bluuebunny/crossref_metadata_2025_split huggingface dataset:
49 Predicting Breeding Values of Purebred Pigs for Crossbred Performance Using Crossbred Phenotypes and Genotypes
Authors: Leite Natalia , Chen Ching-Yi , Herring Willian O , Tsuruta Shogo , Lourenco Daniela 
Published: October 2021

Abstract
Phenotyping a large number of crossbred progeny for the evaluation of purebred animals can be expensive. As genotyping with low-density panels is becoming cheaper, we aimed to evaluate the tradeoff between having different percentages of genotypes and phenotypes for crossbred progeny of candidate boars. We used the linear regression (LR) method to investigate changes in accuracy, bias, and inflation of breeding values for crossbred traits in purebred boars. A total of 304,582 purebred and 147,474 crossbred animals were phenotyped for average daily gain (ADG) and backfat thickness (BF), out of which 46,691 purebred and 13,117 crossbred animals were genotyped. Genomic information consisted of imputed genotypes for 40,247 SNP markers after quality control. A four-trait animal model under single-step GBLUP was used that included phenotypes recorded in purebred and crossbred animals as correlated traits. The LR statistics were calculated based on breeding values of young purebred sires from complete and partial data. The first complete data included genotypes for purebreds and phenotypes for purebreds and crossbreds, whereas the second included also genotypes for crossbreds. The partial data included phenotypes on 50% or none of the progeny of validation sires, with or without genotypes for crossbred animals. When 50% of the progeny has phenotypes, adding genotypes for crossbred progeny marginally increased accuracy of ADG (0.77 vs 0.78) for 47 boars with more than 150 progeny with phenotypes. No increase was observed for BF. A small increase in bias and inflation by adding crossbred genotypes was observed for ADG but not for BF. When no phenotypes were available for crossbred progeny, accuracy for both traits was lower but improved with crossbred genotypes for ADG (0.61 vs 0.64) for boars with more than 150 progeny. The tradeoff between phenotypes and genotypes should be further investigated in larger datasets with more validation boars.
42 An Improved, High-quality Ovine Reference Genome Assembly
Authors: Davenport Kimberly M , Bickhart Derek M , Worley Kim , Murali Shwetha C , Cockett Noelle , Heaton Michael P , Smith Timothy P L , Murdoch Brenda M , Rosen Benjamin D 
Published: October 2021

Abstract
Sheep are an important agricultural species used for both food and fiber in the United States and globally. A high-quality reference genome enhances the ability to discover genetic and biological mechanisms influencing important traits, such as meat and wool quality. The rapid advances in genome assembly algorithms and emergence of increasingly long sequence read length provide the opportunity for an improved de novo assembly of the sheep reference genome. Tissue was collected postmortem from an adult Rambouillet ewe selected by USDA-ARS for the Ovine Functional Annotation of Animal Genomes project. Short-read (55x coverage), long-read PacBio (75x coverage), and Hi-C data from this ewe were retrieved from public databases. We generated an additional 50x coverage of Oxford Nanopore data and assembled the combined long-read data with canu v1.9. The assembled contigs were polished with Nanopolish v0.12.5 and scaffolded using Hi-C data with Salsa v2.2. Gaps were filled with PBsuite v15.8.24 and polished with Nanopolish v0.12.5 followed by removal of duplicate contigs with PurgeDups v1.0.1. Chromosomes were oriented by identifying centromeres and telomeres with RepeatMasker v4.1.1, indicating a need to reverse the orientation of chromosome 11 relative to Oar_rambouillet_v1.0. Final polishing was performed with two rounds of a pipeline which consisted of freebayes v1.3.1 to call variants, Merfin to validate them, and BCFtools to generate the consensus fasta. The ARS-UI_Ramb_v2.0 assembly has improved continuity (contig N50 of 43.19 Mb) with a 19-fold and 38-fold decrease in the number of scaffolds compared with Oar_rambouillet_v1.0 and Oar_v4.0. ARS-UI_Ramb_v2.0 has greater per-base accuracy and fewer insertions and deletions identified from mapped RNA sequence than previous assemblies. This significantly improved reference assembly, public at NCBI GenBank under accession number GCA_016772045, will optimize the functional annotation of the sheep genome and facilitate improved mapping accuracy of genetic variant and expression data for traits relevant the sheep industry.
47 Genomic Studies of Reproductive Performance in American Mink
Authors: Valipour Shafagh , Karimi Karim , Miar Younes 
Published: October 2021

