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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. Cryopreservation induces transcriptomic and epigenetic modifications that strongly impairs sperm quality and function, and thus decrease reproductive performance. N6-methyladenosine (m6A) RNA methylation varies i...

    Authors: Ziyue Qin, Wencan Wang, Malik Ahsan Ali, Yihan Wang, Yan Zhang, Ming Zhang, Guangbin Zhou, Jian-dong Yang and Changjun Zeng

    Citation: BMC Genomics 2021 22:588

    Content type: Research article

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  2. Our previous genome-wide association study (GWAS) on milk fatty acid traits in Chinese Holstein cows revealed, the SNP, BTB-01556197, was significantly associated with C10:0 at genome-wide level (P = 0.0239). It ...

    Authors: Mingyue Cao, Lijun Shi, Peng Peng, Bo Han, Lin Liu, Xiaoqing Lv, Zhu Ma, Shengli Zhang and Dongxiao Sun

    Citation: BMC Genomics 2021 22:575

    Content type: Research article

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  3. Chinese indigenous rabbits have distinct characteristics, such as roughage resistance, stress resistance and environmental adaptability, which are of great significance to the sustainable development of the ra...

    Authors: Chenmiao Liu, Shuhui Wang, Xianggui Dong, Jiping Zhao, Xiangyang Ye, Ruiguang Gong and Zhanjun Ren

    Citation: BMC Genomics 2021 22:573

    Content type: Research article

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  4. Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our first objective was to perform, for the first time, a genome-w...

    Authors: Neža Pogorevc, Mojca Simčič, Negar Khayatzadeh, Johann Sölkner, Beate Berger, Danijela Bojkovski, Minja Zorc, Peter Dovč, Ivica Medugorac and Simon Horvat

    Citation: BMC Genomics 2021 22:546

    Content type: Research article

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  5. Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), estimating these ef...

    Authors: Pattarapol Sumreddee, El Hamidi Hay, Sajjad Toghiani, Andrew Roberts, Samuel E. Aggrey and Romdhane Rekaya

    Citation: BMC Genomics 2021 22:538

    Content type: Methodology article

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  6. Genetic improvement for disease resilience is anticipated to be a practical method to improve efficiency and profitability of the pig industry, as resilient pigs maintain a relatively undepressed level of perf...

    Authors: Xuechun Bai, Tianfu Yang, Austin M. Putz, Zhiquan Wang, Changxi Li, Frédéric Fortin, John C. S. Harding, Michael K. Dyck, Jack C. M. Dekkers, Catherine J. Field and Graham S. Plastow

    Citation: BMC Genomics 2021 22:535

    Content type: Research article

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  7. Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but...

    Authors: Cuili Pan, Zhaoxiong Lei, Shuzhe Wang, Xingping Wang, Dawei Wei, Xiaoyan Cai, Zhuoma Luoreng, Lei Wang and Yun Ma

    Citation: BMC Genomics 2021 22:532

    Content type: Research article

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  8. The all-electronic Single Molecule Break Junction (SMBJ) method is an emerging alternative to traditional polymerase chain reaction (PCR) techniques for genetic sequencing and identification. Existing work ind...

    Authors: Yiren Wang, Mashari Alangari, Joshua Hihath, Arindam K. Das and M. P. Anantram

    Citation: BMC Genomics 2021 22:525

    Content type: Methodology article

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  9. Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of non-additive geneti...

    Authors: Akio Onogi, Toshio Watanabe, Atsushi Ogino, Kazuhito Kurogi and Kenji Togashi

    Citation: BMC Genomics 2021 22:512

    Content type: Research article

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  10. Improving feed efficiency (FE) is an important goal due to its economic and environmental significance for farm animal production. The FE phenotype is complex and based on the measurements of the individual fe...

    Authors: Farouk Messad, Isabelle Louveau, David Renaudeau, Hélène Gilbert and Florence Gondret

    Citation: BMC Genomics 2021 22:501

    Content type: Research article

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  11. The accumulation of carotenoids in adipose tissue leading to yellow fat is, in sheep, a heritable recessive trait that can be attributed to a nonsense mutation in the beta-carotene oxygenase 2 (BCO2) gene. Howeve...

    Authors: Matthew Kent, Michel Moser, Inger Anne Boman, Kristine Lindtveit, Mariann Árnyasi, Kristil Kindem Sundsaasen and Dag Inge Våge

    Citation: BMC Genomics 2021 22:492

    Content type: Research article

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  12. Metabolic stress, as negative energy balance on one hand or obesity on the other hand can lead to increased levels of free fatty acids in the plasma and follicular fluid of animals and humans. In an earlier st...

