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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 17

  2. Content type: Research article

    Cattle populations are highly amenable to the genetic mapping of male reproductive traits because longitudinal data on ejaculate quality and dense microarray-derived genotypes are available for thousands of ar...

    Authors: Terhi Iso-Touru, Christine Wurmser, Heli Venhoranta, Maya Hiltpold, Tujia Savolainen, Anu Sironen, Konrad Fischer, Krzysztof Flisikowski, Ruedi Fries, Alejandro Vicente-Carrillo, Manuel Alvarez-Rodriguez, Szabolcs Nagy, Mervi Mutikainen, Jaana Peippo, Juhani Taponen, Goutam Sahana…

    Citation: BMC Genomics 2019 20:286

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  3. Content type: Research article

    The interferon-induced transmembrane (IFITM) protein family comprises a class of restriction factors widely characterised in humans for their potent antiviral activity. Their biological activity is well docume...

    Authors: Irene Bassano, Swee Hoe Ong, Maximo Sanz-Hernandez, Michal Vinkler, Adebabay Kebede, Olivier Hanotte, Ebele Onuigbo, Mark Fife and Paul Kellam

    Citation: BMC Genomics 2019 20:272

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  4. Content type: Research article

    The Russian White is a gene pool breed, registered in 1953 after crossing White Leghorns with local populations and, for 50 years, selected for cold tolerance and high egg production (EL). The breed has great ...

    Authors: Andrei A. Kudinov, Natalia V. Dementieva, Olga V. Mitrofanova, Olga I. Stanishevskaya, Elena S. Fedorova, Tatiana A. Larkina, Arina I. Mishina, Kirill V. Plemyashov, Darren K. Griffin and Michael N. Romanov

    Citation: BMC Genomics 2019 20:270

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  5. Content type: Research article

    Fertility is among the most important economic traits in dairy cattle. Genomic prediction for cow fertility has received much attention in the last decade, while bull fertility has been largely overlooked. The...

    Authors: Juan Pablo Nani, Fernanda M. Rezende and Francisco Peñagaricano

    Citation: BMC Genomics 2019 20:258

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  6. Content type: Research article

    An unfavorable genetic correlation between milk production and fertility makes simultaneous improvement of milk production and fertility difficult in cattle breeding. Rapid genetic improvement in milk producti...

    Authors: Zexi Cai, Bernt Guldbrandtsen, Mogens Sandø Lund and Goutam Sahana

    Citation: BMC Genomics 2019 20:255

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  7. Content type: Research article

    Placental efficiency (PE) describes the relationship between placental and fetal weights (fetal wt/placental wt). Within litters, PE can vary drastically, resulting in similarly sized pigs associated with diff...

    Authors: Shanice K. Krombeen, Vijay Shankar, Rooksana E. Noorai, Christopher A. Saski, Julia L. Sharp, Matthew E. Wilson and Tiffany A. Wilmoth

    Citation: BMC Genomics 2019 20:254

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  9. Content type: Research article

    Marek’s disease virus (MDV) is an oncogenic herpesvirus that can cause T-cell lymphomas in chicken. Long noncoding RNA (lncRNA) is strongly associated with various cancers and many other diseases. In chickens,...

    Authors: Zhen You, Qinghe Zhang, Changjun Liu, Jiuzhou Song, Ning Yang and Ling Lian

    Citation: BMC Genomics 2019 20:245

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  10. Content type: Research article

    Lactation and associated metabolic stresses during the post-partum period have been shown to impair fertility in dairy cows. The oviduct plays key roles in embryo development and the establishment of pregnancy...

    Authors: Yann Locatelli, Niamh Forde, Helmut Blum, Alexander Graf, Benoît Piégu, Pascal Mermillod, Eckhard Wolf, Patrick Lonergan and Marie Saint-Dizier

    Citation: BMC Genomics 2019 20:233

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  11. Content type: Research article

    Monogenean flatworms are the main fish ectoparasites inflicting serious economic losses in aquaculture. The polyopisthocotylean Sparicotyle chrysophrii parasitizes the gills of gilthead sea bream (GSB, Sparus aur...