Abstract
Improving reproductive efficiency is one of the main breeding goals in mink farming. Understanding the genetics of reproductive performance is essential for the development of effective breeding programs in mink. The objectives of this study are to 1) estimate the phenotypic and genetic parameters for litter sizes (LS), mortality rate at birth. (MB) and gestation-length (GL) traits; 2) perform genome-wide association studies (GWAS) for these reproductive traits; 3) implement GWAS results in the selection of mink for reproductive performance; 4) explore the potential for genomic selection in mink. The detailed reproductive performance on 3,500 female mink has been collected at the Canadian Center for Fur Animal Research at Dalhousie University (Truro, NS, Canada), in which, 1,000 of them will be genotyped with Affymetrix 50k SNP panel. A series of univariate and bivariate analyses were implemented in ASREML software to estimate the genetic and phenotypic parameters. Heritability estimates (±SE) were low-to-moderate, ranged from 0.06±0.02 for total number born to 0.23±0.03 for GL. High positive genetic correlations (±SE) were observed between LS traits, ranged from 0.59±0.18 to 0.85±0.11. There was a moderate genetic correlation (±SE) between MB and total number of kits born (0.46±0.15). However, MB had a favorable strong negative genetic correlation (±SE) with the number of weaned kits (–0.75±0.16). These estimated genetic parameters can be incorporated into Canadian mink breeding programs. Considering the low-to-moderate heritability of reproduction traits, the availability of the mink reference genome and genotyping panel will provide opportunities to accelerate mink breeding through genomics. The results of this project will contribute significantly to the current genetic knowledge of reproductive traits and identify the opportunities for genetic improvement through the application of genomics. The overall project aim is to develop a cost-effective, low-density panel of markers for the implementation of genomic selection for reproductive performance in mink.
59 Insights into Complex Traits from Human Genetics
Authors: Kemper Kathryn 
Published: October 2021

Abstract
Genomic selection has been implemented successfully in many livestock industries for genetic improvement. However, genomic selection provides limited insight into the genetic mechanisms underlying variation in complex traits. In contrast, human genetics has a focus on understanding genetic architecture and the origins of quantitative trait variation. This presentation will discuss a number of examples from human genetics which can inform our understanding of the nature of variation in complex traits. So-called ‘monogenic’ conditions, for example, are proving to have more complex genetic architecture than naïve expectations might suggest. Massive data sets of millions of people are also enabling longstanding questions to be addressed. Traits such as height, for example, are affected by a very large but finite number of loci. We can reconcile seemingly disparate heritability estimates from different experimental designs by accounting for assortative mating. The presentation will provide a brief update on current approaches to genomic prediction in human genetics and discuss the implications of these findings for understanding and predicting complex traits in livestock.
58 Integrating Quantitative Genetics and Epidemiology: Why Selection Against Infectious Diseases Is More Promising Than We Think
Authors: Bijma Piter , Bijma Piter 
Published: October 2021

Abstract
Pathogens have profound effects on livestock. The low heritabilities of individual binary disease status suggest limited prospects for genetic improvement. However, a proper quantitative genetic theory for infectious diseases, including transmission dynamics, is currently lacking. Here we present a quantitative genetic theory for endemic infectious diseases, focussing on the genetic factors that determine the prevalence (P; the mean fraction of the population that is infected). We present simple expressions for breeding values and genetic parameters for the prevalence. Without genetic variation in infectiousness, breeding values for prevalence are a factor 1/P greater than the ordinary breeding values for individual binary disease status (0/1). Hence, even though prevalence is the simple average of individual binary disease status, breeding values for prevalence show much greater variation than our ordinary breeding values. This implies that the genetic variance that determines the potential response of prevalence to selection is largely due to indirect genetic effects (IGE), and thus hidden to ordinary genetic analysis and selection. Hence, the genetic variance that determines the potential of livestock populations to respond to selection must be much greater than currently believed, particularly at low prevalence. We evaluated this implication using simulation of endemics following standard methods in epidemiology. Results show that response of prevalence to selection increases very strongly when prevalence decreases, and is much greater than predicted by our ordinary breeding values. These results supports our theoretical findings, and show that selection against infectious diseases is much more promising than currently believed.
57 The Saga of Just One QTL; From Laying Hen Bone Strength to One Carbon Metabolism
Authors: Dunn Ian C , McCormack Heather , de Koning Dirk-Jan , Navarro Alejandro Rodríguez , Schmutz Matthias , Andersson Björn , Cavero David , Fleming Robert , Wilson Peter , Maidin Maisarah 
Published: October 2021

