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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. Research Article

    On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations

    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 ...

    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

    Genetics Selection Evolution 2016 48:81

    Published on: 28 October 2016

  16. Research Article

    The 1.78-kb insertion in the 3′-untranslated region of RXFP2 does not segregate with horn status in sheep breeds with variable horn status

    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...

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

    Genetics Selection Evolution 2016 48:78

    Published on: 19 October 2016

  17. Research Article

    Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production

    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 ...

    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

    Genetics Selection Evolution 2016 48:79

    Published on: 19 October 2016

  18. Research Article

    Identification of selective sweeps reveals divergent selection between Chinese Holstein and Simmental cattle populations

    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...

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

    Genetics Selection Evolution 2016 48:76

    Published on: 6 October 2016

  19. Research Article

    Genome-wide association studies of immune, disease and production traits in indigenous chicken ecotypes

    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...

    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

    Genetics Selection Evolution 2016 48:74

    Published on: 29 September 2016

  20. Research Article

    Systematic genotyping of groups of cows to improve genomic estimated breeding values of selection candidates

    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...

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

    Genetics Selection Evolution 2016 48:73

    Published on: 28 September 2016

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