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

Location: Livestock and Range Research Laboratory

2019 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. Evaluation of effects of different feeding strategies imposed over three generations revealed generational impacts of nutritional treatments on weight at birth through maturity, loin muscle size and intramuscular fat at year of age, and pregnancy rate at specific ages of test cows. Estimates of genetic potential for growth and carcass characteristic were also shown to be influenced by feeding strategy imposed on dam and granddam. Objective 2, Sub-objective 2A: Establish postweaning heifer development protocols that provide opportunities for differential forage utilization. The field data from this objective has been partially collected. Preliminary analysis shows there are preferences for vegetation sites and some behaviors as influenced by heifer supplementation/management regime. Sub-objective 2B. Results indicate that second 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. Collection of data on pregnancy success in subsequent breeding seasons is ongoing. Objective 3, Sub-objective 3A: A genome wide association study of carcass traits was conducted on the Composite Gene Combination (CGC) cattle and the results were published in the journal of Livestock Science. The study revealed 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. Previously reported QTLs associated with carcass traits were validated. Current methods for detecting genetic variants associated with traits of interest suffer from several limitations. The main limitation is the large amount of genomic data being generated. Therefore, we developed a statistical model that prioritizes genomic information which in turn reduces data dimensionality and improves the prediction accuracy of traits. The proposed model was evaluated using simulated data for a trait with heritability of 0.1 and 0.4 and weaning weight using CGC beef cattle herd. When all animals were genotyped, the model using only 2.5% of prioritized single nucleotide polymorphisms (SNP) exceeded the prediction accuracies of currently used methods by more than 7%. This work is of great importance to the animal genetic evaluation programs since it reduces computational costs and increases prediction accuracies. Sub-objective 3B. Collection of bull fertility phenotypes was completed on 254 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 extended and sent to the Plant and Animal Genetic Resources Preservation Unit in Fort Collins, Colorado, for freezing. 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. In a second experiment, ejaculates from five bulls were divided into two aliquots and one aliquot was purified using magnetic nanoparticles coated with peanut agglutinin to remove acrosome-damaged sperm from the ejaculate. Samples of each ejaculate were analyzed by flowcytometry before and after nanopurification and semen from normal and nanopurified aliquots were extended and frozen for use in a field trial. Percentage of live sperm with intact acrosome was 66.8% and 85.7% in non-purified and nanopurified aliquots. Percentage of DNA fragmentation in sperm was 31.8% and 7.9% for non-purified and nanopurified aliquots. Semen with greater percentages of live sperm with intact acrosome and less DNA damage are expected to result in greater pregnancy rates in field trials. This study enables estimations of genetic mutations caused by specific fertility measures. 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. Genomic inbreeding in Line 1 herd was investigated through the identification and study of runs of homozygosity (ROH). First a grid search type of algorithm was developed to define runs of homozygosity. Runs of homozygosity were defined first based on minimum length and second on the mutation load which is the impact on a given trait. The results showed that a minimum threshold to identify ROH segments could be estimated using available phenotypic data. Furthermore, inbreeding was associated with growth and fertility traits. Across all traits, short ROH segments had limited effect on traits due to purging of deleterious haplotypes through selection. On the other hand, long ROH which represent recent inbreeding contributed to most inbreeding depression. This work was presented at the American Society of Animal Science. A study was conducted using the composite beef cattle herd to investigate the extent of genotype by prenatal nutritional environment interaction (GxE) and its impact on maternally influenced traits. The results showed the existence of GxE effect on birth weight and weaning weight. The genetic correlations of genetic maternal effects between marginal and adequate maternal nutritional environments for birth weight and weaning weight were below the 0.8 threshold suggesting a significant effect of GxE. Maternal genomic estimated breeding values showed re-ranking across the environments and in some instances, animals had a higher maternal genomic estimated breeding value in a less input environment. The genome wide association analysis showed a change in the SNP effects across the two environments. 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. 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. These data were presented at the International Ruminant Reproduction Symposium held in Brazil. 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 (n = 287) were classified as having high (> 5.76 pg/mL) and or low (< 2.6 pg/mL) estradiol at induced ovulation and half of the cows in each of these groups received 3 prostaglandin injections following ovulation to create a low progesterone group. All cows received an embryo on day 7 to establish pregnancy, and pregnancy maintenance was determined on day 34 of gestation. Pregnancy rates were 53% and 33% for cows with high and low estradiol at induced ovulation and 47% and 37% for cows with high and low progesterone during early pregnancy. Therefore, preovulatory estradiol concentrations are more important than early progesterone concentrations related to pregnancy success. These data were presented at Society for the Study of Reproduction Annual Meeting. In a second experiment, fertility classified heifers (high fertility, n = 21; subfertile, n = 14; infertile, n = 6) received 2 in-vivo produced embryos on day 7 following estrus. All heifers were harvested on day 17 for uterine biopsy, uterine lumen fluid, and conceptus recovery. Uterine lumen fluid components and gene expression of uterine and conceptus tissue were compared between high fertility and subfertile heifers. In a third experiment, genomic DNA was compared to first, second, and third-service fertility of a breeding season (artificial insemination + natural service) in beef heifers. Heifers (n = 709) were genotyped using the GeneSeek Bovine GGP50K BeadChip prior to genome-wide association analyses (GWAA). Gene-set enrichment analyses using single nucleotide polymorphism data was performed to identify genetic pathways that might be involved with pregnancy and first-service conception rate.

