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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 5 of 18

  1. Content type: Research article

    A strain of Leghorn chickens (rd/rd), unable to produce a functional riboflavin-binding protein, lays riboflavin-deficient eggs, in which all embryos suddenly die at mid-incubation (days 13-15). This malady, caus...

    Authors: Larry A. Cogburn, Danielle N. Smarsh, Xiaofei Wang, Nares Trakooljul, Wilfrid Carré and Harold B. White III

    Citation: BMC Genomics 2018 19:177

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  2. Content type: Research article

    Southern flounder, Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States. Low year-class strengths over the past few years in the we...

    Authors: Shannon J. O’Leary, Christopher M. Hollenbeck, Robert R. Vega, John R. Gold and David S. Portnoy

    Citation: BMC Genomics 2018 19:163

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  3. Content type: Research article

    The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos ...

    Authors: Josiah T. Wagner, Param Priya Singh, Amie L. Romney, Claire L. Riggs, Patrick Minx, Steven C. Woll, Jake Roush, Wesley C. Warren, Anne Brunet and Jason E. Podrabsky

    Citation: BMC Genomics 2018 19:155

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  4. Content type: Research article

    Improving the efficiency of animal production is a relentless pursuit of ruminant producers. Energy utilization and partition can be affected by dietary composition and nutrient availability. Furthermore, the ...

    Authors: Haitao Shi, Jun Zhang, Shengli Li, Shoukun Ji, Zhijun Cao, Hongtao Zhang and Yajing Wang

    Citation: BMC Genomics 2018 19:148

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  5. Content type: Research article

    RNA is known to play diverse roles in gene regulation. The clues for this regulatory function of RNA are embedded in its ability to fold into intricate secondary and tertiary structure.

    Authors: Kriti Kaushik, Ambily Sivadas, Shamsudheen Karuthedath Vellarikkal, Ankit Verma, Rijith Jayarajan, Satyaprakash Pandey, Tavprithesh Sethi, Souvik Maiti, Vinod Scaria and Sridhar Sivasubbu

    Citation: BMC Genomics 2018 19:147

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  6. Content type: Research article

    The identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypi...

    Authors: Tainã Figueiredo Cardoso, Raquel Quintanilla, Anna Castelló, Rayner González-Prendes, Marcel Amills and Ángela Cánovas

    Citation: BMC Genomics 2018 19:145

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  7. Content type: Research article

    Bovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling ...

    Authors: Hugo A. Carignano, Dana L. Roldan, María J. Beribe, María A. Raschia, Ariel Amadio, Juan P. Nani, Gerónimo Gutierrez, Irene Alvarez, Karina Trono, Mario A. Poli and Marcos M. Miretti

    Citation: BMC Genomics 2018 19:142

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  8. Content type: Research article

    Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted...

    Authors: Zihao Yuan, Shikai Liu, Tao Zhou, Changxu Tian, Lisui Bao, Rex Dunham and Zhanjiang Liu

    Citation: BMC Genomics 2018 19:141

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  9. Content type: Research article

    Infertility is a longstanding limitation in livestock production with important economic impact for the cattle industry. Female reproductive traits are polygenic and lowly heritable in nature, thus selection f...

    Authors: Sarah E. Dickinson, Brock A. Griffin, Michelle F. Elmore, Lisa Kriese-Anderson, Joshua B. Elmore, Paul W. Dyce, Soren P. Rodning and Fernando H. Biase

    Citation: BMC Genomics 2018 19:129

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  10. Content type: Research article

    The purpose of this study was to identify transcripts of retinal rod photoreceptors of the zebrafish. The zebrafish is an important animal model for vision science due to rapid and tractable development, persi...

    Authors: Chi Sun, Carlos Galicia and Deborah L. Stenkamp

    Citation: BMC Genomics 2018 19:127

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  11. Content type: Research article

    The amount of intramuscular fat can influence the sensory characteristics and nutritional value of beef, thus the selection of animals with adequate fat deposition is important to the consumer. There is growin...

    Authors: Gabriella B. Oliveira, Luciana C. A. Regitano, Aline S. M. Cesar, James M. Reecy, Karina Y. Degaki, Mirele D. Poleti, Andrezza M. Felício, James E. Koltes and Luiz L. Coutinho

    Citation: BMC Genomics 2018 19:126

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  12. Content type: Research article

    Numerous studies have established a link between maternal diet and the physiological and metabolic phenotypes of their offspring. In previous studies in sheep, we demonstrated that different maternal diets alt...

    Authors: Hadjer Namous, Francisco Peñagaricano, Marcello Del Corvo, Emanuele Capra, David L. Thomas, Alessandra Stella, John L. Williams, Paolo Ajmone Marsan and Hasan Khatib

    Citation: BMC Genomics 2018 19:123

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  13. Content type: Research article

    Skeletal muscle in livestock develops into meat, an important source of protein and other nutrients for human consumption. The muscle is largely composed of a fixed number of multinucleated myofibers determine...

