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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.

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  1. Gang goose is a native species with gray plumage in Sichuan, China. As a result of overhunting, the number of gray Gang geese has decreased dramatically. To keep the species from extinction, conservation work ...

    Authors: Yang Xi, Lei Wang, Hehe Liu, Shengchao Ma, Yanying Li, Liang Li, Jiwen Wang, Han Chunchun, Lili Bai, Ahsan Mustafa and Hua He

    Citation: BMC Genomics 2020 21:162

    Content type: Research article

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  2. Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption...

    Authors: Madhu Sudhana Saddala, Anton Lennikov, Adam Bouras and Hu Huang

    Citation: BMC Genomics 2020 21:132

    Content type: Research article

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  3. Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings remains poorly understood. To study t...

    Authors: Fengyao Wu, Fengying Lu, Xin Fan, Jin Chao, Chuanmin Liu, Qunxing Pan, Huawei Sun and Xiaofei Zhang

    Citation: BMC Genomics 2020 21:123

    Content type: Research article

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  4. Osmotic stress is a widespread phenomenon in aquatic animal. The ability to cope with salinity stress and alkaline stress is quite important for the survival of aquatic species under natural conditions. Tilapi...

    Authors: Huanhuan Su, Dongmei Ma, Huaping Zhu, Zhigang Liu and Fengying Gao

    Citation: BMC Genomics 2020 21:110

    Content type: Research article

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  5. The fasting-refeeding perturbation has been used extensively to reveal specific genes and metabolic pathways that control energy metabolism in the chicken. Most global transcriptional scans of the fasting-refe...

    Authors: Larry A. Cogburn, Nares Trakooljul, Xiaofei Wang, Laura E. Ellestad and Tom E. Porter

    Citation: BMC Genomics 2020 21:109

    Content type: Research article

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  6. Siberian musk deer, one of the seven species, is distributed in coniferous forests of Asia. Worldwide, the population size of Siberian musk deer is threatened by severe illegal poaching for commercially valuab...

    Authors: Li Yi, Menggen Dalai, Rina Su, Weili Lin, Myagmarsuren Erdenedalai, Batkhuu Luvsantseren, Chimedragchaa Chimedtseren, Zhen Wang and Surong Hasi

    Citation: BMC Genomics 2020 21:108

    Content type: Research article

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  7. Neutrophils are the first effectors of inflammatory response triggered by mastitis infection, and are important defense cells against pathogenic Escherichia coli (E. coli). DNA methylation, as a critical epigenet...

    Authors: Zhihua Ju, Qiang Jiang, Jinpeng Wang, Xiuge Wang, Chunhong Yang, Yan Sun, Yaran Zhang, Changfa Wang, Yaping Gao, Xiaochao Wei, Minghai Hou and Jinming Huang

    Citation: BMC Genomics 2020 21:102

    Content type: Research article

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  8. Sustainability challenges are currently hampering an increase in salmon production. Using sterile salmon can solve problems with precocious puberty and genetic introgression from farmed escapees to wild popula...

    Authors: Lene Kleppe, Rolf Brudvik Edvardsen, Tomasz Furmanek, Eva Andersson, Kai Ove Skaftnesmo, Frida Thyri Segafredo and Anna Wargelius

    Citation: BMC Genomics 2020 21:99

    Content type: Research article

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  9. PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art metho...

    Authors: R. Meyermans, W. Gorssen, N. Buys and S. Janssens

    Citation: BMC Genomics 2020 21:94

    Content type: Methodology article

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  10. Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Je...

    Authors: Young-Lim Lee, Mirte Bosse, Erik Mullaart, Martien A. M. Groenen, Roel F. Veerkamp and Aniek C. Bouwman

    Citation: BMC Genomics 2020 21:89

    Content type: Research article

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  11. Contamination of reagents and cross contamination across samples is a long-recognized issue in molecular biology laboratories. While often innocuous, contamination can lead to inaccurate results. Cantalupo et al.

