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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 19 of 21

  1. We hypothesized that genes that are up-regulated in the uterine endometrium at the initiation of conceptus elongation in cattle, and that encode for secreted proteins, contribute to the composition of the uter...

    Authors: Niamh Forde, Jai P Mehta, Paul A McGettigan, Solomon Mamo, Fuller W Bazer, Thomas E Spencer and Pat Lonergan

    Citation: BMC Genomics 2013 14:321

    Content type: Research article

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  2. The common sole (Solea solea) is a promising candidate for European aquaculture; however, the limited knowledge of the physiological mechanisms underlying larval development in this species has hampered the estab...

    Authors: Serena Ferraresso, Alessio Bonaldo, Luca Parma, Stefano Cinotti, Paola Massi, Luca Bargelloni and Pier Paolo Gatta

    Citation: BMC Genomics 2013 14:315

    Content type: Research article

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  3. When faced with climate change, species must either shift their home range or adapt in situ in order to maintain optimal physiological balance with their environment. The American pika (Ochotona princeps) is a sm...

    Authors: Matthew A Lemay, Philippe Henry, Clayton T Lamb, Kelsey M Robson and Michael A Russello

    Citation: BMC Genomics 2013 14:311

    Content type: Research article

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  4. Genetic information based on molecular markers has increasingly being used in cattle breeding improvement programmes, as a mean to improve conventionally phenotypic selection. Advances in molecular genetics ha...

    Authors: Anis Djari, Diane Esquerré, Bernard Weiss, Frédéric Martins, Cédric Meersseman, Mekki Boussaha, Christophe Klopp and Dominique Rocha

    Citation: BMC Genomics 2013 14:307

    Content type: Research article

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  5. Knowledge of the linkage disequilibrium (LD) between markers is important to establish the number of markers necessary for association studies and genomic selection. The objective of this study was to evaluate...

    Authors: Rafael Espigolan, Fernando Baldi, Arione A Boligon, Fabio RP Souza, Daniel GM Gordo, Rafael L Tonussi, Diércles F Cardoso, Henrique N Oliveira, Humberto Tonhati, Mehdi Sargolzaei, Flavio S Schenkel, Roberto Carvalheiro, Jesus A Ferro and Lucia G Albuquerque

    Citation: BMC Genomics 2013 14:305

    Content type: Research article

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  6. The lactating mammary gland responds to changes in milking frequency by modulating milk production. This response is locally regulated and, in dairy cows, the udder is particularly sensitive during early lacta...

    Authors: Emma H Wall, Jeffrey P Bond and Thomas B McFadden

    Citation: BMC Genomics 2013 14:296

    Content type: Research article

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  7. Aquaculture is the quickest growing sector in agriculture. However, QTL for important traits have been only identified in a few aquaculture species. We conducted QTL mapping for growth traits in an Asian seaba...

    Authors: Jun Hong Xia, Grace Lin, Xiaoping He, Peng Liu, Feng Liu, Fei Sun, Rongjian Tu and Gen Hua Yue

    Citation: BMC Genomics 2013 14:295

    Content type: Research article

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  8. Pigmentation patterns are one of the most recognizable phenotypes across the animal kingdom. They play an important role in camouflage, communication, mate recognition and mate choice. Most progress on underst...

    Authors: Claire T O’Quin, Alexi C Drilea, Matthew A Conte and Thomas D Kocher

    Citation: BMC Genomics 2013 14:287

    Content type: Research article

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  9. Tibial dyschondroplasia (TD) is a common skeletal disorder in broiler chickens. It is characterized by the presence of a non-vascularized and unmineralized cartilage in the growth plate. Previous studies have ...

    Authors: Wen-xia Tian, Jia-kui Li, Ping Qin, Rui Wang, Guan-bao Ning, Jian-gang Qiao, Hong-quan Li, Ding-ren Bi, Si-yi Pan and Ding-zong Guo

    Citation: BMC Genomics 2013 14:276

    Content type: Research article

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  10. Copy number variants contribute to genetic variation in birds. Analyses of copy number variants in chicken breeds had focused primarily on those from commercial varieties with nothing known about the occurrenc...

