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  1. Content type: Research article

    Feed efficiency is an important economic and environmental trait in beef production, which can be measured in terms of residual feed intake (RFI). Cattle selected for low-RFI (feed efficient) have similar prod...

    Authors: Marc G. Higgins, David A. Kenny, Claire Fitzsimons, Gordon Blackshields, Séan Coyle, Clare McKenna, Mark McGee, Derek W. Morris and Sinéad M. Waters

    Citation: BMC Genomics 2019 20:525

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  3. Content type: Correction

    Following the publication of this article [1], the authors reported that the Fig. 2 described in the article had a mistake that two grey blocks in S. moellendorffii was not placed as background color, and in the ...

    Authors: Hong-Rui Zhang, Xian-Chun Zhang and Qiao-Ping Xiang

    Citation: BMC Genomics 2019 20:523

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    The original article was published in BMC Genomics 2019 20:484

  4. Content type: Research article

    Phlebotomine sand flies (Diptera, Nematocera) are important vectors of several pathogens, including Leishmania parasites, causing serious diseases of humans and dogs. Despite their importance as disease vectors, ...

    Authors: Valeria Petrella, Serena Aceto, Vincenza Colonna, Giuseppe Saccone, Remo Sanges, Nikola Polanska, Petr Volf, Luigi Gradoni, Gioia Bongiorno and Marco Salvemini

    Citation: BMC Genomics 2019 20:522

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  5. Content type: Research article

    Splicing is a genetic process that has important implications in several diseases including cancer. Deciphering the complex rules of splicing regulation is crucial to understand and treat splicing-related dise...

    Authors: Fernando Carazo, Marian Gimeno, Juan A. Ferrer-Bonsoms and Angel Rubio

    Citation: BMC Genomics 2019 20:521

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  6. Content type: Research article

    The aim of this study was to use transcriptome RNA-Seq data from longissimus thoracis muscle of uncastrated Nelore males to identify hub genes based on co-expression network obtained from differentially expressed...

    Authors: Danielly Beraldo dos Santos Silva, Larissa Fernanda Simielli Fonseca, Daniel Guariz Pinheiro, Maria Malane Magalhães Muniz, Ana Fabrícia Braga Magalhães, Fernando Baldi, Jesus Aparecido Ferro, Luis Artur Loyola Chardulo and Lucia Galvão de Albuquerque

    Citation: BMC Genomics 2019 20:520

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  8. Content type: Research article

    Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots...

    Authors: Wenbin Li, Xiaolin Wang, Chunqiang Li, Jianbo Sun, Shuxia Li and Ming Peng

    Citation: BMC Genomics 2019 20:519

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  9. Content type: Research article

    The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we...

    Authors: Rayner González-Prendes, Emilio Mármol-Sánchez, Raquel Quintanilla, Anna Castelló, Ali Zidi, Yuliaxis Ramayo-Caldas, Tainã Figueiredo Cardoso, Arianna Manunza, Ángela Cánovas and Marcel Amills

    Citation: BMC Genomics 2019 20:518

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  10. Content type: Research article

    Bovine viral diarrhea virus (BVDV) is an economically important viral pathogen of domestic and wild ruminants. Apart from cattle, small ruminants (goats and sheep) are also the susceptible hosts for BVDV. BVDV...

    Authors: Wenliang Li, Li Mao, Xin Shu, Runxia Liu, Fei Hao, Jizong Li, Maojun Liu, Leilei Yang, Wenwen Zhang, Min Sun, Chunyan Zhong and Jieyuan Jiang

    Citation: BMC Genomics 2019 20:516

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  11. Content type: Research article

    Long non-coding RNAs (lncRNAs) perform crucial roles in biological process involving complex mechanisms. However, information regarding their abundance, characteristics and potential functions linked to fish s...

    Authors: Mingkun Luo, Lanmei Wang, Haoran Yin, Wenbin Zhu, Jianjun Fu and Zaijie Dong

    Citation: BMC Genomics 2019 20:515

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  12. Content type: Research article

    Polyploidization, pervasive among higher plant species, enhances adaptation to water deficit, but the physiological and molecular advantages need to be investigated widely. Long non-coding RNAs (lncRNAs) are i...

