Research Project: Alleviating Rate Limiting Factors that Compromise Beef Production Efficiency

Location: Livestock and Range Research Laboratory

2018 Annual Report

Objectives
Objective 1: Evaluate effects of heifer development and winter supplementation protocols that differ in level and type of harvested feed inputs on the sustainability of beef production systems, including annual reproductive success, lifetime productivity, and progeny performance. Component 1: Problem Statement 1A, 1B Objective 2: Establish postweaning heifer development protocols that provide opportunities for improved fertility and differential forage utilization. Component 1: Problem Statement 1A, 1B Objective 3: Integration of phenomics and genomics data to dissect the genetic basis of reproductive and growth traits in beef cattle. Component 1: Problem Statement 1A, 1B Component 2: Problem Statement 2A, 2B, 2D Objective 4: Study the effect of environment, management and genetic interaction on range beef cattle production. Component 1: Problem Statement 1A, 1B Component 2: Problem Statement 2B, 2D We have proposed a series of experiments that will contribute to the alleviation of rate limiting factors that compromise beef production efficiency by: 1) Collectively increasing knowledge of the phenotypic and genetic interplay between nutrition and lifetime reproductive efficiency (Objectives 1, 2, 3 and 4) thus facilitating the economic optimization of feed level and identification of germplasm that is of less risk of reproductive failure when feed level is reduced; 2) Developing strategies that will provide producers management approaches to better utilize forage and better cope with yearly environmental variation (Objective 1, 2, and 4); 3) Further identifying phenotypic and genomic factors controlling fertility in bulls and establishment and maintenance of pregnancy in females thus leading to targets for managerial interventions that increase pregnancy rate, decrease replacement rate and reduce cost associated with producing replacement females (Objective 1, 3, and 4); 4) Prioritizing weighting of phenotypic and genotypic traits influencing production at the time selection decisions occur (typically at approximately one year of age) targeting lifetime performance (Objectives 1, 2, 3, and 4) thus facilitating selection of breeding stock for efficient low-cost production. Work needed to accomplish our objectives is multi-disciplinary and contributions from more than one scientist are expected in order to bring each objective to fruition.

Approach
Feed consumption and replacement of cows, culled for reproductive failure, are two primary determinants of beef production efficiency. Our overarching goal is to develop strategies and technologies to alleviate these limitations. 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 retention rates. Our approach is, of necessity, long-term and multi-disciplinary, involving both basic and applied aspects of genetics, nutrition, and physiology in a semi-arid grazing production system. This proposal brings to fruition ongoing research and establishes investigations of genetic by environmental interactions and physiological mechanisms limiting reproductive success. Four distinct cattle populations (an intercross of Charolaise (25%), Red Angus (50%) and Tarentaise (25%), Line 1 Hereford, purebred Angus, and Hereford-Angus herd) will be used to facilitate assessment of genetic factors affecting fitness (hybrid vigor). Distinct nutritional environments differing in provision of harvested or grazed forage will be tested to challenge the nutrition-reproduction interface to reveal roles of genetic, physiological, and management factors influencing feed utilization and lifetime 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 most fit for particular production environments. This research will result in the establishment of evidence based beef female development and management protocols that provide producers options for dealing with annual environmental variations.

