Poultry or Avian Science Commons^™

Genomic Analysis Of Metabolic Differences Found In Clostridium Perfringens That Cause Necrotic Enteritis In Poultry, Connor Aylor

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

Clostridium perfringens is a common member of gut microbiota in healthy animals, but can also be an important pathogen in human and veterinary medicine. It produces several protein toxins that contribute to both histotoxic and enteric diseases in animals. Necrotic enteritis in poultry has been associated with the NetB toxin of C. perfringens; however, this toxin alone is insufficient to cause disease in infected chickens. While considerable research has focused on the presence of toxins and virulence factors, little has been done to assess the function of metabolic factors on the ability of the bacteria to cause disease. In …

Recent Advances In The Application Of Crispr/Cas9 Gene Editing System In Poultry Species, Collins N. Khwatenge, Samuel N. Nahashon

Agricultural and Environmental Sciences Faculty Research

CRISPR/Cas9 system genome editing is revolutionizing genetics research in a wide spectrum of animal models in the genetic era. Among these animals, is the poultry species. CRISPR technology is the newest and most advanced gene-editing tool that allows researchers to modify and alter gene functions for transcriptional regulation, gene targeting, epigenetic modification, gene therapy, and drug delivery in the animal genome. The applicability of the CRISPR/Cas9 system in gene editing and modification of genomes in the avian species is still emerging. Up to date, substantial progress in using CRISPR/Cas9 technology has been made in only two poultry species (chicken and …

Transcriptome Analyses Of Liver In Newly-Hatched Chicks During The Metabolic Perturbation Of Fasting And Re-Feeding Reveals Thrspa As The Key Lipogenic Transcription Factor, Larry A. Cogburn, Nares Trakooljul, Xiaofei Wang, Laura E. Ellestad, Tom E. Porter

Biology Faculty Research

Background

The fasting-refeeding perturbation has been used extensively to reveal specific genes and metabolic pathways that control energy metabolism in the chicken. Most global transcriptional scans of the fasting-refeeding response in liver have focused on juvenile chickens that were 1, 2 or 4 weeks old. The present study was aimed at the immediate post-hatch period, in which newly-hatched chicks were subjected to fasting for 4, 24 or 48 h, then refed for 4, 24 or 48 h, and compared with a fully-fed control group at each age (D1-D4).

Results

Visual analysis of hepatic gene expression profiles using hierarchical and K-means …

Expression Of Lysine-Mediated Neuropeptide Hormones Controlling Satiety And Appetite In Broiler Chickens, Collins N. Khwatenge, Boniface M. Kimathi, Thyneice Taylor-Bowden, Samuel N. Nahashon

Agricultural and Environmental Sciences Faculty Research

Lysine is the second most limiting amino acid after methionine and is considered the most limiting amino acid for growth in poultry. Lysine requirement for broiler chickens has changed over the years. Leptin and adiponectin represent 2 adipokines that mediate metabolism by eliciting satiety effects whereas ghrelin peptide hormone influences appetite. We hypothesize that this affects growth performance of chicks. This study evaluates the effect of varying dietary lysine homeostasis on performance of broiler chickens through satiety- and appetite-mediating hormones. In 3 replications, 270 one-day-old chicks were reared for 8 wk feeding on diets comprising 0.85, 1.14, and 1.42% lysine …

Transcriptional Profiling Of Liver During The Critical Embryo-To-Hatchling Transition Period In The Chicken (Gallus Gallus), Larry A. Cogburn, Nares Trakooljul, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Wilfrid Carré, Xiaofei Wang, Harold B. White Iii

Biology Faculty Research

Background

Although hatching is perhaps the most abrupt and profound metabolic challenge that a chicken must undergo; there have been no attempts to functionally map the metabolic pathways induced in liver during the embryo-to-hatchling transition. Furthermore, we know very little about the metabolic and regulatory factors that regulate lipid metabolism in late embryos or newly-hatched chicks. In the present study, we examined hepatic transcriptomes of 12 embryos and 12 hatchling chicks during the peri-hatch period—or the metabolic switch from chorioallantoic to pulmonary respiration.