Accomplishments
1. Reducing computational cost of genomic selection. With the rapid advancement in high-throughput technology, a large amount of genomic data is being generated by researchers at Miles City, Montana. In this study a genome wide association model was developed to reduce the high data dimensionality. This model fits a subset of single nucleotide polymorphisms (SNP) markers selected based on Wright’s fixation index and a classical polygenic effect. The method was first tested using only genotyped animals and then extended to accommodate non-genotyped animals. The proposed model was evaluated using simulated data for a trait with heritability of 0.1 and 0.4 and weaning weight using a composite beef cattle herd. When all animals were genotyped, the hybrid model using only 2.5% of prioritized SNPs exceeded the prediction accuracies of current methods by more than 7%. When non-genotyped animals were incorporated, the proposed model significantly outperformed single-step genomic best linear unbiased prediction (ssGBLUP) method in terms of prediction accuracy under both simulated heritability scenarios. Although the results seem to depend on the genetic complexity of the trait, the proposed model resulted in higher prediction accuracies than current methods. Furthermore, its computational costs in terms of computing time and peak memory are substantially lower than the current methods. This model is capable of computing genomically enhanced breeding values in less computational time and more efficiently for producers and customers to use for selection mating decisions.

2. Defining uterine limitations to pregnancy success in cattle. Identifying limitations to pregnancy success in cattle is vital. The uterus’ role in pregnancy maintenance was evaluated in heifers from Miles City in collaboration with University of Missouri. Uterine gene expression profiles of pregnant and non-pregnant heifers classified as highly fertile or subfertile based on serial embryo transfer (n = 3-4 rounds) and pregnancy were compared. Uterine luminal fluid (ULF) and conceptus gene expression were compared between pregnant highly fertile (HF) and subfertile (SF) heifers. Interferon tau protein was more abundant in ULF from pregnant HF heifers than SF heifers as the conceptus was longer in HF heifers. No differences in interferon-stimulated genes were observed in uterine tissues. Abundance of multiple proteins involved in energy metabolism (ACAA2, ENO1, TKT, PGD), oxidative stress (GSS), amino acid metabolism (PSPH, GOT1, LAP3, WARS, AHCY), and cell proliferation and differentiation (RAC1, HSPB1, CDC42) were greater in the ULF of pregnant HF than SF heifers. Concentrations of glucose in ULF were increased by pregnancy but did not differ between HF and SF heifers. Differences in genes encoding glucose transporters and involved with glycolysis and gluconeogenesis (GLUT2, GLUT4, HK1, FBP1, GALM, ALDOB, and ALDH3B1) were observed between conceptuses of HF and SF heifers. Expression of lipid metabolism genes differed between HF and SF conceptuses, and fatty acids differed between the ULF of HF and SF. Metabolites increasing in ULF of pregnant HF versus SF heifers were associated with energy and amino acid metabolism. Results indicate uterine secretions impact conceptus survival, programs development and is a facet of dysregulated conceptus-uterine interactions causing conceptus death in genetically subfertile heifers. Data demonstrate some of the signals that are obligatory to embryo survival. Overcoming these deficiencies may lessen the 30 to 50% embryonic mortality occurring in beef and dairy cows.