    Authors: M. Carla Piazzon, Ivona Mladineo, Fernando Naya-Català, Ron P. Dirks, Susanne Jong-Raadsen, Anamarija Vrbatović, Jerko Hrabar, Jaume Pérez-Sánchez and Ariadna Sitjà-Bobadilla

    Citation: BMC Genomics 2019 20:200

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  12. Content type: Research article

    Copy number variations (CNVs) are structural variants consisting of large-scale insertions and deletions of genomic fragments. Exploring CNVs and estimating their effects on phenotypes are useful for genome se...

    Authors: Mei Liu, Lingzhao Fang, Shuli Liu, Michael G. Pan, Eyal Seroussi, John B. Cole, Li Ma, Hong Chen and George E. Liu

    Citation: BMC Genomics 2019 20:181

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  13. Content type: Research article

    The power of genome-wide association studies (GWAS) is often limited by the sample size available for the analysis. Milk fatty acid (FA) traits are scarcely recorded due to expensive and time-consuming analyti...

    Authors: G. Gebreyesus, A. J. Buitenhuis, N. A. Poulsen, M. H. P. W. Visker, Q. Zhang, H. J. F. van Valenberg, D. Sun and H. Bovenhuis

    Citation: BMC Genomics 2019 20:178

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  14. Content type: Research article

    With the unprecedented rapid growth rate (up to 2.75 cm/day), velvet antler is an invaluable model for the identification of potent growth factors and signaling networks for extremely fast growing tissues, mai...

    Authors: Hengxing Ba, Datao Wang, Tung On Yau, Yudong Shang and Chunyi Li

    Citation: BMC Genomics 2019 20:173

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  15. Content type: Research article

    Intramuscular fat (IMF) content and composition have a strong impact on the nutritional and organoleptic properties of porcine meat. The goal of the current work was to compare the patterns of gene expression ...

    Authors: Rayner González-Prendes, Raquel Quintanilla, Emilio Mármol-Sánchez, Ramona N. Pena, Maria Ballester, Tainã Figueiredo Cardoso, Arianna Manunza, Joaquim Casellas, Ángela Cánovas, Isabel Díaz, José Luis Noguera, Anna Castelló, Anna Mercadé and Marcel Amills

    Citation: BMC Genomics 2019 20:170

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  16. Content type: Research article

    Korean Hanwoo cattle are known for their high meat quality, especially their high intramuscular fat compared to most other cattle breeds. Different muscles have very different meat quality traits and a study o...

    Authors: Sara de las Heras-Saldana, Ki Yong Chung, Seung Hwan Lee and Cedric Gondro

    Citation: BMC Genomics 2019 20:156

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  17. Content type: Research article

    Meat quality related phenotypes are difficult and expensive to measure and predict but are ideal candidates for genomic selection if genetic markers that account for a worthwhile proportion of the phenotypic v...

    Authors: Joel D. Leal-Gutiérrez, Mauricio A. Elzo, D. Dwain Johnson, Heather Hamblen and Raluca G. Mateescu

    Citation: BMC Genomics 2019 20:151

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  18. Content type: Research article

    Genome-wide association studies (GWAS) are utilized in cattle to identify regions or genetic variants associated with phenotypes of interest, and thus, to identify design strategies that allow for the increase...

    Authors: Luis Orlando Duitama Carreño, Matilde da Conceição Pessoa, Rafael Espigolan, Luciana Takada, Tiago Bresolin, Ligia Cavani, Fernando Baldi, Roberto Carvalheiro, Lucia Galvão de Albuquerque and Ricardo da Fonseca

    Citation: BMC Genomics 2019 20:150

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  19. Content type: Research article

    Hair fibre length is an important economic trait of rabbits in fur production. However, molecular mechanisms regulating rabbit hair growth have remained elusive.

    Authors: Haisheng Ding, Huiling Zhao, Guanglong Cheng, Yongxin Yang, Xiaofei Wang, Xiaowei Zhao, Yunxia Qi and Dongwei Huang

    Citation: BMC Genomics 2019 20:140

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  20. Content type: Research article

    A key developmental transformation in the life of all vertebrates is the transition to sexual maturity, whereby individuals are capable of reproducing for the first time. In the farming of Atlantic salmon, ear...

    Authors: Amin R. Mohamed, Klara L. Verbyla, Hawlader A. Al-Mamun, Sean McWilliam, Bradley Evans, Harry King, Peter Kube and James W. Kijas

    Citation: BMC Genomics 2019 20:139

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  21. Content type: Research article

    Horses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds...

