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

    Maternal nutrient restriction in mid-to-late gestation influences fetal mRNA expression in muscle tissues in beef cattle

    Manipulating maternal nutrition during specific periods of gestation can result in re-programming of fetal and post-natal development. In this experiment we investigated how a feed restriction of 85% compared ...

    Francois Paradis, Katie M. Wood, Kendall C. Swanson, Stephen P. Miller, Brian W. McBride and Carolyn Fitzsimmons

    BMC Genomics 2017 18:632

    Published on: 18 August 2017

  2. Research

    AvBD1 nucleotide polymorphisms, peptide antimicrobial activities and microbial colonisation of the broiler chicken gut

    The importance of poultry as a global source of protein underpins the chicken genome and associated SNP data as key tools in selecting and breeding healthy robust birds with improved disease resistance. SNPs a...

    Kevin Cadwell, Sherko S. Niranji, Vanessa L. Armstrong, Catherine A. Mowbray, Richard Bailey, Kellie A Watson and Judith Hall

    BMC Genomics 2017 18:637

    Published on: 18 August 2017

  3. Research article

    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

    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 a...

    C. W. Resnyk, W. Carré, X. Wang, T. E. Porter, J. Simon, E. Le Bihan-Duval, M. J. Duclos, S. E. Aggrey and L. A. Cogburn

    BMC Genomics 2017 18:626

    Published on: 16 August 2017

  4. Research article

    The genomic architecture of mastitis resistance in dairy sheep

    Mastitis is the most prevalent disease in dairy sheep with major economic, hygienic and welfare implications. The disease persists in all dairy sheep production systems despite the implementation of improved m...

    G. Banos, G. Bramis, S. J. Bush, E. L. Clark, M. E.B. McCulloch, J. Smith, G. Schulze, G. Arsenos, D. A. Hume and A. Psifidi

    BMC Genomics 2017 18:624

    Published on: 16 August 2017

  5. Research article

    Suitable reference gene for quantitative real-time PCR analysis of gene expression in gonadal tissues of minnow Puntius sophore under high-temperature stress

    High ambient temperature is known to affect fish gonadal development and physiology in a variety of ways depending on the severity and duration of exposure; however, the underlying molecular mechanisms are poo...

    Arabinda Mahanty, Gopal Krishna Purohit, Sasmita Mohanty, Nihar Ranjan Nayak and Bimal Prasanna Mohanty

    BMC Genomics 2017 18:617

    Published on: 15 August 2017

  6. Research article

    Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of sex-biased miRNA-mRNA pairs in gonad tissue of dark sleeper (Odontobutis potamophila)

    The dark sleeper (Odontobutis potamophila) is an important commercial fish species which shows a sexually dimorphic growth pattern. However, the lack of sex transcriptomic data is hindering further research and g...

    Cheng Zhao, Guosong Zhang, Shaowu Yin, Zecheng Li, Qintao Wang, Shuqiao Chen and Guoqin Zhou

    BMC Genomics 2017 18:613

    Published on: 14 August 2017

  7. Research article

    Genomic data illuminates demography, genetic structure and selection of a popular dog breed

    Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. ...

    Pamela Wiener, Enrique Sánchez-Molano, Dylan N. Clements, John A. Woolliams, Marie J. Haskell and Sarah C. Blott

    BMC Genomics 2017 18:609

    Published on: 14 August 2017

  8. Research article

    Use of biological priors enhances understanding of genetic architecture and genomic prediction of complex traits within and between dairy cattle breeds

    A better understanding of the genetic architecture underlying complex traits (e.g., the distribution of causal variants and their effects) may aid in the genomic prediction. Here, we hypothesized that the geno...

    Lingzhao Fang, Goutam Sahana, Peipei Ma, Guosheng Su, Ying Yu, Shengli Zhang, Mogens Sandø Lund and Peter Sørensen

    BMC Genomics 2017 18:604

    Published on: 10 August 2017

  9. Research article

    Nutrient supply affects the mRNA expression profile of the porcine skeletal muscle

    The genetic basis of muscle fat deposition in pigs is not well known. So far, we have only identified a limited number of genes involved in the absorption, transport, storage and catabolism of lipids. Such inf...

