bluuebunny/crossref_metadata_2025_split huggingface dataset:
148 Does Increased Gametic Variance Translate to Increased Heterogeneity in progeny?
Authors: Williams Maeve , Naderi Saeid , Berry Donagh P 
Published: November 2023

Abstract
The expected genetic merit of a new-born calf is simply the average genetic merit estimates of its parents. Parents with a very heterogenous genotype could, however, potentially generate a more heterogenous group of progeny than parents with a more homogenous genotype. The objective of the present study was to test this hypothesis, and a secondary objective was to determine the expected progeny variability in their estimates of genetic merit for traits associated with dairy-beef production based on their expected genomic heterogeneity. Gametic variance for calving difficulty, calf mortality, gestation length, docility, feed intake, and carcass weight, fat, and conformation was estimated for 22,038 beef sires of multiple breeds. Sire gametic variance per trait was estimated for each chromosome from all heterozygous single nucleotide polymorphisms (SNP), their location within the genome, and the estimated effect of each SNP on each trait. Gametic variance was estimated for the whole genome as the sum of the estimated gametic variance of all chromosomes. Individual progeny phenotypic records for each trait were adjusted for animal sex, dam parity and dam genetic merit for the trait, heterosis, recombination loss, and contemporary group. The correlations between sire estimated gametic variance and the standard deviation of his (adjusted) progeny phenotypes were then estimated for all sires with at least 20 progeny records; the number of genotyped sires with at least 20 progeny ranged from 2,395 (heifer calving assistance) to 8,545 (calf mortality). The mean gametic variance, relative to the variance of sire genetic merit, for heifer calving difficulty, cow calving difficulty, calf mortality, gestation length, docility, feed intake, carcass weight, carcass conformation, carcass fat were 0.0002, 0.0005, 0.09, 0.07, 0.30, 0.02, 0.25, 0.05, and 0.12, respectively. With the exception of carcass fat and carcass weight, the correlations between the estimated gametic variance per sire and the standard deviation of his (adjusted) progeny phenotypes were non-existent (-0.06 to 0.04); the correlations between the standard deviation of the adjusted progeny phenotypes and the gametic variance for carcass fat and carcass weight were 0.29 and 0.16, respectively. The (weak) correlations between gametic variance and progeny phenotypes for carcass fat and carcass weight suggest that greater gametic variance is associated with increased progeny heterogeneity for both carcass traits. Nevertheless, accounting for gametic variance when selecting beef bulls for use on dairy females seems to provide little benefit.
97 Dissection of Evolution of Cis-Regulatory Elements and Its Application on Genetic Control of Complex Traits in Farm Animals
Authors: Zhou Huaijun 
Published: November 2023

Abstract
Functional Annotation of Animal Genomes (FAANG) has made significant progress on the improvement of the annotation of the functional elements, particularly non-coding regions in farm animal genomes. Different epigenomes including ChIP-seq for 4 histone marks, ATAC-seq, CTCF-seq, RNA-seq, and Hi-C across different tissues in different animal species were generated. Thousands of cis-regulatory elements including promoters and enhancers across different tissues in different species were identified and annotated. A comprehensive characterization and comparison of cis-regulatory elements across tissues and species can help us understand the genetic and evolutionary basis of complex phenotypes. Yet, attempts to dissect the evolution of regulatory elements have generally been small, both regarding the number of tissues and species compared. We demonstrate that genomic variants associated with complex traits and adaptive evolution in farm animals are significantly enriched in active promoters and enhancers. Further analysis suggests that the regulators were significantly enriched in evolutionary breakpoint regions (EBRs) in a tissue-specific and regulator-specific manner. Furthermore, we reveal distinct tissue-specific regulatory elements play important roles in domestication processes. Finally, we provide biological insights on tissue-specific regulatory conservation, and by integrating genome-wide association studies on complex traits, we demonstrate that comparative epigenomic analysis enhances our interpretations of complex traits variations in farm animals and provides novel insights on the role of regulatory elements on the functional conservation across species.
170 Bakery Waste Supplementation to Late Gestating Bos Indicus-Influenced Beef Cows Successfully Impacted Offspring Postnatal Performance
Authors: de Izquierdo Vinicius Souza , Silva Joao , Palmer Elizabeth , Ranches Juliana , Bittar Joao , Pickett Autumn , Cooke Reinaldo F , Vendramini Joao , Moriel Philipe 
Published: November 2023

