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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.

Page 18 of 21

  1. Systems biology enables the identification of gene networks that modulate complex traits. Comprehensive metabolomic analyses provide innovative phenotypes that are intermediate between the initiator of genetic...

    Authors: Philipp Widmann, Antonio Reverter, Marina R S Fortes, Rosemarie Weikard, Karsten Suhre, Harald Hammon, Elke Albrecht and Christa Kuehn

    Citation: BMC Genomics 2013 14:798

    Content type: Research article

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  2. Advances in DNA sequencing and proteomics have facilitated quantitative comparisons of snake venom composition. Most studies have employed one approach or the other. Here, both Illumina cDNA sequencing and LC/...

    Authors: Steven D Aird, Yutaka Watanabe, Alejandro Villar-Briones, Michael C Roy, Kouki Terada and Alexander S Mikheyev

    Citation: BMC Genomics 2013 14:790

    Content type: Research article

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  3. Deep RNA sequencing (RNAseq) has opened a new horizon for understanding global gene expression. The functional annotation of non-model mammalian genomes including bovines is still poor compared to that of huma...

    Authors: Rosemarie Weikard, Frieder Hadlich and Christa Kuehn

    Citation: BMC Genomics 2013 14:789

    Content type: Research article

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  4. In fish breeding, it is essential to discover and generate fish exhibiting an effective phenotype for the aquaculture industry, but screening for natural mutants by only depending on natural spontaneous mutati...

    Authors: Miwa Kuroyanagi, Takashi Katayama, Tadashi Imai, Yoshihisa Yamamoto, Shin-ichi Chisada, Yasutoshi Yoshiura, Tomokazu Ushijima, Tomonao Matsushita, Masashi Fujita, Aoi Nozawa, Yuzuru Suzuki, Kiyoshi Kikuchi and Hiroyuki Okamoto

    Citation: BMC Genomics 2013 14:786

    Content type: Methodology article

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  5. Obesity, excess fat tissue in the body, can underlie a variety of medical complaints including heart disease, stroke and cancer. The pig is an excellent model organism for the study of various human disorders,...

    Authors: Katie E Fowler, Ricardo Pong-Wong, Julien Bauer, Emily J Clemente, Christopher P Reitter, Nabeel A Affara, Stephen Waite, Grant A Walling and Darren K Griffin

    Citation: BMC Genomics 2013 14:784

    Content type: Research article

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  6. Adaptations to a new environment, such as a polluted one, often involve large modifications of the existing phenotypes. Changes in gene expression and regulation during critical developmental stages may explai...

    Authors: Goran Bozinovic, Tim L Sit, Richard Di Giulio, Lauren F Wills and Marjorie F Oleksiak

    Citation: BMC Genomics 2013 14:779

    Content type: Research article

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  7. Blunt snout bream (Megalobrama amblycephala) is an economically important fish species in the Chinese freshwater polyculture system for its delicacy and high economic value. MicroRNAs (miRNAs) play important role...

    Authors: Shaokui Yi, Ze-Xia Gao, Honghao Zhao, Cong Zeng, Wei Luo, Boxiang Chen and Wei-Min Wang

    Citation: BMC Genomics 2013 14:754

    Content type: Research article

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  8. The relationship between fish health and muscle growth is critical for continued expansion of the aquaculture industry. The effect of immune stimulation on the expression of genes related to the energy balance...

    Authors: Nicholas J Pooley, Luca Tacchi, Christopher J Secombes and Samuel AM Martin

    Citation: BMC Genomics 2013 14:747

    Content type: Research article

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  9. Infectious bronchitis virus (IBV), a prototype of the Coronaviridae family, is an economically important causative agent of infectious bronchitis in chickens and causes an acute and highly contagious upper respir...

    Authors: Feng Cong, Xiaoli Liu, Zongxi Han, Yuhao Shao, Xiangang Kong and Shengwang Liu

    Citation: BMC Genomics 2013 14:743

    Content type: Research article

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  10. As consumers continue to request food products that have health advantages, it will be important for the livestock industry to supply a product that meet these demands. One such nutrient is fatty acids, which ...