    Authors: Vengala Rao Yenuganti, Dirk Koczan and Jens Vanselow

    Citation: BMC Genomics 2021 22:486

    Content type: Research article

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  13. Calcium (Ca) and phosphorus (P) are essential nutrients that are linked to a large array of biological processes. Disturbances in Ca and P homeostasis in chickens are associated with a decline in growth and eg...

    Authors: Henry Reyer, Michael Oster, Siriluck Ponsuksili, Nares Trakooljul, Adewunmi O. Omotoso, Muhammad A. Iqbal, Eduard Muráni, Vera Sommerfeld, Markus Rodehutscord and Klaus Wimmers

    Citation: BMC Genomics 2021 22:485

    Content type: Research article

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  14. Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. Howeve...

    Authors: Jenni Harmoinen, Alina von Thaden, Jouni Aspi, Laura Kvist, Berardino Cocchiararo, Anne Jarausch, Andrea Gazzola, Teodora Sin, Hannes Lohi, Marjo K. Hytönen, Ilpo Kojola, Astrid Vik Stronen, Romolo Caniglia, Federica Mattucci, Marco Galaverni, Raquel Godinho…

    Citation: BMC Genomics 2021 22:473

    Content type: Research article

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  15. A number of studies have examined mRNA expression profiles of bovine endometrium at estrus and around the peri-implantation period of pregnancy. However, to date, these studies have been performed on the whole...

    Authors: Wiruntita Chankeaw, Sandra Lignier, Christophe Richard, Theodoros Ntallaris, Mariam Raliou, Yongzhi Guo, Damien Plassard, Claudia Bevilacqua, Olivier Sandra, Göran Andersson, Patrice Humblot and Gilles Charpigny

    Citation: BMC Genomics 2021 22:451

    Content type: Research article

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    The Research article to this article has been published in BMC Genomics 2021 22:450

  16. In post-partum dairy cows, the energy needs to satisfy high milk production induces a status of more or less pronounced Negative Energy Balance (NEB). NEB associated with fat mobilization impairs reproductive ...

    Authors: Wiruntita Chankeaw, Sandra Lignier, Christophe Richard, Theodoros Ntallaris, Mariam Raliou, Yongzhi Guo, Damien Plassard, Claudia Bevilacqua, Olivier Sandra, Göran Andersson, Patrice Humblot and Gilles Charpigny

    Citation: BMC Genomics 2021 22:450

    Content type: Research article

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    The Research article to this article has been published in BMC Genomics 2021 22:451

  17. Transcription is arrested in the late stage oocyte and therefore the maternal transcriptome stored in the oocyte provides nearly all the mRNA required for oocyte maturation, fertilization, and early cleavage o...

    Authors: Gregory M. Weber, Jill Birkett, Kyle Martin, Doug Dixon II, Guangtu Gao, Timothy D. Leeds, Roger L. Vallejo and Hao Ma

    Citation: BMC Genomics 2021 22:448

    Content type: Research article

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  18. Long non-coding RNAs (lncRNAs) structurally resemble mRNAs and exert crucial effects on host immune defense against pathogen infection. Japanese flounder (Paralichthys olivaceus) is an economically important mari...

    Authors: Xianhui Ning and Li Sun

    Citation: BMC Genomics 2021 22:447

    Content type: Research article

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  19. Estrogen plays an essential role in female development and reproductive function. In chickens, estrogen is critical for lipid metabolism in the liver. The regulatory molecular network of estrogen in chicken li...

    Authors: Junxiao Ren, Weihua Tian, Keren Jiang, Zhang Wang, Dandan Wang, Zhuanjian Li, Fengbin Yan, Yanbin Wang, Yadong Tian, Kepeng Ou, Hongjun Wang, Xiangtao Kang, Hong Li and Xiaojun Liu

    Citation: BMC Genomics 2021 22:428

    Content type: Research article

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  20. Tilapia is one of the most abundant species in aquaculture. Hypoxia is known to depress growth rate, but the genetic mechanism by which this occurs is unknown. In this study, two groups consisting of 3140 fish...

    Authors: Xiaofei Yu, Hendrik-Jan Megens, Samuel Bekele Mengistu, John W. M. Bastiaansen, Han A. Mulder, John A. H. Benzie, Martien A. M. Groenen and Hans Komen

    Citation: BMC Genomics 2021 22:426

    Content type: Research article

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  21. Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled...

