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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 1 of 16

  1. Content type: Research article

    Pacific salmon (Oncorhynchus spp.) serve as good biological indicators of the breadth of climate warming effects on fish because their anadromous life cycle exposes them to environmental challenges in both marine...

    Authors: Arash Akbarzadeh, Oliver P Günther, Aimee Lee Houde, Shaorong Li, Tobi J Ming, Kenneth M Jeffries, Scott G Hinch and Kristina M Miller

    Citation: BMC Genomics 2018 19:749

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  2. Content type: Research article

    This study investigated if the allele effect of a given single nucleotide polymorphism (SNP) for crossbred performance in pigs estimated in a genomic prediction model differs depending on its breed-of-origin, ...

    Authors: Claudia A Sevillano, Jan ten Napel, Simone E F Guimarães, Fabyano F Silva and Mario P L Calus

    Citation: BMC Genomics 2018 19:740

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  3. Content type: Research article

    Embryonic and fetal exposure to maternal obesity causes several maladaptive morphological and epigenetic changes in exposed offspring. The timing of these events is unclear, but changes can be observed even af...

    Authors: Sarah R. McCoski, McCauley T. Vailes, Connor E. Owens, Rebecca R. Cockrum and Alan D. Ealy

    Citation: BMC Genomics 2018 19:737

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  5. Content type: Research article

    Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited.

    Authors: Bi Jun Li, Dan Li Jiang, Zi Ning Meng, Yong Zhang, Zong Xian Zhu, Hao Ran Lin and Jun Hong Xia

    Citation: BMC Genomics 2018 19:729

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  6. Content type: Research article

    Captive animal populations, be it for food production or conservation programmes, are often maintained at densities far beyond those in natural environments, which can have profound effects on behaviour, immun...

    Authors: Amy R Ellison, Tamsyn M Uren Webster, Olivier Rey, Carlos Garcia de Leaniz, Sofia Consuegra, Pablo Orozco-terWengel and Jo Cable

    Citation: BMC Genomics 2018 19:723

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  7. Content type: Research article

    Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular ...

    Authors: Claudia M. Arenas Gómez, Ryan M. Woodcock, Jeramiah J. Smith, Randal S. Voss and Jean Paul Delgado

    Citation: BMC Genomics 2018 19:704

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  8. Content type: Research article

    Maternal nutrition has been highlighted as one of the main factors affecting intra-uterine environment. The increase in nutritional requirements by beef cows during late gestation can cause nutritional deficie...

    Authors: Leticia P Sanglard, Moysés Nascimento, Philipe Moriel, Jeffrey Sommer, Melissa Ashwell, Matthew H Poore, Márcio de S Duarte and Nick V L Serão

    Citation: BMC Genomics 2018 19:702

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  9. Content type: Research article

    Natural antibodies (NAb) are an important component of the innate immune system, and fight infections as a part of the first line defence. NAb are poly-reactive and can respond non-specifically to antigens. Th...

    Authors: Britt de Klerk, Mehdi Emam, Kathleen A. Thompson-Crispi, Mehdi Sargolzaei, Johan J. van der Poel and Bonnie A. Mallard

    Citation: BMC Genomics 2018 19:694

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  10. Content type: Research article

    Although hatching is perhaps the most abrupt and profound metabolic challenge that a chicken must undergo; there have been no attempts to functionally map the metabolic pathways induced in liver during the emb...

    Authors: Larry A. Cogburn, Nares Trakooljul, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Wilfrid Carré, Xiaofei Wang and Harold B. White III

    Citation: BMC Genomics 2018 19:695

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  11. Content type: Research article

    Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We us...

    Authors: C. Reimer, C.-J. Rubin, A. R. Sharifi, N.-T. Ha, S. Weigend, K.-H. Waldmann, O. Distl, S. D. Pant, M. Fredholm, M. Schlather and H. Simianer

    Citation: BMC Genomics 2018 19:687

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  12. Content type: Research article

    Numerous long non-coding RNAs (lncRNAs) have been identified and their roles in gene regulation in humans, mice, and other model organisms studied; however, far less research has been focused on lncRNAs in far...

    Authors: Colin Kern, Ying Wang, James Chitwood, Ian Korf, Mary Delany, Hans Cheng, Juan F. Medrano, Alison L. Van Eenennaam, Catherine Ernst, Pablo Ross and Huaijun Zhou

    Citation: BMC Genomics 2018 19:684

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  13. Content type: Research article

    Environmental changes of biotic or abiotic nature during critical periods of early development may exert a profound influence on physiological functions later in life. This process, named developmental program...

