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  1. Content type: Research Article

    Coccidiosis is a major contributor to losses in poultry production. With emerging constraints on the use of in-feed prophylactic anticoccidial drugs and the relatively high costs of effective vaccines, there a...

    Authors: Kay Boulton, Matthew J. Nolan, Zhiguang Wu, Androniki Psifidi, Valentina Riggio, Kimberley Harman, Stephen C. Bishop, Pete Kaiser, Mitchell S. Abrahamsen, Rachel Hawken, Kellie A. Watson, Fiona M. Tomley, Damer P. Blake and David A. Hume

    Citation: Genetics Selection Evolution 2018 50:63

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  2. Content type: Research Article

    Availability of whole-genome sequence data for a large number of cattle and efficient imputation methodologies open a new opportunity to include rare and low-frequency variants (RLFV) in genomic prediction in ...

    Authors: Qianqian Zhang, Goutam Sahana, Guosheng Su, Bernt Guldbrandtsen, Mogens Sandø Lund and Mario P. L. Calus

    Citation: Genetics Selection Evolution 2018 50:62

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  3. Content type: Research Article

    Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems an...

    Authors: Francesca Bertolini, Bertrand Servin, Andrea Talenti, Estelle Rochat, Eui Soo Kim, Claire Oget, Isabelle Palhière, Alessandra Crisà, Gennaro Catillo, Roberto Steri, Marcel Amills, Licia Colli, Gabriele Marras, Marco Milanesi, Ezequiel Nicolazzi, Benjamin D. Rosen…

    Citation: Genetics Selection Evolution 2018 50:57

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  4. Content type: Research Article

    Patterns of homozygosity can be influenced by several factors, such as demography, recombination, and selection. Using the goat SNP50 BeadChip, we genotyped 3171 goats belonging to 117 populations with a world...

    Authors: Francesca Bertolini, Tainã Figueiredo Cardoso, Gabriele Marras, Ezequiel L. Nicolazzi, Max F. Rothschild and Marcel Amills

    Citation: Genetics Selection Evolution 2018 50:59

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  5. Content type: Research Article

    Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We ...

    Authors: Licia Colli, Marco Milanesi, Andrea Talenti, Francesca Bertolini, Minhui Chen, Alessandra Crisà, Kevin Gerard Daly, Marcello Del Corvo, Bernt Guldbrandtsen, Johannes A. Lenstra, Benjamin D. Rosen, Elia Vajana, Gennaro Catillo, Stéphane Joost, Ezequiel Luis Nicolazzi, Estelle Rochat…

    Citation: Genetics Selection Evolution 2018 50:58

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  6. Content type: Research Article

    Genetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diver...

    Authors: Taina F. Cardoso, Marcel Amills, Francesca Bertolini, Max Rothschild, Gabriele Marras, Geert Boink, Jordi Jordana, Juan Capote, Sean Carolan, Jón H. Hallsson, Juha Kantanen, Agueda Pons and Johannes A. Lenstra

    Citation: Genetics Selection Evolution 2018 50:56

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  7. Content type: Editorial

    Authors: Alessandra Stella, Ezequiel Luis Nicolazzi, Curtis P. Van Tassell, Max F. Rothschild, Licia Colli, Benjamin D. Rosen, Tad S. Sonstegard, Paola Crepaldi, Gwenola Tosser-Klopp and Stephane Joost

    Citation: Genetics Selection Evolution 2018 50:61

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  8. Content type: Research Article

    International standard panels of single nucleotide polymorphisms (SNPs) have replaced microsatellites in several species for parentage assessment and assignment (PA) purposes. However, such a resource is still...

    Authors: Andrea Talenti, Isabelle Palhière, Flavie Tortereau, Giulio Pagnacco, Alessandra Stella, Ezequiel L. Nicolazzi, Paola Crepaldi and Gwenola Tosser-Klopp

    Citation: Genetics Selection Evolution 2018 50:55

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  9. Content type: Research Article

    Bacterial cold-water disease, which is caused by Flavobacterium psychrophilum, is one of the major diseases that affect rainbow trout (Oncorhynchus mykiss) and a primary concern for trout farming. Better knowledg...

