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  1. This paper describes a combined heuristic and hidden Markov model (HMM) method to accurately impute missing genotypes in livestock datasets. Genomic selection in breeding programs requires high-density genotyp...

    Authors: Roberto Antolín, Carl Nettelblad, Gregor Gorjanc, Daniel Money and John M. Hickey

    Citation: Genetics Selection Evolution 2017 49:30

    Content type: Research Article

    Published on:

  2. An important issue in genetic evaluation is the comparability of random effects (breeding values), particularly between pairs of animals in different contemporary groups. This is usually referred to as genetic...

    Authors: John B. Holmes, Ken G. Dodds and Michael A. Lee

    Citation: Genetics Selection Evolution 2017 49:29

    Content type: Research Article

    Published on:

  3. DNA-based predictions for hard-to-measure production traits hold great promise for selective breeding programs. DNA pooling might provide a cheap genomic approach to use phenotype data from commercial flocks w...

    Authors: Amy M. Bell, John M. Henshall, Laercio R. Porto-Neto, Sonja Dominik, Russell McCulloch, James Kijas and Sigrid A. Lehnert

    Citation: Genetics Selection Evolution 2017 49:28

    Content type: Research Article

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  4. Large amounts of fat deposition often lead to loss of reproductive efficiency in humans and animals. We used broiler chickens as a model species to conduct a two-directional selection for and against abdominal...

    Authors: Hui Zhang, Wei Na, Hong-Li Zhang, Ning Wang, Zhi-Qiang Du, Shou-Zhi Wang, Zhi-Peng Wang, Zhiwu Zhang and Hui Li

    Citation: Genetics Selection Evolution 2017 49:25

    Content type: Research Article

    Published on:

  5. The availability of dense genotypes and whole-genome sequence variants from various sources offers the opportunity to compile large datasets consisting of tens of thousands of individuals with genotypes at mil...

    Authors: Hubert Pausch, Iona M. MacLeod, Ruedi Fries, Reiner Emmerling, Phil J. Bowman, Hans D. Daetwyler and Michael E. Goddard

    Citation: Genetics Selection Evolution 2017 49:24

    Content type: Research Article

    Published on:

  6. In France, two main diseases threaten Pacific oyster production. Since 2008, Crassostrea gigas spat have suffered massive losses due to the ostreid herpesvirus OsHV-1, and since 2012, significant mortalities in c...

    Authors: Patrick Azéma, Jean-Baptiste Lamy, Pierre Boudry, Tristan Renault, Marie-Agnès Travers and Lionel Dégremont

    Citation: Genetics Selection Evolution 2017 49:23

    Content type: Research article

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  7. Selection acts strongly on individuals that colonise a habitat and have phenotypic traits that deviate from the local optima. Our objective was to investigate the evolutionary rates in Atlantic salmon (Salmo sal...

    Authors: Arne Johan Jensen, Lars Petter Hansen, Bjørn Ove Johnsen and Sten Karlsson

    Citation: Genetics Selection Evolution 2017 49:22

    Content type: Research Article

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  8. Genome-wide association studies (GWAS) have been extensively used to identify genomic regions associated with a variety of phenotypic traits in pigs. Until now, most GWAS have explored single-trait association...

    Authors: Yuanmei Guo, Yixuan Huang, Lijuan Hou, Junwu Ma, Congying Chen, Huashui Ai, Lusheng Huang and Jun Ren

    Citation: Genetics Selection Evolution 2017 49:21

    Content type: Research Article

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  9. Bovine milk is widely regarded as a nutritious food source for humans, although the effects of individual fatty acids on human health is a subject of debate. Based on the assumption that genomic selection offe...

    Authors: Hanne Gro Olsen, Tim Martin Knutsen, Achim Kohler, Morten Svendsen, Lars Gidskehaug, Harald Grove, Torfinn Nome, Marte Sodeland, Kristil Kindem Sundsaasen, Matthew Peter Kent, Harald Martens and Sigbjørn Lien

    Citation: Genetics Selection Evolution 2017 49:20

    Content type: Research Article

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  10. Sheep production in Israel has improved by crossing the fat-tailed local Awassi breed with the East Friesian and later, with the Booroola Merino breed, which led to the formation of the highly prolific Afec-As...

