Genetics and Genomics Commons^™

Biophysical And Functional Characterization Of Rhesus Macaque Igg Subclasses, Austin W. Boesch, Nana Yaw Osei-Owusu, Andrew R. Crowley, Thach H. Chu, Ying Chan, Joshua Weiner, Pranay Bharadwaj, Rufus Hards, Mark Adamo, Scott Gerber, Sarah Cocklin, Joern Schmitz, Adam Miles, Joshua Eckman, Aaron J. Belli, Keith Reimann, Margaret E. Ackerman

Dartmouth Scholarship

Antibodies raised in Indian rhesus macaques [Macaca mulatta (MM)] in many preclinical vaccine studies are often evaluated in vitro for titer, antigen-recognition breadth, neu- tralization potency, and/or effector function, and in vivo for potential associations with protection. However, despite reliance on this key animal model in translation of promising candidate vaccines for evaluation in first in man studies, little is known about the proper- ties of MM immunoglobulin G (IgG) subclasses and how they may compare to human IgG subclasses. Here, we evaluate the binding of MM IgG1, IgG2, IgG3, and IgG4 to human Fc gamma receptors (FcγR) and their …

Whole-Genome Identification, Phylogeny, And Evolution Of The Cytochrome P450 Family 2 (Cyp2) Subfamilies In Birds, Daniela Almeida, Emanuel Maldonado, Imran Khan, Liliana Silva, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O'Brien, Warren E. Johnson, Agostinho Antunes

Biology Faculty Articles

The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized the CYP2 family across 48 avian whole genomes representing all major extant bird clades. Overall,12 CYP2 subfamilies were identified, including the first description of the CYP2F, CYP2G, and several CYP2AF genes in avian genomes. Some of the CYP2 genes previously described as being lineage-specific, such as CYP2K and CYP2W, are ubiquitous to all avian groups. Furthermore, we identified a large number of CYP2J copies, which have …

Blood Mercury Levels Of Zebra Finches Are Heritable: Implications For The Evolution Of Mercury Resistance, Kenton A. Buck, Claire W. Varian-Ramos, Daniel A. Cristol, John P. Swaddle

Arts & Sciences Articles

Mercury is a ubiquitous metal contaminant that negatively impacts reproduction of wildlife and has many other sub-lethal effects. Songbirds are sensitive bioindicators of mercury toxicity and may suffer population declines as a result of mercury pollution. Current predictions of mercury accumulation and biomagnification often overlook possible genetic variation in mercury uptake and elimination within species and the potential for evolution in affected populations. We conducted a study of dietary mercury exposure in a model songbird species, maintaining a breeding population of zebra finches (Taeniopygia guttata) on standardized diets ranging from 0.0–2.4 μg/g methylmercury. We applied a quantitative genetics …

De Novo Sequencing, Assembly And Analysis Of Eight Different Transcriptomes From The Malayan Pangolin, Aini Mohamed Yusoff, Tze King Tan, Ranjeev Hari, Klaus-Peter Koepfli, Wei Yee Wee, Agostinho Antunes, Frankie Thomas Sitam, Jeffrine Japning Rovie-Ryan, Kayal Vizi Karuppannan, Guat Jah Wong, Leonard Lipovich, Wesley C. Warren, Stephen J. O'Brien, Siew Woh Choo

Biology Faculty Articles

Pangolins are scale-covered mammals, containing eight endangered species. Maintaining pangolins in captivity is a significant challenge, in part because little is known about their genetics. Here we provide the first large-scale sequencing of the critically endangered Manis javanica transcriptomes from eight different organs using Illumina HiSeq technology, yielding ~75 Giga bases and 89,754 unigenes. We found some unigenes involved in the insect hormone biosynthesis pathway and also 747 lipids metabolism-related unigenes that may be insightful to understand the lipid metabolism system in pangolins. Comparative analysis between M. javanica and other mammals revealed many pangolin-specific genes significantly over-represented in stress-related processes, …