    Authors: Clémence Fraslin, Nicolas Dechamp, Maria Bernard, Francine Krieg, Caroline Hervet, René Guyomard, Diane Esquerré, Johanna Barbieri, Claire Kuchly, Eric Duchaud, Pierre Boudinot, Tatiana Rochat, Jean-François Bernardet and Edwige Quillet

    Citation: Genetics Selection Evolution 2018 50:60

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  10. Content type: Research Article

    Cross-validation tools are used increasingly to validate and compare genetic evaluation methods but analytical properties of cross-validation methods are rarely described. There is also a lack of cross-validat...

    Authors: Andres Legarra and Antonio Reverter

    Citation: Genetics Selection Evolution 2018 50:53

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  11. Content type: Research Article

    Copy number variations (CNV) are an important source of genetic variation that has gained increasing attention over the last couple of years. In this study, we performed CNV detection and functional analysis f...

    Authors: Wioleta Drobik-Czwarno, Anna Wolc, Janet E. Fulton and Jack C. M. Dekkers

    Citation: Genetics Selection Evolution 2018 50:54

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  12. Content type: Research Article

    A breeding program for commercial broiler chicken that is carried out under strict biosecure conditions can show reduced genetic gain due to genotype by environment interactions (G × E) between bio-secure (B) ...

    Authors: Thinh T. Chu, Setegn W. Alemu, Elise Norberg, Anders C. Sørensen, John Henshall, Rachel Hawken and Just Jensen

    Citation: Genetics Selection Evolution 2018 50:52

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  13. Content type: Research Article

    The single-step single nucleotide polymorphism best linear unbiased prediction (ssSNPBLUP) method, such as single-step genomic BLUP (ssGBLUP), simultaneously analyses phenotypic, pedigree, and genomic informat...

    Authors: Jérémie Vandenplas, Herwin Eding, Mario P. L. Calus and Cornelis Vuik

    Citation: Genetics Selection Evolution 2018 50:51

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  14. Content type: Research Article

    High resistance (the ability of the host to reduce pathogen load) and tolerance (the ability to maintain high performance at a given pathogen load) are two desirable host traits for producing animals that are ...

    Authors: Graham Lough, Andrew Hess, Melanie Hess, Hamed Rashidi, Oswald Matika, Joan K. Lunney, Raymond R. R. Rowland, Ilias Kyriazakis, Han A. Mulder, Jack C. M. Dekkers and Andrea Doeschl-Wilson

    Citation: Genetics Selection Evolution 2018 50:50

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  15. Content type: Research Article

    Genomic prediction (GP) accuracy in numerically small breeds is limited by the small size of the reference population. Our objective was to test a multi-breed multiple genomic relationship matrices (GRM) GP mo...

    Authors: Biaty Raymond, Aniek C. Bouwman, Yvonne C. J. Wientjes, Chris Schrooten, Jeanine Houwing-Duistermaat and Roel F. Veerkamp

    Citation: Genetics Selection Evolution 2018 50:49

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  16. Content type: Research Article

    Heterosis has been suggested to be caused by dominance effects. We performed a joint genome-wide association analysis (GWAS) using data from multi-breed and crossbred beef cattle to identify single nucleotide ...

    Authors: Everestus C. Akanno, Liuhong Chen, Mohammed K. Abo-Ismail, John J. Crowley, Zhiquan Wang, Changxi Li, John A. Basarab, Michael D. MacNeil and Graham S. Plastow

    Citation: Genetics Selection Evolution 2018 50:48

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  17. Content type: Research Article

    Macroparasites, such as ticks, lice, and helminths, are a concern in livestock and aquaculture production, and can be controlled by genetic improvement of the host population. Genetic improvement should aim at...

    Authors: Kasper Janssen, Hans Komen, Helmut W. Saatkamp, Mart C. M. de Jong and Piter Bijma

    Citation: Genetics Selection Evolution 2018 50:47

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  18. Content type: Research Article

    In polytocous livestock species, litter size and offspring weight act antagonistically; in modern pig breeds, selection for increased litter size has resulted in lower mean birth weights, an increased number o...

    Authors: Stephanie M. Matheson, Grant A. Walling and Sandra A. Edwards

    Citation: Genetics Selection Evolution 2018 50:46

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  19. Content type: Research Article

    In this paper, we review the performance of various hidden Markov model-based imputation methods in animal breeding populations. Traditionally, pedigree and heuristic-based imputation methods have been used fo...