Abstract
Skeletal damage is a challenge for laying hens, as the adaptations for egg laying make them susceptible to osteoporosis. We know that activity, growth and puberty influence skeletal quality genetics. However, in this story, we follow the process of resolving a QTL for skeletal quality to a single gene. Providing both a nutritional and a genetic solution and illustrating another level of complexity. Using divergently selected populations in an F2 cross, a QTL for skeletal quality was described. Utilising a series of experiments in the commercial founder line the QTL was fine mapped on chromosome 1 and the differences in physiology of hens that segregated for markers at the locus defined e.g. tibia breaking strength 200.4 vs 218.1 Newton (p&lt; 0.002). Transcriptome profiling of tibia from the high and low bone strength genotype revealed a highly differentially expressed gene co localising to the QTL, the enzyme cystathionine beta synthase (CBS). CBS is a component of one carbon metabolism. Plasma homocysteine, the substrate of CBS had a higher concentration in the genotype associated with poor bone quality. Homocysteine interferes with crosslinking of the collagen matrix, critical to bone formation. Homocysteine can be re-methylated into methionine, a limiting amino acid in laying hens, using betaine as a methyl donor. Testing the hypothesis that reducing plasma homocysteine by feeding betaine, a widely available feed additive, would improve bone quality in laying hens proved successful.This is just one component of a complex trait and its elucidation took us along unexpected routes. However, I am optimistic that with modern tools and an open mind we can progress more quickly. Alongside understanding the factors that determine skeletal quality genetics, the discovery of the mechanisms behind complex traits, although rarely easy, offer the potential for novel interventions to improve animal health and production.
65 Immunological Changes in Response to Treatment of Bovine Respiratory Disease in Newly Received Commercial Stocker Calves
Authors: Akter Afroza , Shepherd Elizabeth , Caldwell Marc , Pighetti Gina , Schneider Liesel G 
Published: October 2021

Abstract
Immunological changes in stocker calves treated for Bovine Respiratory Disease (BRD) could indicate disease progression or treatment success. Our objective was to determine the changes in immune parameters in stocker calves in response to the number of treatments they received for BRD. Forty newly weaned crossbred beef steers purchased from the auction market were kept at a commercial stocker operation at Crossville during winter 2020. Calves were monitored for 4wks and blood samples were collected on days 0, 7, 14, and 21. All calves were assigned a clinical severity scoring (CSS; 0: normal, 3: moribund) on each sampling day. Antibiotic treatment was assigned when calves were categorized as having BRD based on CSS and rectal temperature. Immune parameters (Haptoglobin, IL-8, IL-1β, and TNFα) were determined using commercial ELISA kits. Calves were categorized based on the cumulative number of treatments received by the end of study period (0x, 1x, and ≥2x). Proc GLIMMIX (SAS 9.4) was used to test the fixed effects of treatment number, day of treatment, and their interaction, accounting for day as a repeated measure. To achieve the normality of residuals, log transformation was performed. Significance was determined at α= 0.05. The incidence of BRD was 40% (16 out of 40). Haptoglobin concentration was higher (P = 0.02) in ≥2x (1.85 ± 0.30 mg/mL) compared to 0x (0.74 ± 0.21 mg/mL). A treatment by day interaction (P = 0.03) was observed for IL-8. On day 14, calves that were treated ≥2x times had higher IL-8 compared to the rest of the statuses; no differences were observed for other days between statuses. The lowest IL-1β (P = 0.04) and TNFα (P = 0.001) concentrations were observed on day 0. Results from this study provide an overview of the immunological changes occurring in BRD-affected stocker calves requiring different treatment numbers.
61 Oral Dosing Loline Alkaloid and Its Effects Against Mixed Infection of L4 Teladorsagia Circumcincta, and Trichostrongylus Colubriformis, and Adult Haemonchus Contortus
Authors: Froehlich Kelly , Greer Andrew 
Published: October 2021