Results

Initial hierarchical clustering revealed two distinct, albeit opposing, patterns of hepatic gene expression. Cluster A genes …

Transcriptional Profiling Of Liver In Riboflavin-Deficient Chicken Embryos Explains Impaired Lipid Utilization, Energy Depletion, Massive Hemorrhaging, And Delayed Feathering, Larry A. Cogburn, Danielle N. Smarsh, Xiaofei Wang, Nares Trakooljul, Wilfrid Carré, Harold B. White Iii

Biology Faculty Research

Background

A strain of Leghorn chickens (rd/rd), unable to produce a functional riboflavin-binding protein, lays riboflavin-deficient eggs, in which all embryos suddenly die at mid-incubation (days 13-15). This malady, caused by riboflavin deficiency, leads to excessive lipid accumulation in liver, impaired β-oxidation of lipid, and severe hypoglycemia prior to death. We have used high-density chicken microarrays for time-course transcriptional scans of liver in chicken embryos between days 9-15 during this riboflavin-deficiency-induced metabolic catastrophe. For comparison, half of rd/rd embryos (n = 16) were rescued from this calamity by injection of riboflavin just prior to incubation of fertile …

Transcriptional Analysis Of Abdominal Fat In Chickens Divergently Selected On Bodyweight At Two Ages Reveals Novel Mechanisms Controlling Adiposity: Validating Visceral Adipose Tissue As A Dynamic Endocrine And Metabolic Organ, Christopher W. Resnyk, Wilfrid Carré, Xiaofei Wang, Tom E. Porter, J. Simon, Elisabeth Le Bihan-Duval, Michel J. Duclos, Sammy E. Aggrey, Larry A. Cogburn

Biology Faculty Research

Background

Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today’s broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and disorders of metabolism and reproduction). The present descriptive analysis of the abdominal fat transcriptome aimed to identify functional genes and biological pathways that likely contribute to an extreme difference in visceral fatness of divergently selected broiler chickens.

Methods

We used the Del-Mar 14 K Chicken Integrated Systems microarray to take time-course snapshots of global gene transcription …

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 …

The First Whole Genome And Transcriptome Of The Cinereous Vulture Reveals Adaptation In The Gastric And Immune Defense Systems And Possible Convergent Evolution Between The Old And New World Vultures, Oksung Chung, Seondeok Jin, Yun Sung Cho, Jeongheui Lim, Hyunho Kim, Sungwoong Jho, Hak-Min Kim, Jehoon Jun, Hyejin Lee, Alvin Chon, Junsu Ko, Jeremy Edwards, Jessica A. Weber, Kyudong Han, Stephen J. O'Brien, Andrea Manica, Jong Bhak, Woon Kee Paek

Biology Faculty Articles

Background: The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.

Results: We sequenced the genome of a cinereous vulture, and mapped it to the bald …

Comparative Genomics Reveals Insights Into Avian Genome Evolution And Adaptation, Guojie Zhang, Cai Li, Qiye Li, Bo Li, Dennis M. Larkin, Chul Lee, Jay F. Storz, Agostinho Antunes, Matthew J. Greenwold, Robert W. Meredith, Anders Ödeen, Jie Cui, Qi Zhou, Luohao Xu, Hailin Pan, Zongji Wang, Lijun Jin, Pei Zhang, Haofu Hu, Wei Yang, Jiang Hu, Jin Xiao, Zhikai Yang, Yang Liu, Qiaolin Xie, Hao Yu, Jinmin Lian, Ping Wen, Fang Zhang, Hui Li, Yongli Zeng, Zijun Xiong, Shiping Liu, Long Zhou, Zhiyong Huang, Na An, Jie Wang, Quimei Zheng, Yingqi Xiong, Guangbiao Wang, Bo Wang, Jingjing Wang, Yu Fan, Rute R. Da Fonseca, Alonzo Alfaro-Núñez, Mikkel Schubert, Ludovic Orlando, Tobias Mourier, Jason T. Howard, Ganeshkumar Ganapathy, Andreas Pfenning, Osceola Whitney, Miriam V. Rivas, Erina Hara, Julia Smith, Marta Farré, Jitendra Narayan, Gancho Slavov, Michael N. Romanov, Rui Borges, João Paulo Machado, Imran Khan, Mark S. Springer, John Gatesy, Federico G. Hoffmann, Juan C. Opazo, Olle Håstad, Roger H. Sawyer, Heebal Kim, Kyu-Won Kim, Hyeon Jeong Kim, Seoae Cho, Ning Li, Yinhua Huang, Michael W. Bruford, Xiangjiang Zhan, Andrew Dixon, Mads F. Bertelsen, Elizabeth Derryberry, Wesley Warren, Richard K. Wilson, Shengbin Li, David A. Ray, Richard E. Green, Stephen J. O'Brien, Darren Griffin, Warren E. Johnson, David Haussler, Oliver A. Ryder, Eske Willerslev, Gary R. Graves, Per Alström, Jon Fjeldså, David P. Mindell, Scott V. Edwards, Edward L. Braun, Carsten Rahbek, David W. Burt, Peter Houde, Yong Zhang, Huanming Yang, Jian Wang, Avian Genome Consortium, Erich D. Jarvis, M. Thomas P. Gilbert, Jun Wang