    Authors: Vincent Veron, Lucie Marandel, Jingwei Liu, Emilio J. Vélez, Olivier Lepais, Stéphane Panserat, Sandrine Skiba and Iban Seiliez

    Citation: BMC Genomics 2018 19:677

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  14. Content type: Research article

    Genetically selected modern broiler chickens have acquired outstanding production efficiency through rapid growth and improved feed efficiency compared to unselected chicken breeds. Recently, we analyzed the t...

    Authors: Bhuwan Khatri, Dongwon Seo, Stephanie Shouse, Jeong Hoon Pan, Nicholas J. Hudson, Jae Kyeom Kim, Walter Bottje and Byungwhi C. Kong

    Citation: BMC Genomics 2018 19:683

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  15. Content type: Research article

    The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages...

    Authors: Elisa Peripolli, Julia Metzger, Marcos Vinícius Antunes de Lemos, Nedenia Bonvino Stafuzza, Sabrina Kluska, Bianca Ferreira Olivieri, Fabieli Louise Braga Feitosa, Mariana Piatto Berton, Fernando Brito Lopes, Danísio Prado Munari, Raysildo Barbosa Lôbo, Cláudio de Ulhoa Magnabosco, Fernando Di Croce, Jason Osterstock, Sue Denise, Angélica Simone Cravo Pereira…

    Citation: BMC Genomics 2018 19:680

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  16. Content type: Research article

    Improving resistance to mastitis, one of the costliest diseases in dairy production, has become an important objective in dairy cattle breeding. However, mastitis resistance is influenced by many genes involve...

    Authors: Zexi Cai, Bernt Guldbrandtsen, Mogens Sandø Lund and Goutam Sahana

    Citation: BMC Genomics 2018 19:656

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  17. Content type: Research article

    Exposure to heat stress suppresses poultry immune responses, which can increase susceptibility to infectious diseases and, thereby, intensify the negative effects of heat on poultry welfare and performance. Id...

    Authors: Melissa S. Monson, Angelica G. Van Goor, Christopher M. Ashwell, Michael E. Persia, Max F. Rothschild, Carl J. Schmidt and Susan J. Lamont

    Citation: BMC Genomics 2018 19:643

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  18. Content type: Research article

    Hair follicles (HFs), upon development, undergo repetitive cycles of growth (anagen), regression (catagen), and rest (telogen). The transition between the stages is determined by multiple molecular signals, in...

    Authors: Chao Li, Yan Li, Guangxian Zhou, Ye Gao, Sen Ma, Yulin Chen, Jiuzhou Song and Xiaolong Wang

    Citation: BMC Genomics 2018 19:638

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  19. Content type: Research article

    Delivery of colostrum within the first several hours after birth is vital for establishing successful passive immunity in neonatal dairy calves. However, it is unclear whether a difference in colostrum feeding...

    Authors: Zhixiong He, Amanda Fischer, Yang Song, Michael Steele and Le Luo Guan

    Citation: BMC Genomics 2018 19:635

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  20. Content type: Research article

    During hair growth, cortical cells emerging from the proliferative follicle bulb rapidly undergo a differentiation program and synthesize large amounts of hair keratin proteins. In this process, HOXC13 is one ...

    Authors: Shanhe Wang, Zhixin Luo, Yuelang Zhang, Dan Yuan, Wei Ge and Xin Wang

    Citation: BMC Genomics 2018 19:630

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  21. Content type: Research article

    The success of early reproductive events depends on an appropriate communication between gametes/embryos and the oviduct. Extracellular vesicles (EVs) contained in oviductal secretions have been suggested as n...

    Authors: C. Almiñana, G. Tsikis, V. Labas, R. Uzbekov, J. C. da Silveira, S. Bauersachs and P. Mermillod

    Citation: BMC Genomics 2018 19:622

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  22. Content type: Research article

    In livestock, residual variance has been studied because of the interest to improve uniformity of production. Several studies have provided evidence that residual variance is partially under genetic control; h...

    Authors: Laiza Helena de Souza Iung, Herman Arend Mulder, Haroldo Henrique de Rezende Neves and Roberto Carvalheiro

    Citation: BMC Genomics 2018 19:619

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  23. Content type: Research article

    The expression of microRNAs (miRNAs) is essential for the proper development of the mammalian embryo. A maternal exposure to endocrine disrupting chemicals during preimplantation bears the potential for transg...