Abstract
Loline, an alkaloid produced by Epichloë endophytes in pastoral grass species, is considered non-toxic with suggested antimicrobial and anthelmintic properties. In vivo metabolism of loline suggests ability to reach the abomasum or intestine, and anthelmintic benefit is indicated in vitro when parasites are in either a developmental stage close to the gastric mucus layers or adult stage consuming blood. Therefore, the objective of this project was to investigate the validation of using a loline seed extract as a natural anthelmintic in parasitized lambs. Sixteen Coopworth lambs were individually penned, offered ad-libitum lucerne pellets and water and randomly assigned to 3 treatment groups; CON; no treatment, or treatment with a Festuca pratensis seed extract with (LOL) or without loline (NIL). Lambs were orally infected with 20,0000 L3 Haemonchus contortus on day 0, and 10,000 L3 Teladorsagia circumcincta, and Trichostrongylus colubriformis on day 14. Parasites then matured to determine lolines efficacy on blood feeding adult Haemonchus contortus and L4 mucosal browsers Teladorsagia circumcincta, and Trichostrongylus colubriformis. Loline was orally dosed at 52.5 mg/kg LW starting on day 13, and every other day until slaughter for worm enumeration on day 28. Feed intake and refusals were recorded daily, and fecal samples were taken prior to infection, on loline dose days and at slaughter. Worm and fecal egg counts were transformed to log10 and all data were analyzed in Genstat (18th edition). Significance was declared at P &lt; 0.05. Worm burdens of T. circumcincta (P = 0.96), T. colubriformis (P = 0.43), and H. contortus (P = 0.15) were not different between treatments. No treatment difference (P = 0.39) was observed in fecal egg counts, weight gain (P = 0.51), or feed intake (P = 0.18). Average growth efficiency (kg LWG/ kg DM intake) was 0.18 in CON which was less (P = 0.01) than LOL (0.24) or NIL (0.23). In conclusion, limited evidence supported an in vivo anti-parasitic effect of loline.
69 Occurrence of Mycotoxins in 2020 US Corn Grain and Corn By-product Feeds
Authors: Gott Paige N , Schwandt Erin , Ramirez Shelby M , Hofstetter Ursula , Murugesan Raj 
Published: October 2021

Abstract
Mycotoxins are fungal metabolites that limit animal health and performance through various negative effects including reduced feed intake, diarrhea, and compromised immune function. These toxic metabolites have been detected in a broad range of feedstuffs worldwide. This study investigated mycotoxin occurrence and contamination levels in U.S. corn grain samples marked as 2020 harvest year and corn by-product feed samples submitted since October 2020. Samples were screened via LC-MS/MS for six major mycotoxin groups including: aflatoxins, type A trichothecenes, type B trichothecenes (B-Trich), fumonisins (FUM), zearalenone (ZEN), and ochratoxin A. Results from samples that were above the limit of detection for each respective mycotoxin group were analyzed using the GLIMMIX procedure (SAS 9.4, Cary, NC) to test the effect of harvest year on mean contamination level. Results are presented in Table 1. Occurrence levels of B-Trich, ZEN, and FUM in 2020 corn grain are numerically lower than those from 2019. Mean B-Trich level (parts per billion, ppb) for corn grain samples harvested in 2020 was similar to 2019 crop year. Contamination levels of FUM and ZEN were similar for 2020 crop as compared to prior harvest years. Mycotoxin occurrence in corn by-product feeds continued to be high at 99, 85, and 95% for B-Trich, ZEN, and FUM, respectively. Mean B-Trich and ZEN levels in 2020 corn by-products were similar to respective contamination levels in 2018, but were lower than 2019 samples. Mean FUM contamination in corn by-products has been similar across reported years. Preliminary results of the 2020 corn grain survey indicate mean mycotoxin contamination levels are similar to those observed the past two crop years while levels of B-Trich and ZEN in corn by-product feeds are reduced from 2019. Corn-based feed ingredients may present challenges to producers due to the presence of mycotoxin contamination, therefore, continued monitoring is warranted.
67 Association of Morbidity and Failure of Transfer of Passive Immunity in Beef-dairy Crossbred Calves
Authors: Pereira Jessica , Marcondes Marcos I , Carvalho Pedro H , Silva Del Rio Noelia , Bittar João , Ferreira Fernanda C 
Published: October 2021