3. Genetic by prenatal nutritional environment interactions influence beef cattle progeny. Current beef cattle genetic evaluation programs do not account for the impact of the environment on the animal’s genetics. Genes interact with both pre and postnatal environments potentially affecting several important traits. A study conducted by researchers at Miles City, Montana, evaluated the existence of genotype by prenatal nutritional environment interaction (GxE) in growth traits, birth weight (BW), weaning weight (WW) and yearling weight (YW) in a composite beef cattle breed (50% Red Angus, 25% Charolais and 25% Tarentaise). Dams, randomly assigned to be fed in two levels of harvested supplemental feed from December to March of each year, were expected to result in adequate (ADEQ) or marginal (MARG; ~ 61% of the supplemental feed provided by ADEQ) levels of protein based on average quality and availability of winter forage. This design resulted in two prenatal nutritional environments: MARG and ADEQ. A total of 3,020 records were used in a bi-trait model treating each environment as a different trait. Genetic parameters for all three traits were estimated using genomic information. The direct genetic correlations between environment ADEQ and MARG were 0.97, 0.97 and 0.99 for BW, WW and YW respectively. Contrarily, the maternal genetic correlations between the two environments were 0.62, 0.41 and 0.73 for BW, WW and YW respectively. Direct and maternal genomic estimated breeding values (GEBVs) using single step genomic approach were computed and the solutions of SNP markers were back solved from the resulting GEBVs to compare genomic regions associated with the two environments. The present study demonstrated the existence of maternal genetic by prenatal nutritional environment interaction and warrants the need to account for this interaction in the calculation of expected progeny differences used in genetic evaluations. Having environment specific breeding values will help producers make better selection mating decisions which fits their production system.

4. Defining the mechanisms of genetic limitations to pregnancy success in cattle. Pregnancy loss in cattle ranges from 30 to 50% resulting in an estimated $87 million annual loss to the U.S. cattle industry. Pregnancy losses typically occur in the first month of pregnancy, and we have previously identified 22 genetic markers that differ among fertility classified beef heifers, with 3 primary fertility related genetic markers on the X-chromosome. In a collaborative effort between ARS scientists in Miles City, Montana, and scientists at Montana and Washington State Universities, genome analyses performed on 709 Angus-Saler cross beef heifers that conceived to first service, or within subsequent 20-day periods of a 60-day breeding season revealed a single locus associated with pregnancy on BTA19. This region included the positional candidate gene ASIC2, which is differentially expressed in the endometrium of fertility classified heifers, and the positional candidate gene, SPACA3. Gene-set enrichment analyses identified oxidoreductase activity as enriched among pregnant heifers with nine leading edge genes (MICAL2, PAH, PTGS1, CYP2D14, PHYH, DBH, P4HA3, CYP19A1, HMOX1) involved in catalyzing oxidation-reduction reactions. Imbalances in oxidation-reduction reactions have been associated with oxidative stressors impacting pregnancy success. No loci were associated or gene-sets enriched with first-service conception rate in this dataset. These results provide preliminary information that may enhance use of genomic selection in the beef industry to better select for reproductive superior heifers and improve our understanding of factors contributing to embryonic loss. Selection of reproductively superior heifers for herd replacements will decrease cost of production and increase profitability for beef cattle producers worldwide.

5. 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. ARS scientists in Miles City, Montana, 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/year in the development period.

6. Genomic analysis of inbreeding in Line 1 Hereford. The negative impact of inbreeding on economically important traits beef cattle is widely recognized. However, little is known on the genetic mechanism of inbreeding at the molecular level. In this study, researchers/scientists at Miles City, Montana, investigated inbreeding in Line 1 herd using SNP information to identify and study the effect of runs of homozygosity (ROH) on growth and fertility traits. First a grid search type of algorithm was developed to define runs of homozygosity. Runs of homozygosity were defined first based on minimum length and second on the mutation load which is the impact on a given trait. The results showed that a minimum threshold to identify ROH segments could be estimated using available phenotypic data. Furthermore, inbreeding was associated with growth and fertility traits. Across all traits, short ROH segments had limited effect on traits due to purging of deleterious haplotypes through selection. On the other hand, long ROH which represent recent inbreeding contributed to most inbreeding depression.

