bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSVI-5 Optimizing Limited Deep Phenotyping Capacity for Genetic Studies and Routine Genetic Evaluations: Application to Boar Taint
Authors: Markey Alice , Wavreille José , Mayeres Patrick , Huet Anne-Catherine , Gengler Nicolas 
Published: November 2023

Abstract
In the context of genetic research, but even more for routine genetic evaluations, a recurrent problem is the difficulty to obtain measurements for certain required phenotypes. This can be caused by limited facilities, difficulties in sampling, expensive analyses, limited staff relative to number of animals, and many other reasons. It may therefore be necessary to select which animals to phenotype while maintaining the phenotyping quality and avoiding bias or omitting some animals of interest. This implies developing strategies to do the phenotyping in a non-biased way using a priori available minimum knowledge. An example could be predicting post weaning growth of cattle based on earlier information as birth weight and weaning weight to optimize the use of feed intake or methane measurement facilities. In pigs, similar situations might occur for growth or emissions. However, another important example is boar taint (BT) which shows that not only sequential weighing, but also partial measurements of BT may require attention. BT is defined as urinary and fecal and associated with 2 major compounds, androstenone (AND) and skatole (SKA). The classical method of odor discrimination, “Human Nose Score” (HNS), is notoriously unreliable. Even if odor is known to be complex, adding AND and SKA to HNS would help reveal better the boar taint condition (i.e., phenotype). However, the measurements of AND and SKA or other compounds in fat are expensive. Therefore, it would be important to optimize these measurements by selecting relevant fat samples taken at slaughterhouses. We tested the following optimization strategy. The objective was to obtain a good distribution of a posteriori measured AND and SKA in the selected samples given initial asymmetric populations with positive HNS (3 to 10% declared positives). In a first step, the strategy pooled 2 available HNS for 997 across 22 contemporary groups (CG) and added limited chemical measurements (218/997) available for older samples. The data were obtained from a boar progeny testing scheme; therefore, CG were linked through connecting sires from artificial insemination having sons in different CG. A multi-trait BLUP model was used adjusting for metabolic weight using a 4-generation pedigree. A total of 15% of the animals in the last 6 contemporary groups were selected using first positive HNS (17/300), then keeping the highest and lowest predictions and maintaining diversity by not repeating boars from the same sire-family (i.e., when a family was already present, the next animal was taken). A posteriori chemical analyses were performed on selected samples to compare predicted and observed classifications in tainted and untainted. Research showed an accuracy of 0.73 (Table 1), leading to 58% tainted and 42% untainted compared with the expected ratio. Improvements of this strategy are currently in development, including using genomics.
PSVI-3 Effects of Sprouted Barley on Feeding Behavior and Dry Matter Intake in Growing Steers
Authors: Crump Zachary C , Alberto Anthony F , Brown Bailee , Okamoto Lillian , Sego Mia , Roholt Bryce W , Waddups Allissa , Spurling Ryan A 
Published: November 2023

Abstract
Beef cattle production is a key component to the global food supply and is a valuable source of protein for human consumption. Decreased land and water availability in the Intermountain West region of the U.S. poses challenges for conventional production systems. An alternative option to overcome these challenges is through vertical, controlled environment farming. These systems are used to sprout cereal grains that can be used as feed for beef cattle. In this trial, 60 commercial Angus steers (328.24 ± 6.48 kg) were each stratified into one of four treatment groups (n=15). Treatment groups consisted of a typical ration for the region served as the control and treatments groups had a 5%, 10%, or 20% (DM) inclusion of sprouted barley grain. Animals were fed for 60 days and body weights were measured on days 0, 30, and 60. Intake and feeding behavior were measured throughout the 60 days by Vytelle bunk units. The PROC MIXED procedure of SAS was used to analyze all data where day was used as a repeated measure to determine the main effect of treatment. There was a treatmentxday effect (P = 0.006) on DMI demonstrating steers that received 10% or 20% sprouted barley had a linear increase in intake throughout the trial, where steers that received 0% or 5% sprouted barley showed a linear increase in intake over the first 30 days, but then plateaued the last 30 days of the trial. Additionally, a treatmentxday effect was observed for feed bouts (P = 0.0004) and bunk visits (P = 0.0001), showing that steers receiving 5% or 20% sprouted barley had consistent bunk visits and feed bouts throughout, where 0% sprouted barley increased the first 30 days then decreased the last 30 days, and 10% sprouted barley decreased over the first 30 days then increased the last 30 days. Treatment had no effect (P = 0.85) on weight gain over the trial period. These data demonstrate that including sprouted barley in the ration of backgrounding cattle has no effect on overall animal body weight gain, but does affect dry matter intake and feeding behavior.
