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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 6 of 19

  1. Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. Th...

    Authors: Elisa Peripolli, Nedenia Bonvino Stafuzza, Danísio Prado Munari, André Luís Ferreira Lima, Renato Irgang, Marco Antonio Machado, João Cláudio do Carmo Panetto, Ricardo Vieira Ventura, Fernando Baldi and Marcos Vinícius Gualberto Barbosa da Silva

    Citation: BMC Genomics 2018 19:34

    Content type: Research article

    Published on:

  2. Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are...

    Authors: Madeleine Carruthers, Andrey A. Yurchenko, Julian J. Augley, Colin E. Adams, Pawel Herzyk and Kathryn R. Elmer

    Citation: BMC Genomics 2018 19:32

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2018 19:448

  3. The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery. Genomic resource development is especially important for sp...

    Authors: Catherine M. Purcell, Arun S. Seetharam, Owyn Snodgrass, Sofia Ortega-García, John R. Hyde and Andrew J. Severin

    Citation: BMC Genomics 2018 19:31

    Content type: Research article

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  4. Single nucleotide polymorphism (SNP) panels have been widely used to study genomic variations within and between populations. Methods of SNP discovery have been a matter of debate for their potential of introd...

    Authors: Dorcus Kholofelo Malomane, Christian Reimer, Steffen Weigend, Annett Weigend, Ahmad Reza Sharifi and Henner Simianer

    Citation: BMC Genomics 2018 19:22

    Content type: Research article

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  5. Within the last few years a large amount of genomic information has become available in cattle. Densities of genomic information vary from a few thousand variants up to whole genome sequence information. In or...

    Authors: Mirjam Frischknecht, Hubert Pausch, Beat Bapst, Heidi Signer-Hasler, Christine Flury, Dorian Garrick, Christian Stricker, Ruedi Fries and Birgit Gredler-Grandl

    Citation: BMC Genomics 2017 18:999

    Content type: Research article

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  6. In Japan and East Asia, endemic frogs appear to be tolerant or not susceptible to chytridiomycosis, a deadly amphibian disease caused by the chytrid fungus Batrachochytridium dendrobatidis (Bd). Japanese frogs ma...

    Authors: Quintin Lau, Takeshi Igawa, Ryuhei Minei, Tiffany A. Kosch and Yoko Satta

    Citation: BMC Genomics 2017 18:994

    Content type: Research article

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  7. Newcastle disease virus (NDV) is a threat to poultry production worldwide. A better understanding of mechanisms of resistance and susceptibility to this virus will improve measures for NDV prevention and contr...

    Authors: Melissa S. Deist, Rodrigo A. Gallardo, David A. Bunn, Jack C. M. Dekkers, Huaijun Zhou and Susan J. Lamont

    Citation: BMC Genomics 2017 18:989

    Content type: Research article

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  8. Stress is a generic term used to describe non-specific responses of the body to all kinds of challenges. A very large variability in the response can be observed across individuals, depending on numerous condi...

    Authors: Elena Terenina, Valérie Sautron, Caroline Ydier, Darya Bazovkina, Amélie Sevin-Pujol, Laure Gress, Yannick Lippi, Claire Naylies, Yvon Billon, Laurence Liaubet, Pierre Mormede and Nathalie Villa-Vialaneix

    Citation: BMC Genomics 2017 18:988

    Content type: Research article

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  9. The transition from a high forage to a highly fermentable diet can induce digestive disorders in the rumen. To date, the host mechanisms that regulate the adaption to such dietary transition are largely unknow...

    Authors: K. Zhao, Y. H. Chen, G. B. Penner, M. Oba and L. L. Guan

    Citation: BMC Genomics 2017 18:976

    Content type: Research article

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  10. Understanding the consequences of thermal and chemical variations in aquatic habitats is of importance in a scenario of global change. In ecology, the sex ratio is a major population demographic parameter. So ...

    Authors: Noelia Díaz and Francesc Piferrer

    Citation: BMC Genomics 2017 18:973

    Content type: Research article

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  11. The Sertoli cells act to induce testis differentiation and subsequent development in fetal and post-natal life which makes them key to an understanding of testis biology. As a major step towards characterisati...