    Authors: Mahdi Saatchi, Dorian J Garrick, Richard G Tait Jr, Mary S Mayes, Mary Drewnoski, Jon Schoonmaker, Clara Diaz, Don C Beitz and James M Reecy

    Citation: BMC Genomics 2013 14:730

    Content type: Research article

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  11. The white shark (Carcharodon carcharias) is a globally distributed, apex predator possessing physical, physiological, and behavioral traits that have garnered it significant public attention. In addition to inter...

    Authors: Vincent P Richards, Haruo Suzuki, Michael J Stanhope and Mahmood S Shivji

    Citation: BMC Genomics 2013 14:697

    Content type: Research article

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  12. MicroRNAs (miRNAs) have recently been shown to play important roles in development of the immune system and in fine-tuning of immune responses. Human miR-146 family members are known as inflammation-inducible ...

    Authors: Anita Ordas, Zakia Kanwal, Valesca Lindenberg, Julien Rougeot, Matyas Mink, Herman P Spaink and Annemarie H Meijer

    Citation: BMC Genomics 2013 14:696

    Content type: Research article

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  13. Amur ide (Leuciscus waleckii) is an economically and ecologically important cyprinid species in Northern Asia. The Dali Nor population living in the soda lake Dali Nor can adapt the extremely high alkalinity, pro...

    Authors: Jian Xu, Qiang Li, Liming Xu, Shaolin Wang, Yanliang Jiang, Zixia Zhao, Yan Zhang, Jiongtang Li, Chuanju Dong, Peng Xu and Xiaowen Sun

    Citation: BMC Genomics 2013 14:682

    Content type: Research article

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  14. Release of domesticated strains of fish into nature may pose a threat to wild populations with respect to their evolved genetic structure and fitness. Understanding alterations that have occurred in both physi...

    Authors: Samantha L White, Dionne Sakhrani, Roy G Danzmann and Robert H Devlin

    Citation: BMC Genomics 2013 14:673

    Content type: Research article

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  15. The eastern mosquitofish (Gambusia holbrooki) has the potential to become a bioindicator organism of endocrine disrupting chemicals (EDCs) due to its androgen-driven secondary sexual characteristics. However, the...

    Authors: Erica K Brockmeier, Fahong Yu, David Moraga Amador, Timothy A Bargar and Nancy D Denslow

    Citation: BMC Genomics 2013 14:660

    Content type: Research article

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  16. External development and optical transparency of embryos make zebrafish exceptionally suitable for in vivo insertional mutagenesis using fluorescent proteins to visualize expression patterns of mutated genes. Rec...

    Authors: Jorune Balciuniene, Danielle Nagelberg, Kathleen T Walsh, Diana Camerota, Daphné Georlette, Frédéric Biemar, Gianfranco Bellipanni and Darius Balciunas

    Citation: BMC Genomics 2013 14:619

    Content type: Methodology article

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  17. As economically relevant traits, feeding behavior and food preference domestication determine production cost and profitability. Although there are intensive research efforts on feeding behavior and food intak...

    Authors: Shan He, Xu-Fang Liang, Jian Sun, Ling Li, Ying Yu, Wei Huang, Chun-Mei Qu, Liang Cao, Xiao-Li Bai and Ya-Xiong Tao

    Citation: BMC Genomics 2013 14:601

    Content type: Research article

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  18. The draft genome of the domestic pig (Sus scrofa) has recently been published permitting refined analysis of the transcriptome. Pig breeds have been reported to differ in their resistance to infectious disease...

    Authors: Ronan Kapetanovic, Lynsey Fairbairn, Alison Downing, Dario Beraldi, David P Sester, Tom C Freeman, Christopher K Tuggle, Alan L Archibald and David A Hume

    Citation: BMC Genomics 2013 14:581

    Content type: Research article

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  19. Mammalian hibernators display phenotypes similar to physiological responses to calorie restriction and fasting, sleep, cold exposure, and ischemia-reperfusion in non-hibernating species. Whether biochemical ch...

    Authors: Yichi Xu, Chunxuan Shao, Vadim B Fedorov, Anna V Goropashnaya, Brian M Barnes and Jun Yan

    Citation: BMC Genomics 2013 14:567

    Content type: Research article

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  20. Atlantic halibut (Hippoglossus hippoglossus) is a high-value, niche market species for cold-water marine aquaculture. Production of monosex female stocks is desirable in commercial production since females grow f...