Abstract
The objective of this prospective cohort study was to describe the prevalence of failure of transfer of passive immunity (FTPI) in beef-dairy crossbred calves, and its association with morbidity up to 30 d of life. A total of 393 one d old calves were enrolled upon arrival at a calf facility in Central Valley, California, from Jan-Mar 2021. Farm of origin, breed, sex, and weight were recorded at the day of arrival. Blood was collected at 24 ± 1 h post-arrival to evaluate total serum protein (TSP) and % Brix reading. Calves were classified as having FTPI if TSP &lt; 5.2 g/dL, and brix &lt; 8.2%. Farm personnel performed daily health evaluations and recorded diseases. Descriptive statistics, logistic regression, and survival analysis were conducted using SAS. Calves’ breeds were Angus × Holstein (AN × HO, 58%), Charolais × Jersey (CH × JE, 37%), and Angus × Jersey (AN × JE, 5%). Prevalence of FTPI was 36% (TSP) and 34% (brix). TSP and %Brix readings had a strong correlation (r = 0,99, P &lt; 0.0001). Overall morbidity was 78% (70% had only diarrhea, 7% only respiratory disease and 23% both). The odds of disease up to 30 d was not associated with sex (female vs. male, OR = 0.77, 95% CI = 0.36–1.62), or breed (AN × HO vs. CH × JE, OR = 1.35, CI = 0.63–2.91; AN × JE not included in this analysis). FTPI was associated with greater odds of disease (OR = 2.91, CI = 1.19–7.09, P = 0.01). There was a tendency for association between FTPI and the hazard of disease up to 30 d (HR = 1.43, CI = 0.96–2.10, P = 0.07). Therefore, FTPI may predispose beef-dairy crossbred calves to diarrhea and respiratory disease up to 30 d of life.
73 Antimicrobial Resistance, Agriculture, and the One Health Continuum
Authors: Topp Ed 
Published: October 2021

Abstract
The One Health concept specifies that the microbiomes of humans and animals are connected, both through direct contact, and indirectly through the environment. Managing the flow of microorganisms of human or animal health concern across the One Health continuum requires a transdisciplinary approach to address problems at the intersection of people, animals, and their environments. This presentation will use the management of antimicrobial resistance as an example of how a One Health approach can identify and develop solutions to improve the health and wellness of people, animals, and the environment.
82 Application of Precision Sensor Technologies, Real-time Data Analytics, and Dynamic Models on Extensive Western Rangeland Grazing Systems
Authors: Menendez Hector M , Brennan Jameson 
Published: October 2021

Abstract
Approximately 40% of the land use within the Northern Great Plains is dedicated to livestock production, with much of the 89.9 million head of cattle and calves in the U.S. concentrated in this area. Precision livestock management has ushered in a new era of sensors and technology to monitor individual animal’s health, reproductive, and nutritional status in real-time to improve efficiency. Despite these advances, most of the research has been conducted on dairy operations or within feedlot settings. Incorporation on extensive rangeland production systems remains relatively absent (Brennan et al., 2021). This is primarily due to difficulties in studying animals on rangelands caused by heterogeneity of forage resources, variable environmental conditions, and challenges associated with accessing information across vast distances, often without cellular or internet connection. Advances in communication technology are increasingly connecting remote areas, creating new opportunities to improve livestock production efficiency on extensive rangelands using precision technology. Numerous challenges still exist, including applying and integrating multiple technologies across platforms, effectiveness in a real-world setting, technical skills, and knowledge to utilize real-time data, and achieving economic return for livestock producers. Specifically, we discuss the application of precision technologies and mathematical models for improving ruminant nutrition in rangeland systems (Menendez and Tedeschi, 2020). Opportunities exist to refine or develop the next generation of equations/models that more adequately represent nutrient dynamics such as diet selection, supplementation, movement, behavior, water intake, feed conversion efficiency, heat/cold stress, and gain on an individual animal basis. However, effective adoption and adaptability of new technologies/data analytics merit the consideration of potential intended-and-unintended consequences, such as producer dependency on complex hardware and software systems. Hence, precision capabilities coupled with mathematical models are likely the next step to substantially enhance livestock performance in extensive systems when coupled with feasible and reliable long-term strategies.