    Authors: U. Soffientini, D. Rebourcet, M. H. Abel, S. Lee, G. Hamilton, P. A. Fowler, L. B. Smith and P. J. O’Shaughnessy

    Citation: BMC Genomics 2017 18:972

    Content type: Research article

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  12. Farmed and wild Atlantic salmon are exposed to many infectious and non-infectious challenges that can cause mortality when they enter the sea. Exercise before transfer promotes growth, health and survival in t...

    Authors: Nicholas A. Robinson, Gerrit Timmerhaus, Matthew Baranski, Øivind Andersen, Harald Takle and Aleksei Krasnov

    Citation: BMC Genomics 2017 18:971

    Content type: Research article

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  13. Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to...

    Authors: Thomas J. Lopdell, Kathryn Tiplady, Maksim Struchalin, Thomas J. J. Johnson, Michael Keehan, Ric Sherlock, Christine Couldrey, Stephen R. Davis, Russell G. Snell, Richard J. Spelman and Mathew D. Littlejohn

    Citation: BMC Genomics 2017 18:968

    Content type: Research article

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  14. Avian reovirus (ARV) is an important poultry pathogen that can cause immunosuppression. In this study, RNA-Seq technology was applied to investigate the transcriptome-wide changes of DF-1 cells upon ARV infect...

    Authors: Xiaosai Niu, Yuyang Wang, Min Li, Xiaorong Zhang and Yantao Wu

    Citation: BMC Genomics 2017 18:911

    Content type: Research article

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  15. The detection of quantitative trait loci has accelerated with recent developments in genomics. The introduction of genomic selection in combination with sequencing efforts has made a large amount of genotypic ...

    Authors: Mirjam Frischknecht, Beat Bapst, Franz R. Seefried, Heidi Signer-Hasler, Dorian Garrick, Christian Stricker, Ruedi Fries, Ingolf Russ, Johann Sölkner, Anna Bieber, Maria G. Strillacci, Birgit Gredler-Grandl and Christine Flury

    Citation: BMC Genomics 2017 18:910

    Content type: Research article

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  16. In addition to additive genetic effects, epistatic interactions can play key roles in the control of phenotypic variation of traits of interest. In the current study, 475 male birds from lean and fat chicken l...

    Authors: Hui Zhang, Jia-Qiang Yu, Li-Li Yang, Luke M. Kramer, Xin-Yang Zhang, Wei Na, James M. Reecy and Hui Li

    Citation: BMC Genomics 2017 18:892

    Content type: Research article

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  17. To ensure sustainability of aquaculture, plant-based ingredients are being used in feeds to replace marine-derived products. However, plants contain secondary metabolites which can affect food intake and nutri...

    Authors: L. M. Vera, C. Metochis, J. F. Taylor, M. Clarkson, K. H. Skjærven, H. Migaud and D. R. Tocher

    Citation: BMC Genomics 2017 18:886

    Content type: Research article

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  18. Umami is a Japanese term for the fifth basic taste and is an important sensory property of beef palatability. Inosine 5′-monophosphate (IMP) contributes to umami taste in beef. Thus, t...

    Authors: Yoshinobu Uemoto, Tsuyoshi Ohtake, Nanae Sasago, Masayuki Takeda, Tsuyoshi Abe, Hironori Sakuma, Takatoshi Kojima and Shinji Sasaki

    Citation: BMC Genomics 2017 18:874

    Content type: Research

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  19. The WUR1000125 (WUR) single nucleotide polymorphism (SNP) can be used as a genetic marker for host response to porcine reproductive and respiratory syndrome (PRRS), PRRS vaccination, and co-infection with porcine...

    Authors: Jenelle R. Dunkelberger, Nick V. L. Serão, Ziqing Weng, Emily H. Waide, Megan C. Niederwerder, Maureen A. Kerrigan, Joan K. Lunney, Raymond R. R. Rowland and Jack C. M. Dekkers

    Citation: BMC Genomics 2017 18:865

    Content type: Research article

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  20. Lethal recessive variation can cause prenatal death of homozygous offspring. Although usually present at low-frequency in populations, the impact on individual fitness can be substantial. Until recently, the p...