    Authors: Brandon D. Velie, Mette Lillie, Kim Jäderkvist Fegraeus, Maria K. Rosengren, Marina Solé, Maja Wiklund, Carl-Fredrik Ihler, Eric Strand and Gabriella Lindgren

    Citation: BMC Genomics 2019 20:104

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  22. Content type: Research article

    Circular RNA (circRNA) is a type of noncoding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. The granulosa cells of follicles play a determining role in ovari...

    Authors: Manman Shen, Tingting Li, Genxi Zhang, Pengfei Wu, Fuxiang Chen, Qiuhong Lou, Lan Chen, Xuemei Yin, Tao Zhang and Jinyu Wang

    Citation: BMC Genomics 2019 20:96

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  23. Content type: Research article

    Eggshell formation takes place in the shell gland of the oviduct of laying hens. The eggshell is rich in calcium and various glycoproteins synthesised in the shell gland. Although studies have identified genes...

    Authors: Samiullah Khan, Shu-Biao Wu and Juliet Roberts

    Citation: BMC Genomics 2019 20:89

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  24. Content type: Research article

    Restriction site-associated DNA sequencing (RADseq) has revolutionized the study of wild organisms by allowing cost-effective genotyping of thousands of loci. However, for species lacking reference genomes, it...

    Authors: David L. J. Vendrami, Jaume Forcada and Joseph I. Hoffman

    Citation: BMC Genomics 2019 20:72

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  25. Content type: Research article

    MicroRNAs (miRNAs) are short endogenous, single-stranded, noncoding small RNA molecules of approximately 22 nucleotides in length. They regulate gene expression posttranscriptionally by silencing mRNA expressi...

    Authors: Martin Bilbao-Arribas, Naiara Abendaño, Endika Varela-Martínez, Ramsés Reina, Damián de Andrés and Begoña M. Jugo

    Citation: BMC Genomics 2019 20:62

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  26. Content type: Research article

    The mechanism of latency and the ability of the cyprinid herpesvirus 3 (CyHV-3) to establish life-long infections in carp remains poorly understood. To explain the role of miRNAs in this process we applied a r...

    Authors: Michal Reichert, Anna Lukasik, Piotr Zielenkiewicz, Marek Matras, Joanna Maj-Paluch, Magdalena Stachnik and Ewa Borzym

    Citation: BMC Genomics 2019 20:46

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  27. Content type: Research article

    Long non-coding RNAs (lncRNAs) are important component of mammalian genomes, where their numbers are even larger than that of protein-coding genes. For example, human (Homo sapiens) (96,308 vs. 20,376) and mouse

    Authors: Chang Lu, Yanling Xing, Han Cai, Yirong Shi, Jinhua Liu and Yinhua Huang

    Citation: BMC Genomics 2019 20:36

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  28. Content type: Research article

    Positively correlated with carcass weight and animal growth, the ribeye area (REA) and the backfat thickness (BFT) are economic important carcass traits, which impact directly on producer’s payment. The select...

    Authors: Bárbara Silva-Vignato, Luiz L. Coutinho, Mirele D. Poleti, Aline S. M. Cesar, Cristina T. Moncau, Luciana C. A. Regitano and Júlio C. C. Balieiro

    Citation: BMC Genomics 2019 20:32

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  29. Content type: Research article

    Average daily gain (ADG) is an important trait that contributes to the production efficiency and economic benefits in the beef cattle industry. The molecular mechanisms of ADG have not yet been fully explored ...

    Authors: Lingyang Xu, Liu Yang, Lei Wang, Bo Zhu, Yan Chen, Huijiang Gao, Xue Gao, Lupei Zhang, George E. Liu and Junya Li

    Citation: BMC Genomics 2019 20:31

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  30. Content type: Research article

    A widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. Despite methodological and hardware improvements which have enhanced the efficiency and accuracy o...

    Authors: Veronika N. Laine, Toni I. Gossmann, Kees van Oers, Marcel E. Visser and Martien A. M. Groenen

    Citation: BMC Genomics 2019 20:19

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  31. Content type: Research article

    Duck species are known to have different susceptibility to fatty liver production in response to overfeeding. In order to better describe mechanisms involved in the development of hepatic steatosis and differe...