    Authors: Christos Palaiokostas, Michaël Bekaert, Andrew Davie, Mairi E Cowan, Münevver Oral, John B Taggart, Karim Gharbi, Brendan J McAndrew, David J Penman and Hervé Migaud

    Citation: BMC Genomics 2013 14:566

    Content type: Research article

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  21. This descriptive study of the abdominal fat transcriptome takes advantage of two experimental lines of meat-type chickens (Gallus domesticus), which were selected over seven generations for a large difference in ...

    Authors: Christopher W Resnyk, Wilfrid Carré, Xiaofei Wang, Tom E Porter, Jean Simon, Elisabeth Le Bihan-Duval, Michael J Duclos, Sam E Aggrey and Larry A Cogburn

    Citation: BMC Genomics 2013 14:557

    Content type: Research article

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  22. Physiological processes aiding the conversion of muscle to meat involve many genes associated with muscle structure and metabolic processes. MicroRNAs regulate networks of genes to orchestrate cellular functio...

    Authors: Siriluck Ponsuksili, Yang Du, Frieder Hadlich, Puntita Siengdee, Eduard Murani, Manfred Schwerin and Klaus Wimmers

    Citation: BMC Genomics 2013 14:533

    Content type: Research article

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  23. Hanwoo (Korean cattle), which originated from natural crossbreeding between taurine and zebu cattle, migrated to the Korean peninsula through North China. Hanwoo were raised as draft animals until the 1970s wi...

    Authors: Kyung-Tai Lee, Won-Hyong Chung, Sung-Yeoun Lee, Jung-Woo Choi, Jiwoong Kim, Dajeong Lim, Seunghwan Lee, Gul-Won Jang, Bumsoo Kim, Yun Ho Choy, Xiaoping Liao, Paul Stothard, Stephen S Moore, Sang-Heon Lee, Sungmin Ahn, Namshin Kim…

    Citation: BMC Genomics 2013 14:519

    Content type: Research article

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  24. MicroRNAs (miRNAs) are a large family of endogenous, non-coding RNAs, about 22 nucleotides long, which regulate gene expression through sequence-specific base pairing with target mRNAs. Extensive studies have ...

    Authors: Chao Yuan, Xiaolong Wang, Rongqing Geng, Xiaolin He, Lei Qu and Yulin Chen

    Citation: BMC Genomics 2013 14:511

    Content type: Research article

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  25. Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard c...

    Authors: Julia Metzger, Ute Philipp, Maria Susana Lopes, Artur da Camara Machado, Michela Felicetti, Maurizio Silvestrelli and Ottmar Distl

    Citation: BMC Genomics 2013 14:487

    Content type: Research article

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  26. MicroRNAs (miRNAs) are an abundant class of endogenous small RNA molecules that downregulate gene expression at the posttranscriptional level. They play important roles in multiple biological processes by regu...

    Authors: Rune Andreassen, Merete Molton Worren and Bjørn Høyheim

    Citation: BMC Genomics 2013 14:482

    Content type: Research article

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  27. Meat quality is an important economic trait in chickens. To identify loci and genes associated with meat quality traits, we conducted a genome-wide association study (GWAS) of F2 populations derived from a loc...

    Authors: Yanfa Sun, Guiping Zhao, Ranran Liu, Maiqing Zheng, Yaodong Hu, Dan Wu, Lei Zhang, Peng Li and Jie Wen

    Citation: BMC Genomics 2013 14:458

    Content type: Research article

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  28. Intramuscular fat (IMF) content is positively correlated with aspects of pork palatability, including flavour, juiciness and overall acceptability. The ratio of energy to protein in the finishing diet of growi...

    Authors: Ruth M Hamill, Ozlem Aslan, Anne M Mullen, John V O’Doherty, Jean McBryan, Dermot G Morris and Torres Sweeney

    Citation: BMC Genomics 2013 14:453

    Content type: Research article

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  29. The sablefish (order: Scorpaeniformes) is an economically important species in commercial fisheries of the North Pacific and an emerging species in aquaculture. Aside from a handful of sequences in NCBI and a ...