PSIV-10 Effect of Dietary Inclusion of Fertilized and Unfertilized Sericea Lespedeza Hay on Performance and Plasma Metabolome of Naturally Infected Goats
Authors: Odom Terra , Brown Davia , Pulsifer Chelsea , Terrill Thomas H , Whitley Niki C , Estrada-Reyes Zaira M , Ogunade Ibukun M , Taiwo Godstime A , Idowu Modoluwamu 
Published: November 2023

Abstract
This study was conducted to evaluate the effect of the dietary inclusion of unfertilized (AS) and fertilized (AR) sericea lespedeza (Lespedeza cuneata) hay on body weight (BW), average daily gain, and plasma metabolome of goats. Thirty-six naturally parasite-infected (&gt;5000 eggs/gram) 9-month-old intact male Spanish goats (23.9 ± 0.15 kg) were randomly allocated (12 goats per treatment) into three dietary treatments: a) Control (bermudagrass hay), b) AS (unfertilized lespedeza), and c) AR (fertilized lespedeza) for a 60-day pen feeding trial. All treatments were supplemented with a commercial concentrate following a 70:30 forage:concentrate ratio. Feed samples, blood samples, and BW were collected and recorded weekly to estimate chemical composition, initial and final BW, and average daily gain (ADG). Metabolome analysis of the plasma samples was performed using a chemical isotope labelling/liquid chromatography-mass spectrometry-based technique. Pathway enrichment analysis and analysis of the differentially abundant metabolites were performed using MetaboAnalyst 5.0 software. All other data were analyzed following the GLIMMIX procedure (repeated measures) of SAS, with the fixed effect of treatment, week, and the random effect of animals. Chemical composition revealed greater (P ≤ 0.05) CP (15.6 vs. 12%) and NDF (50 vs. 40.8%) in AR hay compared with AS hay. Compared with the control, dietary AR increased (P &lt; 0.05) final BW (30.1 vs. 27.3 kg) and ADG (130.2 vs. 84.5 g/d) in parasite-infected goats. Compared with the control, nitrogen metabolism was enriched (P ≤ 0.05) in AR and AS goats. Compared with AR, the lysine degradation pathway was enriched in AS (P = 7.51 x 10-6) animals. Moreover, the relative concentration of β-leucine was greater (P &lt; 0.05) in goats on the AR diet compared with the control. Results from this research suggest that both AS and AR sericea lespedeza increased nitrogen metabolism in parasite-infected goats. However, dietary AR hay reduced lysine degradation or increased plasma β-leucine concentration compared with AS and the control, respectively. In conclusion, dietary AR lespedeza hay improved the growth performance of parasite-infected meat goats by preventing amino acid degradation and increasing leucine availability, which may help promote muscle regeneration.