    Authors: Eyal Seroussi, Alexander Rosov, Andrey Shirak, Alon Lam and Elisha Gootwine

    Citation: Genetics Selection Evolution 2017 49:19

    Content type: Research

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  11. Feather pecking and aggressive pecking in laying hens are serious economic and welfare issues. In spite of extensive research on feather pecking during the last decades, the motivation for this behavior is sti...

    Authors: Vanessa Lutz, Patrick Stratz, Siegfried Preuß, Jens Tetens, Michael A. Grashorn, Werner Bessei and Jörn Bennewitz

    Citation: Genetics Selection Evolution 2017 49:18

    Content type: Research Article

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  12. Previously, we have shown that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between...

    Authors: Roger L. Vallejo, Timothy D. Leeds, Guangtu Gao, James E. Parsons, Kyle E. Martin, Jason P. Evenhuis, Breno O. Fragomeni, Gregory D. Wiens and Yniv Palti

    Citation: Genetics Selection Evolution 2017 49:17

    Content type: Research Article

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  13. Genomic selection has been successfully implemented in plant and animal breeding programs to shorten generation intervals and accelerate genetic progress per unit of time. In practice, genomic selection can be...

    Authors: Mehdi Momen, Ahmad Ayatollahi Mehrgardi, Ayoub Sheikhy, Ali Esmailizadeh, Masood Asadi Fozi, Andreas Kranis, Bruno D. Valente, Guilherme J. M. Rosa and Daniel Gianola

    Citation: Genetics Selection Evolution 2017 49:16

    Content type: Research Article

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  14. Sea lice infestations caused by Caligus rogercresseyi are a main concern to the salmon farming industry due to associated economic losses. Resistance to this parasite was shown to have low to moderate genetic var...

    Authors: Katharina Correa, Rama Bangera, René Figueroa, Jean P. Lhorente and José M. Yáñez

    Citation: Genetics Selection Evolution 2017 49:15

    Content type: Short communication

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  15. Environmental exposures, for instance to chemicals, are known to impact plant and animal phenotypes on the long term, sometimes across several generations. Such transgenerational phenotypes were shown to be pr...

    Authors: Sophie Leroux, David Gourichon, Christine Leterrier, Yann Labrune, Vincent Coustham, Sandrine Rivière, Tatiana Zerjal, Jean-Luc Coville, Mireille Morisson, Francis Minvielle and Frédérique Pitel

    Citation: Genetics Selection Evolution 2017 49:14

    Content type: Research Article

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  16. Several examples of structural variation (SV) affecting phenotypic traits have been reported in cattle. Currently the identification of SV from whole-genome sequence data (WGS) suffers from a high false positi...

    Authors: Long Chen, Amanda J. Chamberlain, Coralie M. Reich, Hans D. Daetwyler and Ben J. Hayes

    Citation: Genetics Selection Evolution 2017 49:13

    Content type: Research Article

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    The Erratum to this article has been published in Genetics Selection Evolution 2017 49:31

  17. Selection for sound conformation has been widely used as a primary approach to reduce lameness and leg weakness in pigs. Identification of genomic regions that affect conformation traits would help to improve ...

    Authors: Thu H. Le, Ole F. Christensen, Bjarne Nielsen and Goutam Sahana

    Citation: Genetics Selection Evolution 2017 49:12

    Content type: Research Article

    Published on:

  18. Some genetic studies need to take into account correlations between traits that are repeatedly measured over time. Multiple-trait random regression models are commonly used to analyze repeated traits but suffe...

    Authors: Ingrid David, Hervé Garreau, Elodie Balmisse, Yvon Billon and Laurianne Canario

    Citation: Genetics Selection Evolution 2017 49:11

    Content type: Research Article

    Published on:

  19. Performance recording and genotyping in the multiplier tier of multi-tiered sheep breeding schemes could potentially reduce the difference in the average genetic merit between nucleus and commercial flocks, an...