    Authors: Eric B Rondeau, Amber M Messmer, Dan S Sanderson, Stuart G Jantzen, Kristian R von Schalburg, David R Minkley, Jong S Leong, Graham M Macdonald, Amanda E Davidsen, William A Parker, Rosetta SA Mazzola, Briony Campbell and Ben F Koop

    Citation: BMC Genomics 2013 14:452

    Content type: Research article

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  30. Genome- and population-wide re-sequencing would allow for most efficient detection of causal trait variants. However, despite a strong decrease of costs for next-generation sequencing in the last few years, re...

    Authors: Sandra Jansen, Bernhard Aigner, Hubert Pausch, Michal Wysocki, Sebastian Eck, Anna Benet-Pagès, Elisabeth Graf, Thomas Wieland, Tim M Strom, Thomas Meitinger and Ruedi Fries

    Citation: BMC Genomics 2013 14:446

    Content type: Research article

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  31. The heterogeneous progression of atherosclerotic disease in the peripheral arteries is currently not well understood. In humans, artery specific disease progression is partly attributed to the local hemodynami...

    Authors: Martin Bahls, Christopher A Bidwell, Juan Hu, Armando Tellez, Greg L Kaluza, Juan F Granada, Christian G Krueger, Jess D Reed, M Harold Laughlin, William G Van Alstine and Sean C Newcomer

    Citation: BMC Genomics 2013 14:443

    Content type: Research article

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  32. DNA extracted from historical samples is an important resource for understanding genetic consequences of anthropogenic influences and long-term environmental change. However, such samples generally yield DNA o...

    Authors: Susan E Johnston, Meri Lindqvist, Eero Niemelä, Panu Orell, Jaakko Erkinaro, Matthew P Kent, Sigbjørn Lien, Juha-Pekka Vähä, Anti Vasemägi and Craig R Primmer

    Citation: BMC Genomics 2013 14:439

    Content type: Methodology article

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  33. Salamanders are unique among vertebrates in their ability to completely regenerate amputated limbs through the mediation of blastema cells located at the stump ends. This regeneration is nerve-dependent becaus...

    Authors: Cheng-Han Wu, Mong-Hsun Tsai, Chia-Chuan Ho, Chien-Yu Chen and Hsuan-Shu Lee

    Citation: BMC Genomics 2013 14:434

    Content type: Research article

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  34. Lawsonia intracellularis is an obligate intracellular bacterium and the etiologic agent of proliferative enteropathy. The disease is endemic in pigs, emerging in horses and has been described in various other spe...

    Authors: Fabio A Vannucci, Douglas N Foster and Connie J Gebhart

    Citation: BMC Genomics 2013 14:421

    Content type: Research article

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  35. Sturgeons are a group of Condrostean fish with very high evolutionary, economical and conservation interest. The eggs of these living fossils represent one of the most high prized foods of animal origin. The i...

    Authors: Michele Vidotto, Alessandro Grapputo, Elisa Boscari, Federica Barbisan, Alessandro Coppe, Gilberto Grandi, Abhishek Kumar and Leonardo Congiu

    Citation: BMC Genomics 2013 14:407

    Content type: Research article

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  36. It was recently established that changes in methylation during development are dynamic and involve both methylation and demethylation processes. Yet, which genomic sites are changing and what are the contribut...

    Authors: Béatrice de Montera, Eric Fournier, Habib Allah Shojaei Saadi, Dominic Gagné, Isabelle Laflamme, Patrick Blondin, Marc-André Sirard and Claude Robert

    Citation: BMC Genomics 2013 14:406

    Content type: Research article

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  37. Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNP...

    Authors: Richard PMA Crooijmans, Mark S Fife, Tomas W Fitzgerald, Shurnevia Strickland, Hans H Cheng, Pete Kaiser, Richard Redon and Martien AM Groenen

    Citation: BMC Genomics 2013 14:398

    Content type: Research article

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  38. Previous molecular genetic studies of physiology and pigmentation of sheep skin have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in c...

    Authors: Ruiwen Fan, Jianshan Xie, Junming Bai, Haidong Wang, Xue Tian, Rui Bai, Xiaoyun Jia, Lei Yang, Yunfei Song, Muren Herrid, Wenjun Gao, Xiaoyan He, Jianbo Yao, George W Smith and Changsheng Dong

    Citation: BMC Genomics 2013 14:389

    Content type: Research article

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  39. The domestication and subsequent selection by humans to create breeds and biological types of cattle undoubtedly altered the patterning of variation within their genomes. Strong selection to fix advantageous l...

