bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSVII-5 Detection and Characterization of Copy Number Variation Regions in Three Selection Lines of Nellore Cattle
Authors: Benfica Lorena F , Brito Luiz F F , do Bem Ricardo D , Mulim Henrique A , Braga Larissa G , Cyrillo Joslaine N S G , Mercadante Maria Eugenia Z 
Published: November 2023

Abstract
Copy number variations (CNV) can partially explain phenotypic variability in complex traits. Therefore, we aimed to identify and characterize CNV regions (CNVR) in Nellore cattle from three selection lines. These selection lines were established in 1981 and consist of a line selected based on heavier postweaning weight (NeS, n = 245), a line selected based on heavier postweaning weight and reduced residual feeding Intake (NeT, n = 556), and a line selected based on average postweaning weight (NeC, n = 114). Genotypes (GGP Indicus HD and GGP Indicus 50K panel) of 928 animals were analyzed. The CNV identification was performed per SNP panel using the PennCNV software. After identifying the CNVs, quality control was performed and the following exclusion criteria were used: Log R ratio &gt; 0.30, B allele frequency "drift” &lt; 0.01, and guanine-cytosine wave factor &lt; 0.05. CNVR were determined by grouping individual CNVs with at least one overlapping base pair. The exclusive regions present in at least 10% of the animals from each population were identified. The GALLO R package was used for the annotation of genes in these regions, and the WebGestaltR package was used for the Gene Ontology analyses. Eight-hundred-and-twenty-three CNVRs (143 losses, 650 gains, and 30 mixed), 1,493 CNVRs (327 losses, 1,113 gains, and 53 mixed), and 482 CNVRs (90 losses, 378 gains, and 14 mixed) were identified in the NeS, NeT, and NeC lines, respectively. The CNVRs covered 1.61%, 2.54%, and 0.94% of the cattle genome in NeS, NeT, and NeC, respectively. Only 32 CNVRs were identified in at least 10% of the animals in NeS, 33 in NeT, and 25 in NeC. Of these regions, 2 are NeS exclusive, 4 are NeT exclusive, and 6 are NeC exclusive. Eight candidate genes in NeS, 20 candidate genes in NeT, and 16 genes in NeC overlapped with the exclusive regions. We identified some important genes such as SLC15A1 in NeS herd that have functions associated to nutrient absorption, MAPK1 identified in the NeT population is involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation and development, and IQCA1L in the NeC population is involved in ATP activity. The genes identified are involved in 5 biological processes, such as response to growth factor, in NeT, and in 1 biological process (response to endoplasmic reticulum stress) in NeC. The differences observed in CNVR improve our understanding of the genetic architecture of the three Nellore selection schemes, given that the identification of genes in the CNVR allows the identification of genomic regions and biological processes that could be associated with the phenotypic differences between selection lines.
PSXII-2 Lactation Persistence Analysis and Its Genetic Correlations with Productive, Reproductive, and Health Traits in the First Two Parities in Lucerna Cattle
Authors: Sierra Sergio N Sanchez , Herrera Luis Gabriel Gonzalez , Peñagaricano Francisco 
Published: November 2023

Abstract
Lactation persistency (LP) is a trait of economic relevance in dairy cattle since persistent cows are more profitable by presenting fewer diseases, requiring fewer inputs, and having better reproductive performance. Therefore, the main objective of this study was to estimate genetic relationships between lactation persistency for mastitis (MT), calving interval (CI), and 305–day milk yield (305M) in first and second Lucerna cattle lactations. Records from 67,952 test–day milk, 7,100 CI, and 1,074 clinical-mastitis evaluations from two Colombian farms of Creole dual-purpose cattle were considered. Five three-parameter equations, as reported in previous literature, were graphically and statistically evaluated for fitting a lactation curve (LC) for each parity. The goodness-of-fit criteria included AIC, BIC, RSS, and R2. The most appropriate equation was identified and implemented for predicting 305M for 4,620 lactations (2,716 and 1,904 from first and second parity, respectively) for which LP was estimated. Bi-trait animal models between LP-MT, LP-CI, and LP-M305 for each parity were executed in the BLUPF90+ software (AI-REML algorithm) to estimate heritabilities (h2) and genetic correlations (GC). Fixed effects of herd, year of calving, season of calving, b0 lactation parameter, and age at calving were included. Estimates of goodness-of-fit criteria for all LC equations varied between R2 (0.29 – 0.68), BIC (132,322 – 207,415), AIC (132,289 – 207,389), and RSS (188,231 – 414,007). The incomplete gamma equation best satisfied the goodness-of-fit-criteria and drew the most accurate LC in both parities. Due to the low data density in this work, estimates involving MT and CI had increased standard deviations; therefore, the interpretation should be considered cautiously. The h2 estimates were 0.0 and 0.24 for MT, 0.02 and 0.09 for CI, 0.18 and 0.36 for M305, and 0.14 and 0.15 for LP, for the first and second parity, respectively. The GC estimates were -0.24 and -0.41 for LP–M305, 0.31 – 0.35 for LP–CI, and -0.76 for LP–MT for each parity, respectively. The results of this study suggest that LP could be considered as a selection target in the farms’ breeding program since desirable relationships were found with all evaluated traits for the first and second parity.