    Tainã Figueiredo Cardoso, Raquel Quintanilla, Joan Tibau, Marta Gil, Emilio Mármol-Sánchez, Olga González-Rodríguez, Rayner González-Prendes and Marcel Amills

    BMC Genomics 2017 18:603

    Published on: 10 August 2017

  10. Research article

    Characterization of the peripheral blood transcriptome and adaptive evolution of the MHC I and TLR gene families in the wolf (Canis lupus)

    The wolf (Canis lupus) is one of the most widely distributed terrestrial mammals, because it is well adapted to various ecological niches and their corresponding pathogen environments. Immunological competence is...

    Guangshuai Liu, Honghai Zhang, Guolei Sun, Chao Zhao, Shuai Shang, Xiaodong Gao, Tian Xia and Xiufeng Yang

    BMC Genomics 2017 18:584

    Published on: 7 August 2017

  11. Research article

    Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout

    Coding/functional SNPs change the biological function of a gene and, therefore, could serve as “large-effect” genetic markers. In this study, we used two bioinformatics pipelines, GATK and SAMtools, for discov...

    Rafet Al-Tobasei, Ali Ali, Timothy D. Leeds, Sixin Liu, Yniv Palti, Brett Kenney and Mohamed Salem

    BMC Genomics 2017 18:582

    Published on: 7 August 2017

  12. Research article

    Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

    To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent av...

    Robert J. Schaefer, Mikkel Schubert, Ernest Bailey, Danika L. Bannasch, Eric Barrey, Gila Kahila Bar-Gal, Gottfried Brem, Samantha A. Brooks, Ottmar Distl, Ruedi Fries, Carrie J. Finno, Vinzenz Gerber, Bianca Haase, Vidhya Jagannathan, Ted Kalbfleisch, Tosso Leeb…

    BMC Genomics 2017 18:565

    Published on: 27 July 2017

  13. Research article

    Distinct herpesvirus resistances and immune responses of three gynogenetic clones of gibel carp revealed by comprehensive transcriptomes

    Gibel carp is an important aquaculture species in China, and a herpesvirus, called as Carassius auratus herpesvirus (CaHV), has hampered the aquaculture development. Diverse gynogenetic clones of gibel carp have ...

    Fan-Xiang Gao, Yang Wang, Qi-Ya Zhang, Cheng-Yan Mou, Zhi Li, Yuan-Sheng Deng, Li Zhou and Jian-Fang Gui

    BMC Genomics 2017 18:561

    Published on: 24 July 2017

  14. Research article

    Histological and transcriptomic effects of 17α-methyltestosterone on zebrafish gonad development

    Sex hormones play important roles in teleost ovarian and testicular development. In zebrafish, ovarian differentiation appears to be dictated by an oocyte-derived signal via Cyp19a1a aromatase-mediated estroge...

    Stephanie Ling Jie Lee, Julia A. Horsfield, Michael A. Black, Kim Rutherford, Amanda Fisher and Neil J. Gemmell

    BMC Genomics 2017 18:557

    Published on: 24 July 2017

  15. Research article

    Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx

    The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split...

    Daniel Kleinman-Ruiz, Begoña Martínez-Cruz, Laura Soriano, Maria Lucena-Perez, Fernando Cruz, Beatriz Villanueva, Jesús Fernández and José A. Godoy

    BMC Genomics 2017 18:556

    Published on: 21 July 2017

  16. Research article

    Identification and characterization of long non-coding RNAs in subcutaneous adipose tissue from castrated and intact full-sib pair Huainan male pigs

    Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male ...

    Jing Wang, Liushuai Hua, Junfeng Chen, Jiaqing Zhang, Xianxiao Bai, Binwen Gao, Congjun Li, Zhihai Shi, Weidong Sheng, Yuan Gao and Baosong Xing

    BMC Genomics 2017 18:542

    Published on: 19 July 2017

  17. Research article

    Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus Smith 1828

    The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to ...

    Timothy D. Read, Robert A. Petit III, Sandeep J. Joseph, Md. Tauqeer Alam, M. Ryan Weil, Maida Ahmad, Ravila Bhimani, Jocelyn S. Vuong, Chad P. Haase, D. Harry Webb, Milton Tan and Alistair D. M. Dove

    BMC Genomics 2017 18:532

    Published on: 14 July 2017

  18. Research article

    Identification of long non-coding RNA in the horse transcriptome

    Efforts to resolve the transcribed sequences in the equine genome have focused on protein-coding RNA. The transcription of the intergenic regions, although detected via total RNA sequencing (RNA-seq), has yet ...

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

    BMC Genomics 2017 18:511

    Published on: 4 July 2017

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