Beef Science Commons^™

Using Precision Technology To Measure Cattle Methane Emissions And Intake On Western South Dakota Rangelands, Lillian J. Mcfadden, Ken Olson, Krista Ehlert, Jameson Brennan, Amanda D. Blair, Hector Menendez Iii

SDSU Beef Day 2022 Summary Publication

Study Description:

Cattle DMI is an essential component of calculating cattle stocking rates, determining nutrient requirements, and evaluating feed efficiency. Cattle DMI and digestion of forages impact enteric greenhouse gas (GHG) emissions; a major public and environmental concern. Increased GHG levels indicate energy loss during the rumen fermentation process. Obtaining data for rangeland cattle DMI and GHG emissions is needed to understand and enhance individual animal performance and reduce negative environmental impacts. We will develop enteric emissions and DMI relationships by conducting three feeding trials using the GreenFeed and SmartFeed Pro (C-Lock Inc. Rapid City, SD). The GreenFeed will measure …

Effects Of Environmental Gradients On The Abundance And Diversity Of Helminths Across 7 Bison Herds In The Upper Midwest, Bradly Wehus-Tow, Jeff M. Martin, Jameson Brennan

SDSU Beef Day 2022 Summary Publication

Study Description:

Data were collected from Wind Cave National Park and 6 satellite bison herds across the upper Midwest ranging across South Dakota, Indiana, and Kansas with a MAP gradient ranging from 34 to 82 mm and a MAT gradient ranging from 9 to 13°C. Fecal samples were collected non-invasively from 50 freshly voided bison dung patties at each herd. Helminth eggs were recovered and identified using sugar floatation; Trichostrongyle-type eggs were hatched by coproculture to identify to species. Preliminary findings indicate that general abundance of trichostrongyle-type helminths increases by 2.3 EPG per 1°C and by 0.2 EPG per mm, …

Influence Of Beef Carcass Chilling Rate On Steak Case Life And Quality Traits, Trevor Dehaan, Lydia Hite, Erin Gubbels, Christina Elaine Bakker, Amanda D. Blair, Judson Grubbs, Keith Underwood

SDSU Beef Day 2022 Summary Publication

Study Description:

Twelve head of fed beef cattle were harvested at the SDSU Meat Laboratory over two days. Carcasses were allotted into two weight groups based on hot carcass weight (HCW): Heavyweight (HW) and Lightweight (LW). Data logging thermometers were placed in the left side of each carcass within the round, loin, rib, and chuck primals to track temperature decline. Carcass measurements including 12th rib fat thickness, ribeye area and marbling score were collected approximately 48 hours postmortem. Steaks from each primal were collected to measure Warner-Bratzler shear force (WBSF), objective and subjective color.

Serving Beef In Usda Child Nutrition Programs In South Dakota: Development Of An Faq, Anna Barr, Mikayla Hardy, Andrea Alma, Heather Hopwood, Joanna Studt

SDSU Beef Day 2022 Summary Publication

Study Description:

The project occurred in partnership with four organizations representing state, tribal, and federal affiliations. The authors collaborated to compile and answer questions. Questions that were not answered by the authors’ organizations were asked to the SD Animal Industry Board and USDA Food Safety and Inspection Service.

Bovine Respiratory Microbiota Of Feedlot Cattle And Its Association With Disease, Jianmin Chai, Sarah F. Capik, Beth Kegley, John T. Richeson, Jeremy G. Powell, Jiangchao Zhao

Animal Science Faculty Publications and Presentations

Bovine respiratory disease (BRD), as one of the most common and costly diseases in the beef cattle industry, has significant adverse impacts on global food security and the economic stability of the industry. The bovine respiratory microbiome is strongly associated with health and disease and may provide insights for alternative therapy when treating BRD. The niche-specific microbiome communities that colonize the inter-surface of the upper and the lower respiratory tract consist of a dynamic and complex ecological system. The correlation between the disequilibrium in the respiratory ecosystem and BRD has become a hot research topic. Hence, we summarize the pathogenesis …

Effects Of Increasing Dietary Zinc Sulfate Fed To Gestating Ewes: Ii. Milk Somatic Cell Count, Microbial Populations, And Fatty Acid Composition, C. M. Page, R. M. Knuth, T. W. Murphy, D. C. Rule, B. Bisha, J. B. Taylor, W. C. Stewart

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Objective: The objective of the research was to evaluate the effects of increasing dietary Zn sulfate concentration for primiparous gestating ewes on subsequent milk SCC, intramammary microbial identifications, and fatty acid composition.