    Authors: Ming Tian, Yanqiang Wang, Xiaorong Gu, Chungang Feng, Suyun Fang, Xiaoxiang Hu and Ning Li

    Citation: BMC Genomics 2013 14:262

    Content type: Research article

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  11. Understanding the processes that drive the evolution of snake venom is a topic of great research interest in molecular and evolutionary toxinology. Recent studies suggest that ontogenetic changes in venom comp...

    Authors: Jordi Durban, Alicia Pérez, Libia Sanz, Aarón Gómez, Fabián Bonilla, Santos Rodríguez, Danilo Chacón, Mahmood Sasa, Yamileth Angulo, José M Gutiérrez and Juan J Calvete

    Citation: BMC Genomics 2013 14:234

    Content type: Research article

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  12. Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immu...

    Authors: Nicolas C Nalpas, Stephen DE Park, David A Magee, Maria Taraktsoglou, John A Browne, Kevin M Conlon, Kévin Rue-Albrecht, Kate E Killick, Karsten Hokamp, Amanda J Lohan, Brendan J Loftus, Eamonn Gormley, Stephen V Gordon and David E MacHugh

    Citation: BMC Genomics 2013 14:230

    Content type: Research article

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  13. In recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations...

    Authors: Jiasen Liu, Li Zhang, Lingyang Xu, Hangxing Ren, Jian Lu, Xiaoning Zhang, Shifang Zhang, Xinlei Zhou, Caihong Wei, Fuping Zhao and Lixin Du

    Citation: BMC Genomics 2013 14:229

    Content type: Research article

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  14. The availability of gene expression data that corresponds to pig immune response challenges provides compelling material for the understanding of the host immune system. Meta-analysis offers the opportunity to...

    Authors: Bouabid Badaoui, Christopher K Tuggle, Zhiliang Hu, James M Reecy, Tahar Ait-Ali, Anna Anselmo and Sara Botti

    Citation: BMC Genomics 2013 14:220

    Content type: Research article

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  15. Alternative splicing (AS) is a major mechanism for modulating gene expression of an organism, allowing the synthesis of several structurally and functionally distinct mRNAs and protein isoforms from a unique g...

    Authors: Francisco Hernández-Torres, Alberto Rastrojo and Begoña Aguado

    Citation: BMC Genomics 2013 14:199

    Content type: Research article

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  16. In Piedmontese cattle the double-muscled phenotype is an inherited condition associated to a point mutation in the myostatin (MSTN) gene. The Piedmontese MSTN missense mutation G938A is translated to C313Y myo...

    Authors: Silvia Miretti, Eugenio Martignani, Paolo Accornero and Mario Baratta

    Citation: BMC Genomics 2013 14:194

    Content type: Research article

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  17. The African annual fish Nothobranchius furzeri has over recent years been established as a model species for ageing-related studies. This is mainly based on its exceptionally short lifespan and the presence of ty...

    Authors: Andreas Petzold, Kathrin Reichwald, Marco Groth, Stefan Taudien, Nils Hartmann, Steffen Priebe, Dmitry Shagin, Christoph Englert and Matthias Platzer

    Citation: BMC Genomics 2013 14:185

    Content type: Research article

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  18. Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for esta...

    Authors: Laia Ribas, Belén G Pardo, Carlos Fernández, José Antonio Álvarez-Diós, Antonio Gómez-Tato, María Isabel Quiroga, Josep V Planas, Ariadna Sitjà-Bobadilla, Paulino Martínez and Francesc Piferrer

    Citation: BMC Genomics 2013 14:180

    Content type: Research article

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  19. The gilthead sea bream (Sparus aurata) is the main fish species cultured in the Mediterranean area and constitutes an interesting model of research. Nevertheless, transcriptomic and genomic data are still scarce ...

    Authors: Josep A Calduch-Giner, Azucena Bermejo-Nogales, Laura Benedito-Palos, Itziar Estensoro, Gabriel Ballester-Lozano, Ariadna Sitjà-Bobadilla and Jaume Pérez-Sánchez

    Citation: BMC Genomics 2013 14:178

    Content type: Research article

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  20. Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentr...