    Authors: Holly R Ramey, Jared E Decker, Stephanie D McKay, Megan M Rolf, Robert D Schnabel and Jeremy F Taylor

    Citation: BMC Genomics 2013 14:382

    Content type: Research article

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  40. Identifying genes of adaptive significance in a changing environment is a major focus of ecological genomics. Such efforts were restricted, until recently, to researchers studying a small group of model organi...

    Authors: Steve Smith, Louis Bernatchez and Luciano B Beheregaray

    Citation: BMC Genomics 2013 14:375

    Content type: Research article

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  41. Genomics and metagenomics are currently leading research areas, with DNA sequences accumulating at an exponential rate. Although enormous advances in DNA sequencing technologies are taking place, progress is f...

    Authors: Agnieszka Zylicz-Stachula, Olga Zolnierkiewicz, Jacek Jasiecki and Piotr M Skowron

    Citation: BMC Genomics 2013 14:370

    Content type: Methodology article

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  42. Genomic sequence assemblies are key tools for a broad range of gene function and evolutionary studies. The diploid amphibian Xenopus tropicalis plays a pivotal role in these fields due to its combination of exper...

    Authors: Eva Seifertova, Lyle B Zimmerman, Michael J Gilchrist, Jaroslav Macha, Svatava Kubickova, Halina Cernohorska, Vojtech Zarsky, Nick DL Owens, Abdul K Sesay, Tereza Tlapakova and Vladimir Krylov

    Citation: BMC Genomics 2013 14:357

    Content type: Research article

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  43. Porcine circovirus type 2 (PCV2) is the causal agent of postweaning multisystemic wasting syndrome (PMWS), which has severely impacted the swine industry worldwide. PCV2 triggers a weak and atypical innate imm...

    Authors: Wentao Li, Shuqing Liu, Yang Wang, Feng Deng, Weidong Yan, Kun Yang, Huanchun Chen, Qigai He, Catherine Charreyre and Jean-Christophe Audoneet

    Citation: BMC Genomics 2013 14:353

    Content type: Research article

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  44. MicroRNAs have been suggested to play important roles in the regulation of gene expression in various biological processes. To investigate the function of miRNAs in chicken ovarian development and folliculogen...

    Authors: Li Kang, Xinxing Cui, Yujie Zhang, Chunhong Yang and Yunliang Jiang

    Citation: BMC Genomics 2013 14:352

    Content type: Research article

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  45. Use of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to ...

    Authors: James L Chitwood, Gonzalo Rincon, German G Kaiser, Juan F Medrano and Pablo J Ross

    Citation: BMC Genomics 2013 14:350

    Content type: Research article

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  46. Hyperpigmentation of the visceral peritoneum (HVP) has recently garnered much attention in the poultry industry because of the possible risk to the health of affected animals and the damage it causes to the ap...

    Authors: Chenglong Luo, Hao Qu, Jie Wang, Yan Wang, Jie Ma, Chunyu Li, Chunfen Yang, Xiaoxiang Hu, Ning Li and Dingming Shu

    Citation: BMC Genomics 2013 14:334

    Content type: Research article

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  47. The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the...

    Authors: Harry D Dawson, Jane E Loveland, Géraldine Pascal, James GR Gilbert, Hirohide Uenishi, Katherine M Mann, Yongming Sang, Jie Zhang, Denise Carvalho-Silva, Toby Hunt, Matthew Hardy, Zhiliang Hu, Shu-Hong Zhao, Anna Anselmo, Hiroki Shinkai, Celine Chen…

    Citation: BMC Genomics 2013 14:332

    Content type: Research article

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  48. Animal migration requires adaptations in morphological, physiological and behavioural traits. Several of these traits have been shown to possess a strong heritable component in birds, but little is known about...

    Authors: Max Lundberg, John Boss, Björn Canbäck, Miriam Liedvogel, Keith W Larson, Mats Grahn, Susanne Åkesson, Staffan Bensch and Anthony Wright

    Citation: BMC Genomics 2013 14:330

    Content type: Research article

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