Materials and Methods: Commercial white-face (WF; n = 27) and black-face (BF; n = 24) ewes (age ≈18 mo; BW = 87.48 ± 8.37 kg) were sorted into breed-type groups and within groups ranked by BW, and then, they were randomly divided into 3 dietary supplement treatment groups: CON (n = 13; 40 mg/kg Zn; ≈1 × NASEM recommendations), Zn500 (n = 21; 500 mg/kg Zn; …

Effects Of Harvest Season On Carcass Characteristics Of Lambs In The Intermountain West, J. R. Whaley, T. W. Murphy, C. L. Gifford, W. J. Means, J. P. Ritten, H. N. Mckibben, C. M. Page, W. C. Stewart

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Objective: The objectives of this study were to survey characteristics including hot carcass weight (HCW), 12th rib fat thickness (RFT), body-wall thickness (BWT), longissimus muscle area (LMA), USDA yield grade (USDA YG), percentage closely trimmed retail cuts (RC), and calculated yield grade (Calc YG) of lamb carcasses in the Intermountain West to determine the effects of season of slaughter and interrelationships among carcass characteristics.

Materials and Methods: Lamb carcass characteristics were evaluated in 2 commercial Intermountain West processing plants over one year (n = 10,027). Carcasses were evaluated by season: spring (December–April, n = 2,322) and summer (May–August, n …

Evaluation Of Salmonella Biofilm Cell Transfer From Common Food Contact Surfaces To Beef Products, Rong Wong, David A. King, Norasak Kalchayanand

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Meat contamination by Salmonella enterica is a serious public health concern. Available data have suggested that biofilm formation at processing plants and contaminated contact surfaces might contribute to meat contamination. Because transfer from contact surfaces to food products via direct contact has been deemed the most common bacteria transmission route that can lead to contamination, we evaluated the effect of Salmonella biofilm forming ability, contact surface material, and beef surface tissue type on Salmonella biofilm transfer from hard surfaces to beef products. Salmonella biofilms developed on the common contact surfaces stainless steel (SS) and polyvinylchloride (PVC) were transferred consecutively via …

Transcriptome Profiles Of The Skeletal Muscle Of Mature Cows During Feed Restriction And Realimentation, Hannah C. Cunningham-Hollinger, Larry A. Kuehn, Kristi M. Cammack, Kristin E. Hales, William T. Oliver, Matthew S. Crouse, Celine Chen, Harvey C. Freetly, Amanda K. Lindholm-Perry

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Objective: Realimentation can compensate for weight loss from poor-quality feedstuffs or drought. Mature cows fluctuate in body weight throughout the year due to nutrient availability. The objective of this study was to determine whether cows that differ in weight gain during realimentation also differ in the abundance of transcripts for enzymes associated with energy utilization in skeletal muscle. Mature cows were subjected to feed restriction followed by ad libitum feed. Skeletal muscle transcriptome expression differences during the two feeding periods were determined from cows with greater (n = 6) and less (n = 6) weight gain during the ad libitum …

Considerations And Best Practices In Animal Science 16s Ribosomal Rna Gene Sequencing Microbiome Studies, Margaret D. Weinroth, Aeriel D. Belk, Chris Dean, Noelle Noyes, Dana K. Dittoe, Michael J. Rothrock Jr, Steven C. Ricke, Phillip R. Myer, Madison T. Henniger, Gustavo A. Ramírez, Brian B. Oakley, Katie Lynn Summers, Asha M. Miles, Taylor B. Ault-Seay, Zhongtang Yu, Jessica L. Metcalf, James E. Wells

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, and bioinformatics—in addition to the traditional considerations when conducting an animal science study—makes microbiome studies sometimes intimidating due to the intersection of different fields. The objective of this review is to serve as a jumping-off point for those animal scientists less familiar with 16S rRNA gene sequencing and analyses and to bring up common issues and concerns that arise …

Twenty-Four-Month Longitudinal Study Suggests Little To No Horizontal Gene Transfer In Situ Between Third-Generation Cephalosporin-Resistant Salmonella And Third-Generation Cephalosporin-Resistant Escherichia Coli In A Beef Cattle Feedyard, John W. Schmidt, Sarah A. Murray, Aaron M. Dickey, Tommy L. Wheeler, Dayna M. Harhay, Terrance M. Arthur