    Authors: Deborah A Dawson, Alexander D Ball, Lewis G Spurgin, David Martín-Gálvez, Ian R K Stewart, Gavin J Horsburgh, Jonathan Potter, Mercedes Molina-Morales, Anthony W J Bicknell, Stephanie A J Preston, Robert Ekblom, Jon Slate and Terry Burke

    Citation: BMC Genomics 2013 14:176

    Content type: Methodology article

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  21. A unique feature of fish is that new muscle fibres continue to be produced throughout much of the life cycle; a process termed muscle hyperplasia. In trout, this process begins in the late embryo stage and occ...

    Authors: Pierre-Yves Rescan, Jerome Montfort, Alain Fautrel, Cécile Rallière and Veronique Lebret

    Citation: BMC Genomics 2013 14:173

    Content type: Research article

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  22. The pigeon crop is specially adapted to produce milk that is fed to newly hatched young. The process of pigeon milk production begins when the germinal cell layer of the crop rapidly proliferates in response t...

    Authors: Meagan J Gillespie, Tamsyn M Crowley, Volker R Haring, Susanne L Wilson, Jennifer A Harper, Jean S Payne, Diane Green, Paul Monaghan, John A Donald, Kevin R Nicholas and Robert J Moore

    Citation: BMC Genomics 2013 14:169

    Content type: Research article

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    The Erratum to this article has been published in BMC Genomics 2014 15:185

  23. Ovarian follicular development and hormone secretion are complex and coordinated biological processes which will usually be altered during pregnancy. Ovarian function is tightly regulated by a multitude of gen...

    Authors: Xiao-Dong Zhang, Yun-Hai Zhang, Ying-Hui Ling, Ya Liu, Hong-Guo Cao, Zong-Jun Yin, Jian-Ping Ding and Xiao-Rong Zhang

    Citation: BMC Genomics 2013 14:157

    Content type: Research article

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  24. In China, consumers often prefer indigenous broiler chickens over commercial breeds, as they have characteristic meat qualities requested within traditional culinary customs. However, the growth-rate of these ...

    Authors: Zheya Sheng, Mats E Pettersson, Xiaoxiang Hu, Chenglong Luo, Hao Qu, Dingming Shu, Xia Shen, Örjan Carlborg and Ning Li

    Citation: BMC Genomics 2013 14:151

    Content type: Research article

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  25. In contrast to international pig breeds, the Iberian breed has not been admixed with Asian germplasm. This makes it an important model to study both domestication and relevance of Asian genes in the pig. Besid...

    Authors: Anna Esteve-Codina, Yogesh Paudel, Luca Ferretti, Emanuele Raineri, Hendrik-Jan Megens, Luis Silió, María C Rodríguez, Martein AM Groenen, Sebastian E Ramos-Onsins and Miguel Pérez-Enciso

    Citation: BMC Genomics 2013 14:148

    Content type: Research article

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  26. Copy number variations (CNVs) are widespread in the human or animal genome and are a significant source of genetic variation, which has been demonstrated to play an important role in phenotypic diversity. Adva...

    Authors: Li Jiang, Jicai Jiang, Jie Yang, Xuan Liu, Jiying Wang, Haifei Wang, Xiangdong Ding, Jianfeng Liu and Qin Zhang

    Citation: BMC Genomics 2013 14:131

    Content type: Research article

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  27. Copy number variations (CNVs) represent a significant source of genomic structural variation. Their length ranges from approximately one hundred to millions of base pair. Genome-wide screenings have clarified ...

    Authors: Francesco Cicconardi, Giovanni Chillemi, Anna Tramontano, Cinzia Marchitelli, Alessio Valentini, Paolo Ajmone-Marsan and Alessandro Nardone

    Citation: BMC Genomics 2013 14:124

    Content type: Research article

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  28. High throughput sequencing is beginning to make a transformative impact in the area of viral evolution. Deep sequencing has the potential to reveal the mutant spectrum within a viral sample at high resolution,...

    Authors: Haiyin Chen-Harris, Monica K Borucki, Clinton Torres, Tom R Slezak and Jonathan E Allen

    Citation: BMC Genomics 2013 14:96

    Content type: Methodology article

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  29. A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive rad...

