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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. Research Article

    Insight into the genetic composition of South African Sanga cattle using SNP data from cattle breeds worldwide

    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...

    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

    Genetics Selection Evolution 2016 48:88

    Published on: 15 November 2016

  19. Rsearch Article

    Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

    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.

    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

    Genetics Selection Evolution 2016 48:87

    Published on: 15 November 2016

  20. Short communication

    Inter- and intra-reproducibility of genotypes from sheep technical replicates on Illumina and Affymetrix platforms

    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 ...

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

    Genetics Selection Evolution 2016 48:86

    Published on: 10 November 2016

  21. Research Article

    Selection of performance-tested young bulls and indirect responses in commercial beef cattle herds on pasture and in feedlots

    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...

    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

    Genetics Selection Evolution 2016 48:85

    Published on: 9 November 2016

  22. Research Article

    Semi-supervised learning for genomic prediction of novel traits with small reference populations: an application to residual feed intake in dairy cattle

    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...

    Chen Yao, Xiaojin Zhu and Kent A. Weigel

    Genetics Selection Evolution 2016 48:84

    Published on: 7 November 2016

  23. Research Article

    Dimensionality of genomic information and performance of the Algorithm for Proven and Young for different livestock species

    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...

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

    Genetics Selection Evolution 2016 48:82

    Published on: 31 October 2016

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