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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 15

  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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

  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. Content type: Research article

    Topological association domains (TADs) are chromosomal domains characterised by frequent internal DNA-DNA interactions. The transcription factor CTCF binds to conserved DNA sequence patterns called CTCF bindin...

    Authors: Min Wang, Timothy P. Hancock, Amanda J. Chamberlain, Christy J. Vander Jagt, Jennie E. Pryce, Benjamin G. Cocks, Mike E. Goddard and Benjamin J. Hayes

    Citation: BMC Genomics 2018 19:395

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  30. Content type: Research article

    Aquaculture production is expected to double by 2030, and demands for aquafeeds and raw materials are expected to increase accordingly. Sustainable growth of aquaculture will require the development of highly ...

    Authors: Alexandre Leduc, Céline Zatylny-Gaudin, Marie Robert, Erwan Corre, Gildas Le Corguille, Hélène Castel, Antoine Lefevre-Scelles, Vincent Fournier, Enric Gisbert, Karl B. Andree and Joël Henry

    Citation: BMC Genomics 2018 19:396

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  31. Content type: Research article

    Feathers with complex and fine structure are hallmark avian integument appendages, which have contributed significantly to the survival and breeding for birds. Here, we aimed to explore the differentiation, mo...

    Authors: Jing Yang, Yanhua Qu, Yuan Huang and Fumin Lei

    Citation: BMC Genomics 2018 19:391

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  32. Content type: Research article

    Transposon-mediated, non-viral gene delivery is a powerful tool for generating stable cell lines and transgenic animals. However, as multi-copy insertion is the preferred integration pattern, there is the pote...

    Authors: Soo-Young Yum, Song-Jeon Lee, Sin-Gi Park, In-Gang Shin, Sang-Eun Hahn, Woo-Jae Choi, Hee-Soo Kim, Hyeong-Jong Kim, Seong-Hun Bae, Je-Hyeong Lee, Joo-Yeong Moon, Woo-Sung Lee, Ji-Hyun Lee, Choong-Il Lee, Seong-Jin Kim and Goo Jang

    Citation: BMC Genomics 2018 19:387

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  33. Content type: Research article

    Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity of studies in the literature that report genetic or genomic parameters, especially in the case of sheep popula...

    Authors: G. A. Rovadoscki, S. F. N. Pertile, A. B. Alvarenga, A. S. M. Cesar, F. Pértille, J. Petrini, V. Franzo, W. V. B. Soares, G. Morota, M. L. Spangler, L. F. B. Pinto, G. G. P. Carvalho, D. P. D. Lanna, L. L. Coutinho and G. B. Mourão

    Citation: BMC Genomics 2018 19:375

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  34. Content type: Research article

    Excess fat content in chickens has a negative impact on poultry production. The discovery of QTL associated with fat deposition in the carcass allows the identification of positional candidate genes (PCGs) tha...

    Authors: Gabriel Costa Monteiro Moreira, Clarissa Boschiero, Aline Silva Mello Cesar, James M. Reecy, Thaís Fernanda Godoy, Priscila Anchieta Trevisoli, Maurício E. Cantão, Mônica Corrêa Ledur, Adriana Mércia Guaratini Ibelli, Jane de Oliveira Peixoto, Ana Silvia Alves Meira Tavares Moura, Dorian Garrick and Luiz Lehmann Coutinho

    Citation: BMC Genomics 2018 19:374

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  35. Content type: Research article

    The factors determining sex in teleosts are diverse. Great efforts have been made to characterize the underlying genetic network in various species. However, only seven master sex-determining genes have been i...

    Authors: Wenjing Tao, Jinlin Chen, Dejie Tan, Jing Yang, Lina Sun, Jing Wei, Matthew A. Conte, Thomas D. Kocher and Deshou Wang

    Citation: BMC Genomics 2018 19:363

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  36. Content type: Research article

    In somatic cells, homologous recombination (HR) is a rare event caused by eventual DNA double-strand breaks (DSBs). In contrast, germ cells show high frequency of HR caused by programmed DSBs. Microsatellites ...

    Authors: Jianbo Zheng, Heng Li, Qi Zhang, Lei Sun, Xiangfang Liu and Chen Luo

    Citation: BMC Genomics 2018 19:359

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  37. Content type: Research article

    Tan sheep is an indigenous Chinese breed well known for its beautiful curly fleece. One prominent breed characteristic of this sheep breed is that the degree of curliness differs markedly between lambs and adu...