Characterization, Development And Multiplexing Of Microsatellite Markers In Three Commercially Exploited Reef Fish And Their Application For Stock Identification, Laura Taillebois, Christine Dudgeon, Safia Maher, David Crook, Thor Saunders, Diane P. Barton, Jonathan A. Taylor, David J. Welch, Stephen J. Newman, Michael J. Travers, Richard J. Saunders, Jennifer Ovenden

Fisheries Research Articles

Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass …

Sheep Updates 2016, Mick Keogh, David Cornish, Michael Chilvers, Gerry Hinkley, Danielle England, Rosemary Bartle, Brad Wooldridge, Norm Santich, John Young, Ashley Herbert, Jamie Heinrich, Graeme Howie, Bruce Mullan

Sheep Updates

This session covers eleven papers from different authors:

1. Forward, Dr Bruce Mullan, Director Sheep Industry Development, Department of Agriculture and Food Western Australia

2. The Australian sheep industry in 2025, Mick Keogh, Australian Farm Institute

3. Decision making in a risky environment, David Cornish, Cornish Consulting

4. Business Transitioning, Michael Chilvers, Nile Tasmania

5. Advisory Boards in WA Agriculture - making life 'easier' for everyone, Gerry Hinkley, Producer, Tincurrin and Danielle England, Aginnovate

6. Principles of Successful Family Business Succession Strategies, Rosemary Bartle, Succession Planning Facilitator, Rabobank

7. Diversifying the Feedbase...is the …

Contrasting Origin Of B Chromosomes In Two Cervids (Siberian Roe Deer And Grey Brocket Deer) Unravelled By Chromosome-Specific Dna Sequencing, Alexey I. Makunin, Ilya G. Kichigin, Denis M. Larkin, Patricia C. M. O'Brien, Malcolm A. Ferguson-Smith, Fengtang Yang, Anastasiya A. Proskuryakova, Nadezhda V. Vorobieva, Ekaterina N. Chernyaeva, Stephen J. O'Brien, Alexander S. Graphodatsky, Vladimir Trifonov

Biology Faculty Articles

Background

B chromosomes are dispensable and variable karyotypic elements found in some species of animals, plants and fungi. They often originate from duplications and translocations of host genomic regions or result from hybridization. In most species, little is known about their DNA content. Here we perform high-throughput sequencing and analysis of B chromosomes of roe deer and brocket deer, the only representatives of Cetartiodactyla known to have B chromosomes.

Results

In this study we developed an approach to identify genomic regions present on chromosomes by high-throughput sequencing of DNA generated from flow-sorted chromosomes using degenerate-oligonucleotide-primed PCR. Application of this method …

Polyandry In The Absence Of Fitness Benefits In A Species With Female-Biased Sexual Size Dimorphism, Marie Claire Chelini, Eileen A. Hebets

Eileen Hebets Publications

Most studies exploring the evolution of female mating systems focus on species in which females are either monandric (mate with a single male) or highly polyandric (mate with multiple males), but less is understood about variation in mating decisions within a species. How and why do females of a single species decide whether or not to copulate with additional mates? In this study we attempt to answer this question in the highly dimorphic crab spider, Mecaphesa celer, whose females may be either monandric or polyandric. We tested three hypotheses: (1) a female’s decision to remate is based on sequential mate …

The Maintenance Of Phenotypic Divergence Through Sexual Selection: An Experimental Study In Barn Swallows Hirundo Rustica, Rebecca Safran, Yoni Vortman, Brittany R. Jenkins, Joanna K. Hubbard, Matt Wilkins, Rachel J. Bradley, Arnon Lotem