    Authors: Chris M Rands, Aaron Darling, Matthew Fujita, Lesheng Kong, Matthew T Webster, Céline Clabaut, Richard D Emes, Andreas Heger, Stephen Meader, Michael Brent Hawkins, Michael B Eisen, Clotilde Teiling, Jason Affourtit, Benjamin Boese, Peter R Grant, Barbara Rosemary Grant…

    Citation: BMC Genomics 2013 14:95

    Content type: Research article

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  30. Polymorphism is key to the evolutionary potential of populations. Understanding which factors shape levels of genetic diversity within genomes forms a central question in evolutionary genomics and is of import...

    Authors: Carina F Mugal, Benoit Nabholz and Hans Ellegren

    Citation: BMC Genomics 2013 14:86

    Content type: Research article

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  31. Marek’s disease (MD) is a commercially important neoplastic disease of chickens caused by the Marek’s disease virus (MDV), a naturally occurring oncogenic alphaherpesvirus. Enhancing MD genetic resistance is d...

    Authors: Sudeep Perumbakkam, William M Muir, Alexis Black-Pyrkosz, Ron Okimoto and Hans H Cheng

    Citation: BMC Genomics 2013 14:64

    Content type: Research article

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  32. High density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high r...

    Authors: Andreas Kranis, Almas A Gheyas, Clarissa Boschiero, Frances Turner, Le Yu, Sarah Smith, Richard Talbot, Ali Pirani, Fiona Brew, Pete Kaiser, Paul M Hocking, Mark Fife, Nigel Salmon, Janet Fulton, Tim M Strom, Georg Haberer…

    Citation: BMC Genomics 2013 14:59

    Content type: Research article

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  33. Tilapia is the common name for a group of cichlid fishes and is one of the most important aquacultured freshwater food fish. Mozambique tilapia and its hybrids, including red tilapia are main representatives o...

    Authors: Feng Liu, Fei Sun, Jian Li, Jun Hong Xia, Grace Lin, Rong Jian Tu and Gen Hua Yue

    Citation: BMC Genomics 2013 14:58

    Content type: Research article

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  34. Transcriptomes are powerful resources, providing a window on the expressed portion of the genome that can be generated rapidly and at low cost for virtually any organism. However, because many genes have tissu...

    Authors: Joseph I Hoffman, Michael AS Thorne, Philip N Trathan and Jaume Forcada

    Citation: BMC Genomics 2013 14:52

    Content type: Research article

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  35. The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-a...

    Authors: Walter L Eckalbar, Elizabeth D Hutchins, Glenn J Markov, April N Allen, Jason J Corneveaux, Kerstin Lindblad-Toh, Federica Di Palma, Jessica Alföldi, Matthew J Huentelman and Kenro Kusumi

    Citation: BMC Genomics 2013 14:49

    Content type: Research article

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  36. Network biology (systems biology) approaches are useful tools for elucidating the host infection processes that often accompany complex immune networks. Although many studies have recently focused on Haemophilus ...

    Authors: Ming Zhao, Xiang-dong Liu, Xin-yun Li, Hong-bo Chen, Hui Jin, Rui Zhou, Meng-jin Zhu and Shu-hong Zhao

    Citation: BMC Genomics 2013 14:46

    Content type: Research article

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  37. Erhualian pigs, one of Chinese Taihu pig breeds, are known to have the largest recorded litter size in the world. A lower prenatal death rate is the major contributing factor to the prolificacy of Taihu pigs. ...

    Authors: Hao Zhang, Shouqi Wang, Manqing Liu, Ailing Zhang, Zhenfang Wu, Zhe Zhang and Jiaqi Li

    Citation: BMC Genomics 2013 14:45

    Content type: Research article

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  38. Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiati...

    Authors: Sarika, Vasu Arora, Mir Asif Iquebal, Anil Rai and Dinesh Kumar

    Citation: BMC Genomics 2013 14:43

    Content type: Database

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  39. MicroRNAs (miRNAs) are a family of ~22 nucleotide small RNA molecules that regulate gene expression by fully or partially binding to their complementary sequences. Recently, a large number of miRNAs and their ...

    Authors: Jiajie Sun, Mijie Li, Zhuanjian Li, Jing Xue, Xianyong Lan, Chunlei Zhang, Chuzhao Lei and Hong Chen

    Citation: BMC Genomics 2013 14:42

    Content type: Research article

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  40. The most important disease of dairy cattle is mastitis, caused by the infection of the mammary gland by various micro-organisms. Although the transcriptional response of bovine mammary gland cells to in vitro inf...

