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

    Genome-wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus

    DNA methylation is a frequently studied epigenetic modification due to its role in regulating gene expression and hence in biological processes and in determining phenotypic plasticity in organisms. Rudimentar...

    Stefano Frattini, Emanuele Capra, Barbara Lazzari, Stephanie D. McKay, Beatrice Coizet, Andrea Talenti, Debora Groppetti, Pietro Riccaboni, Alessandro Pecile, Stefania Chessa, Bianca Castiglioni, John L. Williams, Giulio Pagnacco, Alessandra Stella and Paola Crepaldi

    BMC Genomics 2017 18:476

    Published on: 23 June 2017

  2. Research article

    Biological mechanisms discriminating growth rate and adult body weight phenotypes in two Chinese indigenous chicken breeds

    Intensive selection has resulted in increased growth rates and muscularity in broiler chickens, in addition to adverse effects, including delayed organ development, sudden death syndrome, and altered metabolic...

    Tengfei Dou, Sumei Zhao, Hua Rong, Dahai Gu, Qihua Li, Ying Huang, Zhiqiang Xu, Xiaohui Chu, Linli Tao, Lixian Liu, Changrong Ge, Marinus F.W. te Pas and Junjing Jia

    BMC Genomics 2017 18:469

    Published on: 20 June 2017

  3. Research article

    Genome wide association study and genomic prediction for fatty acid composition in Chinese Simmental beef cattle using high density SNP array

    Fatty acid composition of muscle is an important trait contributing to meat quality. Recently, genome-wide association study (GWAS) has been extensively used to explore the molecular mechanism underlying impor...

    Bo Zhu, Hong Niu, Wengang Zhang, Zezhao Wang, Yonghu Liang, Long Guan, Peng Guo, Yan Chen, Lupei Zhang, Yong Guo, Heming Ni, Xue Gao, Huijiang Gao, Lingyang Xu and Junya Li

    BMC Genomics 2017 18:464

    Published on: 14 June 2017

  4. Research article

    Global gene expression in muscle from fasted/refed trout reveals up-regulation of genes promoting myofibre hypertrophy but not myofibre production

    Compensatory growth is a phase of rapid growth, greater than the growth rate of control animals, that occurs after a period of growth-stunting conditions. Fish show a capacity for compensatory growth after all...

    Pierre-Yves Rescan, Aurelie Le Cam, Cécile Rallière and Jérôme Montfort

    BMC Genomics 2017 18:447

    Published on: 7 June 2017

  5. Research article

    Gene-centromere mapping in meiotic gynogenetic European seabass

    Fully isogenic lines in fish can be developed using “mitotic” gynogenesis (suppression of first zygotic mitosis following inactivation of the sperm genome). However, genome-wide verification of the steps in th...

    Münevver Oral, Julie Colléter, Michaël Bekaert, John B Taggart, Christos Palaiokostas, Brendan J. McAndrew, Marc Vandeputte, Béatrice Chatain, Heiner Kuhl, Richard Reinhardt, Stefano Peruzzi and David J Penman

    BMC Genomics 2017 18:449

    Published on: 7 June 2017

  6. Research article

    Construction of a high-density linkage map and mapping of sex determination and growth-related loci in the mandarin fish (Siniperca chuatsi)

    The mandarin fish (Siniperca chuatsi) is an important and widely cultured fish in China. However, the lack of selective breeding of mandarin fish in previous decades has resulted in a decline in the growth rate o...

    Chengfei Sun, Yongchaox Niu, Xing Ye, Junjian Dong, Wushu Hu, Qingkai Zeng, Zhihang Chen, Yuanyuan Tian, Jin Zhang and Maixin Lu

    BMC Genomics 2017 18:446

    Published on: 6 June 2017

  7. Research article

    Identification of conserved genes triggering puberty in European sea bass males (Dicentrarchus labrax) by microarray expression profiling

    Spermatogenesis is a complex process characterized by the activation and/or repression of a number of genes in a spatio-temporal manner. Pubertal development in males starts with the onset of the first spermat...

    Mercedes Blázquez, Paula Medina, Berta Crespo, Ana Gómez and Silvia Zanuy

    BMC Genomics 2017 18:441

    Published on: 5 June 2017

  8. Research article

    The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species

    Understanding the genetic and developmental origins of phenotypic novelty is central to the study of biological diversity. In this study we identify modifications to the expression of genes at four development...

    Ezra S. Lencer, Wesley C. Warren, Richard Harrison and Amy R. McCune

    BMC Genomics 2017 18:424

    Published on: 30 May 2017

  9. Research article

    Dissection of additive, dominance, and imprinting effects for production and reproduction traits in Holstein cattle

    Although genome-wide association and genomic selection studies have primarily focused on additive effects, dominance and imprinting effects play an important role in mammalian biology and development. The degr...