Abstract
This study evaluated the growth and immune function of Bos indicus-influenced offspring born to cows offered prepartum supplementation of bakery waste containing 2 concentrations of crude fat. On day 0 (~90 d before calving), 108 Brangus crossbred cows were stratified by body weight (BW; 551 ± 65 kg) and body condition score (BCS, 5.5 ± 0.9) and were randomly allocated into 1 of 18 bahiagrass pastures (6 cows and 4.3 ha/pasture). Treatments were randomly assigned to pastures (6 pastures/treatment) and consisted of no prepartum supplementation (NOSUP) and 1 kg/d of low-fat (LFAT; 6.4% crude fat) or high-fat (HFAT; 10.7% crude fat) bakery waste-based supplement from day 0 to 70. Calves were weaned on day 292. Then, 15 heifers/treatment were randomly selected, acclimated for 7 d, and assigned to drylot pens from day 300 to 345. Heifers were vaccinated against respiratory pathogens on days 300 and 315. Cow BCS on day 70 was the least (P ≤ 0.05) for NOSUP cows and did not differ (P ≥ 0.12) between LFAT and HFAT cows. Cow BCS on day 140 (start of breeding season) was greater (P = 0.05) for HFAT vs. NOSUP cows and intermediate (P ≥ 0.35) for LFAT cows. Plasma concentrations of total polyunsaturated fatty acids (PUFA) in HFAT cows did not differ (P ≥ 0.76) compared with LFAT cows on day 70, were greater (P ≤ 0.05) compared with NOSUP cows on day 70 and were the greatest on day 140 (P ≤ 0.05). Percentage of cows pregnant on day 292 did not differ (P ≥ 0.26) among treatments but more HFAT cows calved (P ≤ 0.05) their second offspring from day 429 to 450 compared with NOSUP and LFAT cows. First offspring BW on day 292 were greatest (P ≤ 0.05) for LFAT calves and least for NOSUP calves. Maternal treatments did not impact (P ≥ 0.11) post-weaning average daily gain (ADG) and total DM intake. Average plasma cortisol concentrations were greater (P = 0.03) for NOSUP vs. HFAT heifers and intermediate for LFAT heifers (P ≥ 0.26). Final serum titers against infectious bovine rhinotracheitis (IBR) and bovine respiratory syncytial virus (BRSV) were greater (P ≤ 0.08) for LFAT vs. HFAT heifers and intermediate (P ≥ 0.27) for NOSUP heifers. Therefore, crude fat concentration in bakery waste offered to late-gestating beef cows had variable effects on offspring performance. Low-fat bakery waste led to greatest offspring preweaning growth whereas high-fat bakery waste enhanced maternal reproductive success and offspring post-weaning humoral immune response.
175 Effects of Random Metaphylaxis Administered at Feedlot Arrival to 0, 33, 66, Or 100% of High-Risk Beef Cattle on Health Outcomes, Complete Blood Count, and Growth Performance
Authors: Hanratty Ashlee Noelle , Broadway Paul R , Sanchez Nicole C Burdick , Carroll Jeffery A , Hoffman Ashley A , Manahan Jeff L , McDaniel Zach S , Line Dalton J , Dornbach Colten W , Smock Taylor M , Theurer Miles , Galyean Michael , Hales Kristin E 
Published: November 2023

Abstract
Our objective was to evaluate the effects of random metaphylaxis administered on arrival to 0, 33, 66, or 100% of high-risk beef cattle on clinical health, growth performance, and complete blood cell counts during a 35-d receiving period. Crossbred beef steers (n = 216; arrival BW = 197 ± 6.4 kg) were used in a generalized complete block design consisting of 2 source blocks and 4 treatments. Experimental treatments and steers were randomly assigned to pen within source block: 1) negative control, subcutaneous injection with sterile saline (NCON); 2) 33% of steers/pen given metaphylaxis (33M); 3) 66% of steers/pen given metaphylaxis (66M); and 4) positive control; conventional metaphylaxis given to 100% of steers (CONV). Body weight and blood samples for quantification of complete blood count were collected on d 0, 14, and 35. Pen was considered the experimental unit for all analyses. Continuous data were analyzed using PROC MIXED, and categorical data were analyzed as binomial proportions using PROC GLIMMIX. Treatment was included in the model as a fixed effect and source block was a random effect. Complete blood counts were analyzed as repeated measures, where day was the repeated effect and pen within treatment was the subject. The percentage of steers treated with an antibiotic for bovine respiratory disease (BRD) once was greater (P &lt; 0.01) for NCON and 33M than for 66M and CONV. Neither BW on d 35 nor average daily gain from d 0 to 35 differed among treatments (P &gt; 0.65), but dry matter intake (DMI) and DMI as a percentage of BW from d 0 to 35 was greater (P &lt; 0.03) for 66M and CONV than for NCON and 33M. No differences in hematological variables were detected among treatments (P &gt; 0.19), whereas all complete blood count variables were affected by day (P &lt; 0.01), except for mean corpuscular hemoglobin concentration (P = 0.81). Most notably, the neutrophil:lymphocyte ratio was greater (P &lt; 0.01) on d 0 than on d 14 and 35. These data suggest that arrival metaphylaxis can be administered to 66% of cattle at random without increasing BRD morbidity while simultaneously increasing DMI similar to conventional metaphylaxis. Random metaphylaxis may be a viable method to decrease antibiotic use in the feedlot industry, while maintaining health outcomes and growth performance of high-risk beef cattle.
182 Custom Bovine Heifer Development to Advance Onset of Puberty in a Limited-Resource Beef Cow-Calf Operation
Authors: Elder Kasey A , Dunn Rachel , Green Kiana , Odhiambo John F 
Published: November 2023