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Third-generation cephalosporins (3GCs) are preferred treatments for serious human Salmonella enterica infections. Beef cattle are suspected to contribute to human 3GC-resistant Salmonella infections. Commensal 3GC-resistant Escherichia coli are thought to act as reservoirs of 3GC resistance because these strains are isolated more frequently than are 3GC-resistant Salmonella strains at beef cattle feedyards. During each of 24 consecutive months, four samples of pen surface material were obtained from five pens (N = 480) at a Nebraska feedyard to determine to the contribution of 3GC-resistant E. coli to the occurrence of 3GC-resistant Salmonella. Illumina whole genome sequencing was performed, and …

Adaptive Selection Signatures In River Buffalo With Emphasis On Immune And Major Histocompatibility Complex Genes, Yan Ren, Callum Macphillamy, Thu Hien To, Timothy P. L. Smith, John L. Williams, Wai Yee Low

Roman L. Hruska U.S. Meat Animal Research Center: Reports

River buffalo is an agriculturally important species with many traits, such as disease tolerance, which promote its use worldwide. Highly contiguous genome assemblies of the river buffalo, goat, pig, human and two cattle subspecies were aligned to study gene gains and losses and signs of positive selection. The gene families that have changed significantly in river buffalo since divergence from cattle play important roles in protein degradation, the olfactory receptor system, detoxification and the immune system. We used the branch site model in PAML to analyse single-copy orthologs to identify positively selected genes that may be involved in skin differentiation, …

Evaluating Large Spontaneous Deletions In A Bovine Cell Line Selected For Bovine Viral Diarrhea Virus Resistance, Aspen M. Workman, Michael P. Heaton, Dennis A. Webster, Gregory P. Harhay, Theodore S. Kalbfleisch, Timothy P.L. Smith, Shollie M. Falkenberg, Daniel F. Carlson, Tad S. Sonstegard

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Bovine viral diarrhea virus’s (BVDV) entry into bovine cells involves attachment of virions to cellular receptors, internalization, and pH-dependent fusion with endosomal membranes. The primary host receptor for BVDV is CD46; however, the complete set of host factors required for virus entry is unknown. The Madin-Darby bovine kidney (MDBK) cell line is susceptible to BVDV infection, while a derivative cell line (CRIB) is resistant at the level of virus entry. We performed complete genome sequencing of each to identify genomic variation underlying the resistant phenotype with the aim of identifying host factors essential for BVDV entry. Three large compound deletions …

Predicting Carcass Cut Yields In Cattle From Digital Images Using Artificial Intelligence, Darragh Matthews, Thierry Pabiou, Ross D. Evans, Christian Beder, Aengus Daly

Department of Mathematics Publications

Deep Learning (DL) has proven to be a successful tool for many image classification problems but has yet to be applied to carcass images. The aim of this study was to train DL models to predict carcass cut yields and compare predictions to more standard machine learning (ML) methods. Three approaches were undertaken to predict the grouped carcass cut yields of Grilling cuts and Roasting cuts from a large dataset of 54,598 and 69,246 animals respectively. The approaches taken were (1) animal phenotypic data used as features for a range of ML algorithms, (2) carcass images used to train Convolutional …

Localization Of Kisspeptin, Nkb, And Nk3r In The Hypothalamus Of Gilts Treated With The Progestin Altrenogest, Ashley N. Lindo, Jennifer F. Thorson, Michelle N. Bedenbaugh, Richard B. Mccosh, Justin A. Lopez, Samantha A. Young, Lanny J. Meadows, Elizabeth C. Bowdridge, Chrysanthi Fergani, Bradley A. Freking, Michael N. Lehman, Stanley M. Hileman, Clay A. Lents

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Mechanisms in the brain controlling secretion of gonadotropin hormones in pigs, particularly luteinizing hormone (LH), are poorly understood. Kisspeptin is a potent LH stimulant that is essential for fertility in many species, including pigs. Neurokinin B (NKB) acting through neurokinin 3 receptor (NK3R) is involved in kisspeptin-stimulated LH release, but organization of NKB and NK3R within the porcine hypothalamus is unknown. Hypothalamic tissue from ovariectomized (OVX) gilts was used to determine the distribution of immunoreactive kisspeptin, NKB, and NK3R cells in the arcuate nucleus (ARC). Almost all kisspeptin neurons coexpressed NKB in the porcine ARC. Immunostaining for NK3R was distributed …

