Theses and Dissertations

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Open Access
Genetic selection for resistance to bovine respiratory disease using pooled DNA approaches
(Colorado State University. Libraries, 2025) Boldt, Ryan J., author; Enns, R. Mark, advisor; Speidel, Scott, advisor; Keele, John, committee member; Kuehn, Larry, committee member; McDaneld, Tara, committee member; Holt, Tim, committee member
Bovine Respiratory Disease (BRD) is the costliest disease that affects the beef cattle industry. However, the only methods that are currently available to reduce the incidence of the microbial organisms (viruses and bacteria) that cause BRD are vaccination and antibiotic treatment. Examples using other species and diseases have shown that the selection for resistance to disease is an effective method to reduce the economic burden of that disease on the industry. Due to the challenge of collection of phenotypes for a trait like BRD resistance, one of the best methods for selection could be genomic selection. To try and capture a representative sample of commercial genetic makeup of the beef industry, samples for the study were collected from a commercial harvest facilities. To reduce overall genotyping costs, samples were genotyped using a pooled DNA approach. While pooled DNA has been used previously to identify genomic regions that differentiate based on disease status, this has not been done for animals that showed symptoms for BRD during the post weaning period. Therefore, the objectives of this research were to, 1) examine different analysis techniques for pooled DNA information, and 2) identify across breed SNP that are significant for identifying animals more likely to develop clinical signs of BRD. To investigate the first objective of the dissertation, two separate analyses were done. The first analysis evaluated the number of SNPs used to calculate a genomic relationship matrix. While using DNA pooling does reduce the cost of genotyping by grouping samples, the cost could potentially be further reduced by using SNP chips with lower density. For the analysis, 106 pools comprised of 96 individuals each were genotyped using a high-density genomic panel that contained 777,962 SNP. To evaluate the use of lower density SNP chip on pooled DNA analyses, 50 replications of number of SNP from 500 to 770,000 were sampled randomly. For each level and replication, the resulting genomic relationship matrix was compared to the full relationship matrix calculated from 776,749 SNP, after individual SNP were removed for minor allele frequency <0.05. To calculate the equivalence of the matrices, the genomic relationship matrix calculated from the reduced number of SNP was multiplied by the Eigenvalues and Eigenvectors of the genomic relationship matrix formed from all SNP. After this multiplication, the variance of the Eigenvalues of the reduced matrix was standardized by the full matrix variance of the Eigenvalues of the resulting matrix was calculated. The closer the resulting variance is to 0 both matrices were considered to be proportional to one another. When examining the resulting Eigenvalues variances after 2,000 SNP the reduction of variance decreased in magnitude. These results suggest that a low-density panel may be used for pooled DNA data and for calculating genomic relationship matrices. The second analysis that was conducted to address the first objective looked at alternative analysis techniques for identification of simulated important SNP at varying levels of allelic prevalence and effect size. For the analysis, 100 random SNP across all chromosomes were selected to act as the significant SNP among the approximately 770,000 SNP available on the BovineHD chip. All SNP pooling allele frequencies (PAF) were simulated using a beta distribution. For the 100 significant SNP, the PAF were then modified based on differing levels of prevalence and the effect that the disease-causing SNP would have. For prevalence levels from 0.10 to 0.90, increments of 0.10 were simulated and for effect of the SNP values from 0.01 to 0.50 were simulated in increments of 0.01. For each of the 450 combinations of prevalence and effect, two different models were applied to the same dataset. The first model type was a GWAS analysis that has previously been applied to this data type. Under this model each SNP is tested via an F-test. The dependent variable for this analysis was the PAF and the fixed effect was a binary classification of if a pool was a case or a control. Additionally, a relationship matrix was calculated to account for any population stratification that was occurring in the simulated dataset. For each F-test, a p-value was calculated. The second type of analysis that was conducted was a Random Forrest analysis. For the Random Forrest the same number of trees, terminal node size, and number of explanatory variables to try at each node were applied to all combinations. The optimal number was determined to be 2,000 trees, a terminal node size of 1, and to try 60,000 explanatory variables. For each of the combinations the results were ranked based on lowest p-value and highest variable importance factor for the GWAS and Random Forrest analysis, respectively. From there, the top 100 most significant SNP were compared, and the number of pre-identified significant SNP were counted within the subset. Across all levels of prevalence each model was able to identify a subset of the most significant SNP. Across all levels of prevalence, the Random Forrest model started? identifying significant SNP at lower levels of effect of the disease-causing allele. Random Forest model started identifying significant SNP at lower levels of the disease-causing allele. At low (0.10, 0.20, 0.30) and high levels (0.70, 0.80, 0.90) prevalence levels the traditional GWAS model was able to identify a higher number of significant SNP at high effect levels. Whereas at moderate prevalence levels (0.40, 0.50, 0.60) the Random Forest model more correctly identified a larger number of the significant SNP. To address objective two, several analyses were run looking at estimating SNP effects to identify informative variants for selection against development of BRDC. For this analysis samples were collected from three large commercial processing plants in Colorado and Nebraska. DNA samples were collected from ears when the animals were harvested. Samples for the study were collected over a four-year period. For pooling, punches were removed from each ear, and animals were sorted into either a case or control pool. Within each individual pool 96 animals were represented. For each case a corresponding control from the same group from the feedlot was also collected. In total 106 pools were constructed representing 10,176 animals across all pools with a matching case and control strategy. DNA was extracted using a Quigen Kit and pools were sent to Neogen (Lincoln, NE) for genotyping on a Bovine SNP chip that contained approximately 770,000 individual SNP. For each SNP and each pool, a PAF was calculated. To account for population stratification in the analysis a covariance matrix among pools, PAF was calculated. Mixed model methodology was used to solve for effects in the model. In the first analysis, each individual SNP was examined. For each individual SNP an F-test was performed to test for significance. Additionally, analyses were performed using SNP groups. SNP groups were formed using 100, 500, and 1,000 SNP regions. For each region a distance matrix based on the PAF for SNPs in the region was calculated. This was then used as a response variable for an ANOVA analysis. Fixed effects were the A matrix to account for population stratification as well as 2 x 106 matrix to signify if an animal was either in a case or control pool. For all analysis types, no significant SNP were discovered. Additionally, several regions that have been previously reported to be significantly associated with BRDC in previous studies were also examined. To see if similar signal was being picked up, SNP were ranked from being estimated as the most significant to least significant and compared to previous results. Among the previously reported results there were regions on BTA16 (70-71), BTA16 (70-71), BTA14 (9-10), and BTA8 (63-64) that were among the top 1% of most significant SNP in the single SNP analyses. However, in the grouped SNP analyses none of these regions were in the top 1% of significant SNP. Other regions that have been previously identified in other papers were either not in the top 1% of SNP in any analysis or had p-values that were 0.85 or greater.
Open Access
Effects of pre-milking waiting time and selection behavior in cows milked in an automated batch milking system
(Colorado State University. Libraries, 2025) Weng Zheng, Richard, author; Pinedo, Pablo, advisor; Velez, Juan, committee member; Lombard, Jason, committee member
The adoption of automated milking systems (AMS) has transformed the dairy industry by improving efficiency, animal welfare, and milk production. DeLaval's Batch Voluntary Milking System (Batch VMS) provides a structured alternative to traditional AMS for larger dairy herds. Unlike continuous voluntary milking, Batch VMS organizes cows into groups and schedules their milking at set intervals, enhancing herd management while reducing labor demands. As a hybrid approach, it offers a seamless transition from conventional milking methods to automation. Through a literature review and two research studies, this thesis explores how Batch VMS may affect cow health and performance. Chapter 1 contains the literature review. It introduces the changes in the AMS technologies in recent years and compares it to Batch VMS. Secondly, it discusses the effects of pre-milking waiting time on milking performance and cow health in terms of mastitis and lameness. And lastly, it discusses selection behavior in cows, comparing behaviors in conventional and automated milking systems. Chapter 2 explores the effects of pre-milking waiting time (WT) in an automated batch milking system (ABMS). Visit information was collected to calculate pre-milking WT, defined as the time elapsed between the entrance of the cow to the milking barn, as indicated by pedometers attached to each cow that were read by sensors located at the parlor, and the entrance of each individual cow to the robot milking box. WT were categorized into quartiles within each parity group as Q1 ≤ 9 min, Q2 = 10 to 24 min, Q3 = 25 to 46 min and Q4 ≥ 47 mins for primiparous and Q1 ≤ 11 min Q2 = 12 to 30 min, Q3 = 31 to 51 min and Q4 ≥ 52 mins for multiparous. To assess the association between lameness and WT, individual cow WT averages were calculated separately for primiparous and multiparous groups. Lameness was treated as a categorical variable, where 1 indicated a cow diagnosed with lameness and 0 indicated non-lame cow. The results show that the average waiting time for all milking events was 33.6 min (± SD = 28.5), 34.5 ± 28.9 for PP, and 30.7 ± 27.3 for MP. The means for each breed were 25.6 ± 15.2, 42.3 ± 16.8, and 42.3 ± 23.4, for HO, JE, and HJ, respectively. While significant differences in LSM were observed between breeds for most variables, there was little to no significant association between WT and the analyzed outcomes. An increase of 10 minutes in WT was associated with a 23.7% increase in the odds of lameness in multiparous cows (95% CI: 10.2–39.0; p < 0.001). However, no significant association was found in primiparous cows (OR: 1.09, 95% CI: 0.85–1.38, p = 0.462). Chapter 3 discusses selection behavior in an ABMS where cows select between 22 robots each time there are brought to the milking parlor. The objective of this study was to analyze the robotic milking station selection behavior of three breeds including Holstein, Jersey, and Holstein × Jersey crossbred cows in a multibreed dairy farm with a batch milking system with automatic milking units. The study used data from 1,762,461 milking events in 3705 HO (n=1355), JE (1876) and HJ (475) cows from May 2023 to September 2024 in a commercial organic grass-fed dairy in TX. Cows were moved to the milking center twice per day, where they could select their milking visits among 22 robot units (DeLaval, Sweden). For the analysis, robots were also classified by barn location [East (n=11); West] and arm configuration [left (n=11); right]. Milking visit information was collected to determine the frequency of specific robot usage per cow during the study period. Subsequently, the frequencies of selection for the top 1, 3, and 5 robotic milking stations, top barn location, and top arm configuration were calculated for each cow. Preference consistency scores (PCS) were calculated considering the frequency of access to each robotic milking station, barn side, and arm configuration in 30 days periods. Overall, multiparous and HO cows evidenced more consistent behaviors in milking station preference. Dairy cow selection behavior should be considered when analyzing the efficiency of milking procedures.