PSI-7 Vitamin a and D Pre-Exposure to Prime Reproductive Success in Breeding Beef Cows
Authors: Fox Amanda K , Hammerich Michael , Bishop Cecily V 
Published: November 2023

Abstract
Vitamins A and D are important for immunity, reproduction, and overall health. The need for supplementation is often overlooked in beef cattle production because it is assumed that beef cows receive adequate amounts of these micronutrients from their environment. However, there is an increasing incidence of vitamin A and D deficiencies in beef cattle due to challenges of environment, forage access and quality. It is well known that nutrition has a major effect on reproduction, but direct effects of vitamins A and D on beef cow reproduction and fertility are understudied. We previously reported increased rates of fertilization after co-culture of bovine embryos with vitamin A and D in vitro. The objective of this study is to determine how vitamin A and D supplementation in mid- to late gestation affects calving ease and birth weights of calves at parturition, as well as cow fertility at the following breeding. Angus and Angus crossbred females (Bos taurus) of first (n = 20) or second (n = 10) parity were selected based on pregnancy status and gestational age and then randomly assigned to treatment groups. Starting in October 2021, pregnant cows were injected monthly with either a vehicle (control) or a commercial supplement made up of 300,000 IU vitamin A and 45,000 IU vitamin D (Vitamin AD, Vet One; n = 15/ treatment group). Blood samples were collected before each injection for analysis of vitamin and hormone concentrations. All cows were monitored from January-April 2022 for signs of parturition to determine calving date and time, calving ease, birth weight, and to provide assistance if necessary. Serum samples were collected from the calves within 12 hours of parturition for analysis of vitamin D concentrations. There was no effect of vitamin A and D treatment on calving ease (Generalized Linear Model analyses; P = 0.58; 1.44 ± 0.2 treated, 1.29 ± 0.19 control group) or on birth weight (Generalized Linear Model; P = 0.52, 32.6 ± 1.24 kg treated, 33.8 ± 1.38 kg control group). Estrus synchronization, additional blood sampling, vitamin/vehicle injections, and artificial insemination (AI) was performed in late April 2022. Conception rates were determined by transrectal ultrasonography 30 to 40 days post-AI. Interestingly, 7 of 15 controls were determined to be pregnant by AI, while this improved to 10 of14 in AD-injected females (one female could not undergo AI due to late calving). Cows not pregnant by AI were pastured with a bull of proven fertility, and rectal palpation was used in the fall to determine overall pregnancy rates and any pregnancy loss. These data suggest a modest increase in serum vitamin A and D will improve pregnancy rates after AI. Additional studies should reveal if these treatments improve markers of calf health. Supported by The Oregon Beef Council (C. Bishop).