    Authors: Bruno F. S. Santos, Julius H. J. van der Werf, John P. Gibson, Timothy J. Byrne and Peter R. Amer

    Citation: Genetics Selection Evolution 2017 49:10

    Content type: Research Article

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  20. Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the...

    Authors: Robert J. Wallace, Timothy J. Snelling, Christine A. McCartney, Ilma Tapio and Francesco Strozzi

    Citation: Genetics Selection Evolution 2017 49:9

    Content type: Review

    Published on:

    The Erratum to this article has been published in Genetics Selection Evolution 2017 49:27

  21. With the availability of next-generation sequencing technologies, genomic prediction based on whole-genome sequencing (WGS) data is now feasible in animal breeding schemes and was expected to lead to higher pr...

    Authors: Guiyan Ni, David Cavero, Anna Fangmann, Malena Erbe and Henner Simianer

    Citation: Genetics Selection Evolution 2017 49:8

    Content type: Research Article

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  22. Multi-marker methods, which fit all markers simultaneously, were originally tailored for genomic selection purposes, but have proven to be useful also in association analyses, especially the so-called BayesC B...

    Authors: Jörn Bennewitz, Christian Edel, Ruedi Fries, Theo H. E. Meuwissen and Robin Wellmann

    Citation: Genetics Selection Evolution 2017 49:7

    Content type: Research article

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  23. Improving functional annotation of the chicken genome is a key challenge in bridging the gap between genotype and phenotype. Among all transcribed regions, long noncoding RNAs (lncRNAs) are a major component o...

    Authors: Kévin Muret, Christophe Klopp, Valentin Wucher, Diane Esquerré, Fabrice Legeai, Frédéric Lecerf, Colette Désert, Morgane Boutin, Frédéric Jehl, Hervé Acloque, Elisabetta Giuffra, Sarah Djebali, Sylvain Foissac, Thomas Derrien and Sandrine Lagarrigue

    Citation: Genetics Selection Evolution 2017 49:6

    Content type: Research Article

    Published on:

  24. Number of functional teats is an important trait in commercial swine production. As litter size increases, the number of teats must also increase to supply nutrition to all piglets. Therefore, a genome-wide as...

    Authors: Gary A. Rohrer and Dan J. Nonneman

    Citation: Genetics Selection Evolution 2017 49:4

    Content type: Research Article

    Published on:

  25. This paper uses simulation to explore how gene drives can increase genetic gain in livestock breeding programs. Gene drives are naturally occurring phenomena that cause a mutation on one chromosome to copy it...

    Authors: Serap Gonen, Janez Jenko, Gregor Gorjanc, Alan J. Mileham, C. Bruce A. Whitelaw and John M. Hickey

    Citation: Genetics Selection Evolution 2017 49:3

    Content type: Research Article

    Published on:

  26. Genomic predictions from BayesA and BayesB use training data that include animals with both phenotypes and genotypes. Single-step methodologies allow additional information from non-genotyped relatives to be i...

    Authors: Joonho Lee, Hao Cheng, Dorian Garrick, Bruce Golden, Jack Dekkers, Kyungdo Park, Deukhwan Lee and Rohan Fernando

    Citation: Genetics Selection Evolution 2017 49:2

    Content type: Research Article

    Published on:

  27. Hanwoo beef is known for its marbled fat, tenderness, juiciness and characteristic flavor, as well as for its low cholesterol and high omega 3 fatty acid contents. As yet, there has been no comprehensive inves...

    Authors: Hossein Mehrban, Deuk Hwan Lee, Mohammad Hossein Moradi, Chung IlCho, Masoumeh Naserkheil and Noelia Ibáñez-Escriche

    Citation: Genetics Selection Evolution 2017 49:1

    Content type: Research Article

    Published on:

  28. Two types of models have been used for single-step genomic prediction and genome-wide association studies that include phenotypes from both genotyped animals and their non-genotyped relatives. The two types ar...

    Authors: Rohan L. Fernando, Hao Cheng, Bruce L. Golden and Dorian J. Garrick

    Citation: Genetics Selection Evolution 2016 48:96

    Content type: Research Article

    Published on:

  29. Whole-genome sequence data is expected to capture genetic variation more completely than common genotyping panels. Our objective was to compare the proportion of variance explained and the accuracy of genomic ...