Open Access
Individual quarter dry-off procedure in dairy cows
(Colorado State University. Libraries, 2025) Ibarguren, Clara, author; Pinedo, Pablo, advisor; Velez, Juan, committee member; Lombard, Jason, committee member
Mastitis, defined as inflammation of the mammary gland, has a major impact on the dairy industry, affecting profitability and animal welfare due to reduced milk production, increased antibiotic use, and pain and discomfort in the affected animals. This health disorder concerns researchers, producers, and consumers worldwide. The "individual quarter dry-off" procedure, which consists of stopping milking the affected quarter is an alternative to the use of antibiotic treatment in unresponsive cases. Understanding the relationship between the multiple factors involved in the disease and this procedure is crucial. Through an extensive review of mastitis and a descriptive statistical analysis of this dry-off practice, this thesis focuses on understanding the dynamics of this procedure within a lactating dairy herd. Chapter 1 includes a literature review on mastitis, and the possible management practices conducted by the dairy industry to mitigate the problem. Due to the limited information available on individual quarter dry-off, the information provided in this chapter consists of a discussion of the anatomy of the mammary gland, physiology, pathology of mastitis disease, and management practices. Once general knowledge of the root of the problem is established, technical implications regarding the individual dry-off procedure are explained in the following chapter. The objective of chapter 2 is to describe the dynamics of individual quarter dry-offs in certified organic dairies. The data were collected from PCDart (©DRMS) spanning from 2018 to 2023 from four organic dairies in CO, USA. The dataset included 2,881 cows with at least one dried quarter (QDO), of which 769 cows (26%) had a second dried quarter (QDO2). The variables considered in this study were quarter location, parity, days in milk (DIM), season, and survival after the first quarter dry-off (QDO). The statistical analysis was completed in SAS (SAS Institute Inc.), employing chi-square goodness of fit, logistic regression, and ANOVA. The results showed that QDO was more prevalent in front quarters among both primiparous (PP) and multiparous (MP) cows, with higher frequencies observed during winter across both parity categories. The mean ± SE of days in milk at QDO was smaller for primiparous cows compared to multiparous cows, and it took approximately one year to have a second dried quarter to occur. Parity category had no effect on the likelihood of QDO2, and the number of days to culling after QDO were not significantly different between parities, averaging around 365 days. Additionally, cows with QDO had lower actual and projected 305 milk yield compared to healthy cows (597 kg [PP] and 436 kg [MP] less for actual 305 milk production; 628 kg [PP] and 495 kg [MP] less for projected 305 milk production). Overall, milk yield was consistently lower in cows with QDO compared to their herdmates. These findings provide valuable insights into the dynamics of quarter dry-off, contributing novel information to support the control of mastitis in certified organic dairies. Chapter 3 explores the dynamics of milk yield following the individual dry-off of quarters (QDO) in dairy cows. The study focused on cows that had one quarter dried off due to a chronic mastitis event and had milking records available for 30 days post-procedure. Data were collected from 144 cows on an automatic milking system (AMS) dairy farm in Colorado, of which 79% (n=144) were multiparous and 21% (n=30) primiparous. Information was sourced from DelPro and DairyComp on-farm software, and linear mixed models with repeated measures and estimated marginal means (emmeans) were generated using RStudio. Although the sample size of primiparous cows was limited, results showed a slight decrease in milk production following QDO. Conversely, multiparous cows displayed increased production in the opposite quarters, with an overall milk yield rising over the 30-day period after the dry-off. Total milk production following QDO was higher in cows ≤120 days in milk (DIM) compared to those with >120 DIM. Additionally, cows experienced greater milk yields when the dry-off procedure was performed on rear quarters versus front quarters. Of the variables analyzed, the number of days in milk after the procedure showed the most statistically significant relationship with milk production, while presence of other diseases did not exhibit a significant effect. These findings offer valuable insights into milk yield dynamics and implications for management strategies in dairy herds.
Open Access
Effects of growth implants on animal performance, intake, carcass characteristics, feeding behavior, enteric methane emissions, and economic profitability of finishing Angus steers
(Colorado State University. Libraries, 2025) Swenson, Maya, author; Place, Sara, advisor; Stackhouse-Lawson, Kim, committee member; Engle, Terry, committee member; DeLay, Nathan, committee member
Methane (CH4) is a potent greenhouse gas (GHG) with a global warming potential 28-34 times greater than carbon dioxide (CO2), making it a significant contributor to climate change (IPCC, 2019). Livestock production, particularly feedlot systems, is a major source of CH4 emissions from cattle, influenced by diet composition, microbial fermentation, and animal-specific traits (FAO, 2013; Beauchemin et al., 2020). Advances in CH4 measurement techniques including respiration chambers, SF 6 tracer methods, and automated head chamber systems (AHCS), have improved emissions quantification in feedlot settings (Harper et al., 1999; McGinn et al., 2019; Ungerfeld et al., 2022). Mitigations strategies include dietary interventions like high-concentrate diets, which promote propionate production over methanogenesis, and feed additives like 3-nitrooxypropanol (3-NOP), ionophores, seaweed, and nitrates, which can reduce CH4 emissions by 10-80% (Vyas et al., 2018; Almeida et al., 2021; Kebreab et al., 2023; Ungerfeld & Pitta, 2024). Additionally, manure management practices, such as anaerobic digesters and composting, can further reduce CH4 emissions from the livestock operations (EPA, 2024). Anabolic growth promoting implants, widely used in the beef industry, enhance G:F and ADG, have the potential to indirectly reduce CH4 emissions per unit of beef produced by 12-20% (Stackhouse et al., 2013; Reichhardt et al., 2021). Implants containing trenbolone acetate (TBA) and estradiol (E2) have been shown to increase average daily gain (ADG) by up to 28% and improve feed efficiency (G:F), reducing overall emissions intensity (Parr et al., 2011; Smith & Johnson, 2020). Therefore, the study's objective was to assess the relationship between animal performance, feed intake, carcass characteristics, feeding behavior, enteric CH4 emissions, and economic profitability of implanted and nonimplanted finishing Angus steers. Sixty-two cattle were housed at the Climate Smart Research pens at Colorado State University and blocked by body weight into two pens. Each pen was equipped with GreenFeed automated head chambers and SmartFeed feeder for feed intake and behavior measurement (C-Lock, Rapid City, SD). The study was conducted as a randomized complete block design. Animals within each pen were randomly assigned a treatment: implanted with Component TE200 (IMP) (Elanco Animal Health, Greenfield, IN) or not implanted (CON). Body weight (BW) gain, feed intake, and enteric emissions were collected from each individual animal for 80 and 52 d. Data were analyzed in JMP Pro and significance was declared at P < 0.05 with tendencies at P < 0.1. IMP animals had a greater final BW (709 kg vs 670 kg) and ADG (2.4 kg/d vs 1.7 kg/d, P < 0.0001) compared to CON animals. A greater dry matter intake (DMI) was observed in IMP animals (11.3 kg/d) compared to CON animals (10.9 kg/d, P = 0.01). IMP animals had improved feed conversion (F:G) and G:F efficiencies when compared with CON animals (P < 0.0001). A difference was observed in hot carcass weight (HCW) between IMP and CON animals (414.8 kg vs 386.5 kg, P < 0.0001). Similarly, ribeye area (REA) was larger in IMP animals compared to CON animals (P = 0.01). No differences were observed in marbling score and USDA yield grade (YG) between the two treatments (P > 0.05). There was a difference in USDA quality grade (QG), where CON animals graded more frequently in higher grade categories (Choice, Choice+, and Prime) compared to IMP animals (P = 0.04). IMP animals tended to have larger session size (SS) (g DM/visit) than CON animals (P = 0.08). An interaction was observed where IMP animals fed for 80 d had greater enteric CH4 emissions compared to CON animals within the same pen (199 g CH4/d vs 177 g CH4/d, P = 0.04). IMP animals had greater oxygen (O2) consumption and hydrogen (H2) emission than CON animals (P < 0.05). With animals fed for 52 d, IMP animals had reduced CH4 emissions intensity (g CH4/kg ADG) compared to CON animals (P < 0.05). Relative profitability was greater than $0 in both weight groups with mean differences of $111.76 and $143.39 for 52 and 80 DOF, respectively. In summary, anabolic implants improve feedlot animal productivity and efficiency, potentially reducing emissions per unit of beef produced while improving economic profitability.