    Authors: Wilson Nandolo, Gábor Mészáros, Maria Wurzinger, Liveness J. Banda, Timothy N. Gondwe, Henry A. Mulindwa, Helen N. Nakimbugwe, Emily L. Clark, M. Jennifer Woodward-Greene, Mei Liu, George E. Liu, Curtis P. Van Tassell, Benjamin D. Rosen and Johann Sölkner

    Citation: BMC Genomics 2021 22:398

    Content type: Research article

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  22. Subfertility is a major problem in modern horse breeding. Especially, mares without clinical signs of reproductive diseases, without known uterine pathogens and no evidence of inflammation but not becoming pre...

    Authors: Katharina S. Weber, Karen Wagener, Miguel Blanco, Stefan Bauersachs and Heinrich Bollwein

    Citation: BMC Genomics 2021 22:377

    Content type: Research article

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  23. Hybridization, which can quickly merge two or more divergent genomes and form new allopolyploids, is an important technique in fish genetic breeding. However, the merged subgenomes must adjust and coexist with...

    Authors: Wuhui Li, Shi Wang, Jie Hu, Chenchen Tang, Chang Wu, Junmei Liu, Li Ren, Chengfei Sun, Junjian Dong, Shaojun Liu and Xing Ye

    Citation: BMC Genomics 2021 22:362

    Content type: Research article

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  24. Brown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) is native to East Asia but has invaded many countries in the world. BMSB is a polyphagous insect pest and causes significant economic...

    Authors: Juncong Yan, Gábor Vétek, Chandan Pal, Jinping Zhang, Rania Gmati, Qing-Hai Fan, Disna N. Gunawardana, Allan Burne, Diane Anderson, Rebijith Kayattukandy Balan, Sherly George, Péter Farkas and Dongmei Li

    Citation: BMC Genomics 2021 22:355

    Content type: Research article

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  25. Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. W...

    Authors: Anna Carolina Fernandes, Vinicius Henrique da Silva, Carolina Purcell Goes, Gabriel Costa Monteiro Moreira, Thaís Fernanda Godoy, Adriana Mércia Guaratini Ibelli, Jane de Oliveira Peixoto, Maurício Egídio Cantão, Mônica Corrêa Ledur, Fernanda Marcondes de Rezende and Luiz Lehmann Coutinho

    Citation: BMC Genomics 2021 22:354

    Content type: Research article

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  26. Bovine TB (bTB), caused by infection with Mycobacterium bovis, is a major endemic disease affecting global cattle production. The key innate immune cell that first encounters the pathogen is the alveolar macropha...

    Authors: Thomas J. Hall, Michael P. Mullen, Gillian P. McHugo, Kate E. Killick, Siobhán C. Ring, Donagh P. Berry, Carolina N. Correia, John A. Browne, Stephen V. Gordon and David E. MacHugh

    Citation: BMC Genomics 2021 22:343

    Content type: Research article

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  27. In the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not...

    Authors: Yibin Qiu, Rongrong Ding, Zhanwei Zhuang, Jie Wu, Ming Yang, Shenping Zhou, Yong Ye, Qian Geng, Zheng Xu, Sixiu Huang, Gengyuan Cai, Zhenfang Wu and Jie Yang

    Citation: BMC Genomics 2021 22:332

    Content type: Research article

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  28. Circular RNA (circRNA), a novel class of non-coding RNA, has a closed-loop structure with important functions in skeletal muscle growth. The purpose of this study was to investigate the role of differentially ...

    Authors: Meng Li, Na Zhang, Wanfeng Zhang, Wei Hei, Chunbo Cai, Yang Yang, Chang Lu, Pengfei Gao, Xiaohong Guo, Guoqing Cao and Bugao Li

    Citation: BMC Genomics 2021 22:320

    Content type: Research article

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  29. The mechanism of egg formation in the oviduct of laying hens is tightly controlled; each segment of the oviduct contributes a unique component of the egg. Several genes/proteins are involved in the synthesis o...

    Authors: Nirvay Sah, Donna Lee Kuehu, Vedbar Singh Khadka, Youping Deng, Rajesh Jha, Sanjeev Wasti and Birendra Mishra

    Citation: BMC Genomics 2021 22:318

    Content type: Research article

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  30. In Iran, river buffalo is of great importance. It plays an important role in the economy of the Country, because its adaptation to harsh climate conditions and long productive lifespan permitting its farming a...

    Authors: Maria G. Strillacci, Hossein Moradi-Shahrbabak, Pourya Davoudi, Seyed Mohammad Ghoreishifar, Mahdi Mokhber, Anoar Jamai Masroure and Alessandro Bagnato

    Citation: BMC Genomics 2021 22:305

    Content type: Research article

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  31. Cytidine monophospho-n-acetylneuraminic acid hydroxylase (CMAH) gene associated with blood groups in cats encodes CMAH enzyme that converts Neu5Ac to Neu5Gc. Although variations in CMAH gene of pedigree cats have...