    Authors: Sara R. Selitsky, David Marron, Daniel Hollern, Lisle E. Mose, Katherine A. Hoadley, Corbin Jones, Joel S. Parker, Dirk P. Dittmer and Charles M. Perou

    Citation: BMC Genomics 2020 21:79

    Content type: Research article

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  12. This study used a genome-wide screen of gene expression to better understand the metabolic and functional differences between commercially valuable intramuscular fat (IMF) and commercially wasteful subcutaneou...

    Authors: Nicholas J. Hudson, Antonio Reverter, William J. Griffiths, Eylan Yutuc, Yuqin Wang, Angela Jeanes, Sean McWilliam, David W. Pethick and Paul L. Greenwood

    Citation: BMC Genomics 2020 21:77

    Content type: Research article

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  13. Spermatogenesis is an intricate process regulated by a finely organized network. The orange-spotted grouper (Epinephelus coioides) is a protogynous hermaphroditic fish, but the regulatory mechanism of its spermat...

    Authors: Xi Wu, Yang Yang, Chaoyue Zhong, Yin Guo, Shuisheng Li, Haoran Lin and Xiaochun Liu

    Citation: BMC Genomics 2020 21:73

    Content type: Research article

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  14. Gene targeting by homology-directed repair (HDR) can precisely edit the genome and is a versatile tool for biomedical research. However, the efficiency of HDR-based modification is still low in many model orga...

    Authors: Haipeng Bai, Lijun Liu, Ke An, Xiaochan Lu, Michael Harrison, Yanqiu Zhao, Ruibin Yan, Zhijie Lu, Song Li, Shuo Lin, Fang Liang and Wei Qin

    Citation: BMC Genomics 2020 21:67

    Content type: Methodology article

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  15. Reproductive capacity can be altered by challenges experienced during critical periods of development, including fetal development and early neonatal life. Gossypol is a polyphenolic compound, commonly found i...

    Authors: Helder Louvandini, Patricia S. Corrêa, Rocío Amorín, Lihe Liu, Egon H. Ieda, Carolina R. Jimenez, Siu M. Tsai, Concepta M. McManus and Francisco Peñagaricano

    Citation: BMC Genomics 2020 21:59

    Content type: Research article

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  16. Fatty acid composition contributes greatly to the quality and nutritional value of meat. However, the molecular regulatory mechanisms underlying fatty acid accumulation in poultry have not yet been cleared. Th...

    Authors: Wenlei Fan, Wenjing Liu, Hehe Liu, Qingshi Meng, Yaxi Xu, Yuming Guo, Baowei Wang, Zhengkui Zhou and Shuisheng Hou

    Citation: BMC Genomics 2020 21:58

    Content type: Research article

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  17. Carotenoids contribute significantly to animal body coloration, including the spectacular color pattern diversity among fishes. Fish, as other animals, derive carotenoids from their diet. Following uptake, tra...

    Authors: Ehsan Pashay Ahi, Laurène A. Lecaudey, Angelika Ziegelbecker, Oliver Steiner, Ronald Glabonjat, Walter Goessler, Victoria Hois, Carina Wagner, Achim Lass and Kristina M. Sefc

    Citation: BMC Genomics 2020 21:54

    Content type: Research article

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  18. The Tibial dyschondroplasia (TD) in fast-growing chickens is mainly caused by improper blood circulation. The exact mechanism underlying angiogenesis and vascularization in tibial growth plate of broiler chick...

    Authors: Ali Raza Jahejo, Ding Zhang, Sheng Niu, Raza Ali Mangi, Afrasyab Khan, Muhammad Farhan Qadir, Ajab Khan, Huan-chun Chen and Wen-xia Tian

    Citation: BMC Genomics 2020 21:50

    Content type: Research article

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  19. Health traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to iden...

    Authors: Ellen Freebern, Daniel J. A. Santos, Lingzhao Fang, Jicai Jiang, Kristen L. Parker Gaddis, George E. Liu, Paul M. VanRaden, Christian Maltecca, John B. Cole and Li Ma

    Citation: BMC Genomics 2020 21:41

    Content type: Research article

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  20. Genome wide association studies (GWAS) were conducted on 7,853,211 imputed whole genome sequence variants in a population of 3354 to 3984 animals from multiple beef cattle breeds for five carcass merit traits ...

