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  1. Content type: Research Article

    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

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

  2. Content type: Research Article

    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

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  3. Content type: Research Article

    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

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  4. Content type: Research Article

    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

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  5. Content type: Review

    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

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

  6. Content type: Research Article

    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

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  7. Content type: Research article

    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

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  8. Content type: Research Article

    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

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  9. Content type: Research Article

    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

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  10. Content type: Research Article

    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

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  11. Content type: Research Article

    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

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  12. Content type: Research Article

    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

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  13. Content type: Research Article

    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

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  14. Content type: Research Article

    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

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  15. Content type: Research Article

    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

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  16. Content type: Research Article

    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

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  17. Content type: Research Article

    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

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  18. Content type: Research Article

    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

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  19. Content type: Research Article

    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

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  20. Content type: Research Article

    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

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  21. Content type: Research Article

    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

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  22. Content type: Rsearch Article

    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

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  23. Content type: Short communication

    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

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  24. Content type: Research Article

    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

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  25. Content type: Research Article

    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

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  26. Content type: Research Article

    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

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  27. Content type: Research Article

    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

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  28. Content type: Research Article

    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

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  29. Content type: Research Article

    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

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  30. Content type: Research Article

    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

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  31. Content type: Research Article

    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

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  32. Content type: Research Article

    Traditional genomic prediction models using multiple regression on single nucleotide polymorphisms (SNPs) genotypes exploit associations between genotypes of quantitative trait loci (QTL) and SNPs, which can b...

    Authors: Xiaochen Sun, Rohan Fernando and Jack Dekkers

    Citation: Genetics Selection Evolution 2016 48:77

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  33. Content type: Research Article

    The identification of signals left by recent positive selection provides a feasible approach for targeting genomic variants that underlie complex traits and fitness. A better understanding of the selection mec...

    Authors: Minhui Chen, Dunfei Pan, Hongyan Ren, Jinluan Fu, Junya Li, Guosheng Su, Aiguo Wang, Li Jiang, Qin Zhang and Jian-Feng Liu

    Citation: Genetics Selection Evolution 2016 48:76

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  34. Content type: Research Article

    The majority of chickens in sub-Saharan Africa are indigenous ecotypes, well adapted to the local environment and raised in scavenging production systems. Although they are generally resilient to disease chall...

    Authors: Androniki Psifidi, Georgios Banos, Oswald Matika, Takele T. Desta, Judy Bettridge, David A. Hume, Tadelle Dessie, Rob Christley, Paul Wigley, Olivier Hanotte and Pete Kaiser

    Citation: Genetics Selection Evolution 2016 48:74

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  35. Content type: Research Article

    Extending the reference set for genomic predictions in dairy cattle by adding large numbers of cows with genotypes and phenotypes has been proposed as a means to increase reliability of selection decisions for...

    Authors: Laura Plieschke, Christian Edel, Eduardo C. G. Pimentel, Reiner Emmerling, Jörn Bennewitz and Kay-Uwe Götz

    Citation: Genetics Selection Evolution 2016 48:73

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  36. Content type: Research Article

    Feed efficiency of farm animals has greatly improved through genetic selection for production. Today, we are faced with the limits of our ability to predict the effect of selection on feed efficiency, partly b...

    Authors: Laurence Puillet, Denis Réale and Nicolas C. Friggens

    Citation: Genetics Selection Evolution 2016 48:72

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  37. Content type: Research Article

    Genotype imputation is a key element of the implementation of genomic selection within the New Zealand sheep industry, but many factors can influence imputation accuracy. Our objective was to provide practical...

    Authors: Ricardo V. Ventura, Stephen P. Miller, Ken G. Dodds, Benoit Auvray, Michael Lee, Matthew Bixley, Shannon M. Clarke and John C. McEwan

    Citation: Genetics Selection Evolution 2016 48:71

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  38. Content type: Research Article

    The management of genetic variation in a breeding scheme relies very much on the control of the average relationship between selected parents. Optimum contribution selection is a method that seeks the optimum ...

    Authors: Binyam S. Dagnachew and Theo H. E. Meuwissen

    Citation: Genetics Selection Evolution 2016 48:70

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  39. Content type: Research Article

    Mortality due to cannibalism causes both economic and welfare problems in laying hens. To limit mortality due to cannibalism, laying hens are often beak-trimmed, which is undesirable for animal welfare reasons...

    Authors: Setegn W. Alemu, Mario P. L. Calus, William M. Muir, Katrijn Peeters, Addie Vereijken and Piter Bijma

    Citation: Genetics Selection Evolution 2016 48:68

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  40. Content type: Research Article

    Dominance and imprinting genetic effects have been shown to contribute to genetic variance for certain traits but are usually ignored in genomic prediction of complex traits in livestock. The objectives of thi...

    Authors: Xiangyu Guo, Ole Fredslund Christensen, Tage Ostersen, Yachun Wang, Mogens Sandø Lund and Guosheng Su

    Citation: Genetics Selection Evolution 2016 48:67

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  41. Content type: Short communication

    Structural chromosome abnormalities are well known as factors that reduce fertility rate in domestic pigs. According to large-scale national cytogenetic screening programs that are implemented in France, it is...

    Authors: Anh T. Quach, Tamas Revay, Daniel A. F. Villagomez, Mariana P. Macedo, Alison Sullivan, Laurence Maignel, Stefanie Wyss, Brian Sullivan and W. Allan King

    Citation: Genetics Selection Evolution 2016 48:66

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  42. Content type: Software

    Identification of genes or even nucleotides that are responsible for quantitative and adaptive trait variation is a difficult task due to the complex interdependence between a large number of genetic and envir...

    Authors: Strahil Ristov, Vladimir Brajkovic, Vlatka Cubric-Curik, Ivan Michieli and Ino Curik

    Citation: Genetics Selection Evolution 2016 48:65

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  43. Content type: Research Article

    In shrimp farming, major production losses are caused by viruses. Hepatopancreatic parvovirus (HPV) is one of the viral pathogens that infect banana shrimp (Fenneropenaeus merguiensis). HPV is thought to slow dow...

    Authors: Chontida Phuthaworn, Nguyen Hong Nguyen, Jane Quinn and Wayne Knibb

    Citation: Genetics Selection Evolution 2016 48:64

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  44. Content type: Research Article

    Selective breeding for genetic improvement is expected to leave distinctive selection signatures within genomes. The identification of selection signatures can help to elucidate the mechanisms of selection and...

    Authors: Xing Guo, Qi Fang, Chendong Ma, Bangyuan Zhou, Yi Wan and Runshen Jiang

    Citation: Genetics Selection Evolution 2016 48:62

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  45. Content type: Research Article

    For some species, animal production systems are based on the use of crossbreeding to take advantage of the increased performance of crossbred compared to purebred animals. Effects of single nucleotide polymorp...

    Authors: Jérémie Vandenplas, Mario P. L. Calus, Claudia A. Sevillano, Jack J. Windig and John W. M. Bastiaansen

    Citation: Genetics Selection Evolution 2016 48:61

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