School of Biological Sciences: Faculty Publications

Previous studies have shown that sexual signals can rapidly diverge among closely related species. However, we lack experimental studies to demonstrate that differences in trait-associated reproductive performance maintain sexual trait differences between closely related populations, in support for a role of sexual selection in speciation. Populations of Northern Hemisphere distributed barn swallows Hirundo rustica are closely related, yet differ in two plumage-based traits: ventral color and length of the outermost tail feathers (streamers). Here we provide experimental evidence that manipulations of these traits result in different reproductive consequences in two subspecies of barn swallow: (H. r. erythrogaster in North …

Divergent Activity Of The Gonadotropin Releasing Hormone Receptor Gene Promoter Among Genetic Lines Of Pigs Is Partially Conferred By Nuclear Factor (Nf)-Kb, Specificity Protein (Sp)1-Like And Gata-4 Binding Sites, Emily A. Mcdonald, Jacqueline E. Smith, Rebecca A. Cederberg, Brett R. White

Department of Animal Science: Faculty Publications

BACKGROUND: Binding of gonadotropin-releasing hormone (GnRH) to its receptor (GnRHR) on gonadotropes within the anterior pituitary gland is essential to reproduction. In pigs, the GnRHR gene is also located near a genetic marker for ovulation rate, a primary determinant of prolificacy. We hypothesized that pituitary expression of the GnRHR gene is alternatively regulated in genetic strains with elevated ovulation rates (Chinese Meishan and Nebraska Index) vs. standard white crossbred swine (Control).

METHODS: Luciferase reporter vectors containing 5118 bp of GnRHR gene promoter from either the Control, Index or Meishan swine lines were generated. Transient transfection of line-specific, full length, deletion …

Alcohol Discrimination And Preferences In Two Species Of Nectar-Feeding Primate, Samuel R. Gochman, Michael B. Brown, Nathaniel J. Dominy

Dartmouth Scholarship

Recent reports suggest that dietary ethanol, or alcohol, is a supplemental source of calories for some primates. For example, slow lorises (Nycticebus coucang) consume fermented nectars with a mean alcohol concentration of 0.6% (range: 0.0–3.8%). A similar behaviour is hypothesized for aye-ayes (Daubentonia madagascariensis) based on a single point mutation (A294V) in the gene that encodes alcohol dehydrogenase class IV (ADH4), the first enzyme to catabolize alcohol during digestion. The mutation increases catalytic efficiency 40-fold and may confer a selective advantage to aye-ayes that consume the nectar of Ravenala madagascariensis. It is uncertain, however, whether alcohol exists in this nectar …

Description Of Mesocriconema Ericaceum N. Sp. (Nematoda: Criconematidae) And Notes On Other Nematode Species Discovered In An Ericaceous Heath Bald Community In Great Smoky Mountains National Park, Usa, Thomas O. Powers, Peter Mullin, Rebecca Higgins, Timothy Harris, Kirsten S. Powers

Department of Plant Pathology: Faculty Publications

A new species of Mesocriconema and a unique assemblage of plant-parasitic nematodes was discovered in a heath bald atop Brushy Mountain in Great Smoky Mountains National Park. Mesocriconema ericaceum n. sp., a species with males, superficially resembles M. xenoplax. DNA barcoding with the mitochondrial COI gene provided evidence of the new species as a distinct lineage. SEM revealed significant variability in arrangement of labial submedian lobes, plates, and anterior and posterior annuli. Three other nematodes in the family Criconematidae were characterized from the heath bald. Ogma seymouri, when analyzed by statistical parsimony, established connections with isolates from north-eastern Atlantic …

Cooled Perch Effects On Performance And Well-Being Traits In Caged White Leghorn Hens, J Y. Hu, P Y. Hester, M M. Makagon, G Vezzoli, R S. Gates, Y Xiong, H W. Cheng