    Authors: Yining Wang, Feng Zhang, Robert Mukiibi, Liuhong Chen, Michael Vinsky, Graham Plastow, John Basarab, Paul Stothard and Changxi Li

    Citation: BMC Genomics 2020 21:38

    Content type: Research article

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  21. Genome wide association studies (GWAS) on residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) were conducted i...

    Authors: Feng Zhang, Yining Wang, Robert Mukiibi, Liuhong Chen, Michael Vinsky, Graham Plastow, John Basarab, Paul Stothard and Changxi Li

    Citation: BMC Genomics 2020 21:36

    Content type: Research article

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  22. Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local ...

    Authors: Meenu Bhati, Naveen Kumar Kadri, Danang Crysnanto and Hubert Pausch

    Citation: BMC Genomics 2020 21:27

    Content type: Research article

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  23. Early sex differentiation genes of zebrafish remain an unsolved mystery due to the difficulty to distinguish the sex of juvenile zebrafish. However, aromatase inhibitors (AIs) could direct juvenile zebrafish s...

    Authors: Lu Chen, Li Wang, Qiwei Cheng, Yi-Xuan Tu, Zhuang Yang, Run-Ze Li, Zhi-Hui Luo and Zhen-Xia Chen

    Citation: BMC Genomics 2020 21:22

    Content type: Research article

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  24. The domestic cat (Felis catus) is an important companion animal and is used as a large animal model for human disease. However, the comprehensive study of adaptive immunity in this species is hampered by the lack...

    Authors: Araya Radtanakatikanon, Stefan M. Keller, Nikos Darzentas, Peter F. Moore, Géraldine Folch, Viviane Nguefack Ngoune, Marie-Paule Lefranc and William Vernau

    Citation: BMC Genomics 2020 21:20

    Content type: Research article

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  25. Production conditions of layer chicken can vary in terms of temperature or diet energy content compared to the controlled environment where pure-bred selection is undertaken. The aim of this study was to bette...

    Authors: F. Jehl, C. Désert, C. Klopp, M. Brenet, A. Rau, S. Leroux, M. Boutin, L. Lagoutte, K. Muret, Y. Blum, D. Esquerré, D. Gourichon, T. Burlot, A. Collin, F. Pitel, A. Benani…

    Citation: BMC Genomics 2019 20:1033

    Content type: Research article

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  26. The proximal femoral head separation (FHS) or epiphysiolysis is a prevalent disorder affecting the chicken femur epiphysis, being considered a risk factor to infection which can cause bacterial chondronecrosis...

    Authors: Jane de Oliveira Peixoto, Igor Ricardo Savoldi, Adriana Mércia Guaratini Ibelli, Maurício Egídio Cantão, Fátima Regina Ferreira Jaenisch, Poliana Fernanda Giachetto, Matthew Lee Settles, Ricardo Zanella, Jorge Augusto Petroli Marchesi, José Rodrigo Pandolfi, Luiz Lehmann Coutinho and Mônica Corrêa Ledur

    Citation: BMC Genomics 2019 20:1031

    Content type: Research article

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  27. Hip dysplasia and osteoarthritis continue to be prevalent problems in veterinary and human medicine. Canine hip dysplasia is particularly problematic as it massively affects several large-sized breeds and can ...

    Authors: Lea Mikkola, Saila Holopainen, Tiina Pessa-Morikawa, Anu K. Lappalainen, Marjo K. Hytönen, Hannes Lohi and Antti Iivanainen

    Citation: BMC Genomics 2019 20:1027

    Content type: Research article

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  28. Transcriptomic responses to immune stimulation were investigated in coho salmon (Oncorhynchus kisutch) with distinct growth phenotypes. Wild-type fish were contrasted to strains with accelerated growth arising ei...

    Authors: Jin-Hyoung Kim, Daniel J. Macqueen, James R. Winton, John D. Hansen, Hyun Park and Robert H. Devlin

    Citation: BMC Genomics 2019 20:1024

    Content type: Research article

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  29. Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of ...