    Authors: Jochen T. Bick, Veronika L. Flöter, Mark D. Robinson, Stefan Bauersachs and Susanne E. Ulbrich

    Citation: BMC Genomics 2018 19:590

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  24. Content type: Research article

    The Mediterranean diet is considered one of the healthier food habits and olive oil is one of its key components. Olive oil polyphenols are known to induce beneficial effects in several pathological conditions...

    Authors: Marcella Sabino, Katia Cappelli, Stefano Capomaccio, Luisa Pascucci, Ilaria Biasato, Andrea Verini-Supplizi, Andrea Valiani and Massimo Trabalza-Marinucci

    Citation: BMC Genomics 2018 19:576

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  25. Content type: Research article

    Severe equine asthma, also known as recurrent airway obstruction (RAO), is a debilitating, performance limiting, obstructive respiratory condition in horses that is phenotypically similar to human asthma. Past...

    Authors: Victor C. Mason, Robert J. Schaefer, Molly E. McCue, Tosso Leeb and Vinzenz Gerber

    Citation: BMC Genomics 2018 19:581

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  26. Content type: Research article

    Genomic methods can provide extraordinary tools to explore the genetic background of wild species and domestic breeds, optimize breeding practices, monitor and limit the spread of recessive diseases, and disco...

    Authors: Romolo Caniglia, Elena Fabbri, Pavel Hulva, Barbora Černá Bolfíková, Milena Jindřichová, Astrid Vik Stronen, Ihor Dykyy, Alessio Camatta, Paolo Carnier, Ettore Randi and Marco Galaverni

    Citation: BMC Genomics 2018 19:533

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  27. Content type: Research article

    Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate gene transcription or RNA splicing. To identify variants with regulatory functions in cattle, an important economic and m...

    Authors: Ruidong Xiang, Ben J. Hayes, Christy J. Vander Jagt, Iona M. MacLeod, Majid Khansefid, Phil J. Bowman, Zehu Yuan, Claire P. Prowse-Wilkins, Coralie M. Reich, Brett A. Mason, Josie B. Garner, Leah C. Marett, Yizhou Chen, Sunduimijid Bolormaa, Hans D. Daetwyler, Amanda J. Chamberlain…

    Citation: BMC Genomics 2018 19:521

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  28. Content type: Research article

    Beak deformity, typically expressed as the crossing of upper and lower mandibles, is found in several indigenous chicken breeds, including the Beijing-You chickens studied here. Beak deformity severely impairs...

    Authors: Hao Bai, Yanyan Sun, Nian Liu, Fuguang Xue, Yunlei Li, Songshan Xu, Jianhua Ye, Lei Zhang, Yu Chen and Jilan Chen

    Citation: BMC Genomics 2018 19:501

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  29. Content type: Research article

    Anuran metamorphosis, which is obligatorily initiated and sustained by thyroid hormone (TH), is a dramatic example of extensive morphological, biochemical and cellular changes occurring during post-embryonic d...

    Authors: Lusha Liu, Wei Zhu, Jiongyu Liu, Shouhong Wang and Jianping Jiang

    Citation: BMC Genomics 2018 19:507

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  30. Content type: Research article

    The liver is mainly hematopoietic in the embryo, and converts into a major metabolic organ in the adult. Therefore, it is intensively remodeled after birth to adapt and perform adult functions. Long non-coding...

    Authors: Shengru Wu, Yanli Liu, Wei Guo, Xi Cheng, Xiaochun Ren, Si Chen, Xueyuan Li, Yongle Duan, Qingzhu Sun and Xiaojun Yang

    Citation: BMC Genomics 2018 19:498

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  31. Content type: Research article

    Integration of high throughput DNA genotyping and RNA-sequencing data allows for the identification of genomic regions that control gene expression, known as expression quantitative trait loci (eQTL), on a who...

    Authors: Aline S. M. Cesar, Luciana C. A. Regitano, James M. Reecy, Mirele D. Poleti, Priscila S. N. Oliveira, Gabriella B. de Oliveira, Gabriel C. M. Moreira, Maurício A. Mudadu, Polyana C. Tizioto, James E. Koltes, Elyn Fritz-Waters, Luke Kramer, Dorian Garrick, Hamid Beiki, Ludwig Geistlinger, Gerson B. Mourão…

    Citation: BMC Genomics 2018 19:499

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  32. Content type: Research article

    Long intergenic noncoding RNAs (lincRNAs) have been recognized in recent years as key regulators of biological processes. However, lincRNAs in goat remain poorly characterized both across various tissues and d...

