Non-human and non-rodent vertebrate genomics

Section edited by Shane Burgess and Jacqueline Smith

This section covers all aspects of the genomics of vertebrates, excluding humans, primates and rodents, including livestock species.

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  1. Research article

    Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment

    Motility and the coordination of moving food through the gastrointestinal tract rely on a complex network of neurons known as the enteric nervous system (ENS). Despite its critical function, many of the molecu...

    Sweta Roy-Carson, Kevin Natukunda, Hsien-chao Chou, Narinder Pal, Caitlin Farris, Stephan Q. Schneider and Julie A. Kuhlman

    BMC Genomics 2017 18:290

    Published on: 12 April 2017

  2. Research Article

    Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos

    Infertility in dairy cattle is a concern where reduced fertilization rates and high embryonic loss are contributing factors. Studies of the paternal contribution to reproductive performance are limited. Howeve...

    Jenna Kropp, José A. Carrillo, Hadjer Namous, Alyssa Daniels, Sana M. Salih, Jiuzhou Song and Hasan Khatib

    BMC Genomics 2017 18:280

    Published on: 5 April 2017

  3. Research article

    RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

    The selective breeding of cattle with high-feed efficiencies (FE) is an important goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues can be used to study the functions...

    M. S. Salleh, G. Mazzoni, J. K. Höglund, D. W. Olijhoek, P. Lund, P. Løvendahl and H. N. Kadarmideen

    BMC Genomics 2017 18:258

    Published on: 24 March 2017

  4. Research article

    Analysis of hepatic transcript profile and plasma lipid profile in early lactating dairy cows fed grape seed and grape marc meal extract

    It was recently reported that dairy cows fed a polyphenol-rich grape seed and grape marc meal extract (GSGME) during the transition period had an increased milk yield, but the underlying reasons remained uncle...

    Denise K. Gessner, Anne Winkler, Christian Koch, Georg Dusel, Gerhard Liebisch, Robert Ringseis and Klaus Eder

    BMC Genomics 2017 18:253

    Published on: 23 March 2017

  5. Research article

    A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

    Animal’s efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of ...

    Florence Gondret, Annie Vincent, Magalie Houée-Bigot, Anne Siegel, Sandrine Lagarrigue, David Causeur, Hélène Gilbert and Isabelle Louveau

    BMC Genomics 2017 18:244

    Published on: 21 March 2017

  6. Research article

    Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development

    Gut microbial colonization and development of immune competence are intertwined and are influenced by early-life nutritional, environmental, and management factors. Perturbation of the gut microbiome at young ...

    Dirkjan Schokker, Alfons J. M. Jansman, Gosse Veninga, Naomi de Bruin, Stephanie A. Vastenhouw, Freddy M. de Bree, Alex Bossers, Johanna M. J. Rebel and Mari A. Smits

    BMC Genomics 2017 18:241

    Published on: 20 March 2017

  7. Research article

    Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

    The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to inve...

    Luiz F. Brito, James W. Kijas, Ricardo V. Ventura, Mehdi Sargolzaei, Laercio R. Porto-Neto, Angela Cánovas, Zeny Feng, Mohsen Jafarikia and Flávio S. Schenkel

    BMC Genomics 2017 18:229

    Published on: 14 March 2017

  8. Research article

    Effects of exposure to Streptococcus iniae on microRNA expression in the head kidney of genetically improved farmed tilapia (Oreochromis niloticus)

    Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are susceptible to infection by Streptococcus iniae when maintained in modern intensive culture systems. GIFT are commercially important fishes th...

    Jun Qiang, Fanyi Tao, Jie He, Lanyi Sun, Pao Xu and Wenjin Bao

    BMC Genomics 2017 18:190

    Published on: 20 February 2017

  9. Commentary

    Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

    Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and bree...

    Hisham Abdelrahman, Mohamed ElHady, Acacia Alcivar-Warren, Standish Allen, Rafet Al-Tobasei, Lisui Bao, Ben Beck, Harvey Blackburn, Brian Bosworth, John Buchanan, Jesse Chappell, William Daniels, Sheng Dong, Rex Dunham, Evan Durland, Ahmed Elaswad…

    BMC Genomics 2017 18:191

    Published on: 20 February 2017

    The Erratum to this article has been published in BMC Genomics 2017 18:235

  10. Research article

    Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis

    The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainab...

    Richard Osei-Amponsah, Benjamin M. Skinner, Dennis O. Adjei, Julien Bauer, Greger Larson, Nabeel A. Affara and Carole A. Sargent

    BMC Genomics 2017 18:193

    Published on: 20 February 2017

  11. Research article

    Understanding the response to endurance exercise using a systems biology approach: combining blood metabolomics, transcriptomics and miRNomics in horses

    Endurance exercise in horses requires adaptive processes involving physiological, biochemical, and cognitive-behavioral responses in an attempt to regain homeostasis. We hypothesized that the identification of...

    Núria Mach, Yuliaxis Ramayo-Caldas, Allison Clark, Marco Moroldo, Céline Robert, Eric Barrey, Jesús Maria López and Laurence Le Moyec

    BMC Genomics 2017 18:187

    Published on: 17 February 2017

  12. Research article

    The origin of chow chows in the light of the East Asian breeds

    East Asian dog breeds are one of the most ancient groups of dogs that radiated after the domestication of the dog and represent the most basal lineages of dog evolution. Among these, the Chow Chow is an ancien...

    Hechuan Yang, Guodong Wang, Meng Wang, Yaping Ma, Tingting Yin, Ruoxi Fan, Hong Wu, Li Zhong, David M. Irwin, Weiwei Zhai and Yaping Zhang

    BMC Genomics 2017 18:174

    Published on: 16 February 2017

  13. Research article

    Variant discovery in the sheep milk transcriptome using RNA sequencing

    The identification of genetic variation underlying desired phenotypes is one of the main challenges of current livestock genetic research. High-throughput transcriptome sequencing (RNA-Seq) offers new opportun...

    Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser-Klopp and Juan José Arranz

    BMC Genomics 2017 18:170

    Published on: 15 February 2017

  14. Research article

    Screening and evaluating of long noncoding RNAs in the puberty of goats

    Long noncoding RNAs (lncRNAs) are involved in regulating animal development, however, their function in the onset of puberty in goats remain largely unexplored. To identify the genes controlling the regulation...

    Xiaoxiao Gao, Jing Ye, Chen Yang, Kaifa Zhang, Xiumei Li, Lei Luo, Jianping Ding, Yunsheng Li, Hongguo Cao, Yinghui Ling, Xiaorong Zhang, Ya Liu, Fugui Fang and Yunhai Zhang

    BMC Genomics 2017 18:164

    Published on: 14 February 2017

  15. Research article

    Transcriptome analysis of coding and long non-coding RNAs highlights the regulatory network of cascade initiation of permanent molars in miniature pigs

    In diphyodont mammals, the additional molars (permanent molars) bud off from the posterior-free end of the primary dental lamina compared with successional teeth (replacement teeth) budding off from the second...

    Fu Wang, Yang Li, Xiaoshan Wu, Min Yang, Wei Cong, Zhipeng Fan, Jinsong Wang, Chunmei Zhang, Jie Du and Songlin Wang

    BMC Genomics 2017 18:148

    Published on: 10 February 2017

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