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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 21

  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. Long non-coding RNA (lncRNA) as an important regulator has been demonstrated playing an indispensable role in the biological process of hair follicles (HFs) growth. However, their function and expression profi...

    Authors: Xiaolan Zhang, Qi Bao, Congjun Jia, Chen Li, Yongfang Chang, Xiaoyun Wu, Chunnian Liang, Pengjia Bao and Ping Yan

    Citation: BMC Genomics 2020 21:681

    Content type: Research article

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  15. The clupeoid fishes are ecologically and commercially important fish species worldwide that exhibit a high level of population fluctuation, accompanied by alteration of reproductive traits. However, knowledge ...

    Authors: Mitsuo Nyuji, Yuki Hongo, Michio Yoneda and Masahiro Nakamura

    Citation: BMC Genomics 2020 21:668

    Content type: Research article

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  16. Meat quality is a complex trait affected by genotypic and environmental factors. In a previous study, it was found that feedstuffs have various effects on the growth rate and meat quality of lambs. However, th...

    Authors: Jianghong Wu, Ding Yang, Husile Gong, Yunxia Qi, Hailian Sun, Yongbin Liu, Yahong Liu and Xiao Qiu

    Citation: BMC Genomics 2020 21:660

    Content type: Research article

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  17. Disease resilience is the ability to maintain performance under pathogen exposure but is difficult to select for because breeding populations are raised under high health. Selection for resilience requires a t...

    Authors: Yulu Chen, Laura E. Tibbs Cortes, Carolyn Ashley, Austin M. Putz, Kyu-Sang Lim, Michael K. Dyck, Frederic Fortin, Graham S. Plastow, Jack C. M. Dekkers and John C. S. Harding

    Citation: BMC Genomics 2020 21:648

    Content type: Research article

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  18. High egg producing hens (HEPH) show increased hypothalamic and pituitary gene expression related to hypothalamo-pituitary-gonadal (HPG) axis stimulation as well as increased in vitro responsiveness to gonadotropi...

    Authors: Kristen Brady, Hsiao-Ching Liu, Julie A. Hicks, Julie A. Long and Tom E. Porter

    Citation: BMC Genomics 2020 21:647

    Content type: Research article

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  19. The Pacific bluefin tuna (Thunnus orientalis) is a regionally endothermic fish that maintains temperatures in their swimming musculature, eyes, brain and viscera above that of the ambient water. Within their skel...

    Authors: Adam Ciezarek, Luke Gardner, Vincent Savolainen and Barbara Block

    Citation: BMC Genomics 2020 21:642

    Content type: Research article

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  20. Chilo suppressalis is a widespread rice pest that poses a major threat to food security in China. This pest can develop resistance to Cry toxins from Bacillus thuringiensis (Bt), threatening the sustainable use o...

    Authors: Geng Chen, Yanhui Wang, Yanmin Liu, Fajun Chen and Lanzhi Han

    Citation: BMC Genomics 2020 21:634

    Content type: Research article

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  21. Seasonal weight loss (SWL) is a very important limitation to the production of ruminants in the Mediterranean and Tropical regions. In these areas, long dry seasons lead to poor pastures with low nutritional v...

    Authors: José Ricardo Parreira, Lorenzo Enrique Hernández-Castellano, Anastasio Argüello, Juan Capote, Noemí Castro, Susana de Sousa Araújo and André Martinho de Almeida

    Citation: BMC Genomics 2020 21:629

    Content type: Research article

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  22. The environmental impact of pig farming need to be reduced, with phosphorus (P) being of particular interest. Specified dietary regimens and management systems contribute to meet environmental concerns and red...

    Authors: Aisanjiang Wubuli, Christian Gerlinger, Henry Reyer, Michael Oster, Eduard Muráni, Nares Trakooljul, Siriluck Ponsuksili, Petra Wolf and Klaus Wimmers

    Citation: BMC Genomics 2020 21:626

    Content type: Research article

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  23. The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the developm...

