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  1. Research Article

    Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture

    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...

    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

    Genetics Selection Evolution 2017 49:17

    Published on: 1 February 2017

  2. Short communication

    The use of genomic information increases the accuracy of breeding value predictions for sea louse (Caligus rogercresseyi) resistance in Atlantic salmon (Salmo salar)

    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...

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

    Genetics Selection Evolution 2017 49:15

    Published on: 31 January 2017

  3. Research Article

    Embryonic environment and transgenerational effects in quail

    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...

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

    Genetics Selection Evolution 2017 49:14

    Published on: 26 January 2017

  4. Research Article

    Detection and validation of structural variations in bovine whole-genome sequence data

    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...

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

    Genetics Selection Evolution 2017 49:13

    Published on: 25 January 2017

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

  5. Research Article

    Genome-wide association study for conformation traits in three Danish pig breeds

    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 ...

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

    Genetics Selection Evolution 2017 49:12

    Published on: 24 January 2017

  6. Research Article

    Multiple-trait structured antedependence model to study the relationship between litter size and birth weight in pigs and rabbits

    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...

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

    Genetics Selection Evolution 2017 49:11

    Published on: 20 January 2017

  7. Research Article

    Genetic and economic benefits of selection based on performance recording and genotyping in lower tiers of multi-tiered sheep breeding schemes

    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...

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

    Genetics Selection Evolution 2017 49:10

    Published on: 17 January 2017

  8. Research Article

    Whole-genome sequence-based genomic prediction in laying chickens with different genomic relationship matrices to account for genetic architecture

    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...

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

    Genetics Selection Evolution 2017 49:8

    Published on: 16 January 2017

  9. Review

    Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism

    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...

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

    Genetics Selection Evolution 2017 49:9

    Published on: 16 January 2017

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

  10. Research article

    Application of a Bayesian dominance model improves power in quantitative trait genome-wide association analysis

    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...

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

    Genetics Selection Evolution 2017 49:7

    Published on: 14 January 2017

  11. Research Article

    Long noncoding RNA repertoire in chicken liver and adipose tissue

    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...

    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

    Genetics Selection Evolution 2017 49:6

    Published on: 10 January 2017

  12. Research Article

    Derivation of economic values for production traits in aquaculture species

    In breeding programs for aquaculture species, breeding goal traits are often weighted based on the desired gains but economic gain would be higher if economic values were used instead. The objectives of this s...

    Kasper Janssen, Paul Berentsen, Mathieu Besson and Hans Komen

    Genetics Selection Evolution 2017 49:5

    Published on: 5 January 2017

  13. Research Article

    Comparison of alternative approaches to single-trait genomic prediction using genotyped and non-genotyped Hanwoo beef cattle

    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...

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

    Genetics Selection Evolution 2017 49:2

    Published on: 4 January 2017

  14. Research Article

    Genetic analysis of teat number in pigs reveals some developmental pathways independent of vertebra number and several loci which only affect a specific side

    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...

    Gary A. Rohrer and Dan J. Nonneman

    Genetics Selection Evolution 2017 49:4

    Published on: 4 January 2017

  15. Research Article

    Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs

    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...

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

    Genetics Selection Evolution 2017 49:3

    Published on: 4 January 2017

  16. Research Article

    Predictive performance of genomic selection methods for carcass traits in Hanwoo beef cattle: impacts of the genetic architecture

    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...

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

    Genetics Selection Evolution 2017 49:1

    Published on: 4 January 2017

  17. Research Article

    Computational strategies for alternative single-step Bayesian regression models with large numbers of genotyped and non-genotyped animals

    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...

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

    Genetics Selection Evolution 2016 48:96

    Published on: 8 December 2016

  18. Research Article

    Genomic prediction using preselected DNA variants from a GWAS with whole-genome sequence data in Holstein–Friesian cattle

    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 ...

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

    Genetics Selection Evolution 2016 48:95

    Published on: 1 December 2016

  19. Research Article

    Thermal sensitivity of growth indicates heritable variation in 1-year-old rainbow trout (Oncorhynchus mykiss)

    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...

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

    Genetics Selection Evolution 2016 48:94

    Published on: 29 November 2016

  20. Research Article

    Divergent selection-induced obesity alters the composition and functional pathways of chicken gut microbiota

    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...

    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

    Genetics Selection Evolution 2016 48:93

    Published on: 28 November 2016

  21. Research Article

    Genomic evaluation by including dominance effects and inbreeding depression for purebred and crossbred performance with an application in pigs

    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...

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

    Genetics Selection Evolution 2016 48:92

    Published on: 25 November 2016

  22. Research Article

    Quantitative genetic analysis of the bTB diagnostic single intradermal comparative cervical test (SICCT)

    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...

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

    Genetics Selection Evolution 2016 48:90

    Published on: 24 November 2016

  23. Research Article

    Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny

    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 ...

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

    Genetics Selection Evolution 2016 48:91

    Published on: 24 November 2016

  24. Research Article

    From cow to cheese: genetic parameters of the flavour fingerprint of cheese investigated by direct-injection mass spectrometry (PTR-ToF-MS)

    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...

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

    Genetics Selection Evolution 2016 48:89

    Published on: 16 November 2016

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