Department of Animal Science: Faculty Publications

We assessed the effects of chilled water cooling perches on hen performance and physiological and behavioral parameters under “natural” high temperatures during the 2013 summer with a 4-hour acute heating episode. White Leghorns at 16 wk of age (N = 162) were randomly assigned to 18 cages (n = 9) arranged into 3 units. Each unit was assigned to one of the 3 treatments through 32 wk of age: 1) cooled perches, 2) air perches, and 3) no perches. Chilled water (10◦C) was circulated through the cooled perches when cage ambient temperature exceeded 25^◦C. At the age of …

Bone-Associated Gene Evolution And The Origin Of Flight In Birds, Joao P. Machado, Warren E. Johnson, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O'Brien, Agostinho Antunes

Biology Faculty Articles

Background

Bones have been subjected to considerable selective pressure throughout vertebrate evolution, such as occurred during the adaptations associated with the development of powered flight. Powered flight evolved independently in two extant clades of vertebrates, birds and bats. While this trait provided advantages such as in aerial foraging habits, escape from predators or long-distance travels, it also imposed great challenges, namely in the bone structure.

Results

We performed comparative genomic analyses of 89 bone-associated genes from 47 avian genomes (including 45 new), 39 mammalian, and 20 reptilian genomes, and demonstrate that birds, after correcting for multiple testing, have an almost …

Nocturnal Foraging Enhanced By Enlarged Secondary Eyes In A Net-Casting Spider, Jay A. Stafstrom, Eileen A. Hebets

Eileen Hebets Publications

Animals that possess extreme sensory structures are predicted to have a related extreme behavioral function. This study focuses on one such extreme sensory structure—the posterior median eyes of the net-casting spider Deinopis spinosa. Although past research has implicated the importance of vision in the nocturnal foraging habits of Deinopis, no direct link between vision in the enlarged eyes and nocturnal foraging has yet been made. To directly test the hypothesis that the enlarged posterior median eyes facilitate visually based nocturnal prey capture, we conducted repeated-measures, visual occlusion trials in both natural and laboratory settings. Our results indicate that D. …

The Asian Arowana (Scleropages Formosus) Genome Provides New Insights Into The Evolution Of An Early Lineage Of Teleosts, Chao Bian, Yinchang Hu, Vydianathan Ravi, Inna S. Kuznetsova, Xueyan Shen, Xidong Mu, Ying Sun, Xinxin You, Jia Li, Xiaofeng Li, Ying Qiu, Boon-Hui Tay, Natascha May Thevasagayam, Aleksey S. Komissarov, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Jianren Luo, Yi Liu, Hongmei Song, Chao Liu, Xuejie Wang, Dangen Gu, Yexin Yang, Wujiao Li, Gianluca Polgar, Guangyi Fan, Peng Zeng, He Zhang, Zijun Xiong, Zhujing Tang, Chao Peng, Zhiqiang Ruan, Hui Yu, Jieming Chen, Mingjun Fan, Yu Huang, Min Wang, Xiaomeng Zhao, Guojun Hu, Huanming Yang, Jian Wang, Jun Wang, Xun Xu, Linsheng Song, Gangchun Xu, Junmin Xu, Stephen J. O'Brien, Laszlo Orban, Byrappa Venkatesh, Qiong Shi

Biology Faculty Articles

The Asian arowana (Scleropages formosus), one of the world’s most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining …

Chromosomal-Level Assembly Of The Asian Seabass Genome Using Long Sequence Reads And Multi-Layered Scaffolding, Shubha Vij, Heiner Kuhl, Inna S. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, Kathiresan Purushothaman, Jolly M. Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Hin Yan Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S. Hon, James P. Drake, Matthew Boitano, Richard Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, Gopikrishna Gopalapillai, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O'Brien, Michael C. Schatz, Tamas Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, Laszlo Orban

Biology Faculty Articles

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species’ native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications …

Molecular Analysis Confirming The Introduction Of Nile Crocodiles, Crocodylus Niloticus Laurenti 1768 (Crocodylidae), In Southern Florida, With An Assessment Of Potential For Establishment, Spread, And Impacts., Michael R. Rochford, Kenneth L. Krysko, Frank J. Mazzotti, Matthew W. Shirley, Mark W. Parry, Joseph A. Wasilewski, Jeffrey S. Beauchamp, Christpher R. Gillette, Edward F. Metzger Iii, Michiko A. Squires, Louis A. Somma