    Authors: Liang Xiao, Xiao-Hong Shang, Sheng Cao, Xiang-Yu Xie, Wen-Dan Zeng, Liu-Ying Lu, Song-Bi Chen and Hua-Bing Yan

    Citation: BMC Genomics 2019 20:514

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  13. Content type: Methodology article

    RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have focused on adapt...

    Authors: Carrie Wright, Anandita Rajpurohit, Emily E. Burke, Courtney Williams, Leonardo Collado-Torres, Martha Kimos, Nicholas J. Brandon, Alan J. Cross, Andrew E. Jaffe, Daniel R. Weinberger and Joo Heon Shin

    Citation: BMC Genomics 2019 20:513

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  14. Content type: Research article

    Dermal papilla cells (DPCs), the “signaling center” of hair follicle (HF), delicately master continual growth of hair in mammals including cashmere, the fine fiber annually produced by secondary HF embedded in...

    Authors: Sen Ma, Ying Wang, Guangxian Zhou, Yi Ding, Yuxin Yang, Xiaolong Wang, Enping Zhang and Yulin Chen

    Citation: BMC Genomics 2019 20:512

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  15. Content type: Research article

    Non-coding gene regulatory enhancers are essential to transcription in mammalian cells. As a result, a large variety of experimental and computational strategies have been developed to identify cis-regulatory enh...

    Authors: Mary Lauren Benton, Sai Charan Talipineni, Dennis Kostka and John A. Capra

    Citation: BMC Genomics 2019 20:511

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  16. Content type: Research article

    In female mammals, the initiation of puberty, coupling with the dramatically morphological changes in ovaries, indicates the sexual and follicular maturation. Previous studies have suggested that the disrupted...

    Authors: Xiaolong Yuan, Shaopan Ye, Zitao Chen, Xiangchun Pan, Shuwen Huang, Zhonghui Li, Yuyi Zhong, Ning Gao, Hao Zhang, Jiaqi Li and Zhe Zhang

    Citation: BMC Genomics 2019 20:510

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  17. Content type: Research article

    Livestock production aims to provide meats of high and consistent eating quality. Insufficient intramuscular (IM) fat and excessive subcutaneous (SC) fat are paramount pork quality challenges. IM fat and SC fa...

    Authors: Wenjing Wu, Dawei Zhang, Yajun Yin, Miao Ji, Ke Xu, Xin Huang, Yongjia Peng and Jin Zhang

    Citation: BMC Genomics 2019 20:509

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  18. Content type: Research article

    DNA methylation is an important epigenetic modification. Recently the developed single-molecule real-time (SMRT) sequencing technology provided an efficient way to detect DNA N6-methyladenine (6mA) modificatio...

    Authors: Mei-Wei Luan, Wei Chen, Jian-Feng Xing, Chuan-Le Xiao, Ying Chen and Shang-Qian Xie

    Citation: BMC Genomics 2019 20:508

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  19. Content type: Research article

    Whiteflies (Bemisia tabaci) are phloem sap-sucking pests that because of their broad host range and ability to transmit viruses damage crop plants worldwide. B. tabaci are now known to be a complex of cryptic spe...

    Authors: Sonia Hussain, Muhammad Farooq, Hassan Jamil Malik, Imran Amin, Brian E. Scheffler, Jodi A. Scheffler, Shu-Sheng Liu and Shahid Mansoor

    Citation: BMC Genomics 2019 20:507

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  21. Content type: Research article

    Environmental toxicity from non-essential heavy metals such as cadmium (Cd), which is released from human activities and other environmental causes, is rapidly increasing. Wheat can accumulate high levels of C...

    Authors: Min Zhou, Shigang Zheng, Rong Liu, Jing Lu, Lu Lu, Chihong Zhang, Zehou Liu, Congpei Luo, Lei Zhang, Levi Yant and Yu Wu

    Citation: BMC Genomics 2019 20:505

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  22. Content type: Research article

    Enterohemorrhagic Escherichia coli (E. coli) are intestinal pathogenic bacteria that cause life-threatening disease in humans. Their cardinal virulence factor is Shiga toxin (Stx), which is encoded on lambdoid ph...