Relationship Of Molecular Breeding Value For Beef Tenderness With Heifer Traits Through Weaning Of Their First Calf, Robert A. Cushman, Gary L. Bennett, Richard G. Tait, Anthony K. Mcneel, Eduardo Casas, Timothy P.L. Smith, Harvey C. Freetly

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Polymorphisms in μ-calpain (CAPN1) that beneficially associate with beef tenderness are reported to antagonistically associate with calving day in beef heifers and post-partum interval to estrus in beef cows. We, therefore, hypothesized that a molecular breeding value for slice shear force, calculated based on CAPN1 and calpastatin (CAST) genotypes, would demonstrate an antagonistic relationship between genomically predicted slice shear force and ordinal calving date in replacement beef heifers. A secondary objective of this study was to evaluate the association of a polymorphism in diacylglycerol O-acyltransferase (DGAT1) with reproductive traits in beef heifers. One hundred eighty-seven MARC III heifers (¼ Angus, …

Validation Of High-Resolution Melting Assays For The Detection Of Virulent Strains Of Escherichia Coli O26 And O111 In Beef And Pork Enrichment Broths, Frank J. Velez, Joseph M. Bosilevac, Prashant Singh

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Extensive validation of diagnostic assays using widely collected surveillance samples is critical for developing pathogen detection assays. The detection of potentially virulent E. coli strains is critical to the red meat industry. We previously developed two high-resolution melting (HRM) assays for detecting potentially virulent and avirulent E. coli O26 and O111 strains. Assays were validated using enriched beef (n = 36) and pork (n = 36) samples collected as part of a U.S. federal regulatory surveillance program. Data from this study showed more than 90% sensitivity and specificity for both the HRM assays, demonstrating suitability for the red meat industry …

Genomic Analysis Of Shiga Toxin-Containing Escherichia Coli O157:H7 Isolated From Argentinean Cattle, Ariel Amadio, James L. Bono, Matías Irazoqui, Mariano Larzábal, Wanderson Marques Da Silva, María Florencia Eberhardt, Nahuel A. Riviere, David Gally, Shannon D. Manning, Angel Cataldi

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Cattle are the main reservoir of Enterohemorrhagic Escherichia coli (EHEC), with O157:H7 the distinctive serotype. EHEC is the main causative agent of a severe systemic disease, Hemolytic Uremic Syndrome (HUS). Argentina has the highest pediatric HUS incidence worldwide with 12–14 cases per 100,000 children. Herein, we assessed the genomes of EHEC O157:H7 isolates recovered from cattle in the humid Pampas of Argentina. According to phylogenetic studies, EHEC O157 can be divided into clades. Clade 8 strains that were classified as hypervirulent. Most of the strains of this clade have a Shiga toxin stx2a-stx2c genotype. To better understand the molecular bases …

Characterisation Of Early Positive Mcr‐1 Resistance Gene And Plasmidome In Escherichia Coli Pathogenic Strains Associated With Variable Phylogroups Under Colistin Selection, Guerrino Macori, Scott V. Nguyen, Ankita Naithani, Daniel Hurley, Li Bai, Farid El Garch, Frédérique Woehrlé, Christine Miossec, Benjamin Roques, Peadar O’Gaora, James L. Bono, Séamus Fanning

Roman L. Hruska U.S. Meat Animal Research Center: Reports

An antibiotic susceptibility monitoring programme was conducted from 2004 to 2010, re-sulting in a collection of 143 Escherichia coli cultured from bovine faecal samples (diarrhoea) and milk‐aliquots (mastitis). The isolates were subjected to whole‐genome sequencing and were distrib-uted in phylogroups A, B1, B2, C, D, E, and G with no correlation for particular genotypes with pathotypes. In fact, the population structure showed that the strains belonging to the different phy-logroups matched broadly to ST complexes; however, the isolates are randomly associated with the diseases, highlighting the necessity to investigate the virulence factors more accurately in order to identify the mechanisms …

Meat Tenderness: Advances In Biology, Biochemistry, Molecular Mechanisms And New Technologies, Robyn D. Warner, Tommy L. Wheeler, Minh Ha, Xin Li, Alaa El-Din Bekhit, James Morton, Rozita Vaskoska, Frank R. Dunshea, Rui Lui, Peter Purslow, Wangang Zhang

