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Non-human and non-rodent vertebrate genomics

This section covers all aspects of the genomics of vertebrates, excluding humans, primates and rodents, including livestock species.

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  1. Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this s...

    Authors: Chao Yuan, Zengkui Lu, Tingting Guo, Yaojing Yue, Xijun Wang, Tianxiang Wang, Yajun Zhang, Fujun Hou, Chune Niu, Xiaopin Sun, Hongchang Zhao, Shaohua Zhu, Jianbin Liu and Bohui Yang

    Citation: BMC Genomics 2021 22:78

    Content type: Research article

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  2. Canine hip dysplasia (CHD) is a common disease, with a complex genetic background. Dogs with severe CHD sometimes also suffer from osteoarthritis (OA), an inflammatory, often painful and incurable condition. P...

    Authors: Lea Mikkola, Kaisa Kyöstilä, Jonas Donner, Anu K. Lappalainen, Marjo K. Hytönen, Hannes Lohi and Antti Iivanainen

    Citation: BMC Genomics 2021 22:68

    Content type: Research article

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  3. Avian infectious bronchitis virus (IBV) is a gamma coronavirus that severely affects the poultry industry worldwide. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs with a length of more than 200 n...

    Authors: Hao Li, Pengfei Cui, Xue Fu, Lan Zhang, Wenjun Yan, Yaru Zhai, Changwei Lei, Hongning Wang and Xin Yang

    Citation: BMC Genomics 2021 22:67

    Content type: Research article

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  4. miRNAs play critical roles in growth and development. Various studies of chicken muscle development have focused on identifying miRNAs that are important for embryo or adult muscle development. However, littl...

    Authors: Jie Liu, Fuwei Li, Xin Hu, Dingguo Cao, Wei Liu, Haixia Han, Yan Zhou and Qiuxia Lei

    Citation: BMC Genomics 2021 22:64

    Content type: Research article

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  5. Chinese domestic pig breeds are reputed for pork quality, but their low ratio of lean-to-fat carcass weight decreases production efficiency. A better understanding of the genetic regulation network of subcutan...

    Authors: Dawei Zhang, Wenjing Wu, Xin Huang, Ke Xu, Cheng Zheng and Jin Zhang

    Citation: BMC Genomics 2021 22:61

    Content type: Research article

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  6. The mechanism of body growth in mammals is poorly understood. Here, we investigated the regulatory networks involved in body growth through transcriptomic analysis of pituitary and epiphyseal tissues of smalle...

    Authors: Jun Fang, Dong Zhang, Jun Wei Cao, Li Zhang, Chun Xia Liu, Yan Ping Xing, Feng Wang, Hong Yang Xu, Shi Chao Wang, Yu Ling, Wei Wang, Yan Ru Zhang and Huan Min Zhou

    Citation: BMC Genomics 2021 22:58

    Content type: Research article

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  7. Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by ...

    Authors: Grazyella M. Yoshida and José M. Yáñez

    Citation: BMC Genomics 2021 22:57

    Content type: Research article

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  8. With the intensification of global warming, rainbow trout (Oncorhynchus mykiss) suffer from varying degrees of thermal stimulation, leads to mass mortality, which severely restrict the development of aquaculture....

    Authors: Jinqiang Quan, Yujun Kang, Zhicheng Luo, Guiyan Zhao, Lanlan Li and Zhe Liu

    Citation: BMC Genomics 2021 22:48

    Content type: Research article

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  9. Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GW...

    Authors: Gabriele Flossmann, Christine Wurmser, Hubert Pausch, Amabel Tenghe, Jörg Dodenhoff, Günther Dahinten, Kay-Uwe Götz, Ingolf Russ and Ruedi Fries

    Citation: BMC Genomics 2021 22:38

    Content type: Research article

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  10. Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resol...

    Authors: Sonia Rey, Xingkun Jin, Børge Damsgård, Marie-Laure Bégout and Simon Mackenzie

    Citation: BMC Genomics 2021 22:33

    Content type: Research article

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  11. The use of sex-sorted sperm in cattle assisted reproduction is constantly increasing. However, sperm fertility can substantially differ between unsorted (conventional) and sex-sorted semen batches of the same ...

