bluuebunny/crossref_metadata_2025_split huggingface dataset:
85 Genomic regions associated with electronic measures indicative of structural soundness in pigs
Authors: Rohrer Gary A , Ostrand Lexi , Rempel Lea A , Keel Brittney N , Schmidt Ty B , Mote Benny E 
Published: September 2024

Abstract
The objective was to determine the genetic factors influencing mobility traits recorded from 5 mo-old gilts. Mobility was measured using a pressure-sensing mat (GAIT4) and 7 d of video recorded activity (NUtrack). Gilts (n = 3,659) were evaluated for the study, but only 2,172 gilts had data for both systems. GAIT4 system creates a series of measurements for each foot related to pressure, duration and step length of each foot generating a lameness score for each foot. Traits studied summarized values for all 4 feet: average stride length, average stance time, standard deviation of stance time, lameness score and total scaled pressure. NUtrack measurements were rotations, velocity, and distance walked as well as the time spent eating, sitting, standing, lying sternal and lying lateral. All NUtrack traits were standardized to a mean of zero and standard deviation of 1.0 based on each pen-day subgroup. Mixed model analyses were conducted in R fitting animal as a random effect and fixed effects of breed of sire and contemporary group, with day included for NUtrack data. ssGBLUP analyses were conducted in WOMBAT using animal effects from R models as phenotypes. Three generations of pedigree were included and genotypic data from the NeoGen Porcine 50K beadchip on 3,186 animals representing 60% of gilts with NUtrack data, 67% of gilts with GAIT4 data and most parents (&gt;99%). Single trait analyses were conducted for all traits, gEBVs estimated and then SNP effects estimated by back-solving equations. Significance values were determined by 5,000 permutations and a Bonferroni adjustment factor applied. Estimates of heritability ranged from 0.08 to 0.41 and traits from the NUtrack system tended to have greater heritability than GAIT4 traits. There were 343 significant SNP effects in 39 unique chromosomal regions. There were 133 significant SNP associations located on chromosome 14 between 45-47 Mb associated with rotations, distance and times standing and lying. Pathway analysis identified proteoglycan and apelin pathways to be over-represented based on associations with SNP located at 2:45, 2:51, 13:79 and 14:40 (SSC:Mb). Proteoglycans are a subunit of cartilage and apelins affect blood flow and angiogenesis which make them candidates for the development of osteochondrosis, a leading cause of lameness in pigs. These results will facilitate selection of more robust animals capable of withstanding commercial production environments and group sow housing. USDA is an equal opportunity employer.
117 Population structure and genetic diversity of U.S. Polypay Sheep in the National Sheep Improvement Program
Authors: Wilson Carrie S , Petersen Jessica L , Brito Luiz F , Freking Brad A , Nilson Sara M , Lewis Ronald M 
Published: September 2024

Abstract
The development of the Polypay breed focused on improving the lifetime productivity of the Western range ewe with the objective of ewes lambing twice a year starting at 1 yr of age. The Polypay was developed at the U.S. Sheep Experiment Station (USSES) in 1968 as a four-breed composite with 25% each of Dorset, Rambouillet, Targhee, and Finnsheep. The breed is versatile and rugged enough to be used extensively in Western sheep production and throughout the Central and Eastern U.S. in intensive accelerated lambing systems. Our objective was to define the current population structure and genetic diversity in this breed using pedigree- and genomic-based methods as the industry adopts genomic selection. Pedigree records from Polypay breeders participating in the National Sheep Improvement Program representing 193 flocks were combined with pedigree records from USSES (n = 162,997) tracing back to the origins of the breed. A subset of these pedigreed sheep from 32 flocks born from 2011 to 2023 were genotyped with the GGP Ovine 50K BeadChip (n = 1,856). Quality control measures were applied for marker and animal call rates and to remove markers in high linkage disequilibrium. Pedigree completeness and quality was 9.6, 2.3, and 4.6 for mean maximum, mean complete, and mean equivalent generations, respectively. Pedigree-based inbreeding for the full data was 2.19%; for the subset of pedigreed animals also genotyped, it was 2.94%. The rate of inbreeding