    Authors: Andrew Whalen, Gregor Gorjanc, Roger Ros-Freixedes and John M. Hickey

    Citation: Genetics Selection Evolution 2018 50:44

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  20. Content type: Research Article

    Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplo...

    Authors: Wilson Nandolo, Yuri T. Utsunomiya, Gábor Mészáros, Maria Wurzinger, Negar Khayadzadeh, Rafaela B. P. Torrecilha, Henry A. Mulindwa, Timothy N. Gondwe, Patrik Waldmann, Maja Ferenčaković, José F. Garcia, Benjamin D. Rosen, Derek Bickhart, Curt P. van Tassell, Ino Curik and Johann Sölkner

    Citation: Genetics Selection Evolution 2018 50:43

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  21. Content type: Research Article

    Records on groups of individuals rather than on single individuals could be valuable for predicting breeding values (BV) of the traits that are difficult or costly to measure individually, such as feed intake ...

    Authors: Guosheng Su, Per Madsen, Bjarne Nielsen, Tage Ostersen, Mahmoud Shirali, Just Jensen and Ole F. Christensen

    Citation: Genetics Selection Evolution 2018 50:42

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  22. Content type: Research Article

    Genomic models that link phenotypes to dense genotype information are increasingly being used for infering variance parameters in genetics studies. The variance parameters of these models can be inferred using...

    Authors: Beatriz C. D. Cuyabano, A. Christian Sørensen and Peter Sørensen

    Citation: Genetics Selection Evolution 2018 50:41

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  23. Content type: Research Article

    In recent years, there has been increased interest in the study of the molecular processes that affect semen traits. In this study, our aim was to identify quantitative trait loci (QTL) regions associated with...

    Authors: Daniele B. D. Marques, John W. M. Bastiaansen, Marleen L. W. J. Broekhuijse, Marcos S. Lopes, Egbert F. Knol, Barbara Harlizius, Simone E. F. Guimarães, Fabyano F. Silva and Paulo S. Lopes

    Citation: Genetics Selection Evolution 2018 50:40

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  24. Content type: Research Article

    A common measure employed to evaluate the efficacy of livestock improvement schemes is the genetic trend, which is calculated as the means of predicted breeding values for animals born in successive time perio...

    Authors: Karin Meyer, Bruce Tier and Andrew Swan

    Citation: Genetics Selection Evolution 2018 50:39

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  25. Content type: Research Article

    Cannibalism is an important welfare problem in the layer industry. Cannibalism is a social behavior where individual survival is affected by direct genetic effects (DGE) and indirect genetic effects (IGE). Pre...

    Authors: Tessa Brinker, Piter Bijma, Addie Vereijken and Esther D. Ellen

    Citation: Genetics Selection Evolution 2018 50:38

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  26. Content type: Research Article

    The origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we inv...

    Authors: Alexander A. Sermyagin, Arsen V. Dotsev, Elena A. Gladyr, Alexey A. Traspov, Tatiana E. Deniskova, Olga V. Kostyunina, Henry Reyer, Klaus Wimmers, Mario Barbato, Ivan A. Paronyan, Kirill V. Plemyashov, Johann Sölkner, Ruslan G. Popov, Gottfried Brem and Natalia A. Zinovieva

    Citation: Genetics Selection Evolution 2018 50:37

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  27. Content type: Research Article

    It has been known for almost a century that the belted phenotype in cattle follows a pattern of dominant inheritance. In 2009, the approximate position of the belt locus in Brown Swiss cattle was mapped to a 922-...

    Authors: Sophie Rothammer, Elisabeth Kunz, Stefan Krebs, Fanny Bitzer, Andreas Hauser, Natalia Zinovieva, Nikolai Klymiuk and Ivica Medugorac

    Citation: Genetics Selection Evolution 2018 50:36

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  28. Content type: Research Article

    High levels of pairwise linkage disequilibrium (LD) in single nucleotide polymorphism (SNP) array or whole-genome sequence data may affect both performance and efficiency of genomic prediction models. Thus, th...

    Authors: Mario P. L. Calus and Jérémie Vandenplas

    Citation: Genetics Selection Evolution 2018 50:34

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  29. Content type: Research Article

    In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still fa...