    Authors: Esin Keles, Eleni Malama, Siyka Bozukova, Mathias Siuda, Sarah Wyck, Ulrich Witschi, Stefan Bauersachs and Heinrich Bollwein

    Citation: BMC Genomics 2021 22:30

    Content type: Research article

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  12. Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). DNA-based biomarkers contributing to BRD resistance are potentially present in non-protein-coding regulatory regions of...

    Authors: Dayle Johnston, JaeWoo Kim, Jeremy F. Taylor, Bernadette Earley, Matthew S. McCabe, Ken Lemon, Catherine Duffy, Michael McMenamy, S. Louise Cosby and Sinéad M. Waters

    Citation: BMC Genomics 2021 22:14

    Content type: Research article

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  13. Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome...

    Authors: Shenping Zhou, Rongrong Ding, Fanming Meng, Xingwang Wang, Zhanwei Zhuang, Jianping Quan, Qian Geng, Jie Wu, Enqin Zheng, Zhenfang Wu, Jianhui Yang and Jie Yang

    Citation: BMC Genomics 2021 22:12

    Content type: Research article

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  14. DNA methylation, a biochemical modification of cytosine, has an important role in lipid metabolism. Fatty liver hemorrhagic syndrome (FLHS) is a serious disease and is tightly linked to lipid homeostasis. Here...

    Authors: Xiaodong Tan, Ranran Liu, Yonghong Zhang, Xicai Wang, Jie Wang, Hailong Wang, Guiping Zhao, Maiqing Zheng and Jie Wen

    Citation: BMC Genomics 2021 22:8

    Content type: Research article

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  15. Bovine frontonasal dysplasias like arhinencephaly, synophthalmia, cyclopia and anophthalmia are sporadic congenital facial malformations. In this study, computed tomography, necropsy, histopathological examina...

    Authors: Marina Braun, Annika Lehmbecker, Deborah Eikelberg, Maren Hellige, Andreas Beineke, Julia Metzger and Ottmar Distl

    Citation: BMC Genomics 2021 22:1

    Content type: Research article

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  16. Porcine epidemic diarrhea virus (PEDV) is a causative agent of serious viral enteric disease in suckling pigs. Such diseases cause considerable economic losses in the global swine industry. Enhancing our knowl...

    Authors: Zhengzheng Hu, Yuchen Li, Heng Du, Junxiao Ren, Xianrui Zheng, Kejian Wei and Jianfeng Liu

    Citation: BMC Genomics 2020 21:891

    Content type: Research article

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  17. Voice disorders are a worldwide problem impacting human health, particularly for occupational voice users. Avoidance of surface dehydration is commonly prescribed as a protective factor against the development...

    Authors: Taylor W. Bailey, Andrea Pires dos Santos, Naila Cannes do Nascimento, Shaojun Xie, Jyothi Thimmapuram, M. Preeti Sivasankar and Abigail Cox

    Citation: BMC Genomics 2020 21:888

    Content type: Research article

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  18. The electrosensory ampullary organs (AOs) and mechanosensory neuromasts (NMs) found in sturgeon and some other non-neopterygian fish or amphibians are both originated from lateral line placodes. However, these...

    Authors: Jian Wang, Chengcheng Lu, Yifan Zhao, Zhijiao Tang, Jiakun Song and Chunxin Fan

    Citation: BMC Genomics 2020 21:875

    Content type: Research article

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  19. Distichiasis, an ocular disorder in which aberrant cilia (eyelashes) grow from the opening of the Meibomian glands of the eyelid, has been reported in Friesian horses. These misplaced cilia can cause discomfor...

    Authors: E. A. Hisey, H. Hermans, Z. T. Lounsberry, F. Avila, R. A. Grahn, K. E. Knickelbein, S. A. Duward-Akhurst, M. E. McCue, T.S. Kalbfleisch, M. E. Lassaline, W. Back and R. R. Bellone

    Citation: BMC Genomics 2020 21:848

    Content type: Research article

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  20. Post-traumatic osteoarthritis (PTOA) is a common and significant problem in equine athletes. It is a disease of the entire joint, with the synovium thought to be a key player in disease onset and progression d...