    Authors: Petya Berger, Ivan U. Kouzel, Michael Berger, Nadja Haarmann, Ulrich Dobrindt, Gerald B. Koudelka and Alexander Mellmann

    Citation: BMC Genomics 2019 20:504

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  23. Content type: Research article

    Accurate classification of breast cancer using gene expression profiles has contributed to a better understanding of the biological mechanisms behind the disease and has paved the way for better prognosticatio...

    Authors: Rolf Søkilde, Helena Persson, Anna Ehinger, Anna Chiara Pirona, Mårten Fernö, Cecilia Hegardt, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Lao Saal, Åke Borg, Johan Vallon-Christerson and Carlos Rovira

    Citation: BMC Genomics 2019 20:503

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  24. Content type: Research article

    We present results from a computational analysis developed to integrate transcriptome and metabolomic data in order to explore the heat stress response in the liver of the modern broiler chicken. Heat stress i...

    Authors: Allen H. Hubbard, Xiaoke Zhang, Sara Jastrebski, Abhyudai Singh and Carl Schmidt

    Citation: BMC Genomics 2019 20:502

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  25. Content type: Research article

    Feed efficiency is one of the most important parameters that affect beef production costs. The energy metabolism of skeletal muscle greatly contributes to variations in feed efficiency. However, information re...

    Authors: Elisa B. Carvalho, Mateus P. Gionbelli, Rafael T. S. Rodrigues, Sarah F. M. Bonilha, Charles J. Newbold, Simone E. F. Guimarães, Walmir Silva, Lucas L. Verardo, Fabyano F. Silva, Edenio Detmann and Marcio S. Duarte

    Citation: BMC Genomics 2019 20:501

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  26. Content type: Methodology article

    The wide variety of specialized permissive and repressive mechanisms by which germ cells regulate developmental gene expression are not well understood genome-wide. Isolation of germ cells with high integrity ...

    Authors: Mei Han, Guifeng Wei, Catherine E. McManus, LaDeana W. Hillier and Valerie Reinke

    Citation: BMC Genomics 2019 20:500

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  27. Content type: Research article

    Seed aging in soybean is a serious challenge for agronomic production and germplasm preservation. However, its genetic basis remains largely unclear in soybean. Unraveling the genetic mechanism involved in see...

    Authors: Xi Zhang, Aiman Hina, Shiyu Song, Jiejie Kong, Javaid Akhter Bhat and Tuanjie Zhao

    Citation: BMC Genomics 2019 20:499

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  28. Content type: Research article

    The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultiva...

    Authors: Yasmin A. Mohamoud, Lisa S. Mathew, Maria F. Torres, Shameem Younuskunju, Robert Krueger, Karsten Suhre and Joel A. Malek

    Citation: BMC Genomics 2019 20:498

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  29. Content type: Methodology article

    The introduction of genome-wide shRNA and CRISPR libraries has facilitated cell-based screens to identify loss-of-function mutations associated with a phenotype of interest. Approaches to perform analogous gai...

    Authors: Charlotte R. Feddersen, Lexy S. Wadsworth, Eliot Y. Zhu, Hayley R. Vaughn, Andrew P. Voigt, Jesse D. Riordan and Adam J. Dupuy

    Citation: BMC Genomics 2019 20:497

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  30. Content type: Software

    Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. ...

    Authors: Matteo Soverini, Silvia Turroni, Elena Biagi, Patrizia Brigidi, Marco Candela and Simone Rampelli

    Citation: BMC Genomics 2019 20:496

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  31. Content type: Research article

    Puccinia graminis f. sp. tritici (Pgt) race TTKSK and its lineage pose a threat to barley production world-wide justifying the extensive efforts to identify, clone, and characterize the rpg4-mediated resistance l...

    Authors: Shyam Solanki, Jonathan Richards, Gazala Ameen, Xue Wang, Atiya Khan, Harris Ali, Alex Stangel, Prabin Tamang, Thomas Gross, Patrick Gross, Thomas G. Fetch and Robert S. Brueggeman

    Citation: BMC Genomics 2019 20:495

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  32. Content type: Research article

    Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs.