    Authors: Roni Tadmor-Levi, Adi Doron-Faigenboim, Evgeniya Marcos-Hadad, Jules Petit, Gideon Hulata, Maria Forlenza, Geert F. Wiegertjes and Lior David

    Citation: BMC Genomics 2019 20:1019

    Content type: Research article

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  30. As a newly characterized type of noncoding RNA, circular RNA (circRNA) has been shown to have functions in diverse biological processes of animals. It has been reported that several noncoding RNAs may regulate...

    Authors: Haojie Zhang, Baoyu Hu, Jiali Xiong, Ting Chen, Qianyun Xi, Junyi Luo, Qingyan Jiang, Jiajie Sun and Yongliang Zhang

    Citation: BMC Genomics 2019 20:1013

    Content type: Research article

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  31. Genetic resistance in cattle is considered a suitable way to control tick burden and its consequent losses for livestock production. Exploring tick-resistant (R) and tick-susceptible (S) hosts, we investigated...

    Authors: Daniela D. Moré, Fernando F. Cardoso, Maurício A. Mudadu, Wilson Malagó-Jr, Claudia C. Gulias-Gomes, Bruna P. Sollero, Adriana M. G. Ibelli, Luiz L. Coutinho and Luciana C. A. Regitano

    Citation: BMC Genomics 2019 20:998

    Content type: Research article

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  32. The compromised performance of laying hens in the late phase of production relative to the peak production was thought to be associated with the impairment of intestinal functionality, which plays essential ro...

    Authors: Wei-wei Wang, Jing Wang, Hai-jun Zhang, Shu-geng Wu and Guang-hai Qi

    Citation: BMC Genomics 2019 20:970

    Content type: Research article

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  33. Melanocytes are derived from neural crest stem cells in the embryonic stage. In mature melanocytes, a series of complex enzyme-catalyzed reactions leads to the production of melanins, which determine the hair ...

    Authors: Xuexian Liu, Bin Du, Pengqian Zhang, Junzhen Zhang, Zhiwei Zhu, Bo Liu and Ruiwen Fan

    Citation: BMC Genomics 2019 20:962

    Content type: Research article

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  34. Sperm epigenetics is an emerging area of study supported by observations reporting that abnormal sperm DNA methylation patterns are associated with infertility. Here, we explore cytosine-guanine dinucleotides ...

    Authors: Emanuele Capra, Barbara Lazzari, Federica Turri, Paola Cremonesi, Antônia Moemia Rodrigues Portela, Paolo Ajmone-Marsan, Alessandra Stella and Flavia Pizzi

    Citation: BMC Genomics 2019 20:940

    Content type: Research article

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  35. Genome-wide association studies (GWAS) are extensively used to identify single nucleotide polymorphisms (SNP) underlying the genetic variation of complex traits. However, much uncertainly often still exists ab...

    Authors: Sara de las Heras-Saldana, Samuel A. Clark, Naomi Duijvesteijn, Cedric Gondro, Julius H. J. van der Werf and Yizhou Chen

    Citation: BMC Genomics 2019 20:939

    Content type: Research article

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  36. Spinibarbus hollandi is an economically important fish species in southern China. This fish is known to have nutritional and medicinal properties; however, its farming is limited by its slow growth rate. In the p...

    Authors: Yang Yang, Huiqiang Zhou, Liping Hou, Ke Xing and Hu Shu

    Citation: BMC Genomics 2019 20:938

    Content type: Research article

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  37. MicroRNAs (miRNAs) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aur...

    Authors: Shaoyang Ma, Chao Tong, Eveline M. Ibeagha-Awemu and Xin Zhao

    Citation: BMC Genomics 2019 20:934

    Content type: Research article

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  38. Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population di...

    Authors: Qiong Wang, Yaxiong Jia, Yuan Wang, Zhihua Jiang, Xiang Zhou, Zebin Zhang, Changsheng Nie, Junying Li, Ning Yang and Lujiang Qu

    Citation: BMC Genomics 2019 20:933

    Content type: Research article

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  39. Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide...