    Authors: Martijn F. L. Derks, Hendrik-Jan Megens, Mirte Bosse, Marcos S. Lopes, Barbara Harlizius and Martien A. M. Groenen

    Citation: BMC Genomics 2017 18:858

    Content type: Research article

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  21. Negative energy balance (NEB) is an imbalance between energy intake and energy requirements for lactation and body maintenance affecting high-yielding dairy cows and is of considerable economic importance due ...

    Authors: Daragh Matthews, Michael G. Diskin, David A. Kenny, Christopher J. Creevey, Kate Keogh and Sinead M. Waters

    Citation: BMC Genomics 2017 18:857

    Content type: Research article

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  22. Global trend of the introduction of high levels of relatively cheap carbohydrates to reduce the amount of costly protein in the aquatic animal feed production has affected the aquaculture of an economically im...

    Authors: Wassana Prisingkorn, Panita Prathomya, Ivan Jakovlić, Han Liu, Yu-Hua Zhao and Wei-Min Wang

    Citation: BMC Genomics 2017 18:856

    Content type: Research article

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  23. Tissue regeneration requires a series of steps, beginning with generation of the necessary cell mass, followed by cell migration into damaged area, and ending with differentiation and integration with surround...

    Authors: Ke’ale W. Louie, Alfonso Saera-Vila, Phillip E. Kish, Justin A. Colacino and Alon Kahana

    Citation: BMC Genomics 2017 18:854

    Content type: Research article

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  24. Genotyping and whole-genome sequencing data have been generated for hundreds of thousands of cattle. International consortia used these data to compile imputation reference panels that facilitate the imputatio...

    Authors: Hubert Pausch, Reiner Emmerling, Birgit Gredler-Grandl, Ruedi Fries, Hans D. Daetwyler and Michael E. Goddard

    Citation: BMC Genomics 2017 18:853

    Content type: Research

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  25. Our understanding of the molecular mechanisms implementing pubertal maturation of the testis in vertebrates is incomplete. This topic is relevant in Atlantic salmon aquaculture, since precocious male puberty n...

    Authors: K. O. Skaftnesmo, R. B. Edvardsen, T. Furmanek, D. Crespo, E. Andersson, L. Kleppe, G. L. Taranger, J. Bogerd, R. W. Schulz and A. Wargelius

    Citation: BMC Genomics 2017 18:801

    Content type: Research article

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  26. If unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating ...

    Authors: Jesse L. Hoff, Jared E. Decker, Robert D. Schnabel and Jeremy F. Taylor

    Citation: BMC Genomics 2017 18:799

    Content type: Research article

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  27. The intramuscular fat content (IMF) refers to the amount of fat within muscles, including the sum of phospholipids mainly found in cell membranes, triglycerides and cholesterol, and is determined both by hyper...

    Authors: Yuding Wang, Cai Ma, Yi Sun, Yi Li, Li Kang and Yunliang Jiang

    Citation: BMC Genomics 2017 18:780

    Content type: Research article

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  28. The impact of nutritional status and diet composition on mitochondrial oxidative phosphorylation (OXPHOS) in fish remains largely unknown. To identify biomarkers of interest in nutritional studies, herein we o...

    Authors: Jonás I. Silva-Marrero, Alberto Sáez, Albert Caballero-Solares, Ivan Viegas, María Pilar Almajano, Felipe Fernández, Isabel V. Baanante and Isidoro Metón

    Citation: BMC Genomics 2017 18:768

    Content type: Research article

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  29. Cashmere growth is a seasonal and cyclic phenomenon under the control of photoperiod and multiple stimulatory and inhibitory signals. Beyond relevant coding genes, microRNA (miRNA) and long non coding RNA (lnc...

    Authors: Shanhe Wang, Wei Ge, Zhixin Luo, Yang Guo, Beilei Jiao, Lei Qu, Zhiying Zhang and Xin Wang

    Citation: BMC Genomics 2017 18:767

    Content type: Research article

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  30. The bulldog calf syndrome is a lethal form of the inherited congenital chondrodysplasias. Among the progeny of the polled Holstein bull Energy P cases of lethal chondrodysplasia were observed. Pedigrees of the...