Abstract
Age at puberty in bovine heifers is controlled largely by genetic and environmental factors, among which nutrition has a major influence. This study evaluated the utility of cool-season forages for heifer development in a limited-resource beef cow-calf system. Beef heifer development was evaluated at 4 time periods: Period 1 (Birth-Weaning) heifers sucked dams until weaning, Period 2 (Weaning-Puberty) heifers grazed natural pastures and supplements in Fall and Winter, Period 3 (Puberty-Breeding) heifers grazed cool-season forages, Period 4 (Breeding-Pregnancy) heifers were maintained on Spring and Summer forages. The supplements were fed at a rate of 0.45 kg/68.2 kg. calf BW and consisted of a 1:1 ratio of cracked corn and commercial grower pellets. Cool-season pasture consisted mainly of Rye grass and clovers. Hay, water, and minerals were provided free choice. Heifer body weights were obtained at quarterly intervals. They were synchronized with two doses of prostaglandin F (PGF) 2α, 14 days apart before bull introduction on June 1st. Pregnancy was confirmed by ultrasonography at the end of breeding in August. The growth trajectory was evaluated by mixed procedures of SAS. A stair-step pattern of body weight gain was observed from birth to pregnancy. There was rapid growth pre-weaning, average daily gain (ADG) = 0.95 ± 0.0.17kg ∙heifer-1∙day-1. Limited growth during the juvenile period (ADG = 0.24 ± 0.17kg∙heifer-1∙day-1) and compensatory growth during the pre-pubertal period (ADG = 1.32 ± 0.17kg∙heifer-1∙day-1). These preliminary results indicate that limited-resource beef cow-calf producers should utilize winter forages to leverage compensatory growth in their heifer development programs. Funded by FAMU World Class Scholars Program and NIFA CBG # 2021-38821-34599
413 Awardee Talk: Reproductive Efficiency: Managing Cows to Improve Reproductive Efficiency
Authors: Perry George A 
Published: November 2023

Abstract
Management of a herd has a tremendous impact on reproductive efficiency, and estrous synchronization can be used as a tool to help get more animals to conceive early. In comparisons among synchronization protocols, pregnancy success did not differ between newer protocols. The factors that had the greatest impact on pregnancy success were estrous cycling status before the breeding season (estrous cycling &gt; non-cycling; P &lt; 0.01) and expression of estrus before fixed-time AI (estrual &gt; non-estrual; P &lt; 0.01). Thus, herd management, before the breeding season, has a large impact on reproductive success. Timing and type of vaccine used prebreeding can impact pregnancy success and luteal function (killed vaccine &gt; modified live; P &lt; 0.05). Nutritional changes can also impact reproductive efficiency. A decrease in available energy pre- (P = 0.05) or post-breeding (P = 0.02) decreased embryo quality (stage and grade, respectively) and subsequent concentrations of progesterone (P &lt; 0.01). Cattle fertility is not only controlled by the female but is also controlled by the male. Stage of sexual maturity in bulls impacted scrotal circumference P &lt; 0.0003), motility (P &lt; 0.001), as well as mitochondrial membrane potential (P &lt; 0.01), but stage of bull maturity did not influence viability, chromatin structure, nor amount of reactive oxygen species. Prenatal stress of a bull impacted the portion of sperm with DNA damage (control &gt; prenatal stress; P = 0.04), but did not impact scrotal circumference, motility, mitochondrial membrane potential, or reactive oxygen species. Furthermore, sperm from bulls that were stressed in utero did not have differences in fertilization compared with control bulls; however, possible epigenetic modifications, to the sperm produced, resulted in fewer embryos making it to blastocyst stage (P = 0.03). Thus, management decisions made throughout the year can have a tremendous impact on reproductive efficiency and the percentage of animals that conceive early not only in the present breeding season but also in future breeding seasons as well.
22 Greenhouse Gas Emission Measurement and Modeling in Complex Beef Production Systems
Authors: Campbell Terra N 
Published: November 2023