Open Access
Preweaned calf transportation practices in the United States: a survey of dairies, calf raisers, and haulers
(Colorado State University. Libraries, 2025) Machuca, Erica, author; Cramer, Catie, advisor; Edwards-Callaway, Lily, committee member; Roman-Muniz, Noa, committee member; Keller, Kaleigh, committee member
Transport is recognized as a welfare concern for livestock, but young calves are especially vulnerable to transport challenges. Despite this knowledge, little research is available describing transportation practices of preweaned dairy calves in the United States. Therefore, the objectives of this study were to (1) describe the current industry practices regarding the transportation of preweaned dairy and beef-on-dairy crossbred calves, (2) determine differences in pre-transport management on dairies between replacement heifers, beef-on-dairy crossbreds, and dairy bull calves, and (3) identify outreach and research needs to address calf welfare concerns related to transportation. Individuals who make decisions about transporting and receiving preweaned dairy or beef-on-dairy calves within the United States were recruited through digital advertisement, email, and extension agents to complete an online survey in 2023. A total of 123 responses were accepted for analysis and consisted of 69 dairy operations that sold or shipped preweaned calves, 29 operations that received preweaned calves, and 25 hauling companies that transported preweaned calves in 2022. The survey used a branching method to direct respondents to complete one of four surveys, each containing different questions based on their selected role: 1) dairies that sell or contract out calf raising for preweaned calves, 2) dairies that transport and raise preweaned calves at another location, 3) operations that receive preweaned calves after transport (e.g., auctions, livestock markets, calf ranches, etc.), and 4) haulers that transport preweaned calves. Question topics for dairy operations included pre-transport practices such as colostrum management, health evaluations, and marketing practices. Questions for operations that received calves included calf condition upon arrival, disease incidence during the preweaning period, and preconditioning requirements. Questions for hauling companies included distances traveled, number of operations, and calves' final destination. Bhapkar, Kruskal-Wallis, or McNemar tests were conducted to determine differences in management practices at the dairy prior to transport. The predictor of interest was calf class: replacement heifer, beef-on-dairy, and dairy bull. Outcomes of interest included: age at transport, timing after birth to first colostrum feeding, total colostrum quantity, milk feeding prior to transport, and access to water immediately prior to transport, median distance, and median duration. Out of the 69 dairy operations accepted for analysis, 40 dairy operations transported 284,597 replacement heifers, 58 dairy operations transported 263,104 beef-on-dairy crosses, and 57 dairy operations transported 33,146 dairy bull calves prior to weaning. The age at transport for the majority of calves differed between calf class (P < 0.009). A difference in timing to first colostrum feeding was seen between replacement heifer and beef-on-dairy calves (P = 0.02). A difference in timing to first colostrum feeding was seen between replacement heifer and dairy bull calves as well (P = 0.02). Some preconditioning practices differed between replacement heifer and beef-on-dairy calves and between beef-on-dairy and dairy bull calves (P < 0.05). Operations that received preweaned calves reported wide variabilities in the prevalences of morbidity and mortality in calves following transport, suggesting a lack of uniformity in calf care across the industry. While the study was limited by a small sample size, our findings provide a deeper understanding of transport management practices in the United States that can help guide future research and outreach efforts to promote the health and welfare of dairy calves and support the longevity of the dairy industry.
Open Access
Characterizing the vitamin and mineral status of farmed American bison in the United States
(Colorado State University. Libraries, 2025) Okoren, Claire, author; Edwards-Callaway, Lily, advisor; Engle, Terry, advisor; Torres-Henderson, Camille, committee member
The American bison (Bison bison) has become increasingly prevalent within the agricultural sector, yet limited research exists on their specific nutritional needs, particularly for vitamins and minerals. Minerals play a critical role in physiological processes like muscle development, reproduction, and enzyme activation, while vitamins act as coenzymes essential for metabolic pathways and immune functions. This study aimed to establish baseline mineral and vitamin concentrations in farmed American bison tissues and to analyze mineral and vitamin contents of feed and water across locations within the United States. Post-mortem samples, including blood, liver, kidney, and muscle, were collected from bison processed at USDA-inspected facilities. Seasonal sampling captured variations in feed and water composition. Tissue samples underwent mineral analysis using inductively coupled plasma-optical emission spectrometry (ICP-OES), while vitamin levels were determined via liquid chromatography-tandem mass spectrometry (LC-MS/MS). To provide context, a scoping review of existing literature on mineral and vitamin concentrations in bison and related species was conducted, yielding weighted means for comparison. Results highlight the nutritional variability across ranches, seasons, ages, and sexes offering foundational data for developing species-specific dietary recommendations. These findings address a critical knowledge gap in farmed American bison mineral and vitamin status, and hopes to drive future research in bison agriculture, enhancing animal health, welfare, and productivity in these farmed settings.
Open Access
Development of a multi-breed heifer pregnancy genetic evaluation in beef cattle
(Colorado State University. Libraries, 2024) Giess, Lane Kurtis, author; Enns, R. Mark, advisor; Speidel, Scott E., advisor; Doyle, S. Patrick, committee member; Koontz, Stephen R., committee member
Heifer fertility represents a primary influence on the profitability of a beef cow-calf enterprise. Reproductive rates determine the number of calves born and thus influence the amount of beef product produced at the commercial level driving income for cow-calf operators. Heifer fertility then is an economically relevant trait, though in most cases pregnancy data are cumbersome, untimely to collect, and are considered a rare phenotype in national cattle evaluations (NCE). Despite this, there are successful examples of existing evaluations for heifer pregnancy (HP) across several beef breed associations. These HP genetic evaluations typically rely on categorical exposure (1 = exposed; 0 = not exposed) and pregnancy outcome (1 = pregnant; 0 = not pregnant) data and involve the use of threshold animal models (TM) to convert these binary observations to an underlying normally distributed range of values known as liabilities. These liabilities are then expressed as a percentage that predicts the likelihood of a bull's daughters becoming pregnant and giving birth as two-year-olds in the form of an expected progeny difference (EPD). However, despite these existing HP genetic evaluations, little improvement in the genetic trends in HP has been observed. Perhaps the reason for meager improvement in genetic trend is seedstock producers are not placing enough emphasis on HP, or with pregnancy rates already at or near 90% there is an assumption there is no need for genetic improvement. Additionally, though TM have been successfully implemented in genetic evaluations of HP, a common challenge with the methodology is the inability to evaluate data from contemporary groups that all have the same observation. Even more important is that TM are not supported in some software used for single-step genomic evaluation, such as BOLT by Theta Solutions. Because of these challenges, this study investigated the development of a multi-breed genetic evaluation for HP by performing a series of HP evaluations using TM, linear animal model (LM), and random regression model (RRM) methods. This study used HP data collected on heifers from 1974 to 2020 provided by the International Genetic Solutions (IGS) genetic evaluation, sourced from 9 partner breed associations. Because each breed organization may have its own nuanced definition of HP or differences in how data are reported, inconsistencies in HP data need to be investigated. For example, the American Simmental Association (ASA) does not have an upload format for producers to report HP data but instead uses a system of logic converting whole herd reporting (WHR) codes into HP phenotypes. The first study described the framework for how the ASA converted productivity, culling, and enrollment codes into HP phenotypes. It then evaluated the relative proportions of reasons why heifers/cows were culled. The proportion of heifers culled due to reproductive failure using this method of establishing HP phenotypes was 14%, which is consistent with the national average. The summary statistics for HP observations were cohesive with other HP observations reported to IGS partner breed organizations. Evaluating the effectiveness of these created phenotypes were investigated in the second study. Using data from the American Gelbvieh Association, the Red Angus Association of America, the North American Limousin Foundation, the American Shorthorn Association, and the Canadian Limousin Association, the second study estimated variance components, breed effects, and heterosis effects using LM and TM evaluation methods. Evaluations of HP were performed first within breed before a multibreed population was developed. The average heritability estimate across evaluations performed on 7 different breed