    Authors: Roel F. Veerkamp, Aniek C. Bouwman, Chris Schrooten and Mario P. L. Calus

    Citation: Genetics Selection Evolution 2016 48:95

    Content type: Research Article

    Published on:

  30. Rainbow trout is an important aquaculture species, which has a worldwide distribution across various production environments. The diverse locations of trout farms involve remarkable variation in environmental...

    Authors: Matti Janhunen, Juha Koskela, Nguyễn Hữu Ninh, Harri Vehviläinen, Heikki Koskinen, Antti Nousiainen and Ngô Phú Thỏa

    Citation: Genetics Selection Evolution 2016 48:94

    Content type: Research Article

    Published on:

  31. The gastrointestinal tract is populated by a complex and vast microbial network, with a composition that reflects the relationships of the symbiosis, co-metabolism, and co-evolution of these microorganisms wit...

    Authors: Jinmei Ding, Lele Zhao, Lifeng Wang, Wenjing Zhao, Zhengxiao Zhai, Li Leng, Yuxiang Wang, Chuan He, Yan Zhang, Heping Zhang, Hui Li and He Meng

    Citation: Genetics Selection Evolution 2016 48:93

    Content type: Research Article

    Published on:

  32. Improved performance of crossbred animals is partly due to heterosis. One of the major genetic bases of heterosis is dominance, but it is seldom used in pedigree-based genetic evaluation of livestock. Recently...

    Authors: Tao Xiang, Ole Fredslund Christensen, Zulma Gladis Vitezica and Andres Legarra

    Citation: Genetics Selection Evolution 2016 48:92

    Content type: Research Article

    Published on:

  33. In nucleus populations, regions of the genome that have a high frequency of runs of homozygosity (ROH) occur and are associated with a reduction in genetic diversity, as well as adverse effects on fitness. It ...

    Authors: Jeremy T. Howard, Francesco Tiezzi, Yijian Huang, Kent A. Gray and Christian Maltecca

    Citation: Genetics Selection Evolution 2016 48:91

    Content type: Research Article

    Published on:

  34. Bovine tuberculosis (bTB) is a disease of significant economic importance and is a persistent animal health problem with implications for public health worldwide. Control of bTB in the UK has relied on diagnos...

    Authors: Smaragda Tsairidou, Susan Brotherstone, Mike Coffey, Stephen C. Bishop and John A. Woolliams

    Citation: Genetics Selection Evolution 2016 48:90

    Content type: Research Article

    Published on:

  35. Volatile organic compounds determine important quality traits in cheese. The aim of this work was to infer genetic parameters of the profile of volatile compounds in cheese as revealed by direct-injection mass...

    Authors: Matteo Bergamaschi, Alessio Cecchinato, Franco Biasioli, Flavia Gasperi, Bruno Martin and Giovanni Bittante

    Citation: Genetics Selection Evolution 2016 48:89

    Content type: Research Article

    Published on:

  36. Understanding the history of cattle breeds is important because it provides the basis for developing appropriate selection and breed improvement programs. In this study, patterns of ancestry and admixture in A...

    Authors: Sithembile O. Makina, Lindsey K. Whitacre, Jared E. Decker, Jeremy F. Taylor, Michael D. MacNeil, Michiel M. Scholtz, Este van Marle-Köster, Farai C. Muchadeyi, Mahlako L. Makgahlela and Azwihangwisi Maiwashe

    Citation: Genetics Selection Evolution 2016 48:88

    Content type: Research Article

    Published on:

  37. In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability.

    Authors: Mekki Boussaha, Pauline Michot, Rabia Letaief, Chris Hozé, Sébastien Fritz, Cécile Grohs, Diane Esquerré, Amandine Duchesne, Romain Philippe, Véronique Blanquet, Florence Phocas, Sandrine Floriot, Dominique Rocha, Christophe Klopp, Aurélien Capitan and Didier Boichard

    Citation: Genetics Selection Evolution 2016 48:87

    Content type: Rsearch Article

    Published on:

  38. Accurate genomic analyses are predicated upon access to accurate genotype input data. The objective of this study was to quantify the reproducibility of genotype data that are generated from the same genotype ...