    Authors: Shen Song, Min Yang, Yefang Li, Marhaba Rouzi, Qianjun Zhao, Yabin Pu, Xiaohong He, Joram M. Mwacharo, Ning Yang, Yuehui Ma and Lin Jiang

    Citation: BMC Genomics 2018 19:495

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  33. Content type: Research article

    Miniature size in horses represents an extreme reduction of withers height that originated after domestication. In some breeds, it is a highly desired trait representing a breed- or subtype-specific feature. T...

    Authors: Julia Metzger, Janina Rau, Fanny Naccache, Laura Bas Conn, Gabriella Lindgren and Ottmar Distl

    Citation: BMC Genomics 2018 19:492

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  34. Content type: Research article

    The viral hemorrhagic septicemia virus (VHSV) is a major threat for salmonid farming and for wild fish populations worldwide. Previous studies have highlighted the importance of innate factors regulated by a m...

    Authors: Eloi R. Verrier, Carine Genet, Denis Laloë, Florence Jaffrezic, Andrea Rau, Diane Esquerre, Nicolas Dechamp, Céline Ciobotaru, Caroline Hervet, Francine Krieg, Luc Jouneau, Christophe Klopp, Edwige Quillet and Pierre Boudinot

    Citation: BMC Genomics 2018 19:482

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  35. Content type: Research article

    Along with trophoblast elongation (Days 10 to 12), estradiol is secreted in increasing amounts for recognition of pregnancy. Endometrial secretions driven by ovarian progesterone and conceptus signals are esse...

    Authors: Shuqin Zeng, Jochen Bick, Susanne E. Ulbrich and Stefan Bauersachs

    Citation: BMC Genomics 2018 19:459

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  36. Content type: Research article

    Identification of genomic regions that have been targets of selection may shed light on the genetic history of livestock populations and help to identify variation controlling commercially important phenotypes...

    Authors: Mahdi Mokhber, Mohammad Moradi-Shahrbabak, Mostafa Sadeghi, Hossein Moradi-Shahrbabak, Alessandra Stella, Ezequiel Nicolzzi, Javad Rahmaninia and John L. Williams

    Citation: BMC Genomics 2018 19:449

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  38. Content type: Research article

    Assisted reproductive technologies (ART) are widely used to treat fertility issues in humans and for the production of embryos in mammalian livestock. The use of these techniques, however, is not without conse...

    Authors: Alan M. O’Doherty, Paul McGettigan, Rachelle E. Irwin, David A. Magee, Dominic Gagne, Eric Fournier, Abdullah Al-Naib, Marc-André Sirard, Colum P. Walsh, Claude Robert and Trudee Fair

    Citation: BMC Genomics 2018 19:438

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  39. Content type: Research article

    Due to the advancement in high throughput technology, single nucleotide polymorphism (SNP) is routinely being incorporated along with phenotypic information into genetic evaluation. However, this approach ofte...

    Authors: El Hamidi A. Hay, Yuri T. Utsunomiya, Lingyang Xu, Yang Zhou, Haroldo H. R. Neves, Roberto Carvalheiro, Derek M. Bickhart, Li Ma, Jose Fernando Garcia and George E. Liu

    Citation: BMC Genomics 2018 19:441

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  40. Content type: Research article

    Feed intake and body weight gain are economically important inputs and outputs of beef production systems. The purpose of this study was to discover differentially expressed genes that will be robust for feed ...

    Authors: Brittney N. Keel, Christina M. Zarek, John W. Keele, Larry A. Kuehn, Warren M. Snelling, William T. Oliver, Harvey C. Freetly and Amanda K. Lindholm-Perry

    Citation: BMC Genomics 2018 19:430

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  41. Content type: Research article

    The PIWI/piRNA pathway is a conserved machinery important for germ cell development and fertility. This piRNA-guided molecular machinery is best known for repressing derepressed transposable elements (TE) duri...