groups for HP using LM methods was 0.026, with a minimum value of 0 and a maximum of 0.084. The average heritability for HP using TM methods was 0.17, with a minimum of 0.07 and a maximum of 0.28. Breed populations were then combined into a single multi-breed population, and the same stepwise procedure of incorporating heterosis and breed effects as fixed effects was used to generate variance components and fixed effect solutions. The heritability estimates in this multi-breed population were 0.023 and 0.088 using LM and TM methods, respectively. Heritability estimates did not change as additional fixed effects of breed and heterosis were fit. There were no statistically meaningful breed effects; however, heterosis results in a 17.2% increase (P<0.05) in the probability of HP when maximum heterosis is achieved. Results from this statistical method suggested that LM and TM may be performing equivalently for estimating HP breeding values in within-breed populations; however, in a multi-breed population, results were inconsistent, suggesting perhaps the model was over-specified with breed effects. These results suggest that LM as the model type within a genetic evaluation may be an alternative evaluation method for HP due to its simplicity, ability to use all available information, and support in modern genetic evaluation software programs. Due to being relatively simple to collect and economically important for beef producers, the third study performed a series of evaluations for age at first calving (AFC), which also served as an important investigation as AFC was a potential age covariate in HP evaluations. Models were implemented using single-breed populations and then combined into a larger multi-breed population so heterosis and breed effects could be estimated. The heritability estimates of AFC for Simmental and Red Angus were 0.19 ± 0.01 and 0.14 ± 0.01, respectively. These results demonstrate AFC in days is lowly to moderately heritable. However, when evaluating the genetic trend for both breeds the results seemed incongruous as AFC was sharply increasing over time. Many beef producers mass mate heifers at a single fixed breeding date. As a result, older heifers in a CG will not have the ability to have a younger AFC compared their younger counterparts in the same CG if conception occurs on the same day. To account for this systematic management influence which may be creating a disadvantage in some heifers, age differential (DIFF) was included to account for age differences prior to first exposure and was defined as the difference in days between an individual's birth date and the earliest birth date of an animal in a defined contemporary group. In addition to including DIFF as a fixed effect, accounting for heifer body weight prior to breeding was also considered, and subsequent bivariate animal models of AFC that included yearling weight (YW) were performed. Two bivariate multi-trait animal models for AFC and YW with random additive genetic and residual effects and fixed effects of contemporary group, breed proportion, and retained hybrid vigor were used. When DIFF was not included as a fixed effect, the additive, residual, and phenotypic variances for AFC were 126.1, 456.8, and 582.9 d2, respectively, and the genetic correlation between AFC and YW was 0.36 ± 0.02. When DIFF was included as a fixed effect, the additive, residual, and phenotypic variances for AFC were 10.0, 326.0, and 336.0 d2, respectively. The genetic correlation between AFC and YW was 0.19 ± 0.04. In the absence of DIFF, the heritability estimates for AFC and YW were 0.22 ± 0.01 and 0.44 ± 0.01, respectively, but were 0.03 ± 0.003 and 0.44 ± 0.01 respectively, when DIFF was included. Age differential had a significant effect on AFC at –0.86 (P < 0.0001). The low additive genetic variance of AFC, when accounting for DIFF, suggests that the influence of a female's age going into a fixed breeding date explains much of the variation in AFC. Because of the potential drawbacks associated with LM and TM evaluations of HP, the fourth study investigated alternative definitions of HP using RRM evaluation methods. Two fertility traits evaluated using RRM were proposed; the first being the evaluation of heifer pregnancy by calving week (HPcw), which regresses a binary calving event on the week a heifer calved within her contemporary groups calving window, and the second being the linear evaluation of binary HP which regresses HP on an age covariate such as age at first exposure (AFE) or yearling age (YAGE). In all evaluation methods, Legendre polynomials were used as the base function and observed heritability estimates at different age ranges were transformed from the (co)variances estimated for the intercept and linear term of HPcw or HP. Within the HPcw evaluations, two separate age covariates were proposed as additional fixed effects, with the first being age at first calving (AFC), and the second being AFE. Heritability estimates for HPcw fitting AFC as a fixed effect ranged from 0.39 to 0.56, though this is assuredly from AFC being a biased age estimate. Observed heritability estimates for HPcw across 10 weeks, fitting AFE as a fixed effect ranged from 0.010 to 0.20, which are more realistic and consistent with literature estimates compared to observed HPcw heritability estimates fitting AFC as an age covariate. For the HP evaluation regressing HP on YAGE, heritability estimates ranged from 0.01 to 0.14, suggesting that up to 14% of the variation in HP across ages could be attributed to differences in additive genetics. For the evaluation regressing HP on AFE, heritability estimates were 0 or near zero, so this evaluation method likely requires additional scrutiny. Differences in heifer age covariate and trait definition for the evaluation of HP provided expanded opportunities for the development of national cattle evaluations using RRM. The potential advantages of utilizing RRM in evaluations of categorical or single observation data are that it allows the use of all available data in a dataset and is more adapted to single-step genomic evaluation software systems. Because of this, RRM may be the preferred evaluation method for HP or related fertility traits, though this requires additional testing in global databases. Results from previous studies suggest there are options for evaluating HP in a multi-breed NCE, but no single method is ideal. While LM evaluations validate well, there is low variance in the EBV for the populations evaluated due to low heritability. The TM evaluations validate well and have reasonable predictions, but they cannot appropriately utilize all available data and are not supported by some modern genetic evaluation software programs. The potential of RRM evaluation methods is evident; however, further testing of this methodology must be performed before this approach can be considered.
Open Access
Exploration of bison industry practices and mitochondrial metabolism
(Colorado State University. Libraries, 2024) Velazco, David, author; Nair, Mahesh, advisor; Edwards-Callaway, Lily, advisor; Hess, Ann, committee member; Engle, Terry, committee member
The objectives of this study were to benchmark the United States bison meat industry and to compare the mitochondrial metabolism of beef and bison. The first project evaluated bison industry stakeholder perceptions on management, animal welfare, and meat quality with in-person and online surveys. The stakeholder surveys identified animal handling, bison behavior, employee training, facility design, and transportation duration as the most critical factors that could impact animal welfare in the bison production system. The stakeholders understood that animal welfare is a crucial component of bison production and directly affects meat quality. The second project analyzed multiple live animal factors to benchmark their influence on specific meat quality attributes. Live animal production parameters of bison (n = 2,284; Bulls n = 1,101; Cows n = 199; Heifers n = 984) such as distance traveled, season, number of head bumps in the chute, sex class, and live weight were associated (P < 0.05) with differences in fat thickness, ribeye area, blood splash presence, and instrumental color of bison meat. The third experiment compared the mitochondrial metabolism of bison and beef. The left side masseter muscle of crossbred Angus steers (n = 12) and bison (n = 12) were collected within 60 minutes postmortem. The oxygen consumption rate of permeabilized muscle fibers at specific respiration states was evaluated utilizing the Oroboros O2K high-resolution respirometry system. The abundance of electron transport chain protein in bison and beef muscle was measured using gel electrophoresis. All mitochondrial data were analyzed as mixed models with species as the fixed effect, and day confounded with sex class as the random effect, using JMP Pro 16. No differences were found in oxygen consumption flux (JO2) between bison and beef under baseline, Leak respiration (LEAK; P = 0.8813), rotenone respiration (ROT; P = 0.1071), and carbonyl cyanide m-chlorophenyl hydrazone respiration (CCCP; P = 0.7502) respiration states. Bison permeabilized muscle fibers had a higher (P = 0.0016) JO2 during max OXPHOS (+D) and produced more hydrogen peroxide (P = 0.0234) during this respiration state compared to beef. Respiration control rate (RCR) did not differ (P =0.2928) between beef and bison permeabilized muscle samples. Bison muscle samples contained lower relative abundance of the electron transport chain complexes II (P = 0.0057) and III proteins (P = 0.0020) than beef. Additionally, bison and beef had similar concentrations of citrate synthase in the masseter muscle (P = 0.4650). Results from these experiments can be used as an industry reference to monitor improvements in bison animal welfare and meat quality. Additionally, information regarding mitochondrial metabolism can serve as the foundation for future research to further investigate differences in efficiency between bison and beef.
Open Access
The effect of trace mineral source on solubility, rumen fermentation characteristics, and trace mineral concentration in protozoa and bacteria of steers consuming a lactation dairy type diet
(Colorado State University. Libraries, 2024) Loh, Huey Yi, author; Engle, Terry, advisor; Narayanan Nair, Mahesh, committee member; Coleman, Stephen, committee member; Torres-Henderson, Camille, committee member
A series of experiments were conducted to investigate the influence of trace mineral (TM) source on TM solubility, rumen fermentation characteristics, and trace mineral concentration in protozoa and bacteria of steer consuming a lactation dairy-type diet. Experiments 3 and 4 were classified as experiments 1 and 2 in chapter 3 for publication purposes in academic journal. In the first experiment, hydroxychloride TM (HTM) and sulfate TM (STM) sources of Cu, Mn, and Zn (n = 4/element/source; N = 24) were incubated separately in water for 24 h. Initial pH was measured after adding the TM to the solution, then the tubes were incubated at 39°C with agitation. After a 24-h incubation, samples were filtered to obtain the filtrate for TM analysis, and final pH readings were taken. Initial pH of each solution was greater (P < 0.03) for HTM compared to STM for all elements. Final pH tended to be greater for Cu (P = 0.09) and Zn (P = 0.07) from HTM compared to STM. Water solubility of Cu, Mn, and Zn from STM was greater (P < 0.01) than HTM sources. These data indicate that TM source influences pH and solubility of Cu, Mn, and Zn in water. In Experiment 2, eight steers fitted with rumen cannula were blocked by body weight and randomly assigned to treatments consisting of 10 mg Cu, 40 mg Mn, and 60 mg Zn/kg DM from either STM or HTM sources (n = 4/treatment). Steers were individually fed a cracked corn-corn silage-based diet. Treatments were top-dressed daily. Rumen contents were collected at 0, 2, and 4 h post-feeding on d 1 and 14. On d 15, strained ruminal fluid (SRF) and particle-associated microorganisms (PAO) were obtained. Digesta from HTM-supplemented steers has a lesser (P < 0.01) Mn concentration than STM-supplemented steers on d 14 of the trial. Steers supplemented with STM had a greater (P = 0.0016) soluble Cu concentration in the rumen on d 14 than those fed HTM. Zinc was more tightly bound (P = 0.01) to the digesta in HTM-supplemented steers compared to STM on d 14. The data suggest that dietary TM source can affect rumen soluble Cu concentrations and binding strength of Zn to solid digesta. In Experiment 3, three cannulated steers were adapted to a diet formulated to meet the nutrient requirements for lactating dairy cows. Strained RF was obtained by straining rumen content through 2 layers of cheesecloth. Half of the remaining digesta was washed with McDougall's buffer and filtered through 2 layers of cheesecloth to obtain PAO. Both SRF and PAO were filtered again through 8 layers of cheesecloth. Strained RF was mixed with either McDougall's buffer (SRF) or PAO (SRF+PAO) at a ratio of 1:2 or 1:4 and incubated at 39°C for 12 h using the ground basal diet as the substrate. Digestibility of DM was greater (P < 0.05) in digestion tubes containing SRF and SRF+PAO at a 1:2 ratio. In Experiment 4, eight steers fitted with ruminal cannula were blocked by body weight and assigned to one of two treatment groups. Treatments consisted of 10 mg Cu, 40 mg Mn, and 60 mg Zn/kg DM from either 1) sulfate (STM) or 2) hydroxychloride (HTM) sources. Steers were housed in individual pens and fed the same diet as described in experiment 1. Dietary TM treatments were mixed with dried distillers grains and mixed in the diet by hand, immediately after basal diet delivery. Dietary treatments were fed for 14 d. On day 15, SRF+PAO was collected from each steer (STM-RF and HTM-RF) and used in a series of in vitro crossover experiments. In vitro substrates (S) used were the ground diets consumed by the animals on each treatment (STM-S and HTM-S). Incubations containing HTM-S had greater (P < 0.01) total VFA concentration and propionic acid molar proportions, but lesser (P < 0.01) acetic acid molar proportions than STM-S. Rumen fluid from steers supplemented with HTM had a greater (P < 0.03) total VFA than STM-RF at 24h post incubation. After 12 h post incubation, the molar proportion of propionic acid in HTM-RF was lesser (P = 0.04) than STM-RF. After simulated abomasal digestion, soluble Mn concentration in HTM-S was greater (P < 0.01) than STM-S. These data indicate that the source of trace minerals can influence in vitro rumen fermentation characteristics and Mn solubility under simulated abomasal conditions.
Open Access
The effects of long-term molybdenum exposure in drinking water on molybdenum metabolism and production performance of beef cattle consuming a high forage diet
(Colorado State University. Libraries, 2024) Thorndyke, Meghan, author; Engle, Terry, advisor; Ahola, Jason, committee member; Edwards-Callaway, Lily, committee member; Holt, Timothy, committee member
In the current series of experiments the influence of long term molybdenum (Mo) exposure in the feed or water on copper (Cu) status, metabolic, reproductive, and carcass characteristics was investigated. The objective of experiment 1 was to conduct a life-cycle production and health assessment of lactating and gestating beef cattle, and their calves, exposed to varying doses of Mo. In this experiment Commercial, multiparous beef cows (n=54 in year 1; n= 51 in year 2) with calves (approximately 2 months of age) were used to evaluate the effects of Mo source (feed or water) on reproduction, mineral status, and performance in cows and calves receiving a grass hay diet [dry matter (DM) basis: 6.6% crude protein; 0.15% S, 6.7 mg Cu/kg, 2.4 mg Mo/kg] for 553 d. Cows were stratified by age, body weight (BW), and liver Cu and Mo status, and were then randomly assigned to one of six treatment groups. Treatments were: 1) Negative control (NC; basal diet with no supplemental Mo or Cu); 2) Positive control (PC: NC + Cu; 3 mg of supplemental Cu/kg diet DM from CuSO4·5H2O); 3) NC + 500 µg Mo/L from Na2MoO4·2H2O supplied in drinking water (Mo 500-water); 4) NC + 1000 µg Mo/L of Na2MoO4·2H2O supplied in drinking water (Mo 1000-water); 5) NC + Mo 1000-water + 3 mg of supplemental Cu/kg diet DM from CuSO4·5H2O (Mo 1000-water+Cu); and 6) NC + 3.0 mg of supplemental Mo/kg diet DM from Na2MoO4·2H2O (3.0 Mo-diet). During the winter months, animals were housed in three replicate pens per treatment and during the summer months animals were housed in separate pastures by treatment. Animals were allowed ad libitum access to both feed and water throughout the experiment. Cows were bred via artificial insemination during the summer months of both years of the experiment and calves were weaned at approximately 6 months of age in the fall of both years. All cows and calves were weighed, bled, and feed and water intake were determined every 28d. Cattle receiving diets containing less than 10 mg Cu/kg DM total diet became Cu deficient over the course of the experiment as determined by liver and plasma Cu concentrations. However, no Mo toxicity or Cu deficiency signs (e.g., reduction in growth rates, reproductive performance, or immune function) were observed throughout the course of the experiment for any treatment. Results suggest that Mo supplemented in water or feed at concentrations used in this experiment had minimal impact on Cu status and overall animal performance. However, dietary Cu concentration below 10.0 mg Cu/kg DM total diet reduced liver and plasma Cu concentrations to values indicative of a marginal Cu deficiency in beef cows. The objective of the chapter 3 review was to examine the impact of Mo in drinking water on cattle performance and Mo and Cu metabolism. The majority of Mo research has focused on the antagonist effect of Mo, alone or in combination with elevated dietary S, on Cu absorption and metabolism in ruminants. Diets containing both >5.0 mg of Mo/kg DM and >0.33% S have been reported to reduce the Cu status in cattle and sheep. Therefore, due to the potential for inducing Cu deficiency, Mo and S concentrations in the diet should be monitored and kept within appropriate values. Elevated sulfate concentrations in drinking water can also be detrimental to livestock production, especially in ruminants. High concentrations of sulfate in water have been extensively studied in cattle because high-sulfate water induces polioencephalomalacia in ruminants. However, little research has been conducted investigating the impact of Mo in water on Cu metabolism in ruminants. Based on the limited number of published experiments, it appears that Mo in drinking water may have a lower antagonistic impact on the cu status in cattle when compared to Mo consumed in the diet. This response may be due to a certain percentage of water bypassing the rumen when consumed by ruminants. The chapter 4 experiment objective was to of this experiment was to investigate the influence of prolonged exposure to elevated Mo water concentrations on apparent absorption and retention of both Cu and Mo in pregnant multiparous beef cows. In this experiment twelve multiparous beef cows of similar BW, age, and gestational length, from a larger cow-calf study, were utilized to evaluate the effects of molybdenum (Mo) consumption method (feed or water) on apparent absorption and retention of copper (Cu) and Mo. Cows (n=54) with calves had been assigned to one of six dietary and/or water treatments (n=9 cow-calf pairs per treatment) 301 d prior to selecting a sub-group of 12 cows. Treatments consisted of: 1) negative control (control; basal diet with no supplemental Mo or Cu), 2) positive control (control + 3 mg of supplemental Cu/kg DM), 3) control + 500 µg Mo/L from Na2MoO4·2H2O supplied in drinking water, (4) control + 1000 µg Mo/L of Na2MoO4·2H2O supplied in drinking water, (5) positive control + 1000 µg Mo/L of Na2MoO4·2H2O supplied in drinking water, and (6) control + 3.0 mg of supplemental Mo/kg diet DM from Na2MoO4·2H2O. The sub-group of cows were individually fed a low quality grass hay diet with their respective treatments, n=2 cows/treatment) for 14 d. On day 15, dry matter intake (DMI) was held at 90% of the group's average intake. Total fecal and urine output were then collected for 3 d. Dry matter digestibility and water intake were similar across treatments. Copper intake and apparent absorption and retention of Cu were greater (p < 0.05) in cows receiving supplemental Cu when compared to non-Cu supplemented cows. Apparent absorption of Mo was similar across all treatments. Apparent retention of Mo was greater while apparent absorption of Cu was lesser (p < 0.05) in cows receiving 3 mg of Mo/kg dm and cows receiving 1000 µg Mo/L when compared to all other treatments. These data indicate that Mo source (feed vs water) may impact apparent absorption of Cu in cows receiving a low quality forage diet. The chapter 5 survey of central Rocky Mountain livestock producers objective was to understand the mineral consumption within the forage and water as well as Cu and Mo status of the grazing cattle. Commercial, multiparous, crossbred beef cows from 3 independent cow-calf production operations were selected to assess the molybdenum (Mo) and copper (Cu) status of cattle raised in the Rocky Mountains. Fifteen cows from each operation were selected at random, during early summer and late fall processing. At the time of cattle processing, both jugular venipuncture blood samples and liver biopsies were obtained from each cow. Furthermore, all diet components, forage, water, and supplement samples were obtained from each location. Plasma, liver, water, and feed samples were analyzed for Mo and Cu concentrations via inductively coupled plasma mass spectrometry. Feed samples were also analyzed for moisture, crude protein (CP), ash, ADF and NDF. Water samples were sent to an established laboratory for general water quality analysis. On average, in the current survey forages samples contained 55.61% DM, 8.37% CP, 34.91% ADF, and 54.98 NDF with a Cu:Mo ratio of 2.8:1. Additionally, the water quality of the samples obtained were well within the "safe and should pose no health problems" category for beef cattle. Plasma Mo concentrations of 0.22 (±0.10) mg/kg DM were considered to be elevated in 64% of all samples obtained, likely a result of the elevated Mo forage concentrations in the grazed plant material. Plasma Cu of 0.83 (±0.11) concentrations were within normal ranges for all samples obtained. Molybdenum and Cu liver concentrations of 3.74 (±1.29) and 82.54 (±22.76) respectively, were within ranges considered to be normal for beef cattle for all samples collected. Based on the results of this survey, Mo and Cu plasma and liver concentrations in Colorado cow-calf operations in the central Rocky Mountains were similar to Mo and Cu plasma and liver concentrations in Cu supplemented cows in the previously described 2-year Mo supplementation cow-calf experiment. Furthermore, these data suggest that Cu supplementation at NASEM (2016) recommended concentrations of 10 mg Cu/kg DM total diet (or greater) meets the animals dietary Cu requirement for cattle consuming forages sampled.
Open Access
Hempseed meal as an effective protein supplement for finishing wethers
(Colorado State University. Libraries, 2024) Butts, Mercer, author; Archibeque, Shawn, advisor; Dillon, Jasmine, advisor; Myrick, Chris, committee member
To address the needs of an increasing global population and decreased availability of arable land due to the continued expansion of monoculture farms for the use of feeding livestock, it is necessary that we begin to research more sustainable methods for feeding animals, and the people who consume them. This study aims to address those needs by presenting hempseed meal (HSM) as a protein alternative to more commercially available feeds such as soybean meal commonly used in finishing rations on animal feeding operations (AFOs) across the United States. To complete this task, forty Western White-Faced wethers were used in a completely randomized block design with 5 treatments. These treatments included diets formulated to be near isonitrogenous with 0%, 5%, 10%, 15%, or 20% of diet DM as hemp seed meal, primarily as a substitute for soybean meal. Wethers were fed the diets individually for 90 d, which was followed by a 5 d balance trial with a total collection of urine and feces. There were no differences in DM intake (P = 0.44) or N digestibility (P = 0.467) between treatments, although there was a slight increase in P digestibility as hemp meal inclusion increased until it represented 15% of the dietary DM (P = 0.047). There were no differences in urinary N excretion (P = 0.33) or urinary urea excretion (P = 0.34) between treatments.
Open Access
Liver abscess effects on carcass performance and heritability estimates of liver abscess incidence and severity in beef on dairy heifers
(Colorado State University. Libraries, 2024) Zuvich, Miranda Lee, author; Enns, R. Mark, advisor; Speidel, Scott E., advisor; Woerner, Dale, committee member; Holt, Timothy N., committee member
The economic impact of liver abscesses has been reported to be not only due to loss from condemnation of livers but also from impacts on performance. A primary focus in decreasing liver abscess prevalence has been on prevention methods because with limited or no clinical signs present, diagnosis of liver abscesses in live animals is complicated, and no prevention methods have been highly effective in mitigation. As a result, this study aimed to identify the impacts of liver abscesses on carcass performance and estimate heritability for liver abscess incidence and severity in fed beef on dairy heifers. In the first study, 1,860 beef on dairy heifers were fed and harvested in Kansas. All had phenotypes for hot carcass weight (HCW; kg), rib eye area (REA; cm2), fat thickness (FT; cm), marbling score (MS), calculated visual yield grade (VYG), and liver abscess score. Of the 1,860 individuals, 1,646 had phenotypes for heart score (HS). Carcass impacts were estimated using fixed effects of liver abscess score, contemporary group, and age in days. The contemporary group was a concatenation of kill lot and treatment. Liver abscess score was fit in two different forms: 6 scores ("0", "A-", "A", "A+", "A+AD", "A+O") and 4 scores ("0", "A-", "A", "A+") where "A+" included scores of "A+AD" and "A+O". A score of "0" indicated no abscess and abscess severity increases with "A-", "A", and "A+". The scores of "A+AD", and "A+O" indicate there is adhesion of the liver to nearby organs and ruptured abscess, respectively. A significant increase was identified using the six-score model for FT for animals with scores of "A+O" compared to "A+", with respective least-squares means of 1.94 cm ± 0.12 and 1.59 cm ± 0.06 (P < 0.05). While not significant, tendencies were identified for FT for animals with scores of "A" and "A+AD" compared to "A+O" (0.05 ≤ P < 0.1) with respective least-squares means of 1.61 cm ± 0.06, 1.61 cm ± 0.05, and 1.94 cm ± 0.12. A significant increase was identified using the six-score model for VYG in animals with VYG scores of "A+O" higher than "A+" and "A+AD", with respective least-squares means of 3.75 ± 0.19, 3.20 ± 0.09, and 3.20 ± 0.08 (P < 0.05). When using the 4-score system, HCW was significantly lower for animals with scores of "A+" compared to those with non-abscessed livers. Hot carcass weight least-squares means for animals with no abscesses was 396 kg ± 2.63, and for those with severe abscesses was 391 kg ± 2.92 (P < 0.05). In the second study, 1,492 beef on dairy heifers fed and harvested in Kansas had liver abscess scores and sire information. Nine models were utilized to estimate heritability, all with fixed effects of contemporary group, age in days, and number of bovine respiratory disease treatments. The contemporary group was a concatenation of kill lot and treatment. Models 1, 4, and 7 were from data sets with all sires represented but had liver abscess score represented as a continuous variable, a binary score indicating abscess presence, and a binary score indicating severe abscess ("A+") presence, respectively. Models 2, 5, and 8 followed the same respective scoring systems as Models 1, 4, and 7, but the data set only included heifers from sires with 10 or more progeny. Models 3, 6, and 9 followed the same respective scoring systems as Models 1, 4, and 7, but the data set only included heifers from sires with 100 to 200 progeny in the complete data set. Heritability estimates from a sire model for Models 1, 4, and 7 ranged from 4.26 x 10-8 to 1.06 x 10-7. Heritability estimates from a sire model for Models 2, 5, and 8 ranged from 4.90 x 10-8 to 4.61 x 10-7. Heritability estimates from a sire model for Models 3, 6, and 9 ranged from 1.01 x 10-7 to 2.88 x 10-3. All estimates indicate no genetic component to liver abscess severity or incidence in this data set.
Open Access
Management and benchmarking strategies to improve financial health status of U.S. beef operators
(Colorado State University. Libraries, 2024) Krehbiel, Bethany Cornwell, author; Rhoades, Ryan D., advisor; Ahola, Jason K., advisor; Blackburn, Harvey D., committee member; Mooney, Daniel, committee member
The objective of this dissertation was to obtain, analyze, and summarize historical Standardized Performance Analysis (SPA) benchmark information and subsequently determine significant Key Performance Indicators (KPI) influencing beef producer's Unit Cost of Production (UCOP). Using the KPI's, a Ranch Health Index (RHI) was developed to assist producers in simply analyzing their financial health while analyzing beef production and financial relationships. Lastly, producer information using the significant KPI's incorporated into the RHI was analyzed for sensitivity to explore potential leverage points to enhance overall financial health. The SPA Beef cattle production performance and financial data was obtained from the SPA program conducted by Texas A&M AgriLife Extension which has records from three states: Oklahoma, Texas, and New Mexico. The dataset contained 25 years of beef financial and production metrics from 1992 – 2016. Three models (linear regression, random forest, and step-wise) were used to assess the SPA data for KPI. Upon further analyses, six variables were considered most impactful to predict Unit Cost of Production: Financial Grazing per CWT, Financial Raised/Purchased Feed per CWT, Livestock Cost Basis per CWT, Weaning Pay Weight per CWT, Pounds Weaned, and Number of Adjusted Exposed Females. The RHI was developed from the six variables using a Random Forest machine learning model and their corresponding importance factors as weights in the model. The model selected was tested and showed concordance with all the SPA variables predicting UCOP. Therefore, the RHI results showed utility in usefulness to assess financial health. Subsequently, three producers with 5 consecutive years of data were tested for sensitivity at ± 5% and ± 10% from the original value to determine sensitivity of each KPI variable. Finally, the models were investigated for maximum and minimum RHI values. Results showed changes in RHI up to $13,000 when accounting for all KPI improvements at 10% sensitivity. In conclusion, knowledge of the SPA data and ultimately the RHI provides information to cattle producers on what may be the most indicative variables for enhanced profits. In addition, this research has provided a simple and effective way for producers to analyze their beef operation.
Open Access
Association between beef ribeye area measurements and steak portion size
(Colorado State University. Libraries, 2024) Schiefelbein, Abbey Faith, author; Nair, Mahesh N., advisor; Geornaras, Ifigenia, committee member; Clark, Daniel, committee member; Hess, Ann, committee member
As cattle weights have increased over the past decades, hot carcass weight and ribeye area (REA) have also increased. The REA is an important determinant of carcass value as it impacts the thickness of steaks when portioned to a pre-determined weight. Additionally, previous research has indicated that steak thickness impacts consumers' eating experience potentially due to its impact on the degree of doneness. The objective of this study was to examine the relationship between carcass REA and steak portion size. Beef carcasses (n = 100) were selected from a commercial beef harvesting facility based on REA in 1 in2 (6.45 cm2) increments ranging from less than 11 in2 (70.97 cm2) to greater than 19 in2 (122.58 cm2) based on a United States Department of Agriculture-approved camera (E+V) with 10 total categories. Data (hot carcass weight, back fat thickness, and marbling) were collected from each selected carcass. The REA measurements were obtained using the grading camera, a manual grid, and pen tracing and measured using ImageJ software. Strip loins (IMPS#180) from selected carcasses were collected, and weight, length, and three width (anterior, middle, and posterior) measurements of the strip loins were measured manually. Each strip loin was then scanned through a Marel I-Cut 56 portion cutter to determine the thickness of 12 oz (340.19 g) and 16 oz (453.59 g) portions and to determine the weight of a 1-in (2.54 cm) thick portion. To quantify and describe the relationship between steak thickness (cut to 12 oz and 16 oz portions) and steak weight (cut at 1-in. thickness), linear regression models were developed using traced REA as the independent variable. Additionally, more exhaustive linear regression models were developed to predict steak thickness or weight based on the traced REA, hot carcass weight, fat thickness, strip loin weight, strip loin length, strip loin width, and average maximum height of the strip loin. Each model was evaluated separately for the main effects of each variable, with significance determined at ɑ=0.05. There was a significant (P < 0.001) correlation and linear relationship (P < 0.05) between traced REA measurement and 12 oz (R2 = 0.71), 16 oz (R2 = 0.71), and 1-in.-thick (R2 = 0.75) portions examined in this study. For 12 oz steaks, the steak thickness decreased by an estimated 0.055 in. (0.14 cm) for every 1-in. increase in REA. Similarly, for the 16 oz steaks, the steak thickness decreased by an estimated 0.074 in. (0.19 cm) for every square in. increase in REA. The 1-in. steak portions had a mean weight of 340 g, and the steak weight increased an estimated 18 g for each square in. increase in REA. In addition, using the strip loin measurements, linear regression models were able to predict steak thickness for 12 oz and 16 oz portions with an R2 of 0.95 each and predict the steak weight for the 1-in. portion with an R2 of 0.98. As expected, REA strongly correlated with the portion size of strip loin steaks cut to a specified weight or thickness. Additionally, our results indicated that the weight and length of the strip loin were good predictors of steak thickness (for 12 oz and 16 oz portions) or steak weight (for 1-in.-thick portions). Further research exploring consumer acceptance and degree of doneness for steaks with varying thicknesses would provide data to determine REA ranges and targets that would optimize steak portion sizes and consumer acceptability.
Open Access
Effects of origin on enteric greenhouse gas emissions and growth performance
(Colorado State University. Libraries, 2024) Mesa Gandolfo, María Inés, author; Carvalho, Pedro H. V., advisor; Stackhouse-Lawson, Kim R., committee member; Place, Sara E., committee member; Ritten, John P., committee member
Methane (CH4) emissions from cattle across various origins remain inadequately understood, representing a significant knowledge gap for sustainable beef production. This study investigates enteric CH4 emissions from yearling steers of different origins and under different management practices. The experiment was divided into two phases. In Phase 1, steers were managed according to local practices: grazing in Colorado and confined background feeding in Nebraska and Wyoming. In Phase 2, all steers were moved to a common grazing environment in Colorado. Methane emissions were measured using the Automated Head Chamber System (AHCS). During Phase 1, CH4 emissions and growth performance varied significantly among the groups, influenced by diet and management. Nebraska steers had the greatest CH4 production (MP), while Colorado steers had the least, reflecting differences in diet composition and feed intake. However, CH4 intensity (MI) was similar across all groups due to compensatory differences in average daily gain (ADG). In Phase 2, when all steers grazed under the same conditions, Colorado steers exhibited the greatest ADG and MP, indicating better adaptation and suitability to the grazing system than Nebraska and Wyoming steers. Results suggest that enteric CH4 emissions are influenced by cattle's origin and previous management. This highlights the need for context-specific studies to accurately assess the sustainability and greenhouse gas (GHG) mitigation strategies for grazing beef cattle. Further research should address these variations to improve the accuracy of CH4 emissions estimates in different rangeland ecosystems. This study also evaluated different CH4 prediction equations using various statistical approaches (RMSE, R2, Mean and Slope bias, correlation coefficients, and least square differences). Three equations showed potential for predicting CH4 emissions for the steers of the current study: the one by Ellis et al. (2009), the one by Escobar-Bahamondes et al. (2016), and Moraes et al. (2014). Even though the CH4 estimated by these equations was similar to the observed, there is room for improvement in the development of accurate equations to predict cattle enteric CH4 emissions in grazing systems. Lastly, the animals were ranked in both Phases by their MI and MP, and it was evaluated if the animals changed their ranking in Phase 1 when moved to Phase 2. Animals from all origins experienced shifts in their classification categories, indicating the dynamic nature of CH4 across different contexts. However, it was observed that steers from the Wyoming group exhibited the most significant changes in MP classification categories when transitioning from a confinement system with grain-based diets to a grazing system. Based on the current results, the background of the steers may need to be considered when evaluating sustainability goals in beef cattle production systems.
Open Access
Pre-weaning performance in lambs after nutrient specific restriction in gestation and training cognitive skills to improve integration and application of knowledge in animal physiology
(Colorado State University. Libraries, 2024) Stucke, Rachael, author; Cadaret, Caitlin N., advisor; Ahola, Jason K., committee member; Winger, Quinton A., committee member
Due to seasonal availability and quality of range forage, extensively managed ewes often experience nutrient restriction during gestation. Neonatal lamb performance after severe experimental nutrient restriction during gestation has been well studied; however, there is a gap in understanding of how practical nutrient restriction experienced over the course of a production cycle impacts lamb success. Therefore, the objective of the first study was to investigate early life performance in lambs from ewes fed a diet from 30-125 days of gestation (dGA) that simulates winter forage or one that meets all nutritional requirements for gestation. Maternal BCS and weight losses were evident prior to the standard supplementation period suggesting impacts on the fetus could be happening due to nutrient restriction earlier in gestation. Lambs from dams who received the lower quality diet did not differ by bodyweight but were not able to thermoregulate as well as lambs whose dams had their requirements met during the first week and on specific weeks thereafter. Beginning at six weeks of life through weaning lambs from restricted dams had lower body weights compared to lambs from fully nourished dams. This data demonstrates that nutrient challenge during gestation, even when re-alimented in late gestation, decreases performance. The lamb data showed that while there are no apparent differences in growth during the first week of life, NR animals start to diverge later in life even when provided high quality nutrition. This coupled with reduced thermoregulatory ability suggests tissue specific differences may underlie animal variation and warrants further investigation. Case-based learning immerses students in real-world scenarios, prompting observation, action, and reflection to enhance cognitive skills. The open-ended nature of such learning can challenge students to reach higher levels of critical thinking, however, we have noticed that without guidance, students often do not know how to approach these types of questions. Therefore, the objective of study 2 was to investigate how two low-input interventions strategies may help train cognitive skills and improve student performance. Three semesters of an undergraduate physiology course employed a case-based assessment strategy. Semester 1 (S1) represented no intervention, Semester 2 (S2) included two dedicated class periods of instructor-led guidance on approaching case studies, and Semester 3 (S3) utilized an online peer evaluation platform, where students evaluated and provided feedback to each other. In S2 and S3 pre-surveys were administered to understand changes in students' perceptions of their own cognitive skills. The average grade on case studies after intervention was the highest in S3 where peer intervention was employed. When comparing changes in perceptions, student confidence in their cognitive skills generally increased in S2 and S3. Interestingly, while peer evaluation improved student performance, free response questions indicated that students did not enjoy peer evaluation and felt that it was not beneficial to their learning. Peer evaluation provides a unique opportunity for students to actively engage in the learning process and to practice cognitive skills. This process holds dual benefit as reviewing peers requires students to reflect, analyze, and evaluate, which are cognitive skills also needed to solve the case studies.
Embargo
Transposable elements and early pregnancy in the horse
(Colorado State University. Libraries, 2024) Southerland, Sierra L., author; Coleman, Stephen, advisor; Bruemmer, Jason, committee member; Fedorka, Carleigh, committee member; Pinedo, Pablo, committee member; Chicco, Adam, committee member
Understanding the molecular events and physiological dynamics in the endometrium during early pregnancy is crucial for improving our understanding of reproductive outcomes in horses. Much of the work investigating early pregnancy in the horse has focused on maternal recognition of pregnancy (MRP). This critical signal, which initiates the pathways and regulatory changes to help make the endometrium receptive to pregnancy, remains elusive in the horse. Transposable elements (TEs), once overlooked components of the genome, have been implicated in regulating gene expression during critical stages of embryo and placental development. The current study investigated the expression of TEs during the early phase of pregnancy post-ovulation. The hypothesis tested was that pregnancy status would impact the expression patterns of TE-derived transcripts in the endometrium around the time of maternal recognition. It was anticipated that the TE transcripts would increase in the endometrium of pregnant mares either in response to or as a part of the maternal recognition signal. RNA sequencing data was generated from endometrial biopsies at days 9, 11, and 13 in pregnant and non-pregnant mares. Bioinformatics analyses identified distinct patterns of TE expression across the duration of early pregnancy. Contrary to expectations, these findings did not reveal the accumulation of TE transcripts in the pregnant endometrium compared to the non-pregnant endometrium during early pregnancy. Instead, there was a significant decrease in the number of differentially expressed transcripts over the time points studied. These results challenge the initial assumption and suggest that the regulation of TE transcriptional activity during early pregnancy may be more complex than previously thought, highlighting the need for further research into the roles of TEs in equine reproductive physiology. An alternative explanation for the results of this analysis is that maternal recognition of pregnancy may involve the downregulation of transcripts expressed from TEs, potentially serving as a switch to prevent luteolysis and maintain pregnancy. This study underscores TEs as potential biomarkers and regulators in equine reproduction, providing insights into endometrial processes and offering avenues for improving fertility outcomes and breeding efficiency in horses.
Open Access
The association of lunar phases with pregnancy at first artificial insemination of dairy cows
(Colorado State University. Libraries, 2024) Schatte, Margaret, author; Grandin, Temple, advisor; Pinedo, Pablo, advisor; Keller, Kayleigh, committee member
Myths and old farming legends have circulated the belief that the full moon affects livestock behavior and reproduction. To assess this association in dairy cattle, 13,558 records from 2019 to 2021 at an organic dairy farm in Colorado were analyzed. These records included lactation number, artificial insemination date (AI date), and pregnancy result. AI date was categorized into season and lunar phases. Lunar phases were separated into four equal categorizations: new moon, first quarter, full moon, and third quarter. The primary objective of this study was to identify any associations between the lunar phases and PAI1 (pregnancy rate at first AI). The secondary objective of this study was to use logistic regression to specify which phases had the lowest and greatest PAI1 while accounting for other effects on fertility. Logistic regression was used to complete this by comparing the pregnancy result of lunar phases while accounting for lactation number and season, which are known to affect pregnancy rate. The 4 lunar phase categorizations did have an association on PAI1 (p<0.05). The new moon phase resulted in the lowest PAI1 at 35.3% while the third quarter was the highest at 38.3%. Estimated marginal means were explored to identify the seasonal effect on pregnancy and found that winter had the highest probability of pregnancy and summer had the lowest. This analysis of 3 years of records provides evidence that the week of the new moon is the least probable week out of the month for pregnancy after first AI to occur, while the week before and week of the full moon are the most probable days for pregnancy after first AI to occur within the lunar cycle.
Open Access
Influence of BOVAMINE DEFEND® Plus on growth performance, carcass characteristics, estimated dry matter digestibility, rumen fermentation characteristics, and immune function in finishing beef steers
(Colorado State University. Libraries, 2024) Miller, Alexandra C., author; Engle, Terry E., advisor; Edwards-Callaway, Lily, committee member; Holt, Timothy, committee member
One hundred and eighty crossbred beef steers (406.0 ± 2.2 kg) were used to determine the impact of a novel direct-fed microbial (DFM) on growth performance, carcass characteristics, rumen fermentation characteristics, and immune response in finishing beef cattle. Steers were blocked by body weight and randomly assigned, within block, to 1 of 2 treatments (3 replicates/treatment: 30 steers/replicate). Treatments included: 1) no DFM (control) and 2) DFM supplementation at 50 mg∙animal-1∙d-1 (BOVAMINE DEFEND® Plus). All steers were fed a high-concentrate finishing diet and individual feed intake was recorded daily via the GrowSafe® system. Body weights were collected every 28 d. On d 55, 10 steers per pen were injected with ovalbumin (OVA). Jugular blood samples were collected from each steer on d 0, 7, 14, and 21 post-injection. On d 112, the same steers were injected again with OVA and intramuscularly with a pig red blood cell solution. Jugular blood samples were collected from each steer on d 0, 7, 14, and 21 post-injection. On d 124 rumen fluid was collected from 3 steers per treatment and used to estimate in vitro rumen fermentation characteristics. Equal numbers of steers per treatment were transported to a commercial abattoir on d 145, 167, and 185 of the experiment, harvested, and carcass data collected. Initial body weight (BW) was similar across treatments. On d 28 and 55, steers receiving DFM had heavier BW (P < 0.01) compared to controls. Average daily gain was greater in DFM-supplemented steers from d 0 to 28 (P < 0.01) and d 0 to 55 (P < 0.01) of the experiment compared to controls. Overall dry matter intake was greater (P < 0.04) and overall feed efficiency was similar in DFM-supplemented steers compared to controls. Dressing percentage (P < 0.02) was greater in steers receiving DFM compared to controls. Antibody titers to injected antigens were similar across treatments. However, red blood cell superoxide dismutase activity was greater (P < 0.05) in DFM-supplemented steers compared to controls. In vitro molar proportions of isobutyric and butyric acid were greater (P < 0.01) and dry matter (DM) digestibility tended (P < 0.07) to be greater in rumen fluid obtained from steers supplemented with DFM. These data suggest that BOVAMINE DEFEND® Plus supplementation improves growth performance during the initial period of the finishing phase, increases overall dry matter intake and dressing percentage, and may impact antioxidant status in beef cattle.
Open Access
Effect of hot-iron brand size and meloxicam on behavior, health, and performance of beef calves in a pasture setting
(Colorado State University. Libraries, 2024) Keogh, Lily, author; Edwards-Callaway, Lily, advisor; Cramer, Catie, advisor; Wolfe, Barb, committee member; Engle, Terry, committee member
Animal welfare is of growing importance in beef cattle production and therefore there is heightened interest in regularly practiced, painful management practices. Hot-iron branding is a common method of permanent identification of cattle, created by intense thermal damage to the hide. The main objectives of the study were to quantify the effects of hot-iron brand size and meloxicam on pain related behaviors and health and performance parameters of 2-month-old beef calves on a commercial cow calf operation. A total of 126 calves were enrolled in the study (bulls, n=56; heifers, n=70). Calves were hot-iron branded with one of two iron sizes (small (SM), large (LG)) and administered meloxicam (MEL; dosed for a 113-kg calf at 1mg/kg of bodyweight) or a placebo (PLA)), and castrated (CAS) or not castrated (NCAS), if a heifer calf. Following the treatment application, behavioral observation (2 h periods) using instantaneous scan sampling occurred at 6 h and 24 h post branding; these observation periods (OP) represent the pharmacokinetics of oral meloxicam. A logistic regression (PROC GLIMIX) was used to assess the association between castration status, brand size, medication, observation period, as well as any interactions, on the proportional behavioral outcomes. More LG brand calves were observed standing, lying, and displaying event behaviors as compared to the SM brand calves (P = 0.003, P = 0.011, P = 0.016, respectively). OP affected the display of event and state behaviors, with standing observed more at 6 h and event behaviors displayed more at 24 h (P = 0.0028). Concurrently, CAS and SM or LG branded calves exhibited more event behaviors and standing than NCAS calves (P = 0.022). No effect of the fixed variables on average daily gain (ADG) or morbidity were observed (P > 0.05). MEL did reduce the proportion of branded heifer calves expressing event behaviors as compared to PLA, however it had less of a behavioral impact on the concurrently castrated and branded calves (P = 0.022). The results indicate that pain is present within the 24 h following branding and castration and that concurrent castration and branding elicits a greater behavioral response than only branding. This study highlighted both the feasibility of administering an oral analgesic in a commercial setting and that implementing a smaller brand size may be a strategy to reduce pain associated with hot-iron branding.