Papers in Herpetology

The state of Florida, USA, has more introduced herpetofauna than any other governmental region on Earth. Four species of nonnative crocodilians have been introduced to Florida (all since 1960), one of which is established. Between 2000–2014 we field-collected three nonnative crocodilians in Miami-Dade County, Florida, and one in Hendry County, Florida. We used DNA barcoding and molecular phylogenetics to determine species identification and native range origin. Also, we described diet, movement, and growth for one crocodile. Our molecular analyses illustrated that two of the crocodiles we collected are most closely related to Nile Crocodiles (Crocodylus niloticus) from South Africa, suggesting …

Examining Maternal Obesity Effects On Oogenesis, Follicular Development, And Embryonic Myogenesis, Chris Lindeman, Jennifer Wood

UCARE Research Products

The CDC estimates that more than one-third of U.S. adults (approximately 78.6 million) are obese. Despite national efforts to combat this with diet and exercise, the number of obese adults and children continues to climb. It is critical to emphasize that obesity can lead to lifelong, chronic complications and health risks including hypertension, heart disease, and diabetes.

Diet and obesity also have important impacts on the reproductive health of female including the ability to become pregnant (fertility) and risk for complications during pregnancy. Furthermore, for women who do become pregnant, obesity can affect the development of the embryo and fetus, …

Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography Of Rattlesnakes (Viperidae: Crotalinae: Crotalus And Sistrurus), Christopher Blair, Santiago Sánchez-Ramírez

Publications and Research

Rattlesnakes (Crotalus and Sistrurus) represent a radiation of approximately 42 species distributed throughout the New World from southern Canada to Argentina. Interest in this enigmatic group of snakes continues to accrue due, in part, to their ecomorphological diversity, contributions to global envenomations, and potential medicinal importance. Although the group has garnered substantial attention from systematists and evolutionary biologists for decades, little is still known regarding patterns of lineage diversification. In addition, few studies have statistically quantified broad-scale biogeographic patterns in rattlesnakes to ascertain how dispersal occurred throughout the New World, particularly among the different major biomes of the …

Intrauterine Growth-Restricted Sheep Fetuses Exhibit Smaller Hindlimb Muscle Fibers And Lower Proportions Of Insulin-Sensitive Type I Fibers Near Term, Dustin T. Yates, Caitlin N. Cadaret, Kristin A. Beede, Hannah E. Riley, Antoni R. Macko, Miranda J. Anderson, Leticia E. Camacho, Sean W. Limesand

Department of Animal Science: Faculty Publications

Intrauterine growthrestricted sheep fetuses exhibit smaller hindlimb muscle fibers and lower proportions of insulin-sensitive Type I fibers near term. Am J Physiol Regul Integr Comp Physiol 310: R1020–R1029, 2016. First published April 6, 2016; doi:10.1152/ajpregu.00528.2015.—Intrauterine growth restriction (IUGR) reduces muscle mass and insulin sensitivity in offspring. Insulin sensitivity varies among muscle fiber types, with Type I fibers being most sensitive. Differences in fibertype ratios are associated with insulin resistance in adults, and thus we hypothesized that near-term IUGR sheep fetuses exhibit reduced size and proportions of Type I fibers. Placental insufficiency-induced IUGR fetuses were 54% smaller (P < 0.05) than controls and exhibited hypoxemia and hypoglycemia, which contributed to 6.9- fold greater (P < 0.05) plasma norepinephrine and 53% lower (P < 0.05) plasma insulin concentrations. IUGR semitendinosus muscles contained less (P < 0.05) myosin heavy chain-I protein (MyHC-I) and proportionally fewer (P < 0.05) Type I and Type I/IIa fibers than controls, but MyHC-II protein concentrations, Type II fibers, and Type IIx fibers were not different. IUGR biceps femoris muscles exhibited similar albeit less dramatic differences in fiber type proportions. Type I and IIa fibers are more responsive to adrenergic and insulin regulation than Type IIx and may be more profoundly impaired by the high catecholamines and low insulin in our IUGR fetuses, leading to their proportional reduction. In both muscles, fibers of each type were uniformly smaller (P < 0.05) in IUGR fetuses than controls, which indicates that fiber hypertrophy is not dependent on type but rather on other factors such as myoblast differentiation or protein synthesis. Together, our findings show that IUGR fetal muscles develop smaller fibers and have proportionally fewer Type I fibers, which is indicative of developmental adaptations that may help explain the link between IUGR and adulthood insulin resistance

