bluuebunny/crossref_metadata_2025_split huggingface dataset:
39 Combining Different Marker Prioritization Methods in the Analysis of High-density and Sequence Data
Authors: Ling Ashley S , Hay El Hamidi , Aggrey Samuel E , Rekaya Romdhane 
Published: October 2021

Abstract
High-density and sequence genotypes were expected to increase accuracy of genomic predictions through inclusion of markers in high linkage disequilibrium with causal loci, yet the realized increase has been minimal. Marker preselection has been proposed as a strategy to prioritize the most relevant markers to reduce the dimensionality of the association model and potentially increase accuracy. Strength of association statistics (estimated effect, p-value) and population differentiation measurements (FST score) have both been explored as criteria for preselection, but sensitivity to identify relevant markers decreases as random noise exceeds true signal variation. Combining both criteria into an index would leverage the unique contributions of each criterion and potentially increase prediction accuracies. A simulation consisting of 200 QTL, 777k SNP, and 7 generations under selection was generated (10 replicates). Marker preselection was compared across three criteria: only estimated effect (EFF), only FST score (FST), or an index combining the two previous statistics (COMB). In the COMB scenario, markers from genomic regions with high correlation (&gt;0.7) between estimated effect and FST score were selected along with markers whose estimated effect or FST score exceeded a certain threshold. Across replicates, COMB identified additional markers tagging between 1 and 7 QTL not tagged by EFF or FST that explain 0.2–5.4% of the genetic variance. The highest accuracy for EFF and FST was 0.76 and 0.73 when preselecting 2k and 10k markers, respectively. Under the best-case scenario (3,297 preselected markers), COMB improved accuracy by less than 1% and 4% compared to EFF and FST scenarios, respectively. Though an index combining multiple statistics may increase the number of QTL tagged by preselected markers and genetic variance explained relative to single-statistic preselection, this does not necessarily translate to a meaningful increase in accuracy. However, the results are dependent on the indexing method.
37 Single-step Genomic BLUP Fitting Snps or Haplotypes in Genetically-diverse Populations: A Simulation Study
Authors: Araujo Andre C , Carneiro Paulo , Oliveira Hinayah R , Schenkel Flavio S , Brito Luiz F 
Published: October 2021

Abstract
The successful implementation of genomic selection in more genetically diverse populations (e.g., sheep and goats) require larger training populations. Haplotype-based genomic predictions are hypothesized to perform better in comparison to single-SNP methods mainly due to the possibility of better capturing QTL effects in linkage disequilibrium (LD) with the markers. However, most genomic-prediction studies based on haplotypes were performed in populations with low effective population size (Ne &lt; 150). We aimed to investigate alternative approaches for fitting haplotypes using the single-step GBLUP method (ssGBLUP) in a genetically diverse population (Ne = 400). We simulated a composite sheep population, mimicking real populations based on literature parameters, using the QMSim software, with five replicates. We simulated a HD panel (600K) and two traits with different heritabilites (0.10 and 0.30). Pseudo-SNPs from unique haplotype alleles derived from LD blocks with thresholds of 0.1, 0.3, and 0.6 (LD01, LD03, and LD06, respectively) were used in the analyses. The LD-blocks were constructed using a 50K panel designed from the simulated HD. The training population was composed of 60,000 individuals with phenotypes, 8,000 of them also had genotypes, and 2,000 young genotyped individuals were used as the validation set. The genomic relationship (G) in the ssGBLUP was constructed using both independent markers and pseudo-SNPs (haplotypes). A linear mixed effects model was used to test the effect of the G on the accuracies of prediction, followed by the Tukey test with 5% of significance. No blocks were created with LD06. The accuracies with the 50K panel, LD01, and LD03 for the moderate heritability were 0.41(0.00), 0.40(0.01) and 0.41(0.00), respectively, and 0.24(0.01) 0.23(0.01), and 0.24(0.01) for the low heritability scenario. No statistical differences were observed. Based on our findings, haplotype-based predictions did not improve the accuracy of genomic breeding values in genetically diverse populations.
46 Footprints of Selection in Angus and Hanwoo Beef Cattle Using Imputed Whole Genome Sequence Data
Authors: Nawaz Muhammad Yasir , Savegnago Rodrigo Pelicioni , Gondro Cedric 
Published: October 2021