    Authors: Elisa Peripolli, Christian Reimer, Ngoc-Thuy Ha, Johannes Geibel, Marco Antonio Machado, João Cláudio do Carmo Panetto, Andréa Alves do Egito, Fernando Baldi, Henner Simianer and Marcos Vinícius Gualberto Barbosa da Silva

    Citation: BMC Genomics 2020 21:624

    Content type: Research article

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  24. Phenotypic performances of livestock animals decline with increasing levels of inbreeding, however, the noticeable decline known as inbreeding depression, may not be due only to the total level of inbreeding, ...

    Authors: Bayode O. Makanjuola, Christian Maltecca, Filippo Miglior, Flavio S. Schenkel and Christine F. Baes

    Citation: BMC Genomics 2020 21:605

    Content type: Research article

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  25. Feather pecking (FP) in laying hens reduces animal welfare and leads to economic losses for the layer industry. FP is considered a heritable condition that is influenced by dysregulation of neurotransmitter ho...

    Authors: Clemens Falker-Gieske, Andrea Mott, Siegfried Preuß, Sören Franzenburg, Werner Bessei, Jörn Bennewitz and Jens Tetens

    Citation: BMC Genomics 2020 21:595

    Content type: Research article

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  26. The Quaternary had worldwide consequences in forming the contemporary diversity of many populations, species and communities, which is characterized by marked climatic oscillations between glacial and intergla...

    Authors: Kai Song, Bin Gao, Peter Halvarsson, Yun Fang, Ying-Xin Jiang, Yue-Hua Sun and Jacob Höglund

    Citation: BMC Genomics 2020 21:581

    Content type: Research article

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  27. Tissue-specific fat deposition is regulated by a series of complex regulatory mechanisms. Reports indicate that epigenetic regulators, such as circular RNAs (circRNAs), are crucial in diseases progression, ani...

    Authors: Meng Zhang, Yu Han, Yanhui Zhai, Xiangfei Ma, Xinglan An, Sheng Zhang and Ziyi Li

    Citation: BMC Genomics 2020 21:594

    Content type: Research article

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  28. The DGAT1 gene encodes an enzyme responsible for catalysing the terminal reaction in mammary triglyceride synthesis, and underpins a well-known pleiotropic quantitative trait locus (QTL) with a large influence on...

    Authors: Tania Fink, Thomas J. Lopdell, Kathryn Tiplady, Renee Handley, Thomas J. J. Johnson, Richard J. Spelman, Stephen R. Davis, Russell G. Snell and Mathew D. Littlejohn

    Citation: BMC Genomics 2020 21:591

    Content type: Research article

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  29. A balanced constitutional reciprocal translocation (RT) is a mutual exchange of terminal segments of two non-homologous chromosomes without any loss or gain of DNA in germline cells. Carriers of balanced RTs a...

    Authors: Aniek C. Bouwman, Martijn F. L. Derks, Marleen L. W. J. Broekhuijse, Barbara Harlizius and Roel F. Veerkamp

    Citation: BMC Genomics 2020 21:576

    Content type: Research article

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  30. Rainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The object...

    Authors: J. D’Ambrosio, R. Morvezen, S. Brard-Fudulea, A. Bestin, A. Acin Perez, D. Guéméné, C. Poncet, P. Haffray, M. Dupont-Nivet and F. Phocas

    Citation: BMC Genomics 2020 21:558

    Content type: Research article

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  31. Goldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a mal...

    Authors: Ming Wen, Romain Feron, Qiaowei Pan, Justine Guguin, Elodie Jouanno, Amaury Herpin, Christophe Klopp, Cedric Cabau, Margot Zahm, Hugues Parrinello, Laurent Journot, Shawn M. Burgess, Yoshihiro Omori, John H. Postlethwait, Manfred Schartl and Yann Guiguen

    Citation: BMC Genomics 2020 21:552

    Content type: Research article

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  32. Genomic selection has been successfully implemented in many livestock and crop species. The genomic best linear unbiased predictor (GBLUP) approach, assigning equal variance to all SNP effects, is one of the r...

    Authors: José Luis Gualdrón Duarte, Ann-Stephan Gori, Xavier Hubin, Daniela Lourenco, Carole Charlier, Ignacy Misztal and Tom Druet

    Citation: BMC Genomics 2020 21:545

    Content type: Research article

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  33. The South African claw-toed frog, Xenopus laevis, is uniquely suited for studying differences between regenerative and non-regenerative responses to CNS injury within the same organism, because some CNS neurons (...