PSIV-3 The Effects of Feeding Sprouted Barley on Rumen Health of Backgrounded Steers
Authors: Crump Zachary C , Thornton Kara J , Okamoto Lillian , Alberto Anthony F , Sego Mia , Blackett Brady , Ranathunga Sanjeewa , Harding Rob , Ward Robert , Roholt Bryce W , Brown Bailee 
Published: November 2023

Abstract
By the year 2050 the world population is expected to reach 9.7 billion, which increases the demand for beef production. Urbanization continues to decrease available cropland, resulting in a need for innovative technologies to produce livestock feed. Controlled environment vertical farming systems are an alternative technology that can be used to produce feed. This research assesses the effects of including sprouted grains grown in this type of system in the ration of backgrounding steers. A total of 60 commercial Angus steers (328.24 ± 6.48 kg) were each stratified into one of four treatment groups (n = 15). A typical ration for the region served as the control and treatment groups had a 5%, 10%, or 20% (DM) inclusion of sprouted barley. Rumen fluid was collected on days 0, 30, and 60 of the trial and analyzed for pH and volatile fatty acids (VFA). Data were analyzed using the PROC MIXED procedure of SAS where day was analyzed as a repeated measure to assess the effects of treatment x day, treatment and day. VFA are presented as a percentage of the total VFA analyzed. There was a treatment x day effect (P = 0.006) on rumen pH where steers getting 5 or 20% sprouted barley had a lower rumen pH at days 30 and 60 than the other two treatment groups. However, it is important to note that all rumen pH values were at healthy levels. Additionally, there was a treatment x day effect (P = 0.01) for total VFA where all values were consistent at days 0 and 30 and then steers receiving 5 or 20% sprouted barley decreased compared with the other two treatments. A treatment x day effect (P = 0.0005) was also observed for acetic acid and demonstrated that on day 30 values decreased from day 0, but steers receiving 5 or 10% sprouted barley decreased most drastically, but at day 60 those receiving 10% sprouted barley was less than the other groups. Propionic acid was also altered by treatmentx day (P = 0.008) such that levels increased from day 0 to day 30 in all groups except those receiving 20% sprouted barley, and then a decrease was observed at day 60 in all treatments with steers receiving 5 or 20% sprouted barley having the least amounts. A treatmentx day effect (P = 0.05) was also seen for butyric acid and is described with an increase from day 0 to day 30 and then a slight decrease at day 60 with those receiving the 10% sprouted barley staying consistent from day 30 to day 60. These data demonstrate that including sprouted barley in the ration of backgrounding cattle has an effect on rumen pH and VFA production in the rumen, but all values stayed within an acceptable range.
PSIX-20 Differential Gene Expression in Peripheral White Blood Cells of Fertile and Sub-Fertile Beef Heifers
Authors: Banerjee Priyanka , Da Diniz Wellison Jarles j Silva , Dyce Paul W W 
Published: November 2023

Abstract
Infertility in beef heifers remains a major economic loss to the cow-calf production industry. Identifying beef heifers with superior genetic potential for improved fertility would increase profitability. Therefore, the study aimed to identify differences in transcriptome profile from peripheral white blood cells (pWBCs) of beef heifers with varying reproductive potential. To accomplish this, Angus-Simmental crossbred heifers were subjected to an estrus synchronization and fixed-time artificial insemination (AI) protocol (7-Day CO-Synch + CIDR). Fourteen days after AI, all heifers were exposed to fertile bulls for a 60-day natural breeding season. Depending on the presence or absence of conceptus 120 days post-AI, heifers were classified as fertile (pregnant heifers) or sub-fertile (non-pregnant by AI or bull-breeding). Pregnancies were terminated, and all animals in both groups were cycling when pWBCs were isolated. Total RNA was extracted from the PWBCs and subjected to the library preparation and sequencing on the Nova-Seq platform. The read counts were obtained after data filtering and quality control using FastQC v0.11.9 and MultiQC v1.12 and alignment to the Ensemble’s ARS UCD1.2 Bos taurus genome reference using STAR aligner v2.7.5 for fertile (n = 8) and sub-fertile (n = 5) beef heifers. The filtered data were subjected to differential expression analysis using DESeq2. We identified 300 significantly differentially expressed genes (DEGs) with P-value ≤ 0.05 and absolute (log2 fold change) ≥ 0.5. Among them, 34 genes including FKBP5, ADCY3, REPS1, LAMP1, CTSH, ADGRE5 were identified with padj &lt; 0.05. DEGs were over-represented for pathways such as response to thyroid stimulus, immune response, response to lipid, neutrophil degranulation, and calcium ion binding. Some of these genes were reported as fertility-related, while the other genes are novel and have the potential to predict heifers with varying reproductive potential. A detailed understanding of the underlying biological mechanisms of the top genes and a follow-up study with a higher sample size at different time points could validate the potential candidates identified in this study.