    Authors: Donagh P. Berry, Aine O’Brien, Eamonn Wall, Kevin McDermott, Shane Randles, Paul Flynn, Stephen Park, Jenny Grose, Rebecca Weld and Noirin McHugh

    Citation: Genetics Selection Evolution 2016 48:86

    Content type: Short communication

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  39. Central testing is used to select young bulls which are likely to contribute to increased net income of the commercial beef cattle herd. We present genetic parameters for growth and reproductive traits on perf...

    Authors: Fernanda S. S. Raidan, Dalinne C. C. Santos, Mariana M. Moraes, Andresa E. M. Araújo, Henrique T. Ventura, José A. G. Bergmann, Eduardo M. Turra and Fabio L. B. Toral

    Citation: Genetics Selection Evolution 2016 48:85

    Content type: Research Article

    Published on:

  40. Genomic prediction for novel traits, which can be costly and labor-intensive to measure, is often hampered by low accuracy due to the limited size of the reference population. As an option to improve predictio...

    Authors: Chen Yao, Xiaojin Zhu and Kent A. Weigel

    Citation: Genetics Selection Evolution 2016 48:84

    Content type: Research Article

    Published on:

  41. Sequence data can potentially increase the reliability of genomic predictions, because such data include causative mutations instead of relying on linkage disequilibrium (LD) between causative mutations and pr...

    Authors: Irene van den Berg, Didier Boichard and Mogens S. Lund

    Citation: Genetics Selection Evolution 2016 48:83

    Content type: Research Article

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  42. A genomic relationship matrix (GRM) can be inverted efficiently with the Algorithm for Proven and Young (APY) through recursion on a small number of core animals. The number of core animals is theoretically li...

    Authors: Ivan Pocrnic, Daniela A. L. Lourenco, Yutaka Masuda and Ignacy Misztal

    Citation: Genetics Selection Evolution 2016 48:82

    Content type: Research Article

    Published on:

  43. Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can ...

    Authors: Aldemar González-Rodríguez, Sebastián Munilla, Elena F. Mouresan, Jhon J. Cañas-Álvarez, Clara Díaz, Jesús Piedrafita, Juan Altarriba, Jesús Á. Baro, Antonio Molina and Luis Varona

    Citation: Genetics Selection Evolution 2016 48:81

    Content type: Research Article

    Published on:

  44. The mixed linear model employed for genomic best linear unbiased prediction (GBLUP) includes the breeding value for each animal as a random effect that has a mean of zero and a covariance matrix proportional t...

    Authors: Rohan L. Fernando, Hao Cheng and Dorian J. Garrick

    Citation: Genetics Selection Evolution 2016 48:80

    Content type: Research Article

    Published on:

  45. Clinical mastitis is an inflammation of the mammary gland and causes significant costs to dairy production. It is unfavourably genetically correlated to milk production, and, thus, knowledge of the mechanisms ...

    Authors: Hanne Gro Olsen, Tim Martin Knutsen, Anna M. Lewandowska-Sabat, Harald Grove, Torfinn Nome, Morten Svendsen, Mariann Arnyasi, Marte Sodeland, Kristil K. Sundsaasen, Sandra Rinne Dahl, Bjørg Heringstad, Hanne H. Hansen, Ingrid Olsaker, Matthew Peter Kent and Sigbjørn Lien

    Citation: Genetics Selection Evolution 2016 48:79

    Content type: Research Article

    Published on:

  46. The mode of inheritance of horn status in sheep is far more complex than a superficial analysis might suggest. Observations, which were mostly based on crossbreeding experiments, indicated that the allele that...

    Authors: Gesine Lühken, Stefan Krebs, Sophie Rothammer, Julia Küpper, Boro Mioč, Ingolf Russ and Ivica Medugorac

    Citation: Genetics Selection Evolution 2016 48:78

    Content type: Research Article

    Published on:

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