Progress Report
Objective 1, Sub-objective 1A. Preliminary analysis of association between rate of growth and individual animal variation in amount of consumption of a protein/mineral supplement during post-weaning development on native winter range indicates a quadratic response, with greater unit change at lower levels of intake and less dramatic increments of increase at higher levels of intake. However, with the current data evaluated, no association was observed between variation in supplement consumption and first year breeding success. In heifers developed in a feedlot, where individual variation in total daily feed intake has been recorded, average intake was lower for heifers that failed to get bred compared to heifers that were pregnant after their first breeding season. Heifers developed in the feedlot that failed to get pregnant during the first breeding season were also shown to be larger at birth, grew slower from birth to time of breeding, had smaller ribeye muscle size and less fat (determined by carcass ultrasound) but were similar in height when compared to heifers that did get pregnant during the first breeding season. Objective 2, Sub-objective 2A. The field data from this objective has been partially collected. Preliminary analysis shows there is no effect on forage utilization as influenced by range heifer supplementation regime. Sub-objective 2B. Current data indicate that first year pregnancy rates do not differ among heifers developed in a feedlot and heifers developed on range, even though heifers developed in the feedlot were 40 or 80 lbs. heavier at the start of breeding than range developed heifers supplemented with 4 pounds of cake/day or range heifers provided a self-fed protein mineral supplement. Collection of data on pregnancy success in subsequent breeding seasons is ongoing. Sub-objective 2C. Results from this objective were presented this year at the American Society of Animal Science Annual Meeting. Statistical analysis is currently in progress in preparation of a manuscript. Related to this objective, the effects of pre-breeding and early post-breeding effects on early embryonic development were evaluated. Many beef producers develop and breed heifers in a feedlot and then turn those heifers out on grass immediately after breeding. In some years, forage is limiting, and in all cases, there is a period of about 10 days when the microbes in the rumen need to change to adjust to the drastic change in diet to benefit the heifer. Heifers were fed 70% or 125% of maintenance requirements before and/or after artificial insemination (AI; day 0). Embryos were recovered on day 6 of pregnancy for comparison of fertilization rate and embryo development and both blood and uterine flush media measured for non-esterified fatty acids (NEFA), glucose and protein. Embryo recovery rate and development tended to be greater for high post-AI nutrition (48 vs 27%), however high pre-AI nutrition also accelerated embryo development and tended to improve embryo quality. Nutritional treatment impacted blood concentrations of NEFA and protein. Both NEFA and protein were increased in heifers fed low pre and post-AI diets, likely related to the need to metabolize muscle and fat store, however, NEFA, protein and glucose was not different in uterine flush media. Effects of nutrition on early embryo development could be impacting oocyte quality, fertilization success, oviductal nutrient availability, and gene expression of the oviduct, uterus and early embryo, but effects are detectable during very early embryonic development. Objective 3, Sub-objective 3A: A genome wide association study of carcass traits was conducted on the Composite Gene Combination (CGC) beef cattle breed and the results were published in the journal of Livestock Science. The study revealed several quantitative trait loci (QTLs) in the bovine genome associated with these economically important traits. Specifically, one QTL was found on chromosome 14 in position 24Mb associated with fat depth explaining a large genetic variance. Another QTL associated with ribeye area was detected on chromosome 6 in position 64Mb. Furthermore, several previously reported QTLs associated with carcass traits were validated. Sub-objective 3B. Collection of bull fertility phenotypes was completed on 120 yearling heterosis bulls and included scrotal circumference and the following evaluations on fresh semen ejaculates: progressive motility, morphology, viability, acrosome integrity, DNA integrity, stored energy potential, sperm maturity, and reactive oxygen species as a measure of stress resistance. Ejaculates from each bull were also sent to the Gamete Preservation Lab in Fort Collins, Colorado where semen from each bull was frozen. They plan to conduct multiple additional measures this fall on those frozen-thawed samples and have returned frozen straws to us for further evaluation with flow cytometry. Objective 4, Sub-objective 4A. Phenotypes are being collected. The dataset is relatively small to conduct a heterosis study on the Angus X Line 1 Hereford cross. However, a study evaluating the inbreeding of Line 1 population used in the heterosis study was conducted to assess the level of inbreeding using genomic information and evaluate the impact of inbreeding on economically important traits. The inbreeding coefficient was around 0.3, 0.16, 0.22 using pedigree, genomic information and runs of homozygosity respectively. Four chromosomes (9, 12, 17, and 27) were identified to have a significant association between their homozygosity and growth traits. A manuscript was drafted and submitted for publication. Sub-objective 4B. Collection of RNA from the oocyte and cumulus cells of the preovulatory follicle was completed and 4 pools of each cell type per follicle physiological maturity level were sequenced using NexGen sequencing. We used follicle aspiration to evaluate 3 levels of follicle maturity 1) Fully mature – cows had expressed estrus approximately 20 hours before follicle aspiration, 2) Mostly mature – large preovulatory follicles, and 3) Moderately mature – small preovulatory follicles. Large and small follicles were aspirated approximately 20 hours after gonadotropin-releasing hormone (GnRH)-induction (but just prior to anticipated ovulation). An average of 2.1 million uniquely aligned, single end reads per sample were generated and differential expression analysis between sample groups was performed by fitting the expression data to a general linear model using edgeR robust (False Discovery Rate < 0.10). Comparisons of the oocyte transcriptome revealed relatively few differentially expressed genes (DEG; 11, 15, and 9), whereas 884, 1609, 1491 DEG were revealed between cumulus cells of small vs. large, small vs. spontaneous, and large vs. spontaneous follicles, respectively. An abstract was submitted and accepted for this work to the International Ruminant Reproduction Symposium to be held in Brazil in September 2018 and was selected for an oral presentation. See accomplishment 3. Sub-objective 4C. We previously identified preovulatory estradiol and subsequent luteal progesterone concentrations to be the two greatest factors affecting pregnancy success in cattle. Preovulatory estradiol concentrations, however, directly affect subsequent progesterone concentrations and progesterone receptor concentrations in the uterus. To differentiate the relative impact of estradiol and progesterone on pregnancy success, blood samples were collected, and cows were sorted into high and low estradiol at induced ovulation and half of each of these groups received 3 prostaglandin injections on day 3, 3.5, and 4 following ovulations to create a low progesterone group. All cows received an embryo on day 7 and pregnancy was determined on day 34 of gestation. Pregnancy rates were 54% and 30% for cows with high and low estradiol at induced ovulation and 43% and 41% for cows with high and low progesterone during early pregnancy. Therefore, preovulatory estradiol concentrations are far more important than early progesterone concentrations related to pregnancy success. In a second experiment, heifers with high or low preovulatory estradiol levels received 5 embryos on day 7 and were harvested on day 17 to collect their reproductive tracts. Embryo recovery rate and embryo size were similar, thus the impact of high preovulatory estradiol on pregnancy success occurs after maternal recognition of pregnancy during the period of uterine receptivity for placental attachment. These data were presented at this year’s Society for the Study of Reproduction Annual Meeting.