Adrenal Demedullation And Oxygen Supplementation Independently Increase Glucose-Stimulated Insulin Concentrations In Fetal Sheep With Intrauterine Growth Restriction, Antoni R. Macko, Dustin T. Yates, Xiaochuan Chen, Leslie A. Shelton, Amy C. Kelly, Melissa A. Davis, Leticia E. Camacho, Miranda J. Anderson, Sean W. Limesand

Department of Animal Science: Faculty Publications

In pregnancies complicated by placental insufficiency and intrauterine growth restriction (IUGR), fetal glucose and oxygen concentrations are reduced, whereas plasma norepinephrine and epinephrine concentrations are elevated throughout the final third of gestation. Here we study the effects of chronic hypoxemia and hypercatecholaminemia on β-cell function in fetal sheep with placental insufficiency-induced IUGR that is produced by maternal hyperthermia. IUGR and control fetuses underwent a sham (intact) or bilateral adrenal demedullation (AD) surgical procedure at 0.65 gestation. As expected, AD-IUGR fetuses had lower norepinephrine concentrations than intact-IUGR fetuses despite being hypoxemic and hypoglycemic. Placental insufficiency reduced fetal weights, but the severity …

Comparison Of Joint Angles For Feet And Leg Conformation Traits Between Gilts At Selection And At Their Second Gestation And Sows Parity 5 And Above, Joseph D. Stock, Julia A. Calderón Díaz, Benny E. Mote, Kenneth J. Stalder

Department of Animal Science: Faculty Publications

This study is a portion from the validation process of an objective methodology to measure feet and leg joint angles and to evaluate their relationship with sow longevity. Joint angle measurements from five feet and leg conformation traits (knee, hock, front and rear pasterns and rear stance) that have been previously described in the literature as being related with sow longevity were obtained from maternal gilts at selection and during their second gestation and compared with those obtained from 45 crossbred sows parity 5 and above. Significant differences (P < 0.05) between parities were identified in the knee, both pasterns, hock and rear stance joint angle measurements. These results suggest that as pigs age, structural changes occur. The range of which these changes occur could carry implications for the use of objective feet and leg angles towards future selection programs and protocols.

Genomic Differences Between Preweaning Survival And Mortality Of Piglets Following Pedv Outbreaks, Francesca Bertolini, John C.S. Harding, Benny Mote, Graham S. Plastow, Max Rothschild

Department of Animal Science: Faculty Publications

Porcine Epidemic Diarrhea (PED) is a serious and potentially devastating disease in the US and Canadian pig industries. To investigate if there is genetic resistance to PEDV a total of 156 dead and 106 surviving neonatal piglets infected with PEDV were genotyped with over 60,000 genetic markers to investigate genetic differences between the two groups. This allows for the identification of genomic regions that could be linked to susceptibility/resistance to virus infection and in cellular components that are involved in the PED virus infection cycle, providing new insights on the genetic resistance to this disease.