    Authors: Annette M. McCoy, Ann M. Kemper, Mary K. Boyce, Murray P. Brown and Troy N. Trumble

    Citation: BMC Genomics 2020 21:843

    Content type: Research article

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  21. Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. We investigated CNVs in the domestic goat (Capra hircus)...

    Authors: Jiazhong Guo, Jie Zhong, George E. Liu, Liu Yang, Li Li, Guangling Chen, Tianzeng Song and Hongping Zhang

    Citation: BMC Genomics 2020 21:840

    Content type: Research article

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  22. The scale degeneration is thought to be related to the adaptation to the extreme environment with cold climate and high-altitude in schizothoracine fishes. Gymnocypris eckloni, a schizothoracine fish living in pl...

    Authors: Xiu Feng, Yintao Jia, Ren Zhu, Kemao Li, Zhongzhi Guan and Yifeng Chen

    Citation: BMC Genomics 2020 21:835

    Content type: Research article

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  23. Primary hypoadrenocorticism (or Addison’s disease, AD) is an autoimmune disease that results in destruction of the adrenal cortex and consequent adrenal insufficiency. The disease has been described in purebre...

    Authors: Liza C. Gershony, Janelle M. Belanger, Marjo K. Hytönen, Hannes Lohi, Thomas R. Famula and Anita M. Oberbauer

    Citation: BMC Genomics 2020 21:833

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2020 21:898

  24. Long term preservation of living ovarian tissues is a critical approach in human reproductive medicine as well as in the conservation of rare animal genotypes. Compared to single cell preservation, optimizatio...

    Authors: Olga Amelkina and Pierre Comizzoli

    Citation: BMC Genomics 2020 21:828

    Content type: Research article

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  25. Periparturient cows release fatty acid reserves from adipose tissue (AT) through lipolysis in response to the negative energy balance induced by physiological changes related to parturition and the onset of la...

    Authors: David Salcedo-Tacuma, Jair Parales-Giron, Crystal Prom, Miguel Chirivi, Juliana Laguna, Adam L. Lock and G. Andres Contreras

    Citation: BMC Genomics 2020 21:824

    Content type: Research article

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  26. Salmonella enterica serovar Enteritidis (SE) is one of the pathogenic bacteria, which affects poultry production and poses a severe threat to public health. Chicken meat and eggs are the main sources of human sal...

    Authors: Yuanmei Wang, Liying Liu, Min Li, Lili Lin, Pengcheng Su, Hui Tang, Xinzhong Fan and Xianyao Li

    Citation: BMC Genomics 2020 21:814

    Content type: Research article

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  27. Hundreds of genomes and transcriptomes of fish species have been sequenced in recent years. However, fish scholarship currently lacks a comprehensive, integrated, and up-to-date collection of fish genomic data.

    Authors: Liandong Yang, Zetan Xu, Honghui Zeng, Ning Sun, Baosheng Wu, Cheng Wang, Jing Bo, Lin Li, Yang Dong and Shunping He

    Citation: BMC Genomics 2020 21:801

    Content type: Database

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  28. Sperm miRNAs were reported to regulate spermatogenesis and early embryonic development in some mammals including bovine. The dairy cattle breeding industry now tends to collect semen from younger bulls under h...

    Authors: Chongyang Wu, Patrick Blondin, Christian Vigneault, Rémi Labrecque and Marc-André Sirard

    Citation: BMC Genomics 2020 21:798

    Content type: Research article

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  29. Mitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes. We present here an approach to sequence whole mitochond...

    Authors: Sophie Dhorne-Pollet, Eric Barrey and Nicolas Pollet

    Citation: BMC Genomics 2020 21:785

    Content type: Methodology article

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  30. Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation at the transcriptional and post-transcriptional levels. LncRNAs are belonging to a large class of transcripts with ≥200 nt in length which d...