    Authors: Salvatore Mastrangelo, Elena Ciani, Paolo Ajmone Marsan, Alessandro Bagnato, Luca Battaglini, Riccardo Bozzi, Antonello Carta, Gennaro Catillo, Martino Cassandro, Sara Casu, Roberta Ciampolini, Paola Crepaldi, Mariasilvia D’Andrea, Rosalia Di Gerlando, Luca Fontanesi, Maria Longeri…

    Citation: Genetics Selection Evolution 2018 50:35

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  30. Content type: Research Article

    This study aimed at (1) deriving Bayesian methods to predict breeding values for ratio (i.e. feed conversion ratio; FCR) or linear (i.e. residual feed intake; RFI) traits; (2) estimating genetic parameters for...

    Authors: Mahmoud Shirali, Patrick Francis Varley and Just Jensen

    Citation: Genetics Selection Evolution 2018 50:33

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  31. Content type: Research Article

    Population stratification and cryptic relationships have been the main sources of excessive false-positives and false-negatives in population-based association studies. Many methods have been developed to mode...

    Authors: Ali Toosi, Rohan L. Fernando and Jack C. M. Dekkers

    Citation: Genetics Selection Evolution 2018 50:32

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  32. Content type: Research Article

    In 2017, genomic selection was implemented in French dairy goats using the single-step genomic best linear unbiased prediction (ssGBLUP) method, which assumes that all single nucleotide polymorphisms explain t...

    Authors: Marc Teissier, Hélène Larroque and Christèle Robert-Granié

    Citation: Genetics Selection Evolution 2018 50:31

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  33. Content type: Research Article

    European sea bass (Dicentrarchus labrax) is one of the most important species for European aquaculture. Viral nervous necrosis (VNN), commonly caused by the redspotted grouper nervous necrosis virus (RGNNV), can ...

    Authors: Christos Palaiokostas, Sophie Cariou, Anastasia Bestin, Jean-Sebastien Bruant, Pierrick Haffray, Thierry Morin, Joëlle Cabon, François Allal, Marc Vandeputte and Ross D. Houston

    Citation: Genetics Selection Evolution 2018 50:30

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  34. Content type: Research Article

    Russia has a diverse variety of native and locally developed sheep breeds with coarse, fine, and semi-fine wool, which inhabit different climate zones and landscapes that range from hot deserts to harsh northe...

    Authors: Tatiana E. Deniskova, Arsen V. Dotsev, Marina I. Selionova, Elisabeth Kunz, Ivica Medugorac, Henry Reyer, Klaus Wimmers, Mario Barbato, Alexei A. Traspov, Gottfried Brem and Natalia A. Zinovieva

    Citation: Genetics Selection Evolution 2018 50:29

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  35. Content type: Research Article

    In horned sheep breeds, breeding for polledness has been of interest for decades. The objective of this study was to improve prediction of the horned and polled phenotypes using horn scores classified as polle...

    Authors: Naomi Duijvesteijn, Sunduimijid Bolormaa, Hans D. Daetwyler and Julius H. J. van der Werf

    Citation: Genetics Selection Evolution 2018 50:28

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  36. Content type: Research Article

    Parentage assignment is usually based on a limited number of unlinked, independent genomic markers (microsatellites, low-density single nucleotide polymorphisms (SNPs), etc.). Classical methods for parentage a...

    Authors: Kim E. Grashei, Jørgen Ødegård and Theo H. E. Meuwissen

    Citation: Genetics Selection Evolution 2018 50:26

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  37. Content type: Research Article

    Genomic prediction (GP) across breeds has so far resulted in low accuracies of the predicted genomic breeding values. Our objective was to evaluate whether using whole-genome sequence (WGS) instead of low-dens...

    Authors: Biaty Raymond, Aniek C. Bouwman, Chris Schrooten, Jeanine Houwing-Duistermaat and Roel F. Veerkamp

    Citation: Genetics Selection Evolution 2018 50:27

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  38. Content type: Research Article

    Indirect genetic effects (IGE) are important components of various traits in several species. Although the intensity of social interactions between partners likely vary over time, very few genetic studies have...

    Authors: Ingrid David, Juan-Pablo Sánchez and Miriam Piles

    Citation: Genetics Selection Evolution 2018 50:25

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  39. Content type: Research Article

    Optimal contributions selection (OCS) provides animal breeders with a framework for maximising genetic gain for a predefined rate of inbreeding. Simulation studies have indicated that the source of the selecti...