    Authors: Hüseyin Can, Sedef Erkunt Alak, Ahmet Efe Köseoğlu, Umut Şahar, Berna Bostanbaş, Serdar Baydarlı, Mert Döşkaya and Cemal Ün

    Citation: BMC Genomics 2021 22:282

    Content type: Research article

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  32. The back plays a vital role in horse locomotion, where the spine functions as a spring during the stride cycle. A complex interaction between the spine and the muscles of the back contribute to locomotion soun...

    Authors: Maria K. Rosengren, Heiðrún Sigurðardóttir, Susanne Eriksson, Rakan Naboulsi, Ahmad Jouni, Miguel Novoa-Bravo, Elsa Albertsdóttir, Þorvaldur Kristjánsson, Marie Rhodin, Åsa Viklund, Brandon D. Velie, Juan J. Negro, Marina Solé and Gabriella Lindgren

    Citation: BMC Genomics 2021 22:267

    Content type: Research article

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  33. Increases in ocean temperatures and in the frequency and severity of hypoxic events are expected with climate change, and may become a challenge for cultured Atlantic salmon and negatively affect their growth,...

    Authors: Anne Beemelmanns, Fábio S. Zanuzzo, Xi Xue, Rebeccah M. Sandrelli, Matthew L. Rise and A. Kurt Gamperl

    Citation: BMC Genomics 2021 22:261

    Content type: Research article

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  34. Callithrix marmosets are a relatively young primate radiation, whose phylogeny is not yet fully resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have b...

    Authors: Joanna Malukiewicz, Reed A. Cartwright, Nelson H. A. Curi, Jorge A. Dergam, Claudia S. Igayara, Silvia B. Moreira, Camila V. Molina, Patricia A. Nicola, Angela Noll, Marcello Passamani, Luiz C. M. Pereira, Alcides Pissinatti, Carlos R. Ruiz-Miranda, Daniel L. Silva, Anne C. Stone, Dietmar Zinner…

    Citation: BMC Genomics 2021 22:239

    Content type: Research article

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  35. The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradi...

    Authors: Matyas Cserhati

    Citation: BMC Genomics 2021 22:228

    Content type: Research article

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  36. Many recent studies have shown that miRNAs play important roles in the regulation of animal reproduction, including seasonal reproduction. The pineal gland is a crucial hub in the regulation of seasonal reprod...

    Authors: Ran Di, Qiu-Yue Liu, Shu-Hui Song, Dong-Mei Tian, Jian-Ning He, Ying Ge, Xiang-Yu Wang, Wen-Ping Hu, Joram-Mwashigadi Mwacharo, Zhang-Yuan Pan, Jian-Dong Wang, Qing Ma, Gui-Ling Cao, Hui-Hui Jin, Xiao-Jun Liang and Ming-Xing Chu

    Citation: BMC Genomics 2021 22:217

    Content type: Research article

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  37. Early-onset familial Alzheimer’s disease (EOfAD) is promoted by dominant mutations, enabling the study of Alzheimer’s disease (AD) pathogenic mechanisms through generation of EOfAD-like mutations in animal mod...

    Authors: Yang Dong, Morgan Newman, Stephen M. Pederson, Karissa Barthelson, Nhi Hin and Michael Lardelli

    Citation: BMC Genomics 2021 22:211

    Content type: Research article

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  38. Variation in locomotor capacity among animals often reflects adaptations to different environments. Despite evidence that physical performance is heritable, the molecular basis of locomotor performance and per...

    Authors: Valérie Ducret, Adam J. Richards, Mathieu Videlier, Thibault Scalvenzi, Karen A. Moore, Konrad Paszkiewicz, Camille Bonneaud, Nicolas Pollet and Anthony Herrel

    Citation: BMC Genomics 2021 22:204

    Content type: Research article

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  39. Tilapia (Oreochromis niloticus) cultures are frequently infected by Vibrio vulnificus, causing major economic losses to production units. Previously, tilapia expressing recombinant delta-5 desaturase and delta-6 ...

    Authors: Pin-Yang Tu, Shin-Jie Huang, Venugopal Rajanbabu, Jen-Leih Wu and Jyh-Yih Chen

    Citation: BMC Genomics 2021 22:200

    Content type: Research article

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  40. Oxford Nanopore Technologies’ instruments can sequence reads of great length. Long reads improve sequence assemblies by unambiguously spanning repetitive elements of the genome. Sequencing reads of significant...