Accomplishments
1. Cows fed less winter supplements had higher maternal genomic estimated breeding values. Genes interact with both pre- and postnatal environments affecting several important traits in beef cattle. Although several studies have been conducted on the effects of genotype by environment interaction (GxE) on the performance of animals, little work has been done on evaluating how the maternal and individual nutritional environment interact with the genotypes. Furthermore, including the effects of GxE in national genetic evaluation systems remains problematic. With the advent of sophisticated genotyping technologies, genomic information could easily be generated and utilized to adjust for GxE in genetic evaluation and improvement. In the USDA-ARS laboratory in Miles City, Montana, we have characterized the influence of genetics by pre-natal nutritional environment interaction on maternally influenced traits (birth weight, weaning weight and yearling weight) in a composite beef cattle breed using genomic information. The results showed the existence of GxE on birth weight and weaning weight. Moreover, re-ranking of maternal genomic estimated breeding values (GEBVs) was apparent. Interestingly, in some instances cows that were fed less winter supplements had a higher maternal GEBVs than cows fed the recommended amount of winter supplementation. These findings may significantly alter industry practices and production costs by feeding less to improve maternal breeding values.

2. Defining follicular limitations to pregnancy success in cattle. Identifying the limitations to pregnancy success in cattle is obligatory to mitigating these limitations to improve productivity. The role that egg (oocyte) maturity has in fertility was evaluated at USDA-ARS in Miles City, Montana by comparing gene expression differences between oocytes (and surrounding cumulus cells) derived from 1. Fully mature, 2. Mostly mature (large preovulatory follicle), and 3. Moderately mature (small preovulatory follicle). Comparisons of gene expression revealed relatively few differentially expressed genes (11, 15, and 9) in oocytes, whereas 884, 1609, 1491 differentially expressed genes were revealed between cumulus cells of small vs. large, small vs. spontaneous, and large vs. spontaneous follicles, respectively. Significant enrichment of Glycolysis/Gluconeogenesis energy production pathway in cumulus cells from large compared to small follicles was identified. Oocytes have a poor capacity for metabolizing glucose and rely on cumulus cells to supply pyruvate for energy production. Therefore, an inefficient or immature glycolytic pathway in cumulus cells from small follicles contributes to the decreased competency of oocytes from small follicles in comparison to large or spontaneous follicles when ovulation is induced for assisted reproductive techniques. In summary, mature eggs have been exposed to greater energy substrates prior to ovulation which likely improves their ability to undergo fertilization and development of a healthier embryo that leads to improved pregnancy success. These genomic pathways likely hold a key to female fertility when the nutritional environment is limiting. Overcoming these deficiencies may lessen the 30 to 50% embryonic mortality that occurs in beef and dairy cows.

3. Defining the mechanisms of genetic limitations to pregnancy success in cattle. Pregnancy loss in cattle ranges from 30 to 56% resulting in an estimated $87 million annual loss to the U.S. cattle industry. Much of pregnancy losses occur in the first month of pregnancy, and we have identified 22 genetic markers that differ among fertility classified beef heifers, with 3 primary fertility related genetic markers on the X-chromosome. A major unresolved issue is how the uterus differs among the fertility classified (high-fertile, subfertile or infertile) heifers. Embryonic development and pregnancy rates in high-fertile and subfertile heifers were similar but greater than in infertile heifers on day 17 of gestation. Gene expression profiling of the embryo and uterus in high-fertile and subfertile heifers revealed considerable differences related to embryo-uterine communication that elicit embryonic loss during the placental implantation period in the subfertile heifers. This miscommunication was the cause-effect of multiple differences in gene expression between high-fertile and subfertile heifers, that was identified by ARS scientists in Miles City, Montana, enhancing the technical understanding of the mechanisms that lead to pregnancy loss in domestic animals and humans. In summary, multiple pathways involved in early embryonic growth and development were characterized that are involved in embryonic survival. Evaluation of managerial and nutritional effects on these pathways may identify strategies to improve embryo survival and improve pregnancy and weaning rates in cattle herds.