    Authors: David M. Howard, Ricardo Pong-Wong, Pieter W. Knap, Valentin D. Kremer and John A. Woolliams

    Citation: Genetics Selection Evolution 2018 50:24

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  40. Content type: Research Article

    The replacement of fish oil (FO) and fishmeal with plant ingredients in the diet of farmed Atlantic salmon has resulted in reduced levels of the health-promoting long-chain polyunsaturated omega-3 fatty acids ...

    Authors: Siri S. Horn, Bente Ruyter, Theo H. E. Meuwissen, Borghild Hillestad and Anna K. Sonesson

    Citation: Genetics Selection Evolution 2018 50:23

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  41. Content type: Research article

    This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that...

    Authors: Diercles F. Cardoso, Lucia Galvão de Albuquerque, Christian Reimer, Saber Qanbari, Malena Erbe, André V. do Nascimento, Guilherme C. Venturini, Daiane C. Becker Scalez, Fernando Baldi, Gregório M. Ferreira de Camargo, Maria E. Zerlotti Mercadante, Joslaine N. do Santos Gonçalves Cyrillo, Henner Simianer and Humberto Tonhati

    Citation: Genetics Selection Evolution 2018 50:22

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  42. Content type: Short communication

    Avian influenza (AI) is a devastating poultry disease that currently can be controlled only by liquidation of affected flocks. In spite of typically very high mortality rates, a group of survivors was identifi...

    Authors: Anna Wolc, Wioleta Drobik-Czwarno, Janet E. Fulton, Jesus Arango, Tomasz Jankowski and Jack C. M. Dekkers

    Citation: Genetics Selection Evolution 2018 50:21

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  43. Content type: Research Article

    mRNA-like long non-coding RNAs (lncRNAs) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental s...

    Authors: Stephen J. Bush, Charity Muriuki, Mary E. B. McCulloch, Iseabail L. Farquhar, Emily L. Clark and David A. Hume

    Citation: Genetics Selection Evolution 2018 50:20

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  44. Content type: Research Article

    The distribution of the wild turkey (Meleagris gallopavo) extends from Mexico to southeastern Canada and to the eastern and southern regions of the USA. Six subspecies have been described based on morphological c...

    Authors: Gabriela Padilla-Jacobo, Horacio Cano-Camacho, Rigoberto López-Zavala, María E. Cornejo-Pérez and María G. Zavala-Páramo

    Citation: Genetics Selection Evolution 2018 50:19

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  45. Content type: Research Article

    Deleterious genetic variation can increase in frequency as a result of mutations, genetic drift, and genetic hitchhiking. Although individual effects are often small, the cumulative effect of deleterious genet...

    Authors: Martijn F. L. Derks, Hendrik-Jan Megens, Mirte Bosse, Jeroen Visscher, Katrijn Peeters, Marco C. A. M. Bink, Addie Vereijken, Christian Gross, Dick de Ridder, Marcel J. T. Reinders and Martien A. M. Groenen

    Citation: Genetics Selection Evolution 2018 50:17

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  46. Content type: Research Article

    Genome editing technologies provide new tools for genetic improvement and have the potential to become the next game changer in animal and plant breeding. The aim of this study was to investigate how genome ed...

    Authors: John W. M. Bastiaansen, Henk Bovenhuis, Martien A. M. Groenen, Hendrik-Jan Megens and Han A. Mulder

    Citation: Genetics Selection Evolution 2018 50:18

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  47. Content type: Research Article

    In recent decades, Holstein–Friesian (HF) selection schemes have undergone profound changes, including the introduction of optimal contribution selection (OCS; around 2000), a major shift in breeding goal comp...

    Authors: Harmen P. Doekes, Roel F. Veerkamp, Piter Bijma, Sipke J. Hiemstra and Jack J. Windig

    Citation: Genetics Selection Evolution 2018 50:15

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  48. Content type: Research Article

    Increasing marker density was proposed to have potential to improve the accuracy of genomic prediction for quantitative traits; whole-sequence data is expected to give the best accuracy of prediction, since al...

    Authors: Chunyan Zhang, Robert Alan Kemp, Paul Stothard, Zhiquan Wang, Nicholas Boddicker, Kirill Krivushin, Jack Dekkers and Graham Plastow

    Citation: Genetics Selection Evolution 2018 50:14

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