Abstract
Measuring and modeling gas emissions from cattle production pose unique challenges due to the complex nature of these systems. Several methods exist for measuring gas emissions including chambers, tracers, open path lasers, and eddy covariance systems. Each method comes with challenges and benefits. Accurate measurements are crucial for accounting and model development. Simple emission factor methods of accounting require less data but fail to represent dynamic factors that drive emissions. Whole farm emissions will vary depending on several factors including region, cattle breed and age, diet, climate, and manure management. Dynamic models provide more representative emissions, but require far more data, sophisticated software, and are not always user friendly.
18 Role of the Rumen Microbiome in Beef Cattle Gut Physiology and Performance
Authors: Myer Phillip R 
Published: November 2023

Abstract
The diverse rumen microbiome converts low-quality feedstuffs into usable energy and provides approximately 70% of the energy required by its ruminant host through fermentation byproducts. Due to microbial impacts on host health and productivity, numerous studies have associated rumen microbiome variation with important sustainability phenotypes, such as feed efficiency and methane emissions. Although diet, genetics, and environment contribute to variation in feed efficiency, selection for feed-efficient beef cattle using genetic improvement technologies has helped to understand and improve the persistence and longevity of such phenotypes within the herd. While diet has been considered to be the primary driver for the composition and structure of the rumen microbiome, recent studies have indicated the microbial communities present in the rumen are under low-to-moderate host genetic control. The mutualistic, commensal, and parasitic microorganisms that reside in the rumen and lower gastrointestinal tract of cattle and other ruminants exert enormous influence over animal physiology and performance. The ability to interrogate these systems at great depth has permitted a greater understanding of the microbiological and molecular mechanisms involved in ruminant nutrition and health. The work in our group in the field of beef cattle gut microbiology, as it relates to feed efficiency, permits the exploration of these critical microbial community networks. This knowledge will aid researchers seeking to address the grand challenge of maintaining host-efficient gut microbiomes throughout cattle production operations. This work is supported by the Agriculture and Food Research Initiative grant no. 2020-67015-30832 from the USDA National Institute of Food and Agriculture.
231 Podcasting as an Extension Tool: Limitations and Opportunities
Authors: Corbitt Katie , Bennett Samantha , Martin David , Sawyer Jason T , Rodning Soren P , Mulvaney Donald 
Published: November 2023

Abstract
Extension challenges today include prompts for increased consideration for online platforms for educational content programming to best reach young producers about the latest discoveries in terms of production agriculture. Because of these challenges, research was conducted to evaluate the use of podcasts as an Extension tool. For the purposes of this research, a mixed methods approach was utilized to collect both quantitative and qualitative data. Two separate surveys were written for the purposes of this study, and both were housed on the survey platform Qualtrics (Version 2022, Provo, Utah, U.S.). Of the two surveys regarding perspectives towards podcasting as a Cooperative Extension System (CES) tool, one was written for data collection from CES personnel, and the other was written for the purposes of collecting data from CES stakeholders. Both surveys were reviewed for validity by expert panels consisting of graduate students, university faculty, and CES personnel. Before survey recruitment, survey materials were provided to the Auburn University Institutional Review Board, and study #21-438 was considered exempt. Participant recruitment took place through email and data analyses used SPSS to conduct descriptive statistics and frequencies. Results included perspectives of personnel towards podcasts, the status of use for their work, and viewpoints of stakeholders and current use of already available Extension podcasts. A total of 50% of extension personnel responded that they had not thought of using a podcast to disseminate information and 22% said their priorities lie elsewhere. While the potential for podcast modalities is great, results indicated diverse views, varied levels of podcast understanding, plans for adoption, and perceived barriers for use of podcasts in Extension.
233 Fermentation Characteristics of Brassica and Wheat Mixed Silages
Authors: Harrelson Flint W , Harrelson Patricia L , Roush Caroline R , Skidmore Amanda R , Collick Amy S 
Published: November 2023