    Jicai Jiang, Botong Shen, Jeffrey R. O’Connell, Paul M. VanRaden, John B. Cole and Li Ma

    BMC Genomics 2017 18:425

    Published on: 30 May 2017

  10. Research article

    Long-lasting effect of obesity on skeletal muscle transcriptome

    Reduced physical activity and increased intake of calorically-dense diets are the main risk factors for obesity, glucose intolerance, and type 2 diabetes. Chronic overnutrition and hyperglycemia can alter gene...

    Ilhem Messaoudi, Mithila Handu, Maham Rais, Suhas Sureshchandra, Byung S. Park, Suzanne S. Fei, Hollis Wright, Ashley E. White, Ruhee Jain, Judy L. Cameron, Kerri M. Winters-Stone and Oleg Varlamov

    BMC Genomics 2017 18:411

    Published on: 25 May 2017

    The Erratum to this article has been published in BMC Genomics 2017 18:471

  11. Research article

    Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle

    Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Usin...

    Christopher M. Seabury, David L. Oldeschulte, Mahdi Saatchi, Jonathan E. Beever, Jared E. Decker, Yvette A. Halley, Eric K. Bhattarai, Maral Molaei, Harvey C. Freetly, Stephanie L. Hansen, Helen Yampara-Iquise, Kristen A. Johnson, Monty S. Kerley, JaeWoo Kim, Daniel D. Loy, Elisa Marques…

    BMC Genomics 2017 18:386

    Published on: 18 May 2017

  12. Research article

    Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.)

    Pikes represent an important genus (Esox) harbouring a pre-duplication karyotype (2n = 2x = 50) of economically important salmonid pseudopolyploids. Here, we have characterized the 5S ribosomal RNA genes (rDNA) i...

    Radka Symonová, Konrad Ocalewicz, Lech Kirtiklis, Giovanni Battista Delmastro, Šárka Pelikánová, Sonia Garcia and Aleš Kovařík

    BMC Genomics 2017 18:391

    Published on: 18 May 2017

  13. Research article

    Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N’Dama

    Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. While many studies investigated the adaptation of overa...

    Soo-Jin Kim, Sojeong Ka, Jung-Woo Ha, Jaemin Kim, DongAhn Yoo, Kwondo Kim, Hak-Kyo Lee, Dajeong Lim, Seoae Cho, Olivier Hanotte, Okeyo Ally Mwai, Tadelle Dessie, Stephen Kemp, Sung Jong Oh and Heebal Kim

    BMC Genomics 2017 18:371

    Published on: 12 May 2017

  14. Research article

    Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs

    Fatty acid composition contributes importantly to meat quality and is essential to the nutritional value of the meat. Identification of genetic factors underlying levels of fatty acids can be used to breed for...

    Maren van Son, Eli Gjerlaug Enger, Harald Grove, Roger Ros-Freixedes, Matthew P. Kent, Sigbjørn Lien and Eli Grindflek

    BMC Genomics 2017 18:369

    Published on: 11 May 2017

  15. Research article

    Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements

    RNA editing by ADAR (adenosine deaminase acting on RNA) proteins is a form of transcriptional regulation that is widespread among humans and other primates. Based on high-throughput scans used to identify puta...

    Scott A. Funkhouser, Juan P. Steibel, Ronald O. Bates, Nancy E. Raney, Darius Schenk and Catherine W. Ernst

    BMC Genomics 2017 18:360

    Published on: 9 May 2017

  16. Research article

    Effects of dietary physical or nutritional factors on morphology of rumen papillae and transcriptome changes in lactating dairy cows based on three different forage-based diets

    Rumen epithelial tissue plays an important role in nutrient absorption and rumen health. However, whether forage quality and particle size impact the rumen epithelial morphology is unclear. The current study w...

    Bing Wang, Diming Wang, Xuehui Wu, Jie Cai, Mei Liu, Xinbei Huang, Jiusheng Wu, Jianxin Liu and Leluo Guan

    BMC Genomics 2017 18:353

    Published on: 6 May 2017

  17. Research article

    Response of turkey muscle satellite cells to thermal challenge. I. transcriptome effects in proliferating cells

    Climate change poses a multi-dimensional threat to food and agricultural systems as a result of increased risk to animal growth, development, health, and food product quality. This study was designed to charac...

    Kent M. Reed, Kristelle M. Mendoza, Juan E. Abrahante, Natalie E. Barnes, Sandra G. Velleman and Gale M. Strasburg

    BMC Genomics 2017 18:352

    Published on: 6 May 2017

  18. Research article

    Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics

    The genetic diversity of Neotropical fish fauna is underrepresented in public databases. This distortion is evident for the order Siluriformes, in which the suborders Siluroidei and Loricarioidei share equival...

    Daniel Andrade Moreira, Paulo Andreas Buckup, Carolina Furtado, Adalberto Luis Val, Renata Schama and Thiago Estevam Parente

    BMC Genomics 2017 18:345

    Published on: 4 May 2017

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