    Authors: Sina Reinartz, Hartmut Mohwinkel, Christian Sürie, Maren Hellige, Karsten Feige, Deborah Eikelberg, Andreas Beineke, Julia Metzger and Ottmar Distl

    Citation: BMC Genomics 2017 18:762

    Content type: Research article

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  31. Ovulation rate and litter size are important reproductive traits in sheep with high economic value. Recent work has revealed a potential link between DNA methylation and prolificacy. However, a genome-wide stu...

    Authors: Yanli Zhang, Fengzhe Li, Xu Feng, Hua Yang, Aoxiang Zhu, Jing Pang, Le Han, Tingting Zhang, Xiaolei Yao and Feng Wang

    Citation: BMC Genomics 2017 18:759

    Content type: Research article

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  32. In the domestic dog, corpora lutea (CL) are the only source of progesterone (P4), both in pregnant and non-pregnant cycles because there is no placental steroidogenesis. The absence of an endogenous luteolysin...

    Authors: Sophie Zatta, Hubert Rehrauer, Aykut Gram, Alois Boos and Mariusz Pawel Kowalewski

    Citation: BMC Genomics 2017 18:757

    Content type: Research article

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  33. This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck’s ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangoli...

    Authors: Zelda du Toit, Morné du Plessis, Desiré L. Dalton, Raymond Jansen, J. Paul Grobler and Antoinette Kotzé

    Citation: BMC Genomics 2017 18:746

    Content type: Research article

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  34. Expansions of gene families are predictive for ongoing genetic adaptation to environmental cues. We describe such an expansion of the carcinoembryonic antigen (CEA) gene family in certain bat families. Members of...

    Authors: Robert Kammerer, Martin Mansfeld, Jana Hänske, Sophie Mißbach, Xiaocui He, Bernd Köllner, Susan Mouchantat and Wolfgang Zimmermann

    Citation: BMC Genomics 2017 18:717

    Content type: Research article

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  35. Severe equine asthma is a naturally occurring lung inflammatory disease of mature animals characterized by neutrophilic inflammation, bronchoconstriction, mucus hypersecretion and airway remodeling. Exacerbati...

    Authors: Laurence Tessier, Olivier Côté, Mary Ellen Clark, Laurent Viel, Andrés Diaz-Méndez, Simon Anders and Dorothee Bienzle

    Citation: BMC Genomics 2017 18:708

    Content type: Research article

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  36. Due to the limited availability and high cost of fish oil in the face of increasing aquaculture production, there is a need to reduce usage of fish oil in aquafeeds without compromising farm fish health. There...

    Authors: Khalil Eslamloo, Xi Xue, Jennifer R. Hall, Nicole C. Smith, Albert Caballero-Solares, Christopher C. Parrish, Richard G. Taylor and Matthew L. Rise

    Citation: BMC Genomics 2017 18:706

    Content type: Research article

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  37. Efficient use of feed resources for farm animals is a critical concern in animal husbandry. Numerous genetic and nutritional studies have been conducted to investigate feed efficiency during the regular laying...

    Authors: Jingwei Yuan, Sirui Chen, Fengying Shi, Guiqin Wu, Aiqiao Liu, Ning Yang and Congjiao Sun

    Citation: BMC Genomics 2017 18:699

    Content type: Original Paper

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  38. The transition from embryonic to posthatch development in the chicken represents a massive metabolic switch from primarily lipolytic to primarily lipogenic metabolism. This metabolic switch is essential for th...

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

    Citation: BMC Genomics 2017 18:687

    Content type: Research article

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  39. Many inherited polyneuropathies (PN) observed in dogs have clinical similarities to the genetically heterogeneous group of Charcot-Marie-Tooth (CMT) peripheral neuropathies in humans. The canine disorders coll...

    Authors: Doreen Becker, Katie M. Minor, Anna Letko, Kari J. Ekenstedt, Vidhya Jagannathan, Tosso Leeb, G. Diane Shelton, James R. Mickelson and Cord Drögemüller

    Citation: BMC Genomics 2017 18:662

    Content type: Research article

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  40. Coliform mastitis is a symptom of postpartum dysgalactia syndrome (PDS), a multifactorial infectious disease of sows. Our previous study showed gene expression profile change after bacterial challenge of porci...