was consistently 0.07%/yr across years (P = 0.88). Measures of genomic inbreeding for genotyped sheep were 1.26% for Wright’s inbreeding coefficient, measured as heterozygote deficiency, and 2.90% for inbreeding based on runs of homozygosity. Ten rams from 8 flocks contributed up to 20.3% of the current gene pool. Pedigree-based measures of effective population size ranged from 70 to 249 while the genomic estimate was 118. Fixed and rare (≤ 0.01) alleles accounted for 3.2% and 1.4% of the markers, respectively. The majority of runs of homozygosity (72.1%) were less than 6 Mb, indicative of founder effects and ancient inbreeding rather than recent inbreeding. Based on principal component (PC) analysis, PC 1 suggested a separation of USSES sheep from the rest. Model-based population structure showed differentiation among flocks as did Wright’s Fixation Index (FST) values with a mean of 0.07. High levels of genetic diversity exist in the Polypay as demonstrated by low inbreeding, high heterozygosity, and large effective population sizes. Population substructure exists in the population as shown by PC analysis, model-based population structure, and FST values. These parameters indicate that sufficient genetic diversity is present to move forward with genomic selection. Genetic diversity measures should be revisited periodically once genomic selection is implemented in the breed. USDA is an equal opportunity provider and employer.
205 An autosomal recessive mutation in PYGM causes myophosphorylase deficiency in composite cattle
Authors: Batt Mackenzie C , Venzor Leila G , Gardner Keri , Reith Rachel R , Roberts Kelsey A , Herrera Nicolas J , Fuller Anna M , Sullivan Gary A , Mulliniks Travis , Spangler Matthew L , Valberg Stephanie J , Steffen David J , Petersen Jessica L 
Published: September 2024

Abstract
Between 2020 and 2022, eight calves (6 heifers, 2 bulls) in a Nebraska herd (composite Simmental, Red Angus, Gelbvieh) experienced exercise intolerance during extended physical activity. These calves exhibited an inability to keep pace with the rest of the herd, with some eventually succumbing to physical collapse from which they did not recover. Increased creatine kinase, an indication of muscle degeneration, was confirmed in biopsy and necropsy samples. Available sire pedigrees revealed a common paternal ancestor within 2 to 4 generations in all the affected calves. Dam pedigrees were unavailable; however, the herd retained replacement females that occasionally shared common ancestors with breeding bulls. Thus, a de novo autosomal recessive mutation was hypothesized as the cause of exercise intolerance in these calves. Genomic data (100K SNP) from 6 affected calves and 715 herd mates were initially used for a whole genome-wide association study, pinpointing a significant region on chromosome 29. Whole-genome sequencing of 2 affected calves combined with 145 other sequenced cattle led to the identification of a nonsense mutation in the PYGM gene, also located on chromosome 29. The mutation, confirmed to be present in the skeletal muscle transcriptome, was predicted to produce a premature stop codon. The protein product of PYGM, myophosphorylase, has a crucial role in metabolizing glycogen stored within skeletal muscle to generate energy for muscle cells. As a result, the recessive genotype led to greater (P &lt; 0.05) glycogen concentrations in affected calves (n = 2) compared with heterozygous animals (n = 3) and wild-type controls (n = 2). Immunohistochemistry and label-free quantitative proteomics analysis confirmed the absence of the PYGM protein product in skeletal muscle. Myophosphorylase is needed for efficient glycogen utilization, which is crucial for producing high-quality beef. In the 2 affected calves harvested, increased skeletal muscle glycogen persisted postmortem, resulting in increased pH and dark-cutting beef, which is associated with a negative consumer perception and economic losses to the industry. In addition to identifying the cause of exercise intolerance and welfare concerns in these cattle, this study is among the first to identify a specific genetic mutation associated with dark-cutting beef. Carriers of the mutation did not display any discernible differences in meat quality or measures of animal well-being. While cattle heterozygous for the mutation may not immediately impact the beef industry, identifying carriers is paramount for implementing proactive selection and breeding strategies to prevent the production of affected calves.