PSIX-17 Preliminary Assessment of Preweaning Growth Performance of Dexter and Mashona X Dexter Calves
Authors: Browning Richard , Hayes Emily G , Landskroener Christian , Meador Heather 
Published: November 2023

Abstract
Non-traditional cattle breeds are often considered by managers for niche beef production and marketing systems. Some of these alternative breeds are small-framed and thus desired by small-farm operators but have received little research attention because they do not fit traditional commodity beef production systems. Very few of these small breeds also offer heat tolerance. This project was designed to evaluate preweaning performance of straightbred (n = 76) and F1 crossbred calves (n = 81) produced by mature Dexter cows across three years and two Tennessee State University research farms. Spring-born calves were sired by Dexter (n = 7; DD) and Mashona bulls (n = 6; MD) in single-sire, natural service breeding groups following 60-d breeding seasons. Breed of sire was balanced across cow age and farm locations. Calves were weighed within 24-h of birth, at 4 months (125 d of age) of age, and at weaning (227 d of age). Calves were not creep-fed and bull calves were not castrated until after weaning. No cases of dystocia were observed as a result of crossbreeding. Calf performance traits were evaluated using MIXED models of SAS. Fixed effects included sire breed, sex, farm location, and the interaction of sire breed and sex. Random effect terms were production year and sire nested within sire breed. For all the traits evaluated, models were consistent in that the sire breed x calf sex interaction was not significant (P &gt; 0.1), whereas sire breed and calf sex were consistently important (P &lt; 0.01) sources of variation. Bull calves had greater weight and ADG values than heifer calves from birth to weaning. Mean body weight was heavier for MD than DD calves at birth (28.4 ± 0.8 vs. 23.9 ± 0.7 kg), at 4 months of age (120.6 ± 9.7 vs. 96.7 ± 9.6 kg), and at weaning (154 ± 8.6 vs. 124.4 ± 8.6 kg). The MD calves had greater ADG than DD calves from birth to 4 months of age (715.8 ± 36.1 vs. 599.1 ± 36 g/d), from 4 months of age to weaning (334 ± 44.3 vs. 256.8 ± 44 g/d), and from birth to weaning (547 ± 35.7 vs. 447.1 ± 35.7 g/d). Mean 205-d adjusted body weight was heavier for MD than DD (140.2 ± 7.6 vs. 114.7 ± 7.6 kg). Preliminary results indicated that crossbreeding with Mashona bulls significantly increased preweaning growth of calves produced by Dexter cows, while the F1 calves maintained small statute. The spring-born MD F1 calves likely benefited from heat tolerance provided by the Mashona influence and heterosis generated by crossbreeding.