    Authors: A. Jaeger, F. Hadlich, N. Kemper, A. Lübke-Becker, E. Muráni, K. Wimmers and S. Ponsuksili

    Citation: BMC Genomics 2017 18:660

    Content type: Research article

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  41. Maturity of intestinal functions is critical for neonatal health and survival, but comprehensive description of mechanisms underlying intestinal maturation that occur during late gestation still remain poorly ...

    Authors: Ying Yao, Valentin Voillet, Maeva Jegou, Magali SanCristobal, Samir Dou, Véronique Romé, Yannick Lippi, Yvon Billon, Marie-Christine Père, Gaëlle Boudry, Laure Gress, Nathalie Iannucelli, Pierre Mormède, Hélène Quesnel, Laurianne Canario, Laurence Liaubet…

    Citation: BMC Genomics 2017 18:647

    Content type: Research article

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  42. The use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current...

    Authors: Harry D. Dawson, Celine Chen, Brady Gaynor, Jonathan Shao and Joseph F. Urban Jr

    Citation: BMC Genomics 2017 18:643

    Content type: Database

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  43. The importance of poultry as a global source of protein underpins the chicken genome and associated SNP data as key tools in selecting and breeding healthy robust birds with improved disease resistance. SNPs a...

    Authors: Kevin Cadwell, Sherko S. Niranji, Vanessa L. Armstrong, Catherine A. Mowbray, Richard Bailey, Kellie A Watson and Judith Hall

    Citation: BMC Genomics 2017 18:637

    Content type: Research

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  44. Manipulating maternal nutrition during specific periods of gestation can result in re-programming of fetal and post-natal development. In this experiment we investigated how a feed restriction of 85% compared ...

    Authors: Francois Paradis, Katie M. Wood, Kendall C. Swanson, Stephen P. Miller, Brian W. McBride and Carolyn Fitzsimmons

    Citation: BMC Genomics 2017 18:632

    Content type: Research article

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  45. Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today’s broiler (meat-type) chickens. However, this enhanced growth rate was a...

    Authors: C. W. Resnyk, W. Carré, X. Wang, T. E. Porter, J. Simon, E. Le Bihan-Duval, M. J. Duclos, S. E. Aggrey and L. A. Cogburn

    Citation: BMC Genomics 2017 18:626

    Content type: Research article

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  46. Mastitis is the most prevalent disease in dairy sheep with major economic, hygienic and welfare implications. The disease persists in all dairy sheep production systems despite the implementation of improved m...

    Authors: G. Banos, G. Bramis, S. J. Bush, E. L. Clark, M. E.B. McCulloch, J. Smith, G. Schulze, G. Arsenos, D. A. Hume and A. Psifidi

    Citation: BMC Genomics 2017 18:624

    Content type: Research article

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  47. High ambient temperature is known to affect fish gonadal development and physiology in a variety of ways depending on the severity and duration of exposure; however, the underlying molecular mechanisms are poo...

    Authors: Arabinda Mahanty, Gopal Krishna Purohit, Sasmita Mohanty, Nihar Ranjan Nayak and Bimal Prasanna Mohanty

    Citation: BMC Genomics 2017 18:617

    Content type: Research article

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  48. The dark sleeper (Odontobutis potamophila) is an important commercial fish species which shows a sexually dimorphic growth pattern. However, the lack of sex transcriptomic data is hindering further research and g...

    Authors: Cheng Zhao, Guosong Zhang, Shaowu Yin, Zecheng Li, Qintao Wang, Shuqiao Chen and Guoqin Zhou

    Citation: BMC Genomics 2017 18:613

    Content type: Research article

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  49. Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. ...

    Authors: Pamela Wiener, Enrique Sánchez-Molano, Dylan N. Clements, John A. Woolliams, Marie J. Haskell and Sarah C. Blott

    Citation: BMC Genomics 2017 18:609

    Content type: Research article

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  50. The genetic basis of muscle fat deposition in pigs is not well known. So far, we have only identified a limited number of genes involved in the absorption, transport, storage and catabolism of lipids. Such inf...

    Authors: Tainã Figueiredo Cardoso, Raquel Quintanilla, Joan Tibau, Marta Gil, Emilio Mármol-Sánchez, Olga González-Rodríguez, Rayner González-Prendes and Marcel Amills

    Citation: BMC Genomics 2017 18:603

    Content type: Research article

    Published on:

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