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

    Citation: BMC Genomics 2019 20:494

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  33. Content type: Research article

    Limited accessibility to intestinal epithelial tissue in wild animals and humans makes it challenging to study patterns of intestinal gene regulation, and hence to monitor physiological status and health in fi...

    Authors: Ashok Kumar Sharma, Barbora Pafčo, Klára Vlčková, Barbora Červená, Jakub Kreisinger, Samuel Davison, Karen Beeri, Terence Fuh, Steven R. Leigh, Michael B. Burns, Ran Blekhman, Klára J. Petrželková and Andres Gomez

    Citation: BMC Genomics 2019 20:493

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  34. Content type: Research article

    Epigenetic variation may result from selection for complex traits related to metabolic processes or appear in the course of adaptation to mediate responses to exogenous stressors. Moreover epigenetic marks, in...

    Authors: Siriluck Ponsuksili, Nares Trakooljul, Sajjanar Basavaraj, Frieder Hadlich, Eduard Murani and Klaus Wimmers

    Citation: BMC Genomics 2019 20:492

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  35. Content type: Research article

    Mycobacterium avium subsp. paratuberculosis (MAP), the etiologic agent of Johne’s disease is spread between cattle via the fecal-oral route, yet the functional changes in the salivary gland associated with infect...

    Authors: Sanjay Mallikarjunappa, Mounir Adnane, Paul Cormican, Niel A. Karrow and Kieran G. Meade

    Citation: BMC Genomics 2019 20:491

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  36. Content type: Research article

    Salmonella enterica possess several iron acquisition systems, encoded on the chromosome and plasmids. Recently, we demonstrated that incompatibility group (Inc) FIB plasmid-encoded iron acquisition systems (Sit a...

    Authors: Bijay K. Khajanchi, Joshua Xu, Christopher J. Grim, Andrea R. Ottesen, Padmini Ramachandran and Steven L. Foley

    Citation: BMC Genomics 2019 20:490

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  37. Content type: Research article

    Juncus effusus L. (family: Juncaceae; order: Poales) is a helophytic rush growing in temperate damp or wet terrestrial habitats and is of almost cosmopolitan distribution. The species has been studied intensively...

    Authors: Muhammad Arslan, Upendra Kumar Devisetty, Martin Porsch, Ivo Große, Jochen A. Müller and Stefan G. Michalski

    Citation: BMC Genomics 2019 20:489

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  38. Content type: Research article

    With rising global temperature, understanding plants’ adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the post...

    Authors: Sridhar Ravichandran, Raja Ragupathy, Tara Edwards, Michael Domaratzki and Sylvie Cloutier

    Citation: BMC Genomics 2019 20:488

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  39. Content type: Research article

    Apomixis is considered an evolutionary deviation of the sexual reproductive pathway leading to the generation of clonal maternal progenies by seeds. Recent evidence from model and non-model species suggested t...

    Authors: Juan Pablo A. Ortiz, Olivier Leblanc, Cristian Rohr, Mauricio Grisolia, Lorena A. Siena, Maricel Podio, Carolina Colono, Celeste Azzaro and Silvina C. Pessino

    Citation: BMC Genomics 2019 20:487

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  40. Content type: Research article

    Pectobacterium carotovorum subsp. brasiliense is a broad host range bacterial pathogen, which causes blackleg of potatoes and bacterial soft rot of vegetables worldwide. Production of plant cell wall degrading en...

    Authors: Lei Li, Lifang Yuan, Yanxia Shi, Xuewen Xie, Ali Chai, Qi Wang and Baoju Li

    Citation: BMC Genomics 2019 20:486

    Published on:

  41. Content type: Research

    Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regu...

    Authors: Ehsan Hajiramezanali, Mahdi Imani, Ulisses Braga-Neto, Xiaoning Qian and Edward R. Dougherty

    Citation: BMC Genomics 2019 20(Suppl 6):435

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    This article is part of a Supplement: Volume 20 Supplement 6

  42. Content type: Research

    Biological networks describes the mechanisms which govern cellular functions. Temporal networks show how these networks evolve over time. Studying the temporal progression of network topologies is of utmost im...

