 60 percent, but the causes of this loss are extremely difficult to study because the timing of such losses is unknown. ARS researchers at Miles City, Montana, in collaborative efforts with researchers at Texas A&M AgriLife, previously demonstrated the importance of elevated estradiol at the time of induced ovulation. Continued collaboration by this team revealed that addition of 0.1 mg of estradiol at the time of induced ovulation resulted in pregnancy rates more similar to cows that had expressed estrus and greater than cows that had not received estradiol at induced ovulation. Furthermore, this effort has identified the timing of when greater losses occur among cows that don’t have elevated estradiol at induced ovulation which will allow comparison of differential gene expression by the conceptus and uterus related to conceptus attachment and pregnancy success. Identification of the mechanisms resulting in pregnancy failure will allow development of managerial treatments to mitigate such losses and improve pregnancy rates in beef and dairy cattle.

4. Bull field fertility can be estimated by laboratory measures. The bull breeding soundness evaluation, performed by veterinarians, is a pass/fail exam that does not allow selection for improved fertility within a herd. It is primarily based upon sperm motility and morphology. ARS researchers at Miles City, Montana, in collaboration with colleagues from several universities identified specific traits in frozen/thawed sperm samples that were related to field fertility among bulls that had passed a breeding soundness evaluation. These findings will serve as a starting point for developing a bull fertility index that will allow producers to strategically use the more fertile bulls in their herd and select for improved herd fertility.

5. Heifer nutrition after breeding is critical to embryonic development. Almost half of the reproductive loss in cattle comes from early embryo death. Most of these embryos die between 8 and 16 days after fertilization. Replacement heifers are virgin cows that are developed for herd replacements. After weaning, many heifers are raised in a pen and provided feed. Other heifers are raised on pasture until breeding or raised on pasture until breeding at about 15 months of age. In some years, there is less forage available either before or after breeding. ARS researchers at Miles City, Montana, in collaboration with colleagues at Montana State University are studying effects of reduced energy in heifer diets after breeding on early embryo development. When less energy is fed to heifers for 7 to 14 days after breeding, embryo development and quality is reduced, and differential genes are expressed by these embryos. In addition, the nutrients provided by the uterus do not mimic the nutrients available in blood of heifers, making detection of poor embryonic environments more difficult. Slower developing embryos and are less likely to result in pregnancy success. Producers should ensure heifers are fed sufficient energy after breeding to improve pregnancy rates. Higher pregnancy rates generally lead to greater profit.

Review Publications
Manoukian, M.K., Delcurto, T., Kluth, J., Carlisle, T., Davis, N., Nack, M., Wyffels, S., Van Emon, M.L., Geary, T.W., Scheaffer, A. 2022. Impacts of rumen degradable or rumen undegradable protein supplement on supplement intake behavior and performance of yearling heifers and cows grazing dryland pastures. Animals. 12. Article 3338. https://doi.org/10.3390/ani12233338.
Ketchum, J.N., Perry, G.A., Quail, L.K., Epperson, K.M., Ogg, M.A., Zezeski, A.L., Rich, J.J., Zoca, S.M., Kline, A.C., Andrews, T.N., Ortega, M., Smith, M.F., Geary, T.W. 2023. Influence of preovulatory estradiol treatment on the maintenance of pregnancy in beef cattle receiving in vivo produced embryos. Animal Reproduction Science. 255. Article 107274. https://doi.org/10.1016/j.anireprosci.2023.107274.
Reid, D.S., Geary, T.W., Zezeski, A.L., Waterman, R.C., Van Emon, M.L., Messman, R.D., Burnett, D.D., Lemley, C.O. 2023. Effects of prenatal and postnatal melatonin supplementation on overall performance, male reproductive performance, and testicular hemodynamics in beef cattle. Journal of Animal Science. 101. Article skad111. https://doi.org/10.1093/jas/skad111.
Zoca, S.M., Geary, T.W., Zezeski, A.L., Kerns, K.C., Dalton, J.C., Harstine, B.R., Utt, M.D., Cushman, R.A., Walker, J.A., Perry, G.A. 2023. Bull field fertility differences can be estimated with in vitro sperm capacitation and flow cytometry. Frontiers in Animal Science. 4. Article 1180975. https://doi.org/10.3389/fanim.2023.1180975.
Epperson, K.M., Beck, E.E., Rich, J.J., Northrop-Albrecht, E.J., Perkins, S.D., Zezeski, A.L., Ketchum, J.N., Zoca, S.M., Walker, J.A., Geary, T.W., Perry, G.A. 2022. Modulation of expression of estrus, steroidogenesis and embryo development following peri-Artificial Insemination nutrient restriction in beef heifers. Animal Reproduction Science. 244. Article 107045. https://doi.org/10.1016/j.anireprosci.2022.107045.
Ling, A.S., Hay, E.A., Aggrey, S., Rekaya, R. 2022. Fuzzy logic as a strategy for combining marker statistics to optimize preselection of high-density and sequence genotype data. Genes. 12(11). Article 2100. https://doi.org/10.3390/genes13112100.
Hay, E.A., Roberts, A.J. 2023. Genomic analysis of heterosis in an Angus x Hereford cattle population. Animals. 13(2). Article 191. https://doi.org/10.3390/ani13020191.
Dufek, N.A., Vermeire, L.T., Waterman, R.C., Ganguli, A.C. 2022. Fire and nitrogen effects on Aristida purpurea mineral concentrations. Rangeland Ecology and Management. 86:44-49. https://doi.org/10.1016/j.rama.2022.10.006.
Meki, M.N., Osorio-Leyton, J., Steglich, E.M., Kiniry, J.R., Propato, M., Winchell, M., Rathjens, H., Angerer, J.P., Norfleet, L.M. 2023. Plant parameterization and APEXgraze model calibration and validation for U.S. land resource region H grazing lands. Agricultural Systems. 207. Article 103631. https://doi.org/10.1016/j.agsy.2023.103631.
Rhodes, E.C., Tolleson, D.R., Angerer, J.P. 2022. Modeling herbaceous biomass for grazing and fine fuels management in central Arizona. Land. 11(10). Article 1769. https://doi.org/10.3390/land11101769.