Jay F. Storz Publications

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses …

Parsimony And Model-Based Analyses Of Indels In Avian Nuclear Genes Reveal Congruent And Incongruent Phylogenetic Signals, Tamaki Yuri, Rebecca T. Kimball, John Harshman, Rauri C.K. Bowie, Michael J. Braun, Jena L. Chojnowski, Kin-Lan Han, Shannon J. Hackett, Christopher J. Huddleston, William S. Moore, Sushma Reddy, Frederick H. Sheldon, David W. Steadman, Christopher C. Witt, Edward L. Braun

Faculty Publications

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven …

Genome Empowerment For The Puerto Rican Parrot – Amazona Vittata, Stephen J. O'Brien

Biology Faculty Articles

A unique community-funded project in Puerto Rico has launched whole-genome sequencing of the critically endangered Puerto Rican Parrot (Amazona vittata), with interpretation by genome bioinformaticians and students, and deposition into public online databases. This is the first article that focuses on the whole genome of a parrot species, one endemic to the USA and recently threatened with extinction. It provides invaluable conservation tools and a vivid example of hopeful prospects for future genome assessment of so many new species. It also demonstrates inventive ways for smaller institutions to contribute to a field largely considered the domain of large …

An Initial Map Of Chromosomal Segmental Copy Number Variations In The Chicken, Xiaofei Wang, Samuel N. Nahashon, Tromondae K. Feaster, Ann L. Bohannon-Stewart, Nathaniel Adefope

Agricultural and Environmental Sciences Faculty Research

Background

Chromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory elements. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as a model for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosomal regions that segregate for important agricultural and disease phenotypes.

Results

Ninety six CNVs were identified in three lines of chickens (Cornish Rock broiler, Leghorn and Rhode Island …

Sexual Differentiation Of The Zebra Finch Song System: Potential Roles For Sex Chromosome Genes, Michelle L. Tomaszycki, Camilla Peabody, Kirstin Replogle, David F. Clayton, Robert J. Tempelman, Juli Wade

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Recent evidence suggests that some sex differences in brain and behavior might result from direct genetic effects, and not solely the result of the organizational effects of steroid hormones. The present study examined the potential role for sex-biased gene expression during development of sexually dimorphic singing behavior and associated song nuclei in juvenile zebra finches.

Results

A microarray screen revealed more than 2400 putative genes (with a false discovery rate less than 0.05) exhibiting sex differences in the telencephalon of developing zebra finches. Increased expression in males was confirmed in 12 of 20 by qPCR using cDNA from …

International Registry Of Poultry Genetic Stocks, Ralph G. Somes Jr.

Storrs Agricultural Experiment Station

No abstract provided.

Subject And Author Index For Bulletins Of The Storrs Agricultural Experiment Station, Mohini Mundkur

Storrs Agricultural Experiment Station

Storrs Agricultural Experiment Station Bulletin #453, 68 pages.

Research For Connecticut By The Storrs Agricultural Experiment Station

Storrs Agricultural Experiment Station

No abstract provided.