    Authors: Serafino M. A. Augustino, Qinglei Xu, Xueqin Liu, Siyuan Mi, Liangyu Shi, Yibing Liu, Hui Wen, Di Wang, Lei Liu, Qin Zhang and Ying Yu

    Citation: BMC Genomics 2020 21:780

    Content type: Research article

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  31. Hibernation in an appropriate environment not only is important for the survival of hibernators in winter, but also is crucial for breeding in the following season for many hibernating species. However, the ge...

    Authors: Jian-Qing Lin, Jun Yu, Hua Jiang, Yi Zhang, Qiu-Hong Wan and Sheng-Guo Fang

    Citation: BMC Genomics 2020 21:774

    Content type: Research article

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  32. Imputation accuracy among other things depends on the size of the reference panel, the marker’s minor allele frequency (MAF), and the correct placement of single nucleotide polymorphism (SNP) on the reference ...

    Authors: Isis da Costa Hermisdorff, Raphael Bermal Costa, Lucia Galvão de Albuquerque, Hubert Pausch and Naveen Kumar Kadri

    Citation: BMC Genomics 2020 21:772

    Content type: Research article

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  33. Deep neural networks (DNN) are a particular case of artificial neural networks (ANN) composed by multiple hidden layers, and have recently gained attention in genome-enabled prediction of complex traits. Yet, ...

    Authors: Tiago L. Passafaro, Fernando B. Lopes, João R. R. Dórea, Mark Craven, Vivian Breen, Rachel J. Hawken and Guilherme J. M. Rosa

    Citation: BMC Genomics 2020 21:771

    Content type: Research article

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  34. Lower eggshell quality in the late laying period leads to economic loss. It is a major threat to the quality and safety of egg products. Age-related variations in ultrastructure were thought to induce this det...

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

    Citation: BMC Genomics 2020 21:770

    Content type: Research article

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  35. A pregnant gilt infected with porcine reproductive and respiratory syndrome virus (PRRSV) can transmit the virus to her fetuses across the maternal-fetal-interface resulting in varying disease outcomes. Howeve...

    Authors: Angelica Van Goor, Alex Pasternak, Kristen Walker, Linjun Hong, Carolina Malgarin, Daniel J. MacPhee, John C. S. Harding and Joan K. Lunney

    Citation: BMC Genomics 2020 21:763

    Content type: Research article

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  36. The development of skeletal muscle is closely related to the efficiency of meat production and meat quality. Chicken skeletal muscle development depends on myogenesis and adipogenesis and occurs in two phases—...

    Authors: Jinghui Li, Siyuan Xing, Guiping Zhao, Maiqing Zheng, Xinting Yang, Jiahong Sun, Jie Wen and Ranran Liu

    Citation: BMC Genomics 2020 21:752

    Content type: Research article

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  37. The production of foie gras involves different metabolic pathways in the liver of overfed ducks such as lipid synthesis and carbohydrates catabolism, but the establishment of these pathways has not yet been de...

    Authors: William Massimino, Stéphane Davail, Aurélie Secula, Charlotte Andrieux, Marie-Dominique Bernadet, Tracy Pioche, Karine Ricaud, Karine Gontier, Mireille Morisson, Anne Collin, Stéphane Panserat and Marianne Houssier

    Citation: BMC Genomics 2020 21:742

    Content type: Research article

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  38. Tropical stenothermal fish exhibit special tolerance and response to cold stress. However current knowledge of the molecular mechanisms response to cold stress in aquatic ectotherms is largely drawn from euryt...

    Authors: Lili Liu, Rong Zhang, Xiaowen Wang, Hua Zhu and Zhaohui Tian

    Citation: BMC Genomics 2020 21:737

    Content type: Research article

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  39. Domestic yaks play an indispensable role in sustaining the livelihood of Tibetans and other ethnic groups on the Qinghai-Tibetan Plateau (QTP), by providing milk and meat. They have evolved numerous physiologi...

    Authors: Jinwei Xin, Zhixin Chai, Chengfu Zhang, Qiang Zhang, Yong Zhu, Hanwen Cao, Cidan Yangji, Xiaoying Chen, Hui Jiang, Jincheng Zhong and Qiumei Ji

    Citation: BMC Genomics 2020 21:731

    Content type: Research article

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  40. Infectious bursal disease virus (IBDV) causes acute, highly contagious, immunosuppressive, and lethal infectious disease in young chickens and mainly infects the bursa of Fabricius (BF). To investigate interac...