Abstract
In this study, we detected genome wide footprints of selection in Hanwoo and Angus beef cattle using different allele frequency and haplotype-based methods based on imputed whole genome sequence data. Our dataset included 13,202 Angus and 10,437 Hanwoo animals with 10,057,633 and 13,241,550 imputed SNPs, respectively. A subset of data with 6,873,624 common SNPs between the two populations was used to estimate signatures of selection parameters, both within (runs of homozygosity and extended haplotype homozygosity) and between (allele fixation index, extended haplotype homozygosity) the breeds in order to infer evidence of selection. We observed that correlations between various measures of selection ranged between 0.01 to 0.42. Assuming these parameters were complementary to each other, we combined them into a composite selection signal to identify regions under selection in both beef breeds. The composite signal was based on the average of fractional ranks of individual selection measures for every SNP. We identified some selection signatures that were common between the breeds while others were independent. We also observed that more genomic regions were selected in Angus as compared to Hanwoo. Candidate genes within significant genomic regions may help explain mechanisms of adaptation, domestication history and loci for important traits in Angus and Hanwoo cattle. In the future, we will use the top SNPs under selection for genomic prediction of carcass traits in both breeds.
56 Awardee Talk: Genetic Improvement of Disease Resilience
Authors: Dekkers Jack C , Fortin Frederic , Dyck Michael , Harding John , Plastow Graham 
Published: October 2021

Abstract
Infectious disease represents one of the largest cost components to the swine industry, incurring veterinary costs, loss of pigs due to mortality, reduced performance, and reduced animal welfare. Strategies to reduce the incidence and impact of infectious disease include biosecurity, vaccination, veterinary treatment, and selection for genetic resistance. However, biosecurity protocols that keep most infectious pathogens out are not feasible at the commercial level in hog-dense regions, effective vaccines are only available and/or efficacious for some pathogens, and complete genetic resistance is also limited to only a few pathogens (e.g. F18 E.coli) or is only possible to achieve by gene editing (e.g. the PRRS-resistant pig created by editing the CD163 gene). Given these limitations, commercial pigs will continue to be exposed to and infected by pathogens for the foreseeable future. In such a scenario, the ability of an animal to clear the infection while maintaining performance is an important characteristic, which is referred to as disease resilience and is a useful target for inclusion in breeding programs. However, collection of data on disease resilience for genetic improvement requires animals to be exposed to disease, which is not possible in the nucleus herds of breeding programs that most selection is practiced in. To study the genetic basis of disease resilience and develop phenotypes, genetic tests, or indicator traits that could be used to select for disease resilience, a polymicrobial natural disease challenge model was established in grow-finish pigs at the Center de Développement du Porc du Québec, in collaboration with PigGen Canada. The purpose of this presentation is to present results on phenotypes that are relevant to disease resilience, including estimates of genetic parameters, and on potential indicator traits for disease resilience that could be collected in nucleus herds. Funding by Genome Canada, Genome Alberta, PigGen Canada, and USDA NIFA grant #2017-67007-26144.
60 The Effect of Neomycin Inclusion in Milk Replacer on Gut Health and Development in Preweaned Male Holstein Calves
Authors: Buss Lauralise , Yohe Taylor , Cangiano Lautaro Rostoll , Keunen Aaron , Guan Leluo , Renaud David , Steele Michael A 
Published: October 2021

Abstract
Neomycin is commonly used in calf milk replacers (MR) to prevent diarrhea, however, antimicrobial exposure in early life may have consequences to gut development. The objective of this study was to investigate the effects of neomycin inclusion in MR on calf gut health and development. Thirty-six calves were randomly assigned to one of three treatments: control (CON), non-medicated (MR, n = 12), short-term antimicrobial exposure (ST: 20 mg/kg BW neomycin mixed in MR from d 1–14, n = 12), or long-term antimicrobial exposure (LT: 20 mg/kg BW neomycin in MR from d 1–28, n = 12). Fecal samples were collected weekly to measure total bacteria, and gut permeability was measured in week 2 and 4 by comparing serum recovery of orally dosed lactulose and D-mannitol markers. Calves were dissected at week 5 to collect intestinal tissues, which were used to analyze histology, gene expression and total bacteria abundance. Digesta samples were collected to analyze for total bacteria abundance and volatile fatty acid (VFA) concentrations. No treatment effects were found in the amounts of total bacteria in fecal, digesta, or tissue samples. Marker recovery in serum was higher at week 2 compared to week 4 (P &lt; 0.01), suggesting that calves in early life have higher gut permeability. Histomorphological measures were similar, except for villi length in the distal jejunum, which was longest in ST calves (P = 0.05). Tight-junction, mucus, and inflammatory-associated gene expression was similar overall, although the expression of Tight junction protein-1 in the distal jejunum was lowest in CON calves (P = 0.04). Distal jejunum acetic acid, propionic acid, and total VFA tended to be highest in LT calves (P = 0.09; P = 0.06; P = 0.07, respectively). Although this study found few consequences of neomycin to gut health, the lack of benefits supports the argument that antimicrobials should be used prudently.
78 Opportunities and Limitations of Modeling and Data Analytics for Precision Livestock Farming
Authors: Remus Aline , Pomar Candido , Warner Daniel 
Published: October 2021

Abstract
Precision livestock farming (PLF) involves the use of sensors that captures large amounts of real-time information at the building, herd or animal level, which are later processed to control the system. Data processing can be accomplished using mathematical models (MM), artificial intelligence algorithms (AI) or a combination of these and other methods. The choice of the method must be made according to the volume of data to be processed, its nature and the relationship between the available information and the desired control of the system. Several components of PLF such as precision nutrition, early disease detection, animal welfare among others may require sophisticated data processing methods. MM is today the preferred method to estimate nutrient requirements in the precision nutrition component of PLF. Conventional MM estimate average population responses using historical population information. Important limitations of these models are the assumption that all the individuals of the population have the same response to a given nutrient provision and that they have not been developed for real-time estimations using up-to-date available information. Therefore, MM have to be developed specifically for PLF and operate in real-time at individual or small group level, considering the between and within-animal variation. Growth patterns, nutrient utilization and behavior vary among animals and herds. There are opportunities to combine data-driven AI with knowledge-driven MM to control more complex PLF components. AI thrive in large complex datasets, where establishing connections can be otherwise difficult due to data complexity, volume and where flexibility is needed to process real-time data from individuals. In contrast, knowledge-driven MM can simplify complex biological systems based on well-established concepts and information. In both cases, PLF models must be flexible enough to consider changes over time for the same animal or herd, and among animals and herds, acknowledging the method limitation while using its strength.
95 Effects of Three Implant Programs on Growth Performance, Carcass Outcomes, and Weekly Activity Minutes of Finishing Steers Fed Different Days on Feed
Authors: Martinez Socorro , Word Alyssa B , Holland Ben P , Karr Kendall , Hutcheson John P , Walter Lee-Anne J , Richeson John , Lawrence Ty E , Samuelson Kendall L 
Published: October 2021

Abstract
This study evaluated the effects of a single slow-release implant compared to two re-implant programs administered at either 120 days on feed (DOF) or 80 days from harvest on performance, carcass characteristics, and activity of serially harvested feedlot cattle. Using a randomized complete block design, steers (n = 4,680) were randomly assigned to 72 pens and 1 of 12 treatments in a 3 × 4 factorial arrangement. Treatments were either a slow-release implant (SR), an initial slow-release implant followed by re-implant at 120 DOF (SR+RI-120), or an initial slow-release implant followed by re-implant 80 days from harvest (SR+RI-80) administered to cattle harvested at 166, 180, 194, or 208 DOF. A 3-axis accelerometer ear-tag was used in a subset (n =1,080) of animals to quantify rumination time and activity. No interactions (P ≥ 0.09) were observed for implant × DOF. Implant did not affect (P ≥ 0.25) final BW, ADG, or DMI, but re-implanted steers had a greater (P &lt; 0.01) G:F ratio than SR. Re-implanted steers also had greater (P ≤ 0.03) HCW, dressed yield, and ribeye area, but less (P &lt; 0.01) backfat, marbling, and empty body fat (EBF) compared to SR. Re-implanted steers had less (P &lt; 0.01) choice and yield grade 4 and 5 carcasses than SR steers. As DOF increased, HCW, dressed yield, backfat, marbling, and EBF increased linearly (P &lt; 0.01). The percentage of choice and yield grade 4 and 5 carcasses also increased (P &lt; 0.01) linearly with additional DOF. An implant × day effect (P &lt; 0.01) for weekly activity minutes suggests re-implanted steers had greater activity after re-implant administration. Re-implanting within the payout period of a slow-release implant increases feed efficiency, HCW, dressed yield, and activity minutes, but decreases carcass fatness and reduces quality grade regardless of timing of secondary implant administration.
103 The Economics and Role of Beef X Dairy Calves in the Beef Supply Chain
Authors: Smith Jason K , Piñeiro Juan , Benavidez Justin 
Published: October 2021

Abstract
Utilizing beef genetics in dairy herds to produce terminal beef x dairy (BXD) crosses is a growing trend in the U.S. dairy industry. It has been estimated that more than two million U.S. BXD calves were born in 2020, which is a practice that is expected to continue to grow throughout the foreseeable future. While not a new concept, the widespread adoption, scale, and strategies currently being used to produce BXD calves have recently received considerable industry attention. Although the increased duration of feeding exposes BXD feeders to increased price and production risks when compared to straightbred beef cattle, these risks are met with several potential benefits. A prime example of such benefits includes a consistent supply of uniform, traceable feeder cattle that are easily age and source verified, that also serve as ideal candidates for enrollment in or development of other value-added marketing programs. Current demand, as indicated by newborn calf prices, suggests that the industry perceives BXD calves to be superior when compared to their straightbred dairy breed contemporaries, and at times, suggests that they may be overvalued. Sustaining such demand will require BXD calves to meet or exceed the performance and profitability expectations of the various production sectors of the beef industry. Results of a multi-year analysis of the economics of BXD calves as compared to cattle of straightbred beef or dairy breed composition will be presented. Furthermore, specific factors expected to influence value throughout the production supply chain will be outlined and discussed. Calfhood management practices that promote calf health, paired with genetic selection strategies focused on complementary traits that minimize cost of gain and increase cutability, such as feed efficiency, carcass yield, and muscularity, will play key roles in sustaining the value of BXD calves to all aspects of the beef supply chain.
100 Management Strategies to Optimize Health and Performance of Pre-weaned Calves
Authors: Machado Vinicius , Ballou Michael 
Published: October 2021

Abstract
In the United States, 1 in each 10 dairy replacement heifers were raised in a calf raising facility, and that at least half of farms with 500 or more lactating animals raised some of their calves in a specialized calf ranch. Approximately 80% of calves are individually housed, but the type of housing (e.g., outside hutch, inside a barn) varies based on location of calf-raising operations. Generally, the benchmark for optimal growth of calves is to double their birth weight by weaning. Such benchmark can only be achieved with consistent management and nutrition. Hence, it is not surprising that in large operations, up to 90% of facilities receive regular visits of both veterinarians and nutritionists. Milk-replacer is fed in more than 80% of operations, while milk (sealable or non-sealable) is fed in approximately 30% of calf raising facilities. Health challenges such as scours, and bovine respiratory disease (BRD) can hinder the performance of calves and are major causes of mortality in calf ranches. In addition to optimal colostrum management, vaccination and early diagnosis/ treatment can prevent major economic losses caused by these diseases. Compared to calves raised in their original dairies, calves raised in off-site operations are exposed to additional stressors that can lead to impairment of their immune system and weaken their resistance against pathogens. For instance, transportation at a very young age and comingling with animals from other dairies can increase the risk of diseases. Current research efforts are focusing in determining individual factors such as body weight at arrival or biomarkers of inflammation and stress that can be predictive of disease morbidity, mortality, and performance of calves. Such information could be used in the future to optimize management and to develop targeted preventative strategies to reduce incidence of diseases and mortality during the pre-weaned period.
98 What We Think We “know” About Beef X Dairy Crossbred Cattle in the Feedlot
Authors: Felix Tara L 
Published: October 2021