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Meat tenderness is an important quality trait critical to consumer acceptance, and determines satisfaction, repeat purchase and willingness-to-pay premium prices. Recent advances in tenderness research from a variety of perspectives are presented. Our understanding of molecular factors influencing tenderization are discussed in relation to glycolysis, calcium release, protease activation, apoptosis and heat shock proteins, the use of proteomic analysis for monitoring changes, proteomic biomarkers and oxidative/nitrosative stress. Each of these structural, metabolic and molecular determinants of meat tenderness are then discussed in greater detail in relation to animal variation, postmortem influences, and changes during cooking, with a focus on recent …

Pilot-Scale H2S And Swine Odor Removal System Using Commercially Available Biochar, Kyoung S. Ro, Brian Woodbury, Mindy Spiehs, Ariel A. Szogi, Philip J. Silva, Okhwa Hwang, Sungback Cho

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Although biochars made in laboratory seem to remove H2S and odorous compounds effectively, very few studies are available for commercial biochars. This study evaluated the efficacy of a commercial biochar (CBC) for removing H2S and odorous volatile organic compounds (VOCs). We found that the well-known Ergun equation may not be adequate in predicting pressure drop for properly sizing a ventilation system. The H2S breakthrough adsorption capacity of the CBC was 2.51 mg/g under humid conditions, which was much higher than that for dry conditions. The breakthrough capacity increased with the influent concentration of H2S. The efficacy of a pilot-scale biochar …

The Ovarian Follicle Of Ruminants: The Path From Conceptus To Adult, Jennifer L. Juengel, Robert A. Cushman, Joëlle Dupont, Stéphane Fabre, Richard G. Lea, Graeme B. Martin, Francesca Mossa, Janet L. Pitman, Christopher A. Price, Peter Smith

Roman L. Hruska U.S. Meat Animal Research Center: Reports

This review resulted from an international workshop and presents a consensus view of critical advances over the past decade in our understanding of follicle function in ruminants. The major concepts covered include: (1) the value of major genes; (2) the dynamics of fetal ovarian development and its sensitivity to nutritional and environmental influences; (3) the concept of an ovarian follicle reserve, aligned with the rise of anti-Müllerian hormone as a controller of ovarian processes; (4) renewed recognition of the diverse and important roles of theca cells; (5) the importance of follicular fluid as a microenvironment that determines oocyte quality; (6) …

Evolution Of The Sheep Industry And Genetic Research In The United States: Opportunities For Convergence In The Twenty-First Century, J. W. Thorne, B. M. Murdoch, B. A. Freking, R. R. Redden, Thomas W. Murphy, J. B. Taylor, Harvey D. Blackburn

Roman L. Hruska U.S. Meat Animal Research Center: Reports

The continuous development and application of technology for genetic improvement is a key element for advancing sheep production in the United States. The US sheep industry has contracted over time but appears to be at a juncture where a greater utilization of technology can facilitate industry expansion to new markets and address inefficiencies in traditional production practices. Significant transformations include the increased value of lamb in relation to wool, and a downtrend in large-scale operations but a simultaneous rise in small flocks. Additionally, popularity of hair breeds not requiring shearing has surged, particularly in semi-arid and subtropical US environments. A …

Economic Contribution Of The Agricultural Sector To The Arkansas Economy In 2019, Leah English, Jennie Popp, Wayne Miller

AAES Research Reports and Research Bulletins

Agriculture and associated agricultural activities are major contributors to the Arkansas economy. Agriculture is defined as the sum of agricultural production and processing activities, unless otherwise specified, and includes crop and animal production and processing, agricultural support industries, forestry and forest products, and textile goods. Agriculture contributes to the economy through direct agricultural production and value-added processing, leading to economic activity in other parts of the economy.