    Authors: Kai-Wei Chang, Yen-Tzu Tseng, Yi-Chen Chen, Chih-Yun Yu, Hung-Fu Liao, Yi-Chun Chen, Yu-Fan Evan Tu, Shinn-Chih Wu, I-Hsuan Liu, Marina Pinskaya, Antonin Morillon, Bertrand Pain and Shau-Ping Lin

    Citation: BMC Genomics 2018 19:425

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    The Correction to this article has been published in BMC Genomics 2018 19:480

  42. Content type: Research article

    Aberrant DNA methylation patterns of genes required for development are common in in vitro produced embryos. In this regard, we previously identified altered DNA methylation patterns of in vivo developed blast...

    Authors: Dessie Salilew-Wondim, Mohammed Saeed-Zidane, Michael Hoelker, Samuel Gebremedhn, Mikhaël Poirier, Hari Om Pandey, Ernst Tholen, Christiane Neuhoff, Eva Held, Urban Besenfelder, Vita Havlicek, Franca Rings, Eric Fournier, Dominic Gagné, Marc-André Sirard, Claude Robert…

    Citation: BMC Genomics 2018 19:424

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  43. Content type: Research article

    Vertebrates use different pigmentation strategies to adapt to various environments. A large amount of research has been done on disclosing the mechanisms of pigmentation strategies in vertebrates either under ...

    Authors: Wei Zhu, Lusha Liu, Xungang Wang, Xinyu Gao, Jianping Jiang and Bin Wang

    Citation: BMC Genomics 2018 19:422

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  44. Content type: Research article

    Molecular regulation of the hypothalamic-pituitary-gonadal (HPG) axis plays an essential role in the fine tuning of seasonal estrus in Capra hircus. Noncoding RNAs (ncRNAs) are emerging as key regulators in sexua...

    Authors: Emanuele Capra, Barbara Lazzari, Stefano Frattini, Stefania Chessa, Beatrice Coizet, Andrea Talenti, Bianca Castiglioni, Paolo Ajmone Marsan, Paola Crepaldi, Giulio Pagnacco, John L. Williams and Alessandra Stella

    Citation: BMC Genomics 2018 19:417

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  45. Content type: Research article

    Spermatozoa have a remarkable epigenome in line with their degree of specialization, their unique nature and different requirements for successful fertilization. Accordingly, perturbations in the establishment...

    Authors: Jean-Philippe Perrier, Eli Sellem, Audrey Prézelin, Maxime Gasselin, Luc Jouneau, François Piumi, Hala Al Adhami, Michaël Weber, Sébastien Fritz, Didier Boichard, Chrystelle Le Danvic, Laurent Schibler, Hélène Jammes and Hélène Kiefer

    Citation: BMC Genomics 2018 19:404

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  46. Content type: Research article

    Chinese giant salamander (Andrias davidianus) undergoes a metamorphosis from aquatic larvae to terrestrial adults, with concomitant transfer of respiration from gills to lungs prior to metamorphosis. These two ti...

    Authors: Shengyan Su, Yuheng Wang, Huiwei Wang, Wei Huang, Jun Chen, Jun Xing, Pao Xu, Xinhua Yuan, Caiji Huang and Yulin Zhou

    Citation: BMC Genomics 2018 19:406

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  47. Content type: Research article

    The number of studies of Copy Number Variation in cattle has increased in recent years. This has been prompted by the increased availability of data on polymorphisms and their relationship with phenotypes. In ...

    Authors: M. Mielczarek, M. Frąszczak, E. Nicolazzi, J. L. Williams and J. Szyda

    Citation: BMC Genomics 2018 19:410

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  48. Content type: Research article

    Bovine milk is an important nutrient source for humans. Forage plays a vital role in dairy husbandry via affecting milk quality and quantity. However, the differences in mammary metabolism of dairy cows fed di...

    Authors: Wenting Dai, Quanjuan Wang, Fengqi Zhao, Jianxin Liu and Hongyun Liu

    Citation: BMC Genomics 2018 19:403

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  49. Content type: Research article

    Umbilical hernia is one of the most prevalent congenital defect in pigs, causing economic losses and substantial animal welfare problems. Identification and implementation of genomic regions controlling umbili...

    Authors: Eli Grindflek, Marianne H. S. Hansen, Sigbjørn Lien and Maren van Son

    Citation: BMC Genomics 2018 19:412

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  50. Content type: Research article

    Early feathering and late feathering in chickens are sex-linked phenotypes, which have commercial application in the poultry industry for sexing chicks at hatch and have important impacts on performance traits...

    Authors: Guijun Fang, Xinzheng Jia, Hua Li, Shuwen Tan, Qinghua Nie, Hui Yu and Ying Yang

    Citation: BMC Genomics 2018 19:399

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