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 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. Research article

    Whole genome sequencing identifies missense mutation in MTBP in Shar-Pei affected with Autoinflammatory Disease (SPAID)

    Autoinflammatory diseases in dogs are characterized by complex disease processes with varying clinical signs. In Shar-Pei, signs of inflammation including fever and arthritis are known to be related with a bre...

    Julia Metzger, Anna Nolte, Ann-Kathrin Uhde, Marion Hewicker-Trautwein and Ottmar Distl

    BMC Genomics 2017 18:348

    Published on: 4 May 2017

  10. Research article

    Gene expression profile during proliferation and differentiation of rainbow trout adipocyte precursor cells

    Excessive accumulation of adipose tissue in cultured fish is an outstanding problem in aquaculture. To understand the development of adiposity, it is crucial to identify the genes which expression is associate...

    Marta Bou, Jerôme Montfort, Aurélie Le Cam, Cécile Rallière, Véronique Lebret, Jean-Charles Gabillard, Claudine Weil, Joaquim Gutiérrez, Pierre-Yves Rescan, Encarnación Capilla and Isabel Navarro

    BMC Genomics 2017 18:347

    Published on: 4 May 2017

  11. Research article

    Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection

    MicroRNAs (miRNAs) control multiple biological processes including the innate immune responses by negative post-transcriptional regulation of gene expression. As there were no studies on the role(s) of miRNAs ...

    Rune Andreassen, Nardos Tesfaye Woldemariam, Ine Østråt Egeland, Oleg Agafonov, Hilde Sindre and Bjørn Høyheim

    BMC Genomics 2017 18:349

    Published on: 4 May 2017

  12. Research article

    A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions

    Tilapias are the second most farmed fishes in the world and a sustainable source of food. Like many other fish, tilapias are sexually dimorphic and sex is a commercially important trait in these fish. In this ...

    Matthew A. Conte, William J. Gammerdinger, Kerry L. Bartie, David J. Penman and Thomas D. Kocher

    BMC Genomics 2017 18:341

    Published on: 2 May 2017

  13. Research article

    Transcriptome-wide N 6 -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern

    N 6 -methyladenosine (m6A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes a...

    Xuelian Tao, Jianning Chen, Yanzhi Jiang, Yingying Wei, Yan Chen, Huaming Xu, Li Zhu, Guoqing Tang, Mingzhou Li, Anan Jiang, Surong Shuai, Lin Bai, Haifeng Liu, Jideng Ma, Long Jin, Anxiang Wen…

    BMC Genomics 2017 18:336

    Published on: 28 April 2017

  14. 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

  15. 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

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