Review Publications
Ling, A., Hay, E.A., Aggrey, S., Rekaya, R. 2018. A Bayesian approach for analysis of ordered categorical responses subject to misclassification. PLoS One. 13(12):e0208433. https://doi.org/10.1371/journal.pone.0208433.
Roberts, A.J., Ketchum, J.N., Funston, R.N. 2018. Developmental and reproductive characteristics of beef heifers classified by number of estrous cycles experienced by start of first breeding. Translational Animal Science. 3(1):541-548. https://doi.org/10.1093/tas/txy118.
Sumreddee, P., Toghiani, S., Hay, E.A., Roberts, A.J., Aggrey, S., Rekaya, R. 2018. Inbreeding depression in line 1 Hereford cattle population using pedigree and genomic information. Journal of Animal Science. 97(1):1-18. https://doi.org/10.1093/jas/sky385.
Chang, L., Toghiani, S., Aggrey, S.E., Rekaya, R. 2019. Increasing accuracy of genomic selection in presence of high density marker panels through the prioritization of relevant polymorphisms. BMC Genetics. 1-10. https://doi.org/10.1186/s12863-019-0720-5.
Hay, E.A., Rekaya, R. 2018. Use of observed genomic information to infer linkage disequilibrium between markers and QTLs. Agricultural Sciences. 9(11):4170-4178. https://doi.org/10.4236/as.2018.911102.
Abreu, F.M., Geary, T.W., Coutinho Da Silva, M.A., Cruppe, L.H., Mussard, M.L., Madsen, C.A., Martins, T., Bridges, G.A., Harstine, B.R., Day, M.L. 2018. Role of progesterone concentrations during early follicular development in beef cattle: II. Ovulatory follicle growth and pregnancy rates. Animal Reproduction Science. 196:69-76. https://doi.org/10.1016/j.anireprosci.2018.06.011.
Abreu, F.M., Coutinho Da Silva, M.A., Cruppe, L.H., Mussard, M.L., Bridges, G.A., Harstine, B.R., Smith, G.W., Geary, T.W., Day, M.L. 2018. The role of progesterone concentrations during early follicular development in beef cattle: I. Characteristics of LH secretion and oocyte quality. Animal Reproduction Science. 196:59-68. https://doi.org/10.1016/j.anireprosci.2018.06.020.
Waterman, R.C., Petersen, M.K., Geary, T.W., Vermeire, L.T. 2018. Effects of reduced in utero and post-weaning nutrition on glucose clearance measures and serum metabolites. Agricultural Sciences. 9(8):947-957. https://doi.org/10.4236/as.2018.98066.
Hay, E.A., Utsunomiya, Y.T., Xu, L., Neves, H.H., Carvalheiro, R., Bickhart, D.M., Ma, L., Garcia, J.F., Liu, G. 2018. Genomic predictions combining SNP markers and copy number variations in Nellore cattle. BMC Genomics. 19(1):441-449. https://doi.org/10.1186/s12864-018-4787-6.
Roberts, A.J., Hay, E.A. 2019. Multigenerational Effects. In: Funston, R.N., Mulliniks, J.T., editors. Developmental Programming in Livestock Production. Volume 35, Issue 2. Philadelphia, PA: Elsevier. p. 355-364. https://doi.org/10.1016/j.cvfa.2019.02.009.
Petersen, M.K., Muscha, J.M., Roberts, A.J. 2019. Assessment of variability in yearlong relative loose mineral intake and range cow productivity in North American northern Great Plains. Journal of Animal Research and Nutrition. 4(2):4. https://doi.org/10.21767/2572-5459.100054.
Reese, S.T., Geary, T.W., Franco, G.A., Moraes, J.G., Spencer, T.E., Pohler, K.G. 2019. Pregnancy Associated Glycoproteins (PAGs) and late embryonic mortality in high vs sub fertility heifers. Theriogenology. 135:7-12. https://doi.org/10.1016/j.theriogenology.2019.05.026.
Wyffels, S.A., Petersen, M.K., Boss, D.L., Sowell, B.F., Bowman, J.G., Mcnew, L.B. 2019. Dormant season grazing: effect of supplementation strategies on heifer resource utilization and vegetation use. Rangeland Ecology and Management. https://doi.org/10.1016/j.rama.2019.06.006.