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  1. Content type: Research article

    Quantitative genetic studies suggest the existence of variation at the genome level that affects the ability of cattle to resist to parasitic diseases. The objective of the current study was to identify region...

    Authors: Alan J. Twomey, Donagh P. Berry, Ross D. Evans, Michael L. Doherty, David A. Graham and Deirdre C. Purfield

    Citation: Genetics Selection Evolution 2019 51:15

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  2. Content type: Research article

    In this paper, we simulate deleterious load in an animal breeding program, and compare the efficiency of genome editing and selection for decreasing it. Deleterious variants can be identified by bioinformatics...

    Authors: Martin Johnsson, R. Chris Gaynor, Janez Jenko, Gregor Gorjanc, Dirk-Jan de Koning and John M. Hickey

    Citation: Genetics Selection Evolution 2019 51:14

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  3. Content type: Research article

    We used stable isotope profiling (15N and 13C) to obtain indicator phenotypes for feed efficiency in aquaculture. Our objectives were to (1) examine whether atom percent of stable isotopes of nitrogen and carbon ...

    Authors: Hanne Dvergedal, Jørgen Ødegård, Margareth Øverland, Liv Torunn Mydland and Gunnar Klemetsdal

    Citation: Genetics Selection Evolution 2019 51:13

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  4. Content type: Research article

    In quail, two feather colour phenotypes i.e. fawn-2/beige and yellow are associated with the ASIP locus. The aim of our study was to characterize the structural modifications within this locus that explain the ye...

    Authors: Annie Robic, Mireille Morisson, Sophie Leroux, David Gourichon, Alain Vignal, Noémie Thebault, Valérie Fillon, Francis Minvielle, Bertrand Bed’Hom, Tatiana Zerjal and Frédérique Pitel

    Citation: Genetics Selection Evolution 2019 51:12

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  5. Content type: Correction

    After publication of this work [1], we noted that there was an error in Table 3 Line 4.

    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 2019 51:11

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    The original article was published in Genetics Selection Evolution 2018 50:60

  6. Content type: Research Article

    To date, the molecular mechanisms that underlie residual feed intake (RFI) in pigs are unknown. Results from different genome-wide association studies and gene expression analyses are not always consistent. Th...

    Authors: Miriam Piles, Carlos Fernandez-Lozano, María Velasco-Galilea, Olga González-Rodríguez, Juan Pablo Sánchez, David Torrallardona, Maria Ballester and Raquel Quintanilla

    Citation: Genetics Selection Evolution 2019 51:10

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  7. Content type: Research Article

    In livestock, deleterious recessive alleles can result in reduced economic performance of homozygous individuals in multiple ways, e.g. early embryonic death, death soon after birth, or semi-lethality with inc...

    Authors: Janez Jenko, Matthew C. McClure, Daragh Matthews, Jennifer McClure, Martin Johnsson, Gregor Gorjanc and John M. Hickey

    Citation: Genetics Selection Evolution 2019 51:9

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  8. Content type: Research Article

    In pigs, crossbreeding aims at exploiting heterosis, but heterosis is difficult to quantify. Heterozygosity at genetic markers is easier to measure and could potentially be used as an indicator of heterosis. T...

    Authors: Maja Winther Iversen, Øyvind Nordbø, Eli Gjerlaug-Enger, Eli Grindflek, Marcos Soares Lopes and Theo Meuwissen

    Citation: Genetics Selection Evolution 2019 51:8

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  9. Content type: Research Article

    The animal model is a key tool in quantitative genetics and has been used extensively to estimate fundