bluuebunny/crossref_metadata_2025_split huggingface dataset:
116 Using Theoretical and Realized Accuracies to Estimate Changes in Heritabilities
Authors: Misztal Ignacy , Breen Vivian , Lourenco Daniela 
Published: November 2023

Abstract
Under genomic selection, heritabilities for strongly selected traits are reduced, and antagonism between production and fitness traits can intensify. However, estimating genetic parameters by established methods such as REML or Bayesian with large genomic data is computationally expensive or unfeasible. In this study, we investigated the use of theoretical and realized accuracies to estimate heritabilities. The first dataset for pigs included 161k phenotypic records for a growth trait (GT), 27k phenotypic records for a fitness trait (FT), and 55k animals were genotyped. The second dataset for broilers contained 820K phenotypes for a growth trait (GT), and 154k animals were genotyped. Theoretical accuracies (r) were calculated as r = sqrt(Nh2/(Nh2+Me)) assuming the number of independent chromosome segments (Me) of 5k and the number of observations (N) equal to the number of genotypes or phenotypes, whichever was smaller. Estimated accuracies were calculated by the linear regression (LR) method. Assumed heritabilities were recent estimates for pigs (0.21 for GT and 0.04 for FT) and an older estimate for broilers (0.30). For the pig dataset, the theoretical and realized accuracies were similar: 0.82 and 0.84 for GT, and 0.42 and 0.43 for FT, suggesting that the assumed heritabilities were realistic. For the broiler dataset, the theoretical and realized accuracies differed: 0.94 and 0.56, indicating possible large differences between real and assumed heritabilities. Both accuracies could be made equal at 0.89 by assuming a heritability of 0.13. Such a heritability was also found to provide a realistic estimate of the genetic gain with recent data. Comparisons of theoretical and realized accuracies may be used as a tool to estimate changing heritabilities over successive generations at a low cost. Similar formulas may enable low-cost estimation of genetic correlations.
134 Estimating the Heritability of Nitrogen and Carbon Isotopes in the Tail Hair of Beef Cattle
Authors: e Silva Luis Prada , Moradi Morteza , Warburton Christie 
Published: November 2023

Abstract
The natural abundance of nitrogen isotopes (δ15N) in animal tissues is related to the ability of cattle to lose less nitrogen in the urine and has been used to estimate nitrogen use efficiency and feed efficiency. Carbon isotope enrichment (δ13C) has also been used to estimate feed conversion ratio and grazing behavior in beef cattle. There are significant variations between the individual beef cattle in the same environment for δ15N and δ13C of the tail hair. Thus, the objective was to determine the heritability of δ15N and δ13C in the tail hair of tropically adapted beef cattle to further validate their use in genetic breeding programs. A total of 497 Bos indicus steers (269 Brahman and 228 Droughtmaster) were used, and the steers had reliable pedigree information for three generations as they were part of the beef cattle genetic evaluation system in Australia. Two single, mixed breed, contemporary groups of steers are used including the steers weaned in 2019 (n = 254) and steers weaned in 2020 (n = 243). Samples of tail switch hair representing hair segments growing during the dry season were collected and analyzed for δ15N and δ13C. Fixed effects fitted in the linear regression model were age, breed, year (as contemporary groups), and average daily gain during the different seasons. The heritabilities of δ15N and δ13C in the tail hair were estimated at 0.43 ± 0.14, and 0.41 ± 0.15, respectively, which indicates both are moderately heritable traits. The genetic correlation between δ15N and δ13C was negative at -0.78 ± 0.16, and the phenotypic one was -0.40 ± 0.04. The negative correlation can be explained by the contrasting isotope fractionation in the urine of cattle, as urine has less δ15N and more δ13C than the diet. The findings of this study have shown for the first time that both δ15N and δ13C in the tail hair of cattle are heritable traits. These results support the feasibility of utilizing tail hair isotopes as a promising approach for identifying cattle with greater nitrogen use efficiency, which is a key trait in low-protein diets. Moreover, genetic selection for nitrogen-efficient cattle can reduce the environmental impact of beef production.
136 Evaluation of the Relationship Between Hair Coat Shedding Ability, Apparent Forage Digestibility, and Mineral Status in Angus Cattle
Authors: Loftin Margaret P , Burnett Randy , Rude Brian , Smith Trent 
Published: November 2023

Abstract
The objective of this study was to evaluate the relationship between winter hair coat shedding ability, apparent forage digestibility, and mineral status in Angus females. Data were collected on fall calving purebred Angus females with calves from March until July in 2019 (n = 10), 2020 (n = 31), 2021 (n = 39), and 2022 (n = 41). Dams were observed once monthly by two trained technicians for winter hair coat shedding and were given a visual score of 1 to 5 with 1 indicating complete shed and 5 indicating no shedding of the winter hair coat. Month of first shed (MFS) was determined when a female reached an average winter hair shedding score of &gt; 3.5 for any given month. Fecal samples were collected during the grazing months of March, May, and July for 5 consecutive days and were then analyzed via proximate analysis to calculate apparent digestibility of dry matter (DM), ash, acid detergent fiber (ADF), and neutral detergent fiber (NDF) of forage. Liver and blood plasma samples were collected during the grazing months of March and July and analyzed via ICP-OES for mineral concentrations of K, Ca, Mg, Na, Fe, and Zn. Data were analyzed using the MIXED procedure of SAS with a significance declared at P &lt; 0.05. The model included MFS, grazing month, and MFS by grazing month interaction. Interactions of MFS by month were observed for DM, NDF, ADF and liver Fe concentration. For DM, NDF, and ADF, within the grazing month of May, individuals with MFS in April and May were similar and greater when compared with June and July which were similar. Interpretation of these results show no clear trend of an association between hair shedding ability and apparent digestibility; however, some differences based on MFS existed. Further research into this area is important in understanding changes in overall cow performance due to adaptability.
133 Genetic Parameter Estimation for Dry Matter Required in Angus Cattle
Authors: Sánchez-Castro Miguel A , Passafaro Tiago L , Bernal-Rubio Yeni L , Andersen Kent J , Donald Nkrumah J , Jorgensen Nicholas 
Published: November 2023

Abstract
Dry matter intake (DMI) is critical to determine feed efficiency in cattle. However, this trait is expensive and difficult to measure on an individual basis. An alternative to overcome such limitations is to approximate DMI by using mathematical models to estimate the dry matter required (DMR) for animals originally fed in groups. High genetic correlations (e.g., rg&gt;0.95) have been informed between DMI and DMR. Thus, DMR has been proposed as an indicator trait for DMI in genetic evaluations. Few reports exist about genetic parameters associated to DMR and, when available, estimates have been obtained with datasets of limited size (~1,500 animals with phenotypes). Additionally, previous reports have focused on older animals during the finishing phase, such that mathematical models employed to derive DMR have not explicitly accounted for the presence of weaner calves on the data. Therefore, the objective was to estimate genetic parameters for DMR using a moderately large dataset that included weaning and yearling Angus bulls. A total of 8,121 records of estimated DMR were available for analyses. From these records, 6,324 belonged to weaned males whose phenotype was obtained using an equation proposed by NRC to predict DMR for calves. The 1,797 remaining records pertained to yearling bulls for which a different NRC equation was employed. First, a single-trait animal model was implemented to estimate genetic parameters for DMR, with contemporary group (defined as year of test and pen within the testing facility), test length and age of the animal when entering to the test (linear covariate) being included as fixed effects, while animal was considered a random effect. Afterwards, a bivariate model that included weaning weight (WW) as a correlated trait was implemented. In this model, the same effects were included for DMR but for WW, fixed effects included sex, weaning contemporary group and age of dam (BIF classes), while direct genetic, maternal genetic, and maternal permanent environmental effects were considered as random. For both models, a reduced pedigree was used to estimate variance components by tracing back 5 generations from animals having phenotypes. A total of 12,212 and 56,023 animals were included in the univariate analysis and the bivariate analysis, respectively. Heritability (h2) estimates (± SE) for DMR were 0.43 (± 0.04) and 0.49 (± 0.03) under univariate and bivariate model, respectively. Genetic correlation between DMR and WW was 0.69 (± 0.03), with a h2 estimate of 0.29 (± 0.01) for WW. Heritability estimates for DMR obtained with both models resembled those of DMR reported in literature. Results suggested that substantial additive genetic variation exists for DMR and, consequently, indirect genetic progress for DMI can be attained if selecting for DMR. Further studies are required to validate DMR as an indicator trait for DMI in larger Angus populations.
152 Leveraging Rfid Technology to Investigate the Genetic Associations Between Feeding Behavior and Leg Health in Floor-Raised Broilers
Authors: Carvalho Alves Anderson A , Araujo Fernandes Arthur F , Breen Vivian , Hawken Rachel , Rosa Guilherme J M 
Published: November 2023

Abstract
Leg disorders (LD) pose serious welfare issues in broiler chickens. The objective of this study was to investigate the suitability of using feeding behavior (FB) traits as potential leg health indicators in floor-raised broilers. The data used were recorded from 95,711 pure-line chickens of both sexes. The individual FB was monitored continuously on a feeder visit basis with a radio-frequency antenna system. The visit-log data were clustered into daily observations for different FB traits and averaged for the 1st week period after the trial started. The FB traits were daily feed intake (DFI1), number of visits (NV1), time spent at the feeder (TSF1), visiting activity interval (VAI1), number of visited feeders (NVF1), and walked distance visiting feeders (WD1). The LD traits were tibial dyschondroplasia (TD), hock-burn (HB), footpad (FP), rotated legs (RO), bowed-in (BI), and bowed-out (BO) leg structure deformities. Multi-trait linear-threshold models were fitted using Bayesian inference for estimating (co)variance components. The heritability (h2) posterior averages and standard deviations (within parentheses) ranged between 0.09 (0.01) and 0.52 (0.03) for LD traits, and between 0.09 (0.01) and 0.47 (0.02) for FB traits. Genetic correlations (rg) between FB and LD traits ranged from null to weak. TD presented negative rg with NV1 (-0.13), TSF1 (-0.14), NVF1 (-0.11), and WD1 (-0.14), indicating that some alleles involved in broiler activity are favorably associated with a potential reduction in the risk of TD-caused bone lesions. Conversely, FP presented unfavorable rg with the same traits (ranging from 0.21 to 0.32), except for TSF1 (-0.08). When compared with the remaining FB traits, DFI1 generally presented the opposite relationships with TD and FP, with positive (0.16) and negative (-0.18) genetic correlations observed for the first and the latter, respectively. Angular and rotational deformities (RO, BI, and BO) did not present significant correlations with FB traits, apart from the weak correlation found between BO and TSF1 (0.11). General activity indicators such as NV1, NVF1, and WD1 could represent earlier selection criteria to reduce TD incidence, although the potential undesired selection response for FP must be further investigated.
96 Animal Genomes to Phenomes: Funding and Perspectives from Usda-Nifa
Authors: Van Goor Angelica G , Sullivan Timothy , Tobias Christian 
Published: November 2023

Abstract
The National Institute of Food and Agriculture (NIFA) is the extramural science-funding agency of the USDA that invests in and advances agricultural research, education, and extension to solve societal challenges. Animal genome to phenome (G2P) research is an important area of investment at NIFA. This presentation aims to: 1) highlight past investments in animal G2P; 2) discuss the alignment of animal G2P within current USDA and NIFA priorities; 3) bring awareness to Multistate Committee opportunities; 4) highlight current funding opportunities; and 5) provide perspectives on the future of animal G2P at NIFA with attention to the central dogma of phenomics.
166 Pre-Weaned Calves Have Increased Cortisol Concentrations Post-Wildfire Smoke Exposure
Authors: Ranches Juliana , Hernandez Gracia M P , Santos Aline R , Ferreira Matheus , Cruickshank Jenifer 
Published: November 2023

Abstract
The western states of the U.S., home to some of the largest cattle operations in the country, are increasingly experiencing losses related to wildfire events. Wildfires are predicted to intensify with climate change; rising temperatures, droughts, and drier climatic conditions. Although wildfires do not directly endanger most humans and animals, the resultant smoke can disperse great distances and increase disease susceptibility and death in populations removed from its origin. There is a lack of literature on how wildfire smoke exposure can affect livestock physiology, health, and productivity. Therefore, this study aimed to evaluate changes in blood markers of cattle naturally exposed to wildfire smoke. Eighteen beef-on-dairy calves (Jersey X Simmental) from a commercial farm were enrolled in this study at birth (May to June 2022). Blood samples for analysis of cortisol, acute phase proteins, and pro- and anti-inflammatory cytokines were collected before (June to August), during (September), and after smoke exposure (September and October), in a total of seven collections. Additionally, rectal temperature and health scores were collected from each calf at those time points. Air quality (AQ) data, specifically particulate matter (PM2.5; EPA standard for AQ; 35 µg/m3) near the study location (Vale, OR), was obtained from the AirNow database. For statistical analysis, calf was considered the experimental unit, and all data were analyzed using the MIXED procedure of SAS (SAS Inst. Inc., Cary, NC). Air quality before smoke exposure was considered adequate, and PM 2.5 was, on average, 4.9 µg/m3 from June to August. In September, a wildfire reduced AQ at the study location, increasing PM 2.5 to an average of 44.6 µg/m3 for four consecutive days. After the fire was contained, AQ improved, and PM2.5 dropped to 8.6 ug/m3. Blood cortisol concentrations changed over time (P &lt; 0.001). Cortisol concentrations of samples collected before smoke exposure did not differ (P = 0.89) at 4.4, 2.0, and 1.9 ng/mL (SEM:1.3). Cortisol concentrations increased (P &lt; 0.001) and peaked during smoke exposure, at 10.3 and 7.0 ng/mL (SEM:1.4). Immediately after smoke exposure, cortisol concentrations averaged 6.3 ng/mL, intermediate between those before and during smoke exposure (P = 0.89; SEM:1.3). Interestingly, in the last post-smoke exposure sample, cortisol concentration averaged 9.5 ng/mL, similar to concentrations during smoke exposure (P = 0.99; SEM:1.3). This increase in cortisol concentration post-smoke exposure was unexpected but likely explained by the calves having been weaned two days before this final sampling. In summary, calves naturally exposed to wildfire smoke had increased blood cortisol concentrations with concentrations similar to those observed shortly after post-weaning, a practice known to be challenging and stressful for calves.
103 Development of a Novel, Experimental, Minimally Invasive Model to Investigate the Genesis and Etiology of Liver Abscesses in Cattle
Authors: Broadway Paul R , Nagaraja T G , Lawrence Ty E , Amachawadi Raghavendra G , Carroll Jeffery A , Sanchez Nicole C Burdick , Galyean Michael , Hales Kristin E 
Published: November 2023

Abstract
Most research surrounding liver abscesses involves post-hoc evaluation of naturally occurring abscesses in production settings. Few studies have been designed to experimentally induce abscesses with the purpose of identifying a time course, causality, and associated physiological implications. Therefore, we set out to develop a minimally invasive, reliable, and repeatable model to induce liver abscesses in calves in a controlled research environment to elucidate the genesis and etiology of the disease, with the ultimate goal of developing abscess reduction strategies. Experiment 1 was an attempt to induce abscesses by intraruminal inoculation with Fusobacterium necrophorum, Salmonella lubbock, and Truperella pyogenes (FST) following an intravenous lipopolysaccharide challenge. Holstein steers were harvested 3- and 10-d after inoculation, but no abscesses were detected. Experiments 2 and 3 involved diet manipulation by cycling calves on and off a high-starch, acidotic diet followed by intraruminal inoculation of microbes. In Experiment 2, Holstein calves were fed a negative control diet, an acidotic diet, and an acidotic diet plus bacterial inoculation with FST. No abscesses formed in the control or acidotic diet calves, but 43% of calves fed the acidotic diet with FST inoculation formed liver abscesses, suggesting that acidosis alone is insufficient to produce abscesses. In Experiment 3, treatments consisted of Holstein steers fed a negative control, an acidotic diet, an acidotic diet plus ruminal Fusobacterium necrophorum (F), and an acidotic diet plus Fusobacterium and Salmonella (FS). Again, there were no abscesses in the control or calves fed an acidotic diet alone; however, 40% of calves receiving F presented with an abscess, and 50% of the calves that received FS presented with abscesses. These data suggest that ruminal acidosis in conjunction with a ruminal load of pathogens commonly associated with liver abscesses provides a model that will induce liver abscesses. While the role of barrier dysfunction in the rumen and the lower gastrointestinal tract in formation of abscesses is not fully understood, this work provides a foundation to further explore the etiology of this disease and potential mitigation strategies.
178 Tag Your It: Use of Wearable Biometric and Remote Sensing Technology to Monitor Animal Growth, Performance, and Efficiency in Extensively Managed Landscapes
Authors: Parsons Ira L , Webb Stephen , Karisch Brandi B , Stone Amanda E , Street Garrett 
Published: November 2023

Abstract
Energy budgets in grazing cattle are notoriously difficult to study given complex environmental and physiological interactions between plants and animals, each operating according to individual grazing budgets. However, these synergistic energy pathways can be modeled using a series of mechanistic relationships describing forage resource distribution and animal behavior, each which can be observed with high levels of accuracy and precision using biometric sensors and remote sensing technology. The objective of this study is to demonstrate the coordination of data inputs into a coherent framework utilizing biometric and remote sensing technology. Crossbred steers (n = 10) were fitted with GPS and video tracking collars (Vectronic) and accelerometers (Wildbytes technologies), then managed for 286 days as part of a broader research grazing ecology project on pasture (~11.54 hectare) comprised of bermudagrass (Cynodon dactylon) and tall fescue (Festuca arundinacea) and equipped with an automated walk-over-weigh (TruTest) scale system. Distribution of forage quality was sampled monthly with a ½ m2 quadrat using a 20 x 20-meter grid (n = 297) and remotely assessed via an unmanned aerial vehicle (Matrice 100) mounted hyperspectral camera (MicaSense) at 8 cm resolution. Animal behavior was predicted utilizing a trained randomforest prediction algorithm, and linked to geo-location and forage quality at the spatial-temporal scale in Program R. We then constructed animal ethogram, distribution of forage quality, and spatial-temporal distribution of animal behavior across the grazing landscape for a test period. We found steers allocated the greatest proportion of time to grazing and resting behaviors, 30 and 60% respectively, with the remainder dedicated to ruminating and walking behaviors. A diurnal, circadian rhythm in animal behavior demonstrates that steers grazed between 0900 and 1000 in the morning, and again between 1300 and 2000 in the evening, while resting behavior dominated the hours between 0300 and 0900, with a slight increase in grazing behavior noted at 0600, or approximately sunrise. Animal behavior linked forage availability showed steers selectively grazed areas with higher NDVI signatures, while seeking sources of water and cover to practice resting behavior. Given the need to develop robust models predicting forage intake and energy in grazing animals to improve sustainability and environmental metrics, animal tracking and biometric technologies offer a vital solution to improving management of extensively managed grazing livestock.