    Authors: Frédéric Hérault, Magalie Houée-Bigot, Elisabeth Baéza, Olivier Bouchez, Diane Esquerré, Christophe Klopp and Christian Diot

    Citation: BMC Genomics 2019 20:13

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  32. Content type: Research article

    Ruminants play a great role in sustainable livestock since they transform pastures, silage, and crop residues into high-quality human food (i.e. milk and beef). Animals with better ability to convert food into...

    Authors: Francisco José Novais, Pedro Ratto Lisboa Pires, Pâmela Almeida Alexandre, Robert A Dromms, Amadeu Hoshi Iglesias, José Bento Sterman Ferraz, Mark Philip-Walter Styczynski and Heidge Fukumasu

    Citation: BMC Genomics 2019 20:8

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  33. Content type: Research article

    Economically important growth and meat quality traits in pigs are controlled by cascading molecular events occurring during development and continuing throughout the conversion of muscle to meat. However, litt...

    Authors: Deborah Velez-Irizarry, Sebastian Casiro, Kaitlyn R. Daza, Ronald O. Bates, Nancy E. Raney, Juan P. Steibel and Catherine W. Ernst

    Citation: BMC Genomics 2019 20:3

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  34. Content type: Research article

    The Tibetan highland fish, Gymnocypris przewalskii, migrates from Lake Qinghai to its spawning grounds every summer. This seasonal reproduction is critically regulated by intrinsic and extrinsic signals. However,...

    Authors: Fei Tian, Sijia Liu, Jianquan Shi, Hongfang Qi, Kai Zhao and Baosheng Xie

    Citation: BMC Genomics 2019 20:2

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  35. Content type: Research article

    Pekin duck products have become popular in Asia over recent decades and account for an increasing market share. However, the genetic mechanisms affecting carcass growth in Pekin ducks remain unknown. This stud...

    Authors: Meng-Ting Deng, Feng Zhu, Yu-Ze Yang, Fang-Xi Yang, Jin-ping Hao, Si-Rui Chen and Zhuo-Cheng Hou

    Citation: BMC Genomics 2019 20:1

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  36. Content type: Research article

    Paratuberculosis is a contagious, chronic and enteric disease in ruminants, which is caused by Mycobacterium avium subspecies paratuberculosis (MAP) infection, resulting in enormous economic losses worldwide. The...

    Authors: Yahui Gao, Jianping Jiang, Shaohua Yang, Jie Cao, Bo Han, Yachun Wang, Yi Zhang, Ying Yu, Shengli Zhang, Qin Zhang, Lingzhao Fang, Bonnie Cantrell and Dongxiao Sun

    Citation: BMC Genomics 2018 19:972

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  37. Content type: Research article

    The human chromosome 14 microRNA cluster (C14MC) is a conserved microRNA (miRNA) cluster across eutherian mammals, reported to play an important role in placental development. However, the expression kinetics ...

    Authors: Pouya Dini, Peter Daels, Shavahn C. Loux, Alejandro Esteller-Vico, Mariano Carossino, Kirsten E. Scoggin and Barry A. Ball

    Citation: BMC Genomics 2018 19:954

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  38. Content type: Research article

    Walking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, and sometimes “walks” to sear...

    Authors: Ning Li, Lisui Bao, Tao Zhou, Zihao Yuan, Shikai Liu, Rex Dunham, Yuanning Li, Kun Wang, Xiaoyan Xu, Yulin Jin, Qifan Zeng, Sen Gao, Qiang Fu, Yang Liu, Yujia Yang, Qi Li…

    Citation: BMC Genomics 2018 19:952

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  39. Content type: Research article

    Bovine papillomavirus (BPV) belongs to the Papillomaviridae family and infects epithelial cells of bovines and closely related animals, causing hyperproliferative lesions known as warts or papillomas, which ma...

    Authors: Débora M. Barreto, Gerlane S. Barros, Lucas A. B. O. Santos, Rosilene C. Soares and Marcus V. A. Batista

    Citation: BMC Genomics 2018 19:949

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  40. Content type: Research article

    The sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding pro...