    Authors: Jamie L. Belrose, Aparna Prasad, Morgan A. Sammons, Kurt M. Gibbs and Ben G. Szaro

    Citation: BMC Genomics 2020 21:540

    Content type: Research article

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  34. Closely related species of the carp family (Cyprinidae) have evolved distinctive abilities to survive under cold stress, but molecular mechanisms underlying the generation of cold resistance remain largely unknow...

    Authors: Guodong Ge, Yong Long, Lianyu Shi, Jing Ren, Junjun Yan, Chitao Li, Qing Li and Zongbin Cui

    Citation: BMC Genomics 2020 21:539

    Content type: Research article

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  35. Genetic improvement of fillet quality attributes is a priority of the aquaculture industry. Muscle composition impacts quality attributes such as flavor, appearance, texture, and juiciness. Fat and moisture ma...

    Authors: Ali Ali, Rafet Al-Tobasei, Daniela Lourenco, Tim Leeds, Brett Kenney and Mohamed Salem

    Citation: BMC Genomics 2020 21:529

    Content type: Research article

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  36. Avian eggs have a proteinaceous cuticle. The quantity of cuticle varies and the deposition of a good cuticle in the uterus (Shell-gland) prevents transmission of bacteria to the egg contents.

    Authors: Sandra Poyatos Pertiñez, Peter W. Wilson, Wiebke Icken, David Cavero, Maureen M. Bain, Anita C. Jones and Ian C. Dunn

    Citation: BMC Genomics 2020 21:516

    Content type: Research article

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  37. Aim of the present study was first to identify genetic variants associated with egg number (EN) in female broilers, second to describe the mode of their gene action (additive and/or dominant) and third to prov...

    Authors: Eirini Tarsani, Andreas Kranis, Gerasimos Maniatis, Santiago Avendano, Ariadne L. Hager-Theodorides and Antonios Kominakis

    Citation: BMC Genomics 2020 21:512

    Content type: Research article

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  38. Intensive selection for growth rate (GR) in broiler chickens carries negative after-effects, such as aberrations in skeletal development and the immune system, heart failure, and deterioration of meat quality....

    Authors: Katarzyna Piórkowska, Kacper Żukowski, Katarzyna Połtowicz, Joanna Nowak, Katarzyna Ropka-Molik, Natalia Derebecka, Joanna Wesoły and Dorota Wojtysiak

    Citation: BMC Genomics 2020 21:509

    Content type: Research article

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  39. The incidence of poor semen quality and sub-fertility/infertility is higher in crossbred as compared to Zebu males. Several attempts have been made to understand the possible reasons for higher incidence of fe...

    Authors: Kamaraj Elango, Arumugam Kumaresan, Ankur Sharma, Pradeep Nag, Mani Arul Prakash, Manish Kumar Sinha, Ayyasamy Manimaran, Ebenezer Samuel King John Peter, Sakthivel Jeyakumar, Sellappan Selvaraju, Kerekoppa P. Ramesha and Tirtha K. Datta

    Citation: BMC Genomics 2020 21:502

    Content type: Research article

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  40. In quantitative real-time polymerase chain reaction (qRT-PCR) experiments, accurate and reliable target gene expression results are dependent on optimal amplification of house-keeping genes (HKGs). RNA-seq tec...

    Authors: Jipan Zhang, Chengchen Deng, Jialu Li and Yongju Zhao

    Citation: BMC Genomics 2020 21:493

    Content type: Research article

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  41. Ketosis is a common metabolic disease during the transition period in dairy cattle, resulting in long-term economic loss to the dairy industry worldwide. While genetic selection of resistance to ketosis has be...

    Authors: Ze Yan, Hetian Huang, Ellen Freebern, Daniel J. A. Santos, Dongmei Dai, Jingfang Si, Chong Ma, Jie Cao, Gang Guo, George E. Liu, Li Ma, Lingzhao Fang and Yi Zhang

    Citation: BMC Genomics 2020 21:489

    Content type: Research article

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  42. Follicle selection in chickens refers to the process of selecting one follicle from a group of small yellow follicles (SY, 6–8 mm in diameter) for development into 12–15 mm hierarchical follicles (usually F6 f...