Abstract
To increase profitably, dairy farms across the United States have rapidly adopted breeding a portion of their cows to beef sires, generating crossbred progeny. The resulting progeny have, in some cases, increased the value of the calf to the dairy, due to their perceived potential for improved growth, feed efficiency, and carcass characteristics for beef production. U.S. research is behind our European counterparts in recommending the appropriate beef sires for dairy matings, and U.S. semen trends show Angus sales over many other breeds. However, Kempster et al. (1982) reported that calves sired by British breed bulls were actually at a disadvantage in growth performance compared to even purebred Holstein calves. Finnish researchers agreed, reporting that the resulting crossbreds from Aberdeen Angus and Hereford bulls were extremely variable, making them undesirable for beef production. However, resulting crossbred calves from late maturing breed types (Charolais, Limousine, and Simmental) had better average daily gain and carcass characteristics than their counterparts from early maturing breeds (Huuskonen et al., 2013). A comprehensive review of early crossbred systems similarly suggested that calves sired by Continental breeds, like Charolais, had an advantage in the feedlot and the packing house (Shank, 2003). Going a bit further, another European study examined the used of 3 beef breeds (Belgian Blue, Limousine, and Galacian Blonde) known for heavy muscling, but not common in the United States, for use as crossbreeding sires (Fouz et al., 2012). Holstein cows bred to Belgian Blue sires had the greatest difficulty calving; however, calving difficulties were reduced with increasing dam age (Fouz et al., 2012). Unfortunately, that trial did not go on to evaluate feedlot performance. Thus, there remains a dearth of scientific references for crossbred mating decisions as well as subsequent growth performance and carcass outcomes.
107 Quality Parameters of Pet Treats Generated from Beef Processing Co-products
Authors: Presume Marc R , Soler Rigo F , Sandoval Jorge L , Avila Luis P , Chilenje Moses E , Odom Catherine M , Garner Laura J , Morey Amit U , Mason Robert P , Altom Eric K , Starkey Charles W 
Published: October 2021

Abstract
By-products such as beef liver (BL) and beef heart (BH), while rich in protein, vitamins, and minerals, can be difficult products for incorporation into mixtures. Sodium alginate (SA) and calcium lactate (CL) can be used to improve structure of protein sources. The objective was to determine the quality of restructured BL and BH pet treats using ALGIN as a structure forming agent. Quality parameters assessed were pH, expressible moisture, cooking loss, and water activity of raw and dehydrated pet treats. After grinding, BL and BH, were mixed: 25%BL:75%BH, 50%BL:50%BH, and 75%BL:25%BH. The 3 BL:BH combinations were mixed with 2 dosages of ALGIN (0.5% SA + 0.425% CL, and 1% SA + 0.85% CL) to produce 6 treatments. Each treatment was then extruded into 20-mm-thick jerky slices and refrigerated at 3°C for 48 h. Samples were dehydrated at 93°C for 2.5 h for cooking loss analysis. Ten raw samples (25.4 mm × 25.4 mm) were used to measure expressible moisture, and another ten raw samples were used to measure pH. Water activity was assessed on ten raw and ten dehydrated samples. Data were analyzed with the GLIMMIX procedure of SAS and means were separated at P ≤ 0.05. Cooking loss decreased as ALGIN dosage increased in all BL and BH mixtures (P &lt; 0.0001); however, cooking loss percentage increased as BH proportions increased (P = 0.0001). Water activity of dehydrated samples decreased as BL proportions increased (P &lt; 0.0001), but with increasing ALGIN dosage, water activity of dehydrated treats increased (P = 0.0193). Raw pH was not affected by treatment. Expressible moisture of samples increased with increasing BL proportions (P &lt; 0.0001) but decreased as ALGIN dosage decreased (P &lt; 0.0001). Use of ALGIN allowed for BL and BH to be restructured into an acceptable form for use in pet treats.