    Authors: Kirsty Jensen, Juliane Günther, Richard Talbot, Wolfram Petzl, Holm Zerbe, Hans-Joachim Schuberth, Hans-Martin Seyfert and Elizabeth J Glass

    Citation: BMC Genomics 2013 14:36

    Content type: Research article

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  41. This study is aimed at the analysis of genetic and physiological effects of myostatin on economically relevant meat quality traits in a genetic background of high muscularity. For this purpose, we generated G3 po...

    Authors: Stefan Kärst, Eva M Strucken, Armin O Schmitt, Alexandra Weyrich, Fernando PM de Villena, Hyuna Yang and Gudrun A Brockmann

    Citation: BMC Genomics 2013 14:16

    Content type: Research article

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  42. The annotation of many genomes is limited, with a large proportion of identified genes lacking functional assignments. The construction of gene co-expression networks is a powerful approach that presents a way...

    Authors: Dragana Stanley, Nathan S Watson-Haigh, Christopher JE Cowled and Robert J Moore

    Citation: BMC Genomics 2013 14:13

    Content type: Research article

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  43. New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technolog...

    Authors: Mikhail Ozerov, Anti Vasemägi, Vidar Wennevik, Eero Niemelä, Sergey Prusov, Matthew Kent and Juha-Pekka Vähä

    Citation: BMC Genomics 2013 14:12

    Content type: Methodology article

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  44. The sequencing of the cow genome was recently published (Btau_4.0 assembly). A second, alternate cow genome assembly (UMD2), based on the same raw sequence data, was also published. The two assemblies have bee...

    Authors: Giulia Partipilo, Pietro D'Addabbo, Giovanni M Lacalandra, George E Liu and Mariano Rocchi

    Citation: BMC Genomics 2011 12:639

    Content type: Research article

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  45. Recent advances in next-generation sequencing technologies have drastically increased throughput and significantly reduced sequencing costs. However, the average read lengths in next-generation sequencing tech...

    Authors: Yanliang Jiang, Jianguo Lu, Eric Peatman, Huseyin Kucuktas, Shikai Liu, Shaolin Wang, Fanyue Sun and Zhanjiang Liu

    Citation: BMC Genomics 2011 12:629

    Content type: Research article

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  46. Fish under intensive culture conditions are exposed to a variety of acute and chronic stressors, including high rearing densities, sub-optimal water quality, and severe thermal fluctuations. Such stressors are...

    Authors: Cecilia C Sánchez, Gregory M Weber, Guangtu Gao, Beth M Cleveland, Jianbo Yao and Caird E Rexroad III

    Citation: BMC Genomics 2011 12:626

    Content type: Research article

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  47. The Atlantic salmon genome is in the process of returning to a diploid state after undergoing a whole genome duplication (WGD) event between 25 and100 million years ago. Existing data on the proportion of para...

    Authors: Sigbjørn Lien, Lars Gidskehaug, Thomas Moen, Ben J Hayes, Paul R Berg, William S Davidson, Stig W Omholt and Matthew P Kent

    Citation: BMC Genomics 2011 12:615

    Content type: Research article

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  48. Mycobacterium bovis is the causative agent of bovine tuberculosis (BTB), a pathological infection with significant economic impact. Recent studies have highlighted the role of functional genomics to better unders...

    Authors: Kate E Killick, John A Browne, Stephen DE Park, David A Magee, Irene Martin, Kieran G Meade, Stephen V Gordon, Eamonn Gormley, Cliona O'Farrelly, Karsten Hokamp and David E MacHugh

    Citation: BMC Genomics 2011 12:611

    Content type: Research article

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  49. In livestock populations the genetic contribution to muscling is intensively monitored in the progeny of industry sires and used as a tool in selective breeding programs. The genes and pathways conferring this...

    Authors: Lisette JA Kogelman, Keren Byrne, Tony Vuocolo, Nathan S Watson-Haigh, Haja N Kadarmideen, James W Kijas, Hutton V Oddy, Graham E Gardner, Cedric Gondro and Ross L Tellam

    Citation: BMC Genomics 2011 12:607

    Content type: Research article

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