    Authors: Trent M. Prall, Emma K. Neumann, Julie A. Karl, Cecilia G. Shortreed, David A. Baker, Hailey E. Bussan, Roger W. Wiseman and David H. O’Connor

    Citation: BMC Genomics 2021 22:182

    Content type: Methodology article

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  41. Long noncoding RNA (lncRNA) is highly associated with inflammatory response and virus-induced interferon production. By far the majority of studies have focused on the immune-related lncRNAs of mice and humans...

    Authors: Junxin Gao, Yu Pan, Yunfei Xu, Wenli Zhang, Lin Zhang, Xi Li, Zhijun Tian, Hongyan Chen and Yue Wang

    Citation: BMC Genomics 2021 22:177

    Content type: Research article

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  42. Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis, or Johne’s disease (JD), an incurable bovine disease. The evidence for susceptibility to MAP disease points to multiple ...

    Authors: Olivier Ariel, Jean-Simon Brouard, Andrew Marete, Filippo Miglior, Eveline Ibeagha-Awemu and Nathalie Bissonnette

    Citation: BMC Genomics 2021 22:162

    Content type: Research article

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  43. Maternal hormones, like testosterone, can strongly influence developing offspring, even generating long-term organizational effects on adult behavior; yet, the mechanisms facilitating these effects are still u...

    Authors: Alexandra B. Bentz, Chad E. Niederhuth, Laura L. Carruth and Kristen J. Navara

    Citation: BMC Genomics 2021 22:158

    Content type: Research article

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  44. Growth performance is significant in broiler production. In the growth process of broilers, gene expression varies at different growth stages. However, limited research has been conducted on the molecular mech...

    Authors: Genxi Zhang, Pengfei Wu, Kaizhi Zhou, Mingliang He, Xinchao Zhang, Cong Qiu, Tingting Li, Tao Zhang, Kaizhou Xie, Guojun Dai and Jinyu Wang

    Citation: BMC Genomics 2021 22:157

    Content type: Research article

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  45. China is the country with the most abundant swine genetic resources in the world. Through thousands of years of domestication and natural selection, most of pigs in China have developed unique genetic characte...

    Authors: Qing-bo Zhao, Favour Oluwapelumi Oyelami, Qamar Raza Qadri, Hao Sun, Zhong Xu, Qi-shan Wang and Yu-chun Pan

    Citation: BMC Genomics 2021 22:151

    Content type: Research article

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  46. Retinol (RO) and its active metabolite retinoic acid (RA) are major regulators of gene expression in vertebrates and influence various processes like organ development, cell differentiation, and immune respons...

    Authors: Clemens Falker-Gieske, Andrea Mott, Sören Franzenburg and Jens Tetens

    Citation: BMC Genomics 2021 22:146

    Content type: Research article

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  47. The giant panda (Ailuropoda melanoleuca) is a threatened endemic Chinese species and a flagship species of national and global conservation concern. Life history theory proposes that reproduction and immunity can...

    Authors: Haibo Shen, Caiwu Li, Ming He, Yan Huang, Jing Wang, Minglei Wang, Bisong Yue and Xiuyue Zhang

    Citation: BMC Genomics 2021 22:143

    Content type: Research article

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  48. The transcriptional changes around the time of embryonic genome activation in pre-implantation embryos indicate that this process is highly dynamic. In vitro produced porcine blastocysts are known to be less c...

    Authors: Vera A. van der Weijden, Meret Schmidhauser, Mayuko Kurome, Johannes Knubben, Veronika L. Flöter, Eckhard Wolf and Susanne E. Ulbrich

    Citation: BMC Genomics 2021 22:139

    Content type: Research article

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  49. Bone marrow mesenchymal stem cells are a potential resource for the clinical therapy of certain diseases. Canine, as a companion animal, living in the same space with human, is an ideal new model for human dis...

    Authors: Jinglu Wang, Pengxiu Dai, Tong Zou, Yangou Lv, Wen Zhao, Xinke Zhang and Yihua Zhang

    Citation: BMC Genomics 2021 22:134

    Content type: Research article

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  50. As economical traits, food habits domestication can reduce production cost in aquaculture. However, the molecular mechanism underlying food habits domestication has remained elusive. Mandarin fish (Siniperca chua...

    Authors: Shan He, Jun-Jie You, Xu-Fang Liang, Zhi-Lu Zhang and Yan-Peng Zhang

    Citation: BMC Genomics 2021 22:129

    Content type: Research article

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