PSI-6 Effects of a Postbiotic Program Consisting of Liquid and Solid Saccharomyces Cerevisiae Fermentation Products on Digestibility, Ruminal Fermentation, and Plasma Metabolome of Finishing Beef Steers
Authors: Dhungana Anjan , Odunfa Oluwaseun , Osterman Anthony , Woods Daniel , Cooper Kimberly , Wang Changzheng , Yoon Ilkyu , Jiang Yun 
Published: November 2023

Abstract
The objective of this study was to determine the effects of a postbiotic feeding program consisting of liquid and solid Saccharomyces cerevisiae fermentation products (SCFP) on digestibility, ruminal fermentation, and plasma metabolome of finishing beef steers. Eight Holstein steers (BW 467 ± 13.9 kg) equipped with rumen cannulas were used in a crossover design study, with 21-d per period and 7-d washout period in between periods. Steers were blocked based on initial BW to one of two treatments: 1) Control, basal diet only (CON), or 2) SCFP, one day feeding of LiquiCare RTU (Diamond V, dosed via rumen cannula at 11 mL/100 kg BW) followed by daily feeding of 12 g NaturSafe (Diamond V, top-dressed). Feed and fecal samples were collected during d 17 to 20 for determination of digestibility and fecal excretion of N, P, Cu and Zn using acid-insoluble ash as an internal marker. Blood samples were collected on d 21 before morning feeding. Rumen fluid samples were collected on d 0, 1, 2, 3, 5 and 21 at 0, 4, 8, or 12 h post morning feeding via rumen cannula. Results were analyzed with the GLIMMIX procedure of SAS 9.4 (SAS, 2022). BW, DMI and digestibility were not affected by treatment. There was a tendency of treatment by period interaction (P = 0.09) on feed efficiency, which was improved by feeding SCFP only in period 1. Feeding SCFP did not affect (P &gt; 0.10) ruminal pH. Feeding SCFP tended to reduce ruminal lactate concentration on d 21 (0.09 vs. 0.02 mM, P = 0.10). Supplementing SCFP reduced ruminal NH3-N concentration on d 2 (4.24 vs. 7.31 mg/dL, P = 0.03) and d 21 (4.86 vs. 6.83 mg/dL, P = 0.04). By feeding SCFP, ruminal total VFA concentration was increased 4-h post-feeding on d 5 (139.7 vs. 126.7 mM, P = 0.01) and numerically increased 4-h post-feeding on d 21 (151.2 vs. 133.3 mM, P = 0.12). For VFA composition, no treatment differences were observed on day 21. However, feeding SCFP reduced (P = 0.01) propionate proportion and increased (P = 0.05) butyrate proportion on day 3. The enriched plasma metabolic pathways (P ≤ 0.05) by feeding SCFP are citric acid cycle, pyrimidine metabolism, glycolysis/gluconeogenesis, retinol metabolism, and inositol phosphate metabolism pathways. Overall, our results indicated potential benefits of the SCFP feeding program on improving ruminal fermentation, preventing acidosis and improving N utilization in the rumen. Furthermore, feeding SCFP enriched several important pathways in lipid, protein, and glucose metabolism, which may improve feed efficiency of energy and protein in finishing beef cattle.
PSI-17 Use of Sunn Hemp as Forage for Early-Weaned Beef Calves
Authors: Silva Joao , Vendramini Joao , Silva Hiran , Oliveira Hugo , Garzon Jaime , Cook Daniel , Gardner Dale , Moriel Philipe 
Published: November 2023

Abstract
Sunn hemp (Crotalaria juncea) has been widely used as cover crop in the USA and due to superior biomass accumulation and nutritive value, there is interest from producers to use sunn hemp as forage for livestock. However, sunn hemp has pyrrolizidine alkaloids, which can affect animal performance. The objective of this study was to evaluate the effects of feeding sunn hemp hay to early-weaned beef calves in a dry lot in Florida. The experiment was conducted at the UF/IFAS Range Cattle Research and Education Center, Ona, FL from April to May 2021 (42 d). Treatments were calves receiving sunn hemp or stargrass (Cynodon nlemfuensis) hay distributed in a randomized complete block design with 12 replicates. Calves were supplemented with concentrate at 1.3% BW daily (18% CP and 78% TDN). Twenty-four Angus crossbred calves were weaned with 90 ± 14 kg BW and grazed annual ryegrass (Lolium multiflorum) with 1% BW concentrate supplementation for approximately 60 d. Subsequently, calves were randomly distributed and assigned to experimental units (pen) on 14 April 2021 with initial BW of 184 ± 10 kg. ‘Ubon’ sunn hemp hay was harvested approximately 49 d after seeding when 75% of the plants were initially flowering. Ground hay was fed daily targeting 10% refusals, and the initial CP and in vitro digestible organic matter concentrations of sunn hemp and stargrass hay were 9 and 48%, and 9 and 47%, respectively. The average concentration of pyrrolizidine alkaloids from sunn hemp hay was 58 μg/g DM. Early-weaned calves receiving stargrass had a tendency to have greater ADG than sunn hemp (0.5 vs. 0.4 kg/d, P = 0.09), and had greater forage DM intake (1.2 vs. 1.0% BW, P &lt; 0.01) and total DM intake (2.5 vs. 2.3% BW, P &lt; 0.01). Conversely, diets with sunn hemp had greater in vivo DM digestibility than stargrass (68 vs. 62%, P = 0.04). There was no difference between treatments on parasite egg count (mean = 45 eggs/3 g feces, P = 0.25) and coccidia egg count (log10 eggs/g feces, P = 0.35). Early-weaned calves receiving sunn hemp consumed 0.25 g pyrrolizidine alkaloids/d; however, there was no detectable amount (&lt; 0.05 μg/g DM) of pyrrolizidine alkaloids in the feces. The presence of pyrrolizidine alkaloids in sunn hemp may be the potential cause of decreased early-weaned calves forage intake and animal performance.