This report is the fourteenth in a series that examines agriculture’s economic contribution to the Arkansas economy. The total economic contribution of agriculture (direct, indirect, and induced effects) on value added, employment, and …

Influence Of Estradiol On Bovine Trophectoderm And Uterine Gene Transcripts Around Maternal Recognition Of Pregnancy, Emmalee J. Northrop-Albrecht, Jerica J.J. Rich, Robert A. Cushman, Runan Yao, Xijin Ge, George A. Perry

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Embryo survival and pregnancy success is increased among animals that exhibit estrus prior to fixed time-artificial insemination, but there are no differences in conceptus survival to d16. The objective of this study was to determine effects of preovulatory estradiol on uterine transcriptomes, select trophectoderm (TE) transcripts, and uterine luminal fluid proteins. Beef cows/heifers were synchronized, artificially inseminated (d0), and grouped into either high (highE2) or low (lowE2) preovulatory estradiol. Uteri were flushed (d16); conceptuses and endometrial biopsies (n = 29) were collected. RNA sequencing was performed on endometrium. Real-time polymerase chain reaction (RT-PCR) was performed on TE (n = 21) …

Complete Closed Genome Sequence Of The Extremely Heat- Resistant Strain Escherichia Coli Aw1.7, Manita Guragain, James L. Bono, Joseph M. Bosilevac

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Escherichia coli isolate AW1.7 is an extremely heat-resistant bacterium and has been widely used as a reference strain in extreme heat resistance studies for almost a decade. Here, we report its complete closed genome sequence.

Using Genomics To Measure Phenomics: Repeatability Of Bull Prolificacy In Multiple-Bull Pastures, Gary L. Bennett, John W. Keele, Larry A. Kuehn, Warren M. Snelling, Robert A. Cushman, Tara G. Mcdaneld, Aaron M. Dickey, Darrell Light

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Phenotypes are necessary for genomic evaluations and management. Sometimes genomics can be used to measure phenotypes when other methods are difficult or expensive. Prolificacy of bulls used in multiple-bull pastures for commercial beef production is an example. A retrospective study of 79 bulls aged 2 and older used 141 times in 4–5 pastures across 4 years was used to estimate repeatability from variance components. Traits available before each season’s use were tested for predictive ability. Sires were matched to calves using individual genotypes and evaluating exclusions. A lower-cost method of measuring prolificacy was simulated for five pastures using the bulls’ …

Production Performance Of Cows Raised With Different Postweaning Growth Patterns, Harvey C. Freetly, Robert A. Cushman, Gary L. Bennett

Roman L. Hruska U.S. Meat Animal Research Center: Reports

The period of heifer development is a relatively small fraction of a cow's life; however, her pattern of growth may have permanent effects on her productivity as a cow. We hypothesized that altering the growth pattern during the peri-pubertal period would increase life-time productivity across genetic types of Bos taurus cows. The objective was to determine the stayability, calf production, and weight of calf weaned across six calf crops. Heifers (n = 685) were placed on one of two developmental programs at 256 ± 1 d of age. Control heifers received a diet that provided 228 kcal ME·(body weight [BW], …

The Usda-Ars Ag100pest Initiative: High-Quality Genome Assemblies For Agricultural Pest Arthropod Research, Anna K. Childers, Scott M. Geib, Sheina B. Sim, Monica F. Poelchau, Brad S. Coates, Tyler J. Simmonds, Erin D. Scully, Timothy P. L. Smith, Christopher P. Childers, Renee L. Corpuz, Kevin Hackett, Brian Scheffler

Roman L. Hruska U.S. Meat Animal Research Center: Reports

The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture’s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods that are (or may become) pests to agricultural production and global food security. We describe the project goals, process, status, and future. The first three years of the project were focused on species selection, specimen collection, and the construction of lab and bioinformatics pipelines for the efficient production of assemblies at scale. Contig-level assemblies of 47 species …

Reference Transcriptomes Of Porcine Peripheral Immune Cells Created Through Bulk And Single-Cell Rna Sequencing, Juber Herrera-Uribe, Jayne E. Wiarda, Sathesh K. Sivasankaran, Lance Daharsh, Haibo Liu, Kristen A. Byrne, Timothy P. L. Smith, Joan K. Lunney, Crystal L. Loving, Christopher Tuggle

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Pigs are a valuable human biomedical model and an important protein source supporting global food security. The transcriptomes of peripheral blood immune cells in pigs were defined at the bulk cell-type and single cell levels. First, eight cell types were isolated in bulk from peripheral blood mononuclear cells (PBMCs) by cell sorting, representing Myeloid, NK cells and specific populations of T and B-cells. Transcriptomes for each bulk population of cells were generated by RNA-seq with 10,974 expressed genes detected. Pairwise comparisons between cell types revealed specific expression, while enrichment analysis identified 1,885 to 3,591 significantly enriched genes across all 8 …