Differential Contribution Of Genomic Regions To Marked Genetic Variation And Prediction Of Quantitative Traits In Broiler Chickens, Rostam Abdollaha- Arpanahi, Gota Morota, Bruno D. Valente, Andreas Kranis, Guilherme J. M. Rosa, Daniel Gianola

Department of Animal Science: Faculty Publications

Background: Genome-wide association studies in humans have found enrichment of trait-associated single nucleotide polymorphisms (SNPs) in coding regions of the genome and depletion of these in intergenic regions. However, a recent release of the ENCyclopedia of DNA elements showed that ~80 % of the human genome has a biochemical function. Similar studies on the chicken genome are lacking, thus assessing the relative contribution of its genic and non-genic regions to variation is relevant for biological studies and genetic improvement of chicken populations. Methods: A dataset including 1351 birds that were genotyped with the 600K Affymetrix platform was used. We partitioned …

National Program For Genetic Improvement Of Feed Efficiency In Beef Cattle, Jerry Taylor, Monty Kerley, Robert Schnabel, Daniel Pomp, Dorian Garrick, Stephanie L. Hansen, Dan Loy, J. R. Tait, Robert Weaber, Chris Seabury, Jon Beever, Dan Faulkner, Dan Shike, Scott Fahrenkrug, Matt Spangler, Tad Sonstegard, Harvey C. Freetly, John Pollak, Kris Johnson, Holly Neibergs

Department of Animal Science: Faculty Publications

Our goal is to sustainably reduce feed resources required to produce beef via the rapid development and deployment of novel nutritional, genomic and genetic improvement technologies.

We will strengthen the international competitiveness of US agriculture and enable increased food production by increasing the animal protein produced without additional feed inputs and with a reduced greenhouse gas footprint.

Mesh-Informed Enrichment Analysis And Mesh-Guided Semantic Similarity Among Functional Terms And Gene Products In Chicken, Gota Morota, Timothy M. Beissinger, Francisco Peñagaricano

Department of Animal Science: Faculty Publications

Biomedical vocabularies and ontologies aid in recapitulating biological knowledge. The annotation of gene products is mainly accelerated by Gene Ontology (GO) and more recently by Medical Subject Headings (MeSH). Here we report a suite of MeSH packages for chicken in Bioconductor and illustrate some features of different MeSH-based analyses, including MeSH-informed enrichment analysis and MeSH-guided semantic similarity among terms and gene products, using two lists of chicken genes available in public repositories. The two published data sets that were employed represent (i) differentially expressed genes and (ii) candidate genes under selective sweep or epistatic selection. The comparison of MeSH with …

Effects Of Increasing Soybean Hulls In Finishing Diets With Wet Or Modified Distillers Grains Plus Solubles On Performance And Carcass Characteristics Of Beef Steers, Curtis Bittner, Brandon L. Watson, C. J. Schneider, Dirk Burken, L. J. Johnson, Terry J. Klopfenstein, Galen E. Erickson

Department of Animal Science: Faculty Publications

Two experiments evaluated feeding soybean hulls (SBH) in finishing diets that contain distillers grains plus solubles on performance and carcass characteristics. Dietary concentrations of SBH were 0, 12.5, 25, and 37.5% of diet DM. In Exp. 1, 167 crossbred yearling steers (395 ± 22 kg of BW) were fed for 117 d in a randomized block design in which pelleted SBH replaced dry-rolled corn. All diets contained 25% modified distillers grains plus solubles, 15% corn silage, and 5% liquid supplement. As SBH concentration increased, DMI decreased linearly (P = 0.04). Gain and G:F decreased linearly (P < 0.01) in response to increasing concentrations of SBH, which decreased relative energy value from 91 to 79% of corn. Hot carcass weight linearly decreased (P < 0.01) by 24 kg as SBH increased. In Exp. 2, a randomized block design used 160 backgrounded steer calves (363 ± 16 kg of BW) in a 138-d finishing study with 0, 12.5, 25, or 37.5% SBH in the meal form. Basal ingredients consisted of a 1:1 ratio of high-moisture corn and dry-rolled corn, 40% wet distillers grains plus solubles, 8% sorghum silage, and 4% dry meal supplement. There was a tendency (P = 0.12) for a quadratic increase in ADG and G:F as dietary SBH increased, with numerically greatest ADG and G:F with 12.5% SBH. Feeding 12.5 to 25% SBH with 40% wet distillers grains plus solubles (Exp. 2) had little effect on performance but decreased ADG and G:F in diets with 25% modified distillers grains plus solubles (Exp. 1).