    Authors: Yufang Liu, Jibin Zhang, Qiao Xu, Xiaolong Kang, Kejun Wang, Keliang Wu and Meiying Fang

    Citation: BMC Genomics 2018 19:360

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  38. Content type: Research article

    The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment ...

    Authors: J. Auvinet, P. Graça, L. Belkadi, L. Petit, E. Bonnivard, A. Dettaï, W. H Detrich III, C. Ozouf-Costaz and D. Higuet

    Citation: BMC Genomics 2018 19:339

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  39. Content type: Research article

    The level of fat deposition in carcass is a crucial factor influencing meat quality. Guangling Large-Tailed (GLT) and Small-Tailed Han (STH) sheep are important local Chinese fat-tailed breeds that show distin...

    Authors: Baojun Li, Liying Qiao, Lixia An, Weiwei Wang, Jianhua Liu, Youshe Ren, Yangyang Pan, Jiongjie Jing and Wenzhong Liu

    Citation: BMC Genomics 2018 19:338

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  40. Content type: Research article

    Colostrum and milk are essential sources of antibodies and nutrients for the neonate, playing a key role in their survival and growth. Slight abnormalities in the timing of colostrogenesis/lactogenesis potenti...

    Authors: V. Palombo, J. J. Loor, M. D’Andrea, M. Vailati-Riboni, K. Shahzad, U. Krogh and P. K. Theil

    Citation: BMC Genomics 2018 19:322

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  41. Content type: Research article

    Copy number variation (CNV) is an important type of genetic variation contributing to phenotypic differences among mammals and may serve as an alternative molecular marker to single nucleotide polymorphism (SN...

    Authors: Yang Zhou, Erin E. Connor, George R. Wiggans, Yongfang Lu, Robert J. Tempelman, Steven G. Schroeder, Hong Chen and George E. Liu

    Citation: BMC Genomics 2018 19:314

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  42. Content type: Research article

    Divergent selection for meat and egg production in poultry has resulted in strains of birds differing widely in traits related to these products. Modern strains of meat birds can reach live weights of 2 kg in ...

    Authors: Nicky-Lee Willson, Rebecca E. A. Forder, Rick Tearle, John L. Williams, Robert J. Hughes, Greg S. Nattrass and Philip I. Hynd

    Citation: BMC Genomics 2018 19:309

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  43. Content type: Research article

    The understanding of the biological determinism of meat ultimate pH, which is strongly related to muscle glycogen content, is a key point for the control of muscle integrity and meat quality in poultry. In the...

    Authors: Elisabeth Le Bihan-Duval, Christelle Hennequet-Antier, Cécile Berri, Stéphane A. Beauclercq, Marie Christine Bourin, Maryse Boulay, Olivier Demeure and Simon Boitard

    Citation: BMC Genomics 2018 19:294

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  44. Content type: Research article

    Adipose tissue is a major endocrine organ and is thought to play a central role in the metabolic control of reproductive function in cattle. Plane of nutrition during early life has been shown to influence the...

    Authors: Anne-Marie English, Sineád M. Waters, Paul Cormican, Colin J. Byrne, Seán Fair and David A. Kenny

    Citation: BMC Genomics 2018 19:281

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  45. Content type: Research article

    In food animal agriculture, there is a need to identify the mechanisms that can improve the efficiency of muscle growth and protein accretion. Callipyge sheep provide excellent machinery since the up-regulatio...

    Authors: Hui Yu, Jolena N. Waddell, Shihuan Kuang, Ross L. Tellam, Noelle E. Cockett and Christopher A. Bidwell

    Citation: BMC Genomics 2018 19:283

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  46. Content type: Research article

    Prolongation of superstimulatory treatment appears to be associated with a greater superovulatory response and with greater oocyte maturation in cattle. A genome-wide bovine oligo-microarray was used to compar...

    Authors: F. C. F. Dias, M. I. R. Khan, M. A. Sirard, G. P. Adams and J. Singh

    Citation: BMC Genomics 2018 19:258

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  47. Content type: Research article

    It has been suggested that the high phospholipid (PL) requirement in Atlantic salmon (Salmo salar) fry is due to insufficient intestinal de-novo synthesis causing low lipoprotein (LP) production and reduced trans...

    Authors: Yang Jin, Rolf Erik Olsen, Mari-Ann Østensen, Gareth Benjamin Gillard, Sven Arild Korsvoll, Nina Santi, Arne Bjørke Gjuvsland, Jon Olav Vik, Jacob Seilø Torgersen, Simen Rød Sandve and Yngvar Olsen

    Citation: BMC Genomics 2018 19:253

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