    Authors: Qiuyue Chen, Yiya Wang, Zemin Liu, Xiaoli Guo, Yi Sun, Li Kang and Yunliang Jiang

    Citation: BMC Genomics 2020 21:486

    Content type: Research article

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  43. T zone lymphoma (TZL), a histologic variant of peripheral T cell lymphoma, represents about 12% of all canine lymphomas. Golden Retrievers appear predisposed, representing over 40% of TZL cases. Prior research...

    Authors: Julia D. Labadie, Ingegerd Elvers, Heather Spencer Feigelson, Sheryl Magzamen, Janna Yoshimoto, Jeremy Dossey, Robert Burnett and Anne C. Avery

    Citation: BMC Genomics 2020 21:464

    Content type: Research article

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  44. Cashmere goat is known for its precious undercoat. Being photoperiod-dictated, cashmere growth has been studied focusing mainly on hair follicle cycle phases (anagen, catagen and telogen). An accurate molecula...

    Authors: Cristina Nocelli, Katia Cappelli, Stefano Capomaccio, Luisa Pascucci, Francesca Mercati, Irene Pazzaglia, Samanta Mecocci, Marco Antonini and Carlo Renieri

    Citation: BMC Genomics 2020 21:458

    Content type: Research article

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  45. The gonad is the major factor affecting animal reproduction. The regulatory mechanism of the expression of protein-coding genes involved in reproduction still remains to be elucidated. Increasing evidence has ...

    Authors: Xiao Ma, Shuangshuang Cen, Luming Wang, Chao Zhang, Limin Wu, Xue Tian, Qisheng Wu, Xuejun Li and Xiaoqing Wang

    Citation: BMC Genomics 2020 21:443

    Content type: Research article

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  46. In the past several years, the use of resistant starch (RS) as prebiotic has extensively been studied in pigs, and this mostly in the critical period around weaning. RS is believed to exert beneficial effects ...

    Authors: Martine Schroyen, Julie Leblois, Julie Uerlings, Bing Li, Ester Arévalo Sureda, Sébastien Massart, José Wavreille, Jérôme Bindelle and Nadia Everaert

    Citation: BMC Genomics 2020 21:439

    Content type: Research article

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  47. Sex-related genes play a crucial role in gonadal differentiation into testes or ovaries. However, the genetic control of gonadal differentiation in Muscovy ducks remains unknown. Therefore, the objective of ou...

    Authors: Ding-Ping Bai, Yue Chen, Yu-Qiong Hu, Wen-Feng He, Yu-Zhu Shi, Qin-Ming Fan, Ru-Tang Luo and Ang Li

    Citation: BMC Genomics 2020 21:438

    Content type: Research article

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  48. During goat embryonic morphogenesis and postnatal initiation of hair follicle (HF) regeneration, dermal papilla (DP) cells play a vital role in hair formation. Growing evidence shows that microRNAs (miRNAs) pa...

    Authors: Yuelang Zhang, Sizhe Xia, Tianci Wang, Shanhe Wang, Dan Yuan, Fang Li and Xin Wang

    Citation: BMC Genomics 2020 21:430

    Content type: Research article

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  49. Vespa velutina, one of the most aggressive and fearful wasps in China, can cause grievous allergies and toxic reactions, leading to organ failure and even death. However, there is little evidence on molecular dat...

    Authors: Junjie Tan, Wenbo Wang, Fan Wu, Yunming Li and Quanshui Fan

    Citation: BMC Genomics 2020 21:427

    Content type: Research article

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  50. In recent years, increased attention has been focused on breast muscle yield and meat quality in poultry production. Supplementation with nicotinamide and butyrate sodium can improve the meat quality of broile...

    Authors: Yuqin Wu, Youli Wang, Dafei Yin, Tahir Mahmood and Jianmin Yuan

    Citation: BMC Genomics 2020 21:412

    Content type: Research article

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