    Authors: Xuewei Huang, Junyan Zhang, Zengsu Liu, Meng Wang, Xiaolong Fan, Li Wang, Han Zhou, Yanping Jiang, Wen Cui, Xinyuan Qiao, Yigang Xu, Yijing Li and Lijie Tang

    Citation: BMC Genomics 2020 21:724

    Content type: Research article

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  41. Mutations in the mitochondrial genome have been implicated in mitochondrial disease, often characterized by impaired cellular energy metabolism. Cellular energy metabolism in mitochondria involves mitochondria...

    Authors: Jigme Dorji, Christy J. Vander Jagt, Josie B. Garner, Leah C. Marett, Brett A. Mason, Coralie M. Reich, Ruidong Xiang, Emily L. Clark, Benjamin G. Cocks, Amanda J. Chamberlain, Iona M. MacLeod and Hans D. Daetwyler

    Citation: BMC Genomics 2020 21:720

    Content type: Research article

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  42. In China, although buffaloes are abundant, beef is mainly obtained from cattle, and this preference is mainly attributed to the low intramuscular fat (IMF) content of buffalo. Genetic factors are an important ...

    Authors: Jieping Huang, Xue Feng, Ruirui Zhu, Duo Guo, Yutong Wei, Xiaodan Cao, Yun Ma and Deshun Shi

    Citation: BMC Genomics 2020 21:710

    Content type: Research article

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  43. Intrauterine growth restriction (IUGR) remains a major problem associated with swine production. Thus, understanding the physiological changes of postnatal IUGR piglets would aid in improving growth performanc...

    Authors: Hongmei Gao, Longchao Zhang, Ligang Wang, Xin Liu, Xinhua Hou, Fuping Zhao, Hua Yan and Lixian Wang

    Citation: BMC Genomics 2020 21:701

    Content type: Research article

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  44. A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is ...

    Authors: Guosong Zhang, Jie Li, Jiajia Zhang, Xia Liang, Tao Wang and Shaowu Yin

    Citation: BMC Genomics 2020 21:700

    Content type: Research article

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  45. Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This ...

    Authors: Michelle M. Halstead, Colin Kern, Perot Saelao, Ying Wang, Ganrea Chanthavixay, Juan F. Medrano, Alison L. Van Eenennaam, Ian Korf, Christopher K. Tuggle, Catherine W. Ernst, Huaijun Zhou and Pablo J. Ross

    Citation: BMC Genomics 2020 21:698

    Content type: Research article

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  46. Müllerian ducts are paired embryonic tubes that give rise to the female reproductive tract in vertebrates. Many disorders of female reproduction can be attributed to anomalies of Müllerian duct development. Ho...

    Authors: Zahida Yesmin Roly, Rasoul Godini, Martin A. Estermann, Andrew T. Major, Roger Pocock and Craig A. Smith

    Citation: BMC Genomics 2020 21:688

    Content type: Research article

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  47. Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. RNA-Seq analyses from the liver of these different genetic types fed ad libitum...

    Authors: Xi Liu, Frédéric Hérault, Christian Diot and Erwan Corre

    Citation: BMC Genomics 2020 21:687

    Content type: Research article

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  48. MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contri...

    Authors: Haisheng Ding, Min Liu, Changfan Zhou, Xiangbin You, Tao Su, Youbing Yang and Dequan Xu

    Citation: BMC Genomics 2020 21:686

    Content type: Research article

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  49. Coexpression network analysis is a powerful tool to reveal transcriptional regulatory mechanisms, identify transcription factors, and discover gene functions. It can also be used to investigate changes in coex...

    Authors: Lihe Liu, Rocío Amorín, Philipe Moriel, Nicolás DiLorenzo, Phillip A. Lancaster and Francisco Peñagaricano

    Citation: BMC Genomics 2020 21:684

    Content type: Research article

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