347 Quantifying phenotypic and genetic variation for cow fertility phenotypes in American Simmentals using total herd reporting data
Authors: Catrett Cassidy , Moorey Sarah , Beever Jonathan E , Rowan Troy N 
Published: September 2024

Abstract
Inefficiencies in reproduction are the largest drivers of loss in United States beef production. Nearly all reproductive traits are at least modestly heritable, making genetic selection and improvement possible over the long term. Cow-centric reproductive traits present unique challenges, as they are not expressed in male animals and will not be observed until later in the productive life of a female, if at all. This makes cow-centric fertility traits ideal candidates for selection with Expected Progeny Differences (EPDs). We used a commercially generated dataset from the American Simmental Association (ASA) to explore the phenotypic and genetic variation in these traits. The dataset comprised Total Herd Enrollment (THE) records, which required unbiased reporting of enrollment, calving, and disposal for 303,158 females (132,403 cows and 170,755 heifers). Using the THE data, we calculated three continuous and two discrete traits that are indicators of heifer and cow fertility and rebreeding ability. These traits were: 1) calving date (calving date of the cow relative to the start of the calving season), 2) calving interval (days between calves), 3) first calving interval (calving interval observation between the first and second calving record for a female), 4) heifer pregnancy (did the animal calve as 2-yr-old?), and 5) discrete early calving (did animal calve in the first 30 d of the calving season?). We observed a significant difference in calving date in mature cows that calved in the first 30 d of the calving season of their contemporary group as heifers compared with those that calved later (Table 1). Early calving heifers averaged a nearly 10 d sooner calving date throughout their productive lives compared with those that calved after 30 d as heifers (29.9 d vs. 40.2 d, P-value &lt; 0.01). We used a combined pedigree and genomic approach, implemented in GIBBSF90+, to estimate genetic, environmental, and permanent environmental variance components. We estimated heritabilities of 0.24 (± 0.037215) for heifer pregnancy, 0.06 (± 0.009265) for calving date, 0.07 (± 0.015451) for discrete early calving, 0.04 (± 0.003954) for calving interval, and 0.04 (± 0.009604) for first calving interval. We observed positive phenotypic and genetic correlations between these traits, ranging from 0.01 to 0.96 (Table 2). This work provides an extensive population survey of phenotypic trends in reproductive performance and management in a large seedstock population. The heritable nature of the inspected traits motivates further work in understanding their genetic architectures and how they are affected by heterosis in crossbreeding programs.
348 Repeat breeding syndrome: Dexamethasone decreases the prevalence of anti-sperm antibodies in dairy cows
Authors: Cockrum Rebecca R , McGehee John , Duncan Jane , Daniels Kristy M 
Published: September 2024

Abstract
Cows that require greater than two inseminations to conceive are diagnosed with repeat breeding syndrome (RBS). Anti-sperm antibodies (ASA) in serum are in greater abundance among individuals exhibiting fertility challenges. In humans, treatment with glucocorticoids has been shown to decrease the prevalence of ASA and improve fertility. Therefore, the purpose of this study was to determine the impact of dexamethasone on ASA and pregnancy outcomes in RBS cattle. Holstein multiparous cows (n = 18) diagnosed as having RBS were randomly allotted to one of three treatment groups: Control (C; n = 6), low dexamethasone (LD; n = 6) and high dexamethasone (HD; n = 6). Intramuscular injections of saline (C), 0.05 mg/kg of BW of dexamethasone (LD), or 0.10 mg/kg of BW of dexamethasone (HD) were administered daily starting 4 d prior to insemination (d 0) through insemination (d 4). All treatment volumes were standardized with saline to achieve the same treatment level. Blood was collected on d 0, 4, 8 and 18, with serum extracted on d 0 through 8. Additionally, milk weights were recorded until d 34. For breeding, cows were synchronized using the Double Ovsynch protocol and only one insemination was conducted at the time of breeding. The MIXED procedure in SAS was used to determine the relationship of treatment with the repeated measures of ASA abundance and milk yield. Additionally, a non-parametric chi-square analysis was conducted in SAS using PROC GENMOD to determine the relationship of treatment with immune cell count and pregnancy outcomes. Day, Treatment and Treatment × Day were designated as fixed effects, and a protected post hoc analysis was conducted to account for multiple comparisons. Anti-sperm antibodies tended to decrease (P ≤ 0.082) as dexamethasone increased compared with C, however, there was no Treatment × Day interaction. Daily milk yields for both LD and HD decreased (P &lt; 0.002) compared with C cows, but there was no interaction with day. Though there was an effect for Treatment × Day (P ≤ 0.002) for white blood cell count, percentage lymphocytes, eosinophils, and neutrophils, there was no effect of treatment (P ≥ 0.181). Therefore, interaction differences were largely driven by day (P &lt; 0.001). Surprisingly, there was a trend (P = 0.069) for an increase in pregnancy rates for C cows compared with LD and HD cows. In fact, one-half of the C cows achieved pregnancy compared with just one cow for LD and HD treatments. Overall, dosage of dexamethasone did not differ for ASA or pregnancy outcomes. However, dexamethasone did decrease ASA but did not increase pregnancy rates. Based on these results, we suggest that alternative treatment measures should be explored to improve pregnancy rates in RBS cows.