PSIX-19 Association of the Rumen Microbiota with Carcass Merit and Beef Quality
Authors: Holman Devin B , Gzyl Katherine E , Scott Haley , Prieto Nuria , Lopez-Campos Oscar 
Published: November 2023

Abstract
The microbial community in the rumen has an important role in the health and production of beef cattle providing up to 70% of the daily energy requirements from the metabolism of otherwise non-digestible dietary carbohydrates. Diet is often the largest determinant of rumen microbiome composition, but it is also affected by host age, genetics, and sex. Performance attributes such as average daily gain and feed efficiency have all been linked to the rumen microbiome and recent studies with relatively small numbers of cattle have also suggested there may be an association with certain beef quality traits such as marbling, which largely determines the carcass value. Thus, the objective of this study was to evaluate the association of the rumen microbiota with carcass merit and beef quality traits. Two hundred steers were slaughtered, and rumen samples were collected immediately post-slaughter. Subsequently, carcass merit and meat quality attributes were evaluated. The rumen microbiota of these animals was then characterized using 16S rRNA gene sequencing. Although we did not identify a significant association between marbling score and the structure of the rumen microbiota (PERMANOVA; P &gt; 0.05), there were significant associations between rumen microbial community structure and commercial weight, dressed weight percentage, drip loss, and intramuscular fat content (P &lt; 0.05). There were also individual bacterial taxa that were correlated with various carcass merit and beef quality traits. Members of the Acidaminococcus genus were negatively associated with both intramuscular fat content and marbling score (P &lt; 0.10) while Coprococcus, Christensenellaceae R-7 group, Lachnospiraceae NK3A20 group, Moryella, and Prevotella were among those genera positively correlated with intramuscular fat content (P &lt; 0.10). Christensenellaceae R-7 group, Lachnospiraceae NK3A20 group, Moryella, and Prevotella were also significantly associated with dressed weight percentage. Commercial weight was positively correlated with the genera Catonella, Prevotellaceae NK3B31 group, Pseudoramibacter, Selenomonas, and Sutterella and negatively associated with Oribacterium and Ruminococcaceae UCG-001 (P &lt; 0.10). Therefore, bacteria within these genera may be ideal targets for future microbiome-based strategies to improve carcass merit and beef quality.
PSXII-24 Examining Relationships Between Residual Feed Intake Classification, Enteric Emissions, and Apparent Total Tract Digestibility in Late Gestation Beef Heifers
Authors: Acton Kortney , Duarte Marcio S , Swanson Kendall C , Ellis Jen L , Wood Katharine M 
Published: November 2023

Abstract
Improving feed efficiency on forage-based systems can be an important tool for beef producers to reduce their environmental footprint. The objective of this project is to assess the relationship between traditional residual feed intake (RFI) efficiency classification, enteric gas emissions, and apparent total tract nutrient digestibility in late gestation beef heifers. Pregnant Angus crossbred heifers in late gestation (n = 72, BW = 576 ± 45.8 kg) were blocked by expected calving date and randomly assigned to pen groups. Heifers had ad libitum access to a common haylage-based diet formulated to meet nutritional requirements for the last eight weeks of gestation. Individual feed intake and behavior data were recorded daily using Insentec feeding stations (Insentec B.V., Marknesse, The Netherlands). Groups of heifers were rotated through pens with access to GreenFeed trailers (C-Lock Inc., Rapid City, SD, USA) to measure enteric gas emissions of methane (CH4), carbon dioxide (CO2), and oxygen (O2). To determine individual apparent total tract digestibility, fecal samples were collected from each heifer every 9 h over three days, mixed, dried at 65 °C for 96 h, and analyzed for nutrient values (A&L Canada Laboratories, London, ON, Canada). Nutrient digestibility was determined for each heifer using acid-insoluble ash (AIA) and undigestible neutral detergent fiber (uNDF) as internal markers. Heifer RFI was determined using predicted DM intake as a regression of midpoint BW and ADG, and heifers were classified by RFI quartile group. Data were analyzed using PROC GLIMMIX in SAS, with efficiency quartile group as the fixed effect and pen as a random effect, comparisons between quartile groups were assessed with a Tukey test. Heifers classified as efficient (lowest RFI) had decreased DMI (8.2 vs 10.7 ± 0.21 kg/d, P &lt; 0.01), less bunk visits (43 vs 64 ± 5 visits/day, P &lt; 0.01) and greater time per visit (4.8 vs 3.0 ± 0.53 min/visit, P = 0.05). Efficient heifers also had reduced CH4 (219 vs 245 ± 6.2 g/d, P = 0.03) and CO2 (7,517 vs 8,074 ± 165.9 g/d, P = 0.01) emissions compared with inefficient (greatest RFI) heifers. However, apparent total tract digestibility of organic matter, crude protein, NDF, ADF, starch, and sugar using AIA (P &gt; 0.08) or uNDF (P &gt; 0.06) as internal markers were not correlated with heifer efficiency. These data indicate that more efficient heifers in late gestation consume less feed and have reduced enteric emissions, despite no differences in apparent total tract digestibility.