4. Heifer management improves energy efficiency by allowing for adaption to environment and management. A heifer’s ability to thrive is partially due to behavioral, metabolic and genetic traits. USDA-ARS Miles City, Montana scientists determined the effects of confinement feeding or native range grazing on heart rate (HR) as an indicator of energy expenditure and fitness and behavioral adaption by measurements of activities during the winter. A lower mean resting HR is associated with better fitness. The heifers with the highest level of fitness grazed winter range with an approximate 20% lower resting heart rate. These same heifers had a lower average daily heart rate demonstrating lower energy expenditure. The improved fitness and lower energy expenditure occurred despite a 3-fold greater level of activity. These findings point to management impacts on behavior such as travel and resting time causing better energy use efficiency by reducing energy expenditure and improving fitness. These strategies suggest improvements in energy use efficiency can reduce feed cost by $45 per head in the development period.

Review Publications
Neupane, M., Geary, T.W., Kiser, J.N., Burns, G.W., Hansen, P.J., Spencer, T.E., Neibergs, H.L. 2017. Loci and pathways associated with uterine capacity for pregnancy and fertility in beef cattle. PLoS One. 12(12):e0188997. https://doi.org/10.1371/journal.pone.0188997.
Perry, G.A., Geary, T.W., Walker, J.A., Rich, J.J., Northrop, E.J., Perkins, S.D., Mogck, C.L., Van Emon, M.L., Zezeski, A.L., Daly, R.F. 2018. Influence of vaccination with a combined chemically altered/inactivated BHV-1/BVD vaccine or a modified live BHV-1/BVD vaccine on reproductive performance in beef cows and heifers. Bovine Practitioner Journal. 52:53-58.
Toghiani, S., Hay, E.A., Sumreddee, P., Geary, T.W., Rekaya, R., Roberts, A.J. 2017. Genomic prediction of continuous and binary fertility traits of females in a composite beef cattle breed. Journal of Animal Science. 95:4787-4795. doi:10.2527/jas2017.1944.
Moraes, J.G., Behura, S.K., Geary, T.W., Hansen, P.J., Neibergs, H.L., Spencer, T.E. 2018. Uterine influences on conceptus development in fertility-classified heifers. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1721191115.
Roberts, A.J., Gomes Da Silva, A., Summers, A.F., Geary, T.W., Funston, R.N. 2017. Developmental and reproductive characteristics of beef heifers classified by pubertal status at time of first breeding. Journal of Animal Science. 95(12):5629-5636. doi:10.2527/jas2017.1873.
Hay, E.A., Roberts, A.J. 2018. Genotype x prenatal and post-weaning nutritional environment interaction in a composite beef cattle breed using reaction norms and multi-trait model. Journal of Animal Science. 96:444-453. https://doi.org/10.1093/jas/skx057.
Hay, E.A., Roberts, A.J. 2018. Genome-wide association study for carcass traits in a composite beef cattle breed. Livestock Science. 213:35-43. https://doi.org/10.1016/j.livsci.2018.04.018.
Hay, E.A., MacNeil, M., Cardoso, F. 2017. Genotype by environment interaction effects in genetic evaluation of preweaning gain for Line 1 Hereford cattle from Miles City, Montana. Journal of Animal Science. 95:3833-3838. https://doi.org/10.2527/jas2017.1829.
Chang, L., Toghiani, S., Ling, A., Hay, E.A., Aggrey, S., Romdhane, R. 2017. Analysis of multiple binary responses using a threshold model. Journal of Agricultural, Biological, and Environmental Statistics. 22:640-651. https://doi.org/10.1007/s13253-017-0305-6.
Guo, P., Gao, H., Zhu, B., Gao, X., Xu, L., Hay, E.A., Niu, H., Wang, Z., Li, J., Linag, Y., Chen, Y., Zhang, L., Ni, H., Guo, Y. 2018. Fast genomic prediction of breeding values using parallel Markov chain Monte Carlo with convergence diagnosis. BMC Bioinformatics. 19:1-11. https://doi.org/10.1186/s12859-017-2003-3.
Lauriault, L.M., Guldan, S.J., Popiel-Powers, F.G., Steiner, R.L., Martin, C., Heyduck, R., Falk, C., Petersen, M.K., May, T. 2018. Relay intercropping with cover crops improved autumn forage potential of sweet maize stover. Open Agriculture Journal. 8(7):103-115. https://doi.org/10.3390/agriculture8070103.