    Authors: Johanna L. Smith, Miranda L. Wilson, Sara M. Nilson, Troy N. Rowan, David L. Oldeschulte, Robert D. Schnabel, Jared E. Decker and Christopher M. Seabury

    Citation: BMC Genomics 2019 20:926

    Content type: Research article

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  40. Compensatory growth refers to the phenomenon in which organisms grow faster after the improvement of an adverse environment and is thought to be an adaptive evolution to cope with the alleviation of the hostil...

    Authors: Jirong Jia, Jingkai Qin, Xi Yuan, Zongzhen Liao, Jinfeng Huang, Bin Wang, Caiyun Sun and Wensheng Li

    Citation: BMC Genomics 2019 20:919

    Content type: Research article

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  41. Sperm DNA integrity is considered essential for successful transmission of the paternal genome, fertilization and normal embryo development. DNA fragmentation index (DFI, %) has become a key parameter in the s...

    Authors: Abdolrahman Khezri, Birgitte Narud, Else-Berit Stenseth, Anders Johannisson, Frøydis Deinboll Myromslien, Ann Helen Gaustad, Robert C. Wilson, Robert Lyle, Jane M. Morrell, Elisabeth Kommisrud and Rafi Ahmad

    Citation: BMC Genomics 2019 20:897

    Content type: Research article

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  42. DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others.

    Authors: Shuli Liu, Lingzhao Fang, Yang Zhou, Daniel J.A. Santos, Ruidong Xiang, Hans D. Daetwyler, Amanda J. Chamberlain, John B. Cole, Cong-jun Li, Ying Yu, Li Ma, Shengli Zhang and George E. Liu

    Citation: BMC Genomics 2019 20:888

    Content type: Research article

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  43. The function of Toll-like receptor 2 (TLR2) in host defense against pathogens, especially Mycobacterium tuberculosis (Mtb) is poorly understood. To investigate the role of TLR2 during mycobacterial infection, we ...

    Authors: Wanbin Hu, Shuxin Yang, Yasuhito Shimada, Magnus Münch, Rubén Marín-Juez, Annemarie H. Meijer and Herman P. Spaink

    Citation: BMC Genomics 2019 20:878

    Content type: Research article

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  44. The white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. It has been used as an animal model for studying different scientific questions ranging from the restorat...

    Authors: Íria Gabriela Dias dos Santos, Tiago Antônio de Oliveira Mendes, Gerluza Aparecida Borges Silva, Amanda Maria Sena Reis, Cláudia Barros Monteiro-Vitorello, Patricia Dayane Carvalho Schaker, Roberto Hirochi Herai, André Brait Carneiro Fabotti, Luiz Lehmann Coutinho and Erika Cristina Jorge

    Citation: BMC Genomics 2019 20:866

    Content type: Research article

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  45. Intramuscular fat (IMF) is one of the most important factors positively associated with meat quality. Triglycerides (TGs), as the main component of IMF, play an essential role in muscle lipid metabolism. This ...

    Authors: Lu Liu, Xiaojing Liu, Huanxian Cui, Ranran Liu, Guiping Zhao and Jie Wen

    Citation: BMC Genomics 2019 20:863

    Content type: Research article

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  46. The ureagenesis plays a central role in the homeostatic control of nitrogen metabolism. This process occurs in the liver, the key metabolic organ in the maintenance of energy homeostasis in the body. To date, ...

    Authors: Zhongyan Lu, Zhihui Xu, Zanming Shen, Hong Shen and Jörg R. Aschenbach

    Citation: BMC Genomics 2019 20:854

    Content type: Research article

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  47. Subfertility is a major issue facing the dairy industry as the average US Holstein cow conception rate (CCR) is approximately 35%. The genetics underlying the physiological processes responsible for CCR, the p...

    Authors: Jennifer N. Kiser, Erin Clancey, Joao G. N. Moraes, Joseph Dalton, Gregory W. Burns, Thomas E. Spencer and Holly L. Neibergs

    Citation: BMC Genomics 2019 20:840

    Content type: Research article

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