Abstract
Winter feed management in the temperate regions of the U.S. primarily consists of stored or stockpiled grasses. Recently, forage brassica species have become popular additions to fall and winter grazing programs as an alternative feed source. Most all brassicas incorporated into forage systems are grazed; however, there may be more feeding options, such as fermenting them as silage or baleage. The objective of this project was to determine, utilizing a laboratory scale process, the feasibility and quality characteristics of two different brassica species alone or mixed with winter wheat. Forages were planted in 25.4 cm pots at a seeding rate comparable with field application. Three separate forage varieties were used: a hybrid forage rapeseed (RAPE), a forage turnip (TURNIP) and winter wheat (WHEAT). Along with these 3 varieties, two mixed forage treatments were utilized; a 3-way mix spaced and covered mimicking the effect of being planted with a drill (DRILL) and a 3-way mix randomly sprinkled and left uncovered mimicking a more random application (BROADCAST). Each of these 5 treatments were replicated 5 times and grown in the greenhouse for 76 d. At the conclusion of this growing period, forages were harvested 3 cm above the soil and immediately placed into vacuum-sealed bags. Bags were placed in a dark room and incubated for a total of 83 d. Following incubation, samples were analyzed for fermentation characteristics to determine quality of the ensiling process. Data were analyzed using the MIXED procedures of SAS. There was a treatment effect (P &lt; 0.01) on the DM of the ensiled product whereby WHEAT (31.8%) was the greatest and BROADCAST (7.1%) was the least. The BROADCAST treatment had significantly (P &lt; 0.01) greater ammonia concentration, as well as acetic acid (P &lt; 0.05) concentration compared with all other treatments. No differences (P = 0.26) in pH were observed within the ensiled treatments. Overall, results of this trial suggest that it might be possible to use these brassica species as an ensiled feedstuff, though further testing is necessary to elucidate possible complications or limitations.
243 Translating Maternal Vitamin and Mineral Supplementation Effect on Early Developing Fetus Through Hepatic Long Non-Coding Rnas Profile in Beef Heifers
Authors: Anas Muhammad , Ward Alison , McCarthy Kacie L , Menezes Ana Clara Baiao , Borowicz Pawel P , Reynolds Larry P , Caton Joel S , Dahlen Carl R , Da Silva Diniz Wellison Jarles j 
Published: November 2023

Abstract
Maternal nutrition is critical during pregnancy as the fetus relies on the nutrients from the dam. Fetal organogenesis starts during the first trimester. Thus, an appropriate supply of nutrients, including vitamins and minerals, is indispensable. In the field of fetal developmental programming, there is still a lack of knowledge based on appropriate livestock models to explain the role of regulatory factors in translating the effect of maternal minerals and vitamins on fetal development and metabolic function. Therefore, this study was designed to investigate the effect of maternal vitamin and mineral supplementation (VTM -d 71 periconceptual to d 83 of pregnancy) on fetal liver expression of long non-coding RNAs (lncRNAs) and their potential regulatory metabolic pathways. Angus crossbreed beef heifers (n = 16) were supplemented (VTM, n = 8) or not (NoVTM, n = 8) with 113 g· heifer-1· day-1 of mineral premix (Purina Wind & Rain Storm All-Season 7.5 Complete) and all heifers were bred with female sexed semen from a single sire. Transcriptomic profiles were determined with RNA-Seq in fetal livers collected on d 83 ± 0.27 of gestation. After data quality control and read mapping, lncRNAs were predicted using the FEELnc pipeline. Using the DESeq2 software, we identified 50 differentially expressed novel lncRNAs (expression of 32 lncRNAs was upregulated and 18 were downregulated; FDR &lt; 0.05) located either downstream, upstream, or in exonic, or intronic regions of 51 genes (including PFKP, SLC30A10, KCNH8, ZNF451, MINPP1, BCL9, PAH, ITPR2, AHCY, and ABCG8), potentially regulating their expression. These genes could affect pathways (FDR &lt; 0.1) such as PI3K signaling, mineral storage and transport, and amino acids biosynthetic pathways (i.e., cysteine and methionine biosynthesis). Collectively, these results suggest that periconceptual maternal vitamin and mineral supplementation affects the expression of lncRNAs and potentially regulates the expression of genes involved in fetal liver development and function.