    Authors: Amélie Juanchich, Christelle Hennequet-Antier, Cédric Cabau, Elisabeth Le Bihan-Duval, Michel J. Duclos, Sandrine Mignon-Grasteau and Agnès Narcy

    Citation: BMC Genomics 2018 19:928

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  41. Content type: Research article

    The transcriptional profiles of mammals during brain development and ageing have been characterized. However the global expression patterns of transcriptome in the chicken brain have not been explored. Here, w...

    Authors: Zhongxian Xu, Tiandong Che, Feng Li, Kai Tian, Qing Zhu, Shailendra Kumar Mishra, Yifei Dai, Mingzhou Li and Diyan Li

    Citation: BMC Genomics 2018 19:917

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  42. Content type: Research article

    To reduce costs of rearing replacement heifers, researchers have focused on decreasing age at breeding and first calving. To increase returns upon initiation of lactation the focus has been on increasing mamma...

    Authors: M. Vailati-Riboni, R. E. Bucktrout, S. Zhan, A. Geiger, J. C. McCann, R. M. Akers and J. J. Loor

    Citation: BMC Genomics 2018 19:900

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  44. Content type: Research article

    Even though microsatellite loci frequently have been isolated using recently developed next-generation sequencing (NGS) techniques, this task is still difficult because of the subsequent polymorphism screening...

    Authors: Yun Xia, Wei Luo, Siqi Yuan, Yuchi Zheng and Xiaomao Zeng

    Citation: BMC Genomics 2018 19:886

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  45. Content type: Research article

    The health and resilience of species in natural environments is increasingly challenged by complex anthropogenic stressor combinations including climate change, habitat encroachment, and chemical contamination...

    Authors: Kurt A. Gust, Vijender Chaitankar, Preetam Ghosh, Mitchell S. Wilbanks, Xianfeng Chen, Natalie D. Barker, Don Pham, Leona D. Scanlan, Arun Rawat, Larry G. Talent, Michael J. Quinn Jr, Christopher D. Vulpe, Mohamed O. Elasri, Mark S. Johnson, Edward J. Perkins and Craig A. McFarland

    Citation: BMC Genomics 2018 19:877

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  46. Content type: Research article

    The goat is an important farm animal. Reproduction is an important process of goat farming. The ovary is the most important reproductive organ for goats. In recent years, an increasing number of long non-codin...

    Authors: Yong Liu, Bing Qi, Juan Xie, Xiaoqing Wu, Yinghui Ling, Xinyan Cao, Feng Kong, Jing Xin, Xin Jiang, Qiaoqin Wu, Wenying Wang, Qingmei Li, Shengnan Zhang, Fengrui Wu, Di Zhang, Rong Wang…

    Citation: BMC Genomics 2018 19:866

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  47. Content type: Research article

    The dramatic increase in myotomal muscle mass in post-hatching fish is related to their ability to lastingly produce new muscle fibres, a process termed hyperplasia. The molecular and cellular mechanisms under...

    Authors: Sabrina Jagot, Nathalie Sabin, Aurélie Le Cam, Jérôme Bugeon, Pierre-Yves Rescan and Jean-Charles Gabillard

    Citation: BMC Genomics 2018 19:865

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  48. Content type: Research article

    Corn dried distillers grains with solubles (cDDGS) are a byproduct of biofuel and alcohol production. cDDGS have been used in pig feed for many years, because they are readily available and rich in protein, fi...

    Authors: Maria Oczkowicz, Tomasz Szmatoła, Małgorzata Świątkiewicz, Klaudia Pawlina-Tyszko, Artur Gurgul and Tomasz Ząbek

    Citation: BMC Genomics 2018 19:864

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  49. Content type: Research article

    Increased attention is being paid to breast muscle yield and meat quality in the duck breeding industry. Our previous report has demonstrated that dietary Clostridium butyricum (C. butyricum) can improve meat qua...

    Authors: Yanhan Liu, Yaxiong Jia, Cun Liu, Limin Ding and Zhaofei Xia

    Citation: BMC Genomics 2018 19:844

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  50. Content type: Research article

    Skeletal muscle satellite cells (MSC) are crucial for postnatal growth and regeneration of skeletal muscle. An interaction exists between MSC and intramuscular preadipocytes (IMPA). This study is the first to ...

    Authors: Liping Guo, Huanxian Cui, Guiping Zhao, Ranran Liu, Qinghe Li, Maiqing Zheng, Yuming Guo and Jie Wen

    Citation: BMC Genomics 2018 19:838

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