343 The relationship between pulmonary arterial pressure phenotypes and oxygen consumption in beef cattle
Authors: Griffin MacKenzie L , Speidel Scott E , Place Sara E , Stackhouse-Lawson Kimberly R , Holt Tim N , Giess Lane K , Zuvich Miranda L , Enns R Mark 
Published: September 2024

Abstract
The objective of this study was to determine if a phenotypic relationship between pulmonary arterial pressure (PAP) and oxygen consumption exists in beef cattle. Pulmonary arterial pressure is used as an indicator of pulmonary hypertension in cattle which is indicative of the susceptibility to both high-altitude disease and feedlot heart failure of an individual. Cattle with greater PAP are typically hypoxic and have initiated expression of compensatory mechanisms their cardio-pulmonary systems employ to combat this alveolar hypoxia. In turn, this causes an increase in PAP and, ultimately, right-sided heart failure. If hypoxic individuals consume more oxygen as a compensation mechanism, oxygen consumption as a trait could be used as an indicator of the prediction of PAP and feedlot heart failure and would be especially useful for cattle in deep phenotyping systems. Data used in the study included cattle with PAP measures on a total of 132 individuals. The data consisted of both steers (n = 99) and heifers (n = 33) from a ranch located in southern Wyoming at an elevation of approximately 2,195 m. After weaning on the ranch, cattle were transported to Colorado State University’s Agriculture Research, Development and Education Center located in Fort Collins, CO (elevation: 1,558 m). Oxygen consumption was measured using a Greenfeed system (C-Lock, Rapid City, South Dakota). To determine if a relationship exists between oxygen consumption and PAP, a simple linear regression model was used to regress PAP on average daily oxygen consumption. Effects included in the model were sex and phenotypic PAP. Average daily oxygen consumption was measured in kilograms per day and averaged 6.6 ± 1.66 kg with a range of 2.3 to 10.45 kg. Pulmonary arterial pressure averaged 42.6 ± 7.96 mm Hg and ranged from 33 to 81 mm Hg. In this data, sex did not account for a significant amount of variability in phenotypic PAP (P &gt; 0.05). Oxygen consumption did account for a significant amount of variability in PAP (P &lt; 0.05), and it was found that with every 1 kg increase of oxygen consumption, PAP is estimated to increase 1.02 mm Hg. These results indicate that a statistical relationship between oxygen consumption and PAP exists. Although these findings suggest that greater oxygen consumption leads to greater PAP, further research is required to fully comprehend the relationship between beef cattle PAP and oxygen consumption.
345 Breed differences within heart scores of fattening feedlot cattle
Authors: Kukor Isabella , Enns R Mark , Holt Tim N , Cleveland Matthew , Sardella Grant , Holland Ben P , Word Alyssa B , Ellis Guy , Theurer Miles , Speidel Scott E 
Published: September 2024

Abstract
Feedlot heart disease (FHD) is a condition in fattening beef cattle that arises from right-side heart remodeling resulting from alveolar hypoxia. This hypoxic environment is hypothesized to result from the large body mass of fattened cattle. Sensitive cattle have increased incidence of pulmonary hypertension resulting from compensation mechanisms of the individual. The severity of this remodeling is quantified at harvest by gross examination of the heart utilizing a visual grading system of 1-5, where a score of 1 is a normal heart and a score of 5 is a severely remodeled heart. Previously, heart score was found to contain sire differences and to be moderately heritable. This led to more questions regarding other potential factors influencing heart scores, one of which was breed differences. Therefore, the objective of this study was to examine the prevalence of heart remodeling in beef and dairy cattle breeds and to investigate whether some breeds had a greater prevalence of heart remodeling. Heart scores were collected on Angus-influenced animals raised in the panhandle of Texas (1,103 m) and a Beef x Dairy group raised in western Kansas (846 m). The total number of animal observations was 2,069. Twenty-four percent of the individuals exhibited moderate to severe remodeling (score 3 and greater). Of this cohort, 1,307 animals had breed composition data (i.e., Angus, Simmental, Jersey, and Holstein) suitable for use in the analysis. Breed proportions ranged from 0% to 100% for Angus, 0 to 93.25% for Simmental, 0% to 69.22% for Jersey, and 0% to 78.06% for Holstein. Utilizing a linear regression model with heart score as the response and breed percentages and heart scorers as fixed effects, the importance of breed composition (covariate) was determined. The percentages of Angus influence tended to be associated with heart score (P = 0.0506), with a regression coefficient of -0.005. The percentage of Simmental had an association with the variation in heart score (P &lt; 0.05) and had a regression coefficient of -0.008. Additionally, the percentages of Jersey and Holstein were found to reduce the incidence of heart score by a factor of -0.014 and -0.018 (P &lt; 0.05), respectively. In summary, an increased percentage of either Jersey or Holstein breed resulted in reduced heart scores, while the incidence of beef breeds was found to be associated with some to little difference in the improvement of heart scores, alluding to potential breed advantages in mitigating right sided heart remodeling.
313 Many farmers want a prediction of future performance, not necessarily breeding potential
Authors: Berry Donagh P 
Published: September 2024

Abstract
High heritability is a characteristic of many performance traits in cattle translating to a relatively strong correlation between an (accurate) estimated breeding value for an animal and its (future) production potential. However, the broad sense heritability (i.e., numerator in the formula includes both additive and non-additive genetic variance) is often larger than the narrow sense heritability (i.e., numerator includes only the additive genetic variance) especially for low heritability traits like reproductive performance. Moreover, the repeatability of a trait can be greater again, the difference between the heritability and repeatability is the inclusion of a permanent environmental variance in the numerator. Accurate and pertinent omic-based animal-level features can contribute to an increase in narrow sense heritability owing to a possible reduction in the residual variance; such data can also provide insights into both non-additive genetic variance and the permanent environmental variance. Even at the level of the contemporary group, omic-level data from the likes of bulk blood/saliva/milk sample, can improve how systematic environmental effects are modeled in the mixed model equations thus also reducing the residual variance. The greater heritability will contribute to a strengthening of the correlation between future phenotypic performance potential and estimated additive genetic merit. Importantly, omic measures for individual animals can help predict the permanent environmental effect of that animal capturing the yet untapped contributor to phenotypic variance. Irrespective, predictions need to be replaced by prescriptions; end users are inundated with data yet crave actionable information. Animal breeders have a lush (pardon the pun!) history of distilling estimates of genetic merit for a plethora of traits into a single value per animal (i.e., breeding indexes); this is the first step in transitioning from predictions to prescriptions. Given the familiarity of end users with breeding indexes, the potential exists to develop production indexes to rank commercial animals on future expected performance taking cognizance of genetic and non-genetic effects. Such production indexes align well with the associated breeding index but where the estimates of genetic merit for the traits in question are replaced by estimates of production merit; these estimated production values are the sum of the additive genetic, non-additive genetic and permanent environmental effects. The weighting factors in the production indexes are more short-term using current costs and prices as opposed to breeding indexes which are longer term. In comparison with the breeding indexes, the production indexes can include ancillary information like gender, age, and month of calving/birth. Like breeding indexes, they are updated in real time. Examples of the application of genome-enabled production indexes are guides for valuing animals for purchase or culling.