    Authors: Rasha Elhesha, Aisharjya Sarkar, Christina Boucher and Tamer Kahveci

    Citation: BMC Genomics 2019 20(Suppl 6):434

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 6

  43. Content type: Research article

    The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicid...

    Authors: Christian P. Kubicek, Andrei S. Steindorff, Komal Chenthamara, Gelsomina Manganiello, Bernard Henrissat, Jian Zhang, Feng Cai, Alexey G. Kopchinskiy, Eva M. Kubicek, Alan Kuo, Riccardo Baroncelli, Sabrina Sarrocco, Eliane Ferreira Noronha, Giovanni Vannacci, Qirong Shen, Igor V. Grigoriev…

    Citation: BMC Genomics 2019 20:485

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  44. Content type: Research article

    It is hypothesized that the highly conserved inverted repeats (IR) structure of land plant plastid genomes (plastomes) is beneficial for stabilizing plastome organization, whereas the mechanism of the occurren...

    Authors: Hong-Rui Zhang, Xian-Chun Zhang and Qiao-Ping Xiang

    Citation: BMC Genomics 2019 20:484

    Published on:

    The Correction to this article has been published in BMC Genomics 2019 20:523

  45. Content type: Research article

    In reported plants, the bZIP family is one of the largest transcription factor families. bZIP genes play roles in the light signal, seed maturation, flower development, cell elongation, seed accumulation protein,...

    Authors: Moyang Liu, Yongdi Wen, Wenjun Sun, Zhaotang Ma, Li Huang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Genomics 2019 20:483

    Published on:

  46. Content type: Research article

    Global biodiversity is decreasing at an alarming rate and amphibians are at the forefront of this crisis. Understanding the factors that negatively impact amphibian populations and effectively monitoring their...

    Authors: Timothy A. Clay, Michael A. Steffen, Michael L. Treglia, Carolyn D. Torres, Ana Lilia Trujano-Alvarez and Ronald M. Bonett

    Citation: BMC Genomics 2019 20:482

    Published on:

  47. Content type: Research article

    The mammalian major histocompatibility complex (MHC) harbours clusters of genes associated with the immunological defence of animals against infectious pathogens. At present, no complete MHC physical map is av...

    Authors: Chaokun Li, Longxin Chen, Xuefeng Liu, Xiaoqian Shi, Yu Guo, Rui Huang, Fangyuan Nie, Changming Zheng, Chenglin Zhang and Runlin Z. Ma

    Citation: BMC Genomics 2019 20:479

    Published on:

  48. Content type: Research article

    Salt pond restoration aims to recover the environmental damages that accumulated over the long history of salt production. Of the restoration strategies, phytoremediation that utilizes salt-tolerant plants and...

    Authors: Huyen-Trang Tran, Hao-Chu Wang, Tsai-Wen Hsu, Rakesh Sarkar, Chao-Li Huang and Tzen-Yuh Chiang

    Citation: BMC Genomics 2019 20:478

    Published on:

  49. Content type: Research article

    The redundancy of genomic resources, including transcript and molecular markers, and their uncertain position in the genome have dramatically hindered the study of traits in ramie, an important natural fiber c...

    Authors: Yanzhou Wang, Zheng Zeng, Fu Li, Xiufeng Yang, Xinyue Gao, Yonghong Ma, Jing Rao, Hengyun Wang and Touming Liu

    Citation: BMC Genomics 2019 20:476

    Published on:

  50. Content type: Research article

    When puberty starts before males reach harvest size, animal welfare and sustainability issues occur in Atlantic salmon (Salmo salar) aquaculture. Hallmarks of male puberty are an increased proliferation activity ...

    Authors: Diego Crespo, Jan Bogerd, Elisabeth Sambroni, Florence LeGac, Eva Andersson, Rolf B. Edvardsen, Elisabeth Jönsson Bergman, Björn Thrandur Björnsson, Geir Lasse Taranger and Rüdiger W. Schulz

    Citation: BMC Genomics 2019 20:475

    Published on:

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