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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

  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. Content type: Research article

    Gene ontology analysis using the microarray database generated in a previous study by this laboratory was used to further evaluate how maternal dietary supplementation with pyridoxine combined with different s...

    Authors: Danyel Bueno Dalto, Stephen Tsoi, Michael K. Dyck and Jean-Jacques Matte

    Citation: BMC Genomics 2018 19:836

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  33. Content type: Research article

    Fertility is a complex trait that has a major impact on the development of the buffalo industry. Genome-wide association study (GWAS) has increased the ability to detect genes influencing complex traits, and m...

    Authors: Jun Li, Jiajia Liu, Giuseppe Campanile, Graham Plastow, Chunyan Zhang, Zhiquan Wang, Martino Cassandro, Bianca Gasparrini, Angela Salzano, Guohua Hua, Aixin Liang and Liguo Yang

    Citation: BMC Genomics 2018 19:814

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  34. Content type: Research article

    Dependence on marine natural resources threatens the sustainability of Atlantic salmon aquaculture. In the present study, Atlantic salmon fed for 14 weeks with an experimental diet based on animal by-products ...

    Authors: Albert Caballero-Solares, Xi Xue, Christopher C. Parrish, Maryam Beheshti Foroutani, Richard G. Taylor and Matthew L. Rise

    Citation: BMC Genomics 2018 19:796

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  35. Content type: Research article

    Development of the face and mouth is orchestrated by a large number of transcription factors, signaling pathways and epigenetic regulators. While we know many of these regulators, our understanding of how they...

    Authors: Stacey E. Wahl, Brent H. Wyatt, Stephen D. Turner and Amanda J. G. Dickinson

    Citation: BMC Genomics 2018 19:795

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  36. Content type: Research article

    The mutations changing the expression level of a gene, or expression quantitative trait loci (eQTL), can be identified by testing the association between genetic variants and gene expression in multiple indivi...

    Authors: Majid Khansefid, Jennie E. Pryce, Sunduimijid Bolormaa, Yizhou Chen, Catriona A. Millen, Amanda J. Chamberlain, Christy J. Vander Jagt and Michael E. Goddard

    Citation: BMC Genomics 2018 19:793

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  37. Content type: Research article

    Feed efficiency (FE) is an indicator of efficiency in converting energy and nutrients from feed into a tissue that is of major environmental and economic significance. The molecular mechanisms contributing to ...

    Authors: Justyna Horodyska, Klaus Wimmers, Henry Reyer, Nares Trakooljul, Anne Maria Mullen, Peadar G. Lawlor and Ruth M. Hamill

    Citation: BMC Genomics 2018 19:791

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  38. Content type: Research article

    The molecular mechanism controlling regional specific skin appendage phenotypes is a fundamental question that remains unresolved. We recently identified feather and scale primordium associated genes and with ...

    Authors: Yung-Chih Lai, Ya-Chen Liang, Ting-Xin Jiang, Randall B. Widelitz, Ping Wu and Cheng-Ming Chuong

    Citation: BMC Genomics 2018 19:780

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  39. Content type: Research article

    MicroRNAs (miRNAs) are endogenous, small (21–25 nucleotide), non-coding RNAs that play important roles in numerous biological processes. Koi carp exhibit diverse color patterns, making it an ideal subject for ...

    Authors: Mingkun Luo, Lanmei Wang, Wenbin Zhu, Jianjun Fu, Feibiao Song, Min Fang, Juanjuan Dong and Zaijie Dong

    Citation: BMC Genomics 2018 19:779

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  40. Content type: Research article

    Disrupted diurnal rhythms cause accelerated aging and an increased incidence in age-related disease and morbidity. The circadian clock governs cell physiology and metabolism by controlling transcription and ch...

    Authors: Jinhee Park and William J. Belden

    Citation: BMC Genomics 2018 19:777

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  41. Content type: Research article

    In the past years, our laboratory successfully generated transgenic rainbow trout bearing cecropin P1 transgene. These fish exhibited resistant characteristic to infection by Aeromonas salmonicida, Infectious Hem...

    Authors: Yueh-Chiang Han, Chun-Mean Lin and Thomas T. Chen

    Citation: BMC Genomics 2018 19:760

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  42. Content type: Research article

    Pacific salmon (Oncorhynchus spp.) serve as good biological indicators of the breadth of climate warming effects on fish because their anadromous life cycle exposes them to environmental challenges in both marine...

    Authors: Arash Akbarzadeh, Oliver P Günther, Aimee Lee Houde, Shaorong Li, Tobi J Ming, Kenneth M Jeffries, Scott G Hinch and Kristina M Miller

    Citation: BMC Genomics 2018 19:749

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  43. Content type: Research article

    This study investigated if the allele effect of a given single nucleotide polymorphism (SNP) for crossbred performance in pigs estimated in a genomic prediction model differs depending on its breed-of-origin, ...

    Authors: Claudia A Sevillano, Jan ten Napel, Simone E F Guimarães, Fabyano F Silva and Mario P L Calus

    Citation: BMC Genomics 2018 19:740

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  44. Content type: Research article

    Embryonic and fetal exposure to maternal obesity causes several maladaptive morphological and epigenetic changes in exposed offspring. The timing of these events is unclear, but changes can be observed even af...

    Authors: Sarah R. McCoski, McCauley T. Vailes, Connor E. Owens, Rebecca R. Cockrum and Alan D. Ealy

    Citation: BMC Genomics 2018 19:737

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  45. Content type: Research article

    Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited.

    Authors: Bi Jun Li, Dan Li Jiang, Zi Ning Meng, Yong Zhang, Zong Xian Zhu, Hao Ran Lin and Jun Hong Xia

    Citation: BMC Genomics 2018 19:729

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  46. Content type: Research article

    Captive animal populations, be it for food production or conservation programmes, are often maintained at densities far beyond those in natural environments, which can have profound effects on behaviour, immun...

    Authors: Amy R Ellison, Tamsyn M Uren Webster, Olivier Rey, Carlos Garcia de Leaniz, Sofia Consuegra, Pablo Orozco-terWengel and Jo Cable

    Citation: BMC Genomics 2018 19:723

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  47. Content type: Research article

    Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular ...

    Authors: Claudia M. Arenas Gómez, Ryan M. Woodcock, Jeramiah J. Smith, Randal S. Voss and Jean Paul Delgado

    Citation: BMC Genomics 2018 19:704

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  48. Content type: Research article

    Maternal nutrition has been highlighted as one of the main factors affecting intra-uterine environment. The increase in nutritional requirements by beef cows during late gestation can cause nutritional deficie...

    Authors: Leticia P Sanglard, Moysés Nascimento, Philipe Moriel, Jeffrey Sommer, Melissa Ashwell, Matthew H Poore, Márcio de S Duarte and Nick V L Serão

    Citation: BMC Genomics 2018 19:702

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