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

    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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. Research article

    Genomic predictions can accelerate selection for resistance against Piscirickettsia salmonis in Atlantic salmon (Salmo salar)

    Salmon Rickettsial Syndrome (SRS) caused by Piscirickettsia salmonis is a major disease affecting the Chilean salmon industry. Genomic selection (GS) is a method wherein genome-wide markers and phenotype informat...

    Rama Bangera, Katharina Correa, Jean P. Lhorente, René Figueroa and José M. Yáñez

    BMC Genomics 2017 18:121

    Published on: 31 January 2017

  10. Research Article

    Short bowel syndrome results in increased gene expression associated with proliferation, inflammation, bile acid synthesis and immune system activation: RNA sequencing a zebrafish SBS model

    Much of the morbidity associated with short bowel syndrome (SBS) is attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition (TPN). We hypothesized that acute SBS a...

    Kathy A. Schall, Matthew E. Thornton, Mubina Isani, Kathleen A. Holoyda, Xiaogang Hou, Ching-Ling Lien, Brendan H. Grubbs and Tracy C. Grikscheit

    BMC Genomics 2017 18:23

    Published on: 25 January 2017

  11. Research Article

    Tissue resolved, gene structure refined equine transcriptome

    Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the ho...

    T. A. Mansour, E. Y. Scott, C. J. Finno, R. R. Bellone, M. J. Mienaltowski, M. C. Penedo, P. J. Ross, S. J. Valberg, J. D. Murray and C. T. Brown

    BMC Genomics 2017 18:103

    Published on: 20 January 2017

  12. Research article

    Conserved gene expression in sperm reservoirs between birds and mammals in response to mating

    Spermatozoa are stored in the oviductal functional sperm reservoir in animals with internal fertilization, including zoologically distant classes such as pigs or poultry. They are held fertile in the reservoir...

    Mohammad Atikuzzaman, Manuel Alvarez-Rodriguez, Alejandro Vicente Carrillo, Martin Johnsson, Dominic Wright and Heriberto Rodriguez-Martinez

    BMC Genomics 2017 18:98

    Published on: 18 January 2017

  13. Research Article

    Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens

    Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and te...

    Mette Lillie, Zheya Sheng, Christa F. Honaker, Ben J. Dorshorst, Christopher M. Ashwell, Paul B. Siegel and Örjan Carlborg

    BMC Genomics 2017 18:99

    Published on: 18 January 2017

  14. Research Article

    Genome-wide expression profiling in muscle and subcutaneous fat of lambs in response to the intake of concentrate supplemented with vitamin E

    The objective of this study was to acquire a broader, more comprehensive picture of the transcriptional changes in the L. Thoracis muscle (LT) and subcutaneous fat (SF) of lambs supplemented with vitamin E. Furth...

    Laura González-Calvo, Elda Dervishi, Margalida Joy, Pilar Sarto, Roberto Martin-Hernandez, Magdalena Serrano, Jose M. Ordovás and Jorge H. Calvo

    BMC Genomics 2017 18:92

    Published on: 17 January 2017

  15. Research Article

    Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species

    In the marine environment, where there are few absolute physical barriers, contemporary contact between previously isolated species can occur across great distances, and in some cases, may be inter-oceanic. An...

    Ketil Malde, Bjørghild B. Seliussen, María Quintela, Geir Dahle, Francois Besnier, Hans J. Skaug, Nils Øien, Hiroko K. Solvang, Tore Haug, Rasmus Skern-Mauritzen, Naohisa Kanda, Luis A. Pastene, Inge Jonassen and Kevin A. Glover

    BMC Genomics 2017 18:76

    Published on: 13 January 2017

  16. Research article

    RNA sequencing for global gene expression associated with muscle growth in a single male modern broiler line compared to a foundational Barred Plymouth Rock chicken line

    Modern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive gen...

    Byung-Whi Kong, Nicholas Hudson, Dongwon Seo, Seok Lee, Bhuwan Khatri, Kentu Lassiter, Devin Cook, Alissa Piekarski, Sami Dridi, Nicholas Anthony and Walter Bottje

    BMC Genomics 2017 18:82

    Published on: 13 January 2017

  17. Research article

    Construction of high-resolution recombination maps in Asian seabass

    A high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a ...

    Le Wang, Bin Bai, Peng Liu, Shu Qing Huang, Zi Yi Wan, Elaine Chua, Baoqing Ye and Gen Hua Yue

    BMC Genomics 2017 18:63

    Published on: 10 January 2017

  18. Research article

    Functional changes in mRNA expression and alternative pre-mRNA splicing associated with the effects of nutrition on apoptosis and spermatogenesis in the adult testis

    The effects of nutrition on testis mass in the sexually mature male have long been known, however, the cellular and molecular processes of the testis response to nutrition was not fully understood.

    Yongjuan Guan, Guanxiang Liang, Graeme B. Martin and Le Luo Guan

    BMC Genomics 2017 18:64

    Published on: 10 January 2017

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