Comparison Of Wet And Dry Distillers Grains Plus Solubles To Corn As An Energy Source In Forage-Based Diets, Nerissa Ann Ahern, Brandon L. Wingeyer, Terry J. Klopfenstein, James C. Macdonald, Galen E. Erickson, Andrea K. Watson

Department of Animal Science: Faculty Publications

Four experiments compared wet or dry distillers grains plus solubles (WDGS or DDGS) to corn as energy sources in forage-based diets. In Exp. 1, 66 individually fed steers (268 kg of initial BW) were fed a 60:40 blend of sorghum silage and alfalfa hay and supplemented at 0, 0.33, 0.67, or 1.0% of BW with either WDGS or DDGS. In Exp. 2, 160 steers (286 kg of initial BW) were fed 25% WDGS or 33.6% dry rolled corn (DRC) in 35% sorghum silage and grass hay diets (DM basis). In Exp. 3, 60 individually fed steers (231 kg of initial …

Effect Of Increasing Initial Implant Dosage On Feedlot Performance And Carcass Characteristics Of Long-Fed Steer And Heifer Calves1,2, F. H. Hilscher, M. N. Streeter, K. J. Vander Pol, B. D. Dicke, R. J. Cooper, D. J. Jordon, T. L. Scott, A. R. Vogstad, R. E. Peterson, B. E. Depenbusch, G. E. Erickson

Department of Animal Science: Faculty Publications

Three experiments evaluated initial implant strategies for finishing cattle. In Exp. 1, heifers (n = 1,405; initial BW = 282 kg) were given (1) Revalor-IH followed by Revalor-200 (REV-IH/200), (2) Revalor-H followed by Revalor-200 (REV-H/200), or (3) Revalor-200 followed by Revalor-200 (REV-200/200). Intake, ADG, and G:F were not affected (P ≥ 0.14) by implant strategies, nor were HCW and LM area (P ≥ 0.16). Percent USDA Choice was greater (P < 0.01) for Rev-IH/200 compared with Rev-H/200 and Rev-200/200. Experiment 2 used steers (n = 1,858; initial BW = 250 kg) given (1) Revalor-IS reimplanted with Revalor-200 (Rev-IS/200), (2) Revalor-XS followed by Revalor-IS (Rev-XS/IS), (3) Revalor-XS followed by Revalor-S (Rev-XS/S), or (4) Revalor-XS followed by Revalor-200 (Rev-XS/200). Implanting strategies did not affect (P ≥ 0.32) DMI or G:F. Carcass traits were not different (P ≥ 0.18) among treatments, except steers implanted with Rev-XS/200 had greater (P < 0.01) LM area. In Exp. 3, steers (n = 1,408; initial BW = 305 kg) were given (1) Rev-IS/200, (2) Rev-200/200, or (3) Rev-XS/200. Gain and G:F did not differ (P ≥ 0.36) among the 3 implant strategies, nor did HCW or marbling score (P ≥ 0.15). Steers given Rev-XS/200 had greater (P < 0.01) LM area and decreased (P ≤ 0.05) 12th-rib fat and YG compared with Rev-200/200 and Rev-IS/200. Using Rev-200/200 and Rev-XS/200 increased (P = 0.03) USDA Select compared with Rev-IS/200. Using greater-initial-dose implant strategies may not affect ADG or G:F but appears to increase leanness.