    Authors: Tomasz Sadkowski, Anna Ciecierska, Jolanta Oprządek and Edyta Balcerek

    Citation: BMC Genomics 2018 19:109

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  14. Content type: Research article

    Genomic prediction using Diversity Arrays Technology (DArT) genotype by sequencing platform has not been reported in yellowtail kingfish (Seriola lalandi). The principal aim of this study was to address this know...

    Authors: Nguyen H. Nguyen, H. K. A. Premachandra, Andrzej Kilian and Wayne Knibb

    Citation: BMC Genomics 2018 19:107

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  15. Content type: Research article

    The highly prolific breeds of domestic sheep (Ovis aries) are globally valuable genetic resources for sheep industry. Genetic, nutritional and other environmental factors affect prolificacy traits in sheep. To im...

    Authors: Kisun Pokharel, Jaana Peippo, Mervi Honkatukia, Arja Seppälä, Johanna Rautiainen, Nasser Ghanem, Tuula-Marjatta Hamama, Mark A. Crowe, Magnus Andersson, Meng-Hua Li and Juha Kantanen

    Citation: BMC Genomics 2018 19:104

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  16. Content type: Research article

    While autozygosity as a consequence of selection is well understood, there is limited information on the ability of different methods to measure true inbreeding. In the present study, a gene dropping simulatio...

    Authors: Mehrnush Forutan, Saeid Ansari Mahyari, Christine Baes, Nina Melzer, Flavio Schramm Schenkel and Mehdi Sargolzaei

    Citation: BMC Genomics 2018 19:98

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  17. Content type: Research article

    Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particula...

    Authors: Clarissa Boschiero, Gabriel Costa Monteiro Moreira, Almas Ara Gheyas, Thaís Fernanda Godoy, Gustavo Gasparin, Pilar Drummond Sampaio Corrêa Mariani, Marcela Paduan, Aline Silva Mello Cesar, Mônica Corrêa Ledur and Luiz Lehmann Coutinho

    Citation: BMC Genomics 2018 19:83

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  18. Content type: Research article

    The genetics underlying body mass and growth are key to understanding a wide range of topics in biology, both evolutionary and developmental. Body mass and growth traits are affected by many genetic variants o...

    Authors: Martin Johnsson, Rie Henriksen, Andrey Höglund, Jesper Fogelholm, Per Jensen and Dominic Wright

    Citation: BMC Genomics 2018 19:72

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  19. Content type: Research article

    One of the approaches to detect genetics variants affecting fitness traits is to identify their surrounding genomic signatures of past selection. With established methods for detecting selection signatures and...

    Authors: Christina Marie Rochus, Flavie Tortereau, Florence Plisson-Petit, Gwendal Restoux, Carole Moreno-Romieux, Gwenola Tosser-Klopp and Bertrand Servin

    Citation: BMC Genomics 2018 19:71

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  20. Content type: Research article

    Infectious disease is the single greatest threat to taxa such as amphibians (chytrid fungus), bats (white nose syndrome), Tasmanian devils (devil facial tumor disease), and black-footed ferrets (canine distemp...

    Authors: Jean P. Elbers, Mary B. Brown and Sabrina S. Taylor

    Citation: BMC Genomics 2018 19:64

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  21. Content type: Research article

    The neural crest (NC) is a class of transitory stem cell-like cells unique to vertebrate embryos. NC cells arise within the dorsal neural tube where they undergo an epithelial to mesenchymal transition in orde...

    Authors: Nicole J. Ward, Darrell Green, Janet Higgins, Tamas Dalmay, Andrea Münsterberg, Simon Moxon and Grant N. Wheeler

    Citation: BMC Genomics 2018 19:59

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  22. Content type: Research article

    Intramuscular fat (IMF) is one of the important factors influencing meat quality, however, for chickens, the molecular regulatory mechanisms underlying this trait have not yet been clear. In this study, a syst...

    Authors: Huanxian Cui, Maiqing Zheng, Guiping Zhao, Ranran Liu and Jie Wen

    Citation: BMC Genomics 2018 19:55

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  23. Content type: Research article

    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

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  24. Content type: Research article

    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

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

  25. Content type: Research article

    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

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  26. Content type: Research article

    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

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  27. Content type: Research article

    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

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  28. Content type: Research article

    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

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  29. Content type: Research article

    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

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  30. Content type: Research article

    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

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  31. Content type: Research article

    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

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  32. Content type: Research article

    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

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  33. Content type: Research article

    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

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  34. Content type: Research article

    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

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  35. Content type: Research article

    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

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  36. Content type: Research article

    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

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  37. Content type: Research article

    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

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  38. Content type: Research article

    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

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  39. Content type: Research article

    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

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  40. Content type: Research

    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

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  41. Content type: Research article

    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

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  42. Content type: Research article

    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

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  43. Content type: Research article

    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

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  44. Content type: Research article

    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

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  45. Content type: Research article

    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

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  46. Content type: Research

    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

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  47. Content type: Research article

    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

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  48. Content type: Research article

    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

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  49. Content type: Research article

    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

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  50. Content type: Research article

    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

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