PSIII-8 Extra-Label Bisphosphonate Effects on Intra-Articular Inflammation in Juvenile Horses Challenged with Intra-Articular Lipopolysaccharide
Authors: George James M , Leatherwood Jessica , Arnold Carolyn , Glass Kati G , Paris Brittany L , Conrad Matthew B , Martinez Rafael , Hernandez Fernando Vergara , Nielsen Brian D , Colbath Aimee , Welsh Thomas H , Bradbery Amanda N 
Published: November 2023

Abstract
Anecdotal assertions that bisphosphonates, such as clodronate disodium (CD), exhibit anti-inflammatory properties has led to extra-label use, despite a lack of scientific evidence of its efficacy. The objective of this study was to determine the effects of CD on intra-articular inflammation, hypothesizing that intra-muscular administration of CD would reduce intra-articular inflammation following an acute inflammatory challenge by lipopolysaccharide (LPS). To test this, 32 yearling Quarter horses were stratified by age (500 ± 13 d), BW (336 ± 26 kg), sex (n = 16 female; n = 16 male) and initial bone optical density into 4 treatment groups. The 140-d study consisted of two phases: Phase 1 (d 0 to 83) and Phase 2 (d 84 to 140) emulated sale preparation and early performance training, respectively. Horses were housed individually (3.6 m × 7.3 m) and fed to meet requirements of growing horses undergoing moderate training. Treatments consisted of control (CON; n = 8; no CD), single-dose (1X; n = 8; d 84), two-doses (2X; n = 8; d 0, 84), and four-doses (4X; n = 8; d 0, 42, 84, 126) of CD. All horses received iso-volumetric intramuscular injections of 1.8mg/kg BW clodronate disodium (OSPHOS) or saline (placebo) on d 0, 42, 84, and 126. Following treatment administration on d 126, radial carpal joints of each horse were injected with 0.8 mL of either 0.5 ng sterile LPS derived from Escherichia coli O55:B5 or sterile lactated Ringer’s solution as a contralateral control. Synovial fluid was collected before LPS injection (h 0) and at 6, 12, 24, and 336 h post injection. Synovial fluid was analyzed using an ELISA for prostaglandin E2 (PGE2), an indicator of joint inflammation. Data were log transformed and analyzed using the MIXED procedure of SAS. There was an h × LPS interaction (P &lt; 0.01) confirming an acute, transient inflammatory response with increased PGE2 at 6, 12, and 24 h compared with the contralateral control joint, and resolved (P = 0.62) by h 336 post-injection. There was a treatment × h × LPS interaction (P = 0.02) in which 1X, 2X and 4X CD groups had greater synovial PGE2 concentrations at 6 h post-injection in the LPS joint compared with CON. In summary, intra-articular LPS induced localized inflammation, and the PGE2 response was greater in all horses treated with CD. The results of this study reject the hypothesis, suggesting clodronate disodium administration does not reduce intra-articular inflammation following acute induced synovitis.
PSIII-16 Application and Economic Analysis of Pooled Genome-Wide Association Studies in Commercial Feedlot Cattle
Authors: Prosser Haleigh M , Arnold Chelsea J , Saatchi Mahdi , Scott Matthew , Perkins Tommy L 
Published: November 2023

Abstract
Genotyping an individual animal provides a specified identity of their genetic makeup, which when used in a commercial beef operation, may allow for precise predictions centered around trait quality and production. However, conventional genotyping occurs at the individual level and is fiscally and logistically taxing for commercial cattle producers for whole-herd testing. Therefore, our research objective was to utilize DNA pooling methodology and genome-wide association studies (GWAS) to introduce economically feasible genomic testing in commercial feedlot cattle. A total of 1,956 commercial mixed-breed feedlot cattle (1,715 steers; 241 heifers) with accompanying complete carcass date were enrolled in the project after having their DNA extracted from tissue sampling units collected during feedlot enrollment. Isolated DNA was stratified into 79 pools (mean pool size = 25 individuals) for genotyping via GGP Bovine 100K array (Illumina); pooling was designed to replicate a prospective timeline, utilizing lot number, arrival date, and feedlot entry weight to stratify DNA pools. Data preparation with outlier filtering (OF) and repeated measures (RM) reduced phenotypic variance within pools by removing pools containing outliers, defined as values greater than 150% of the IQR outside of the IQR, and replicating a pool genotype by the number of individuals in a pool to compare to individual phenotype, relying on the concept that pooled DNA is a proxy average of individual genetic makeup, respectively. To complete the GWAS, phenotype files were built using pool average and individual calculated yield grade (CYG) and marbling (MARB) values. To evaluate economic feasibility, we performed a cost comparison of the pooling process itself as compared with individual genotyping, in addition to a cost-benefit analysis for prospective pooling to display the potential increase in income because of the investment in genotyping. Completed GWAS identified 20, 10, 27, and 16 significant SNPs associated with RM CYG, OF CYG, RM MARB, and OF MARB, respectively (P ≤ 0.001). The estimated total cost of genotyping the pooled DNA in the project ($23,460) was 4.5 times less than the estimated cost of genotyping the same cattle individually ($105,354), and the mean potential benefit-cost ratio of utilizing pooled genotypes to make management decisions was 2.33 (SD = 1.91).Our research demonstrated the successful use of DNA pooling in a commercial feedlot setting and showcased a need for further research and more exploration to better define a successful prospective pooling process. Although the dataset was highly variable, these biologically logical associations signify relative success of utilizing pooled DNA in GWAS. The economic efficiency of the DNA pooling process itself warrants further testing, as the economic benefits the process can provide producers outweigh costs.
PSIII-10 Hepatic Mrna Expression of Genes Related to Innate and Adaptive Immune Genes in Beef Steers with Divergent Residual Body Weight Gain
Authors: Idowu Modoluwamu , Ologunagba Deborah , Taiwo Godstime A , Sidney Taylor S , Treon Emily , Leal Yara , Eichie Francisca , Morenikeji Lanre , Pech-Cervantes Andres A , Ogunade Ibukun M 
Published: November 2023

Abstract
Immune function plays an important role in overall animal health and productivity. In this study, we evaluated the hepatic mRNA expression of genes involved in innate and adaptive immunity in crossbred beef steers with positive or negative residual body weight gain (RADG). Positive-RADG beef steers (n = 8; RADG = 0.34 kg/d) and negative-RADG beef steers (n = 8; RADG = -0.27 kg/d) were selected from a group of 108 growing crossbred beef steers (average BW = 556 ± 38 kg) after a 42-d performance testing period. At the end of the 42-d period, liver biopsies were collected from the beef steers for RNA extraction and cDNA synthesis. The mRNA expression of 84 genes involved in innate and adaptive immunity were analyzed using pathway-focused PCR-based arrays. The mRNA expression of genes with false discovery rate-adjusted P-values (FDR) ≤ 0.05 were considered to be differentially expressed. Out of the 84 genes analyzed, four genes (IL-2, MYD88, CD-80, NFkB-1) were differentially expressed and were all upregulated in positive-RADG, compared with negative-RADG beef steers. IL-2 is a cytokine that plays a critical role in the immune response by activating and proliferating T-cells, which are important for fighting infections. MYD88 is an adaptor protein that is essential for signaling by toll-like receptors, which are involved in pathogen recognition. CD80 is a protein that is expressed on the surface of antigen-presenting cells and plays a critical role in the initiation of an immune response. The activation of NF-κB leads to the production of cytokines and chemokines that help to recruit immune cells to the site of infection. The upregulation of the aforementioned genes in positive-RADG beef steers suggests that they had a better ability than negative-RADG beef steers to quickly recognize pathogens and initiate appropriate responses to effectively fight off infections without causing inflammatory reactions. This is essential to optimize immune function and minimize the impact of immune activation on growth and production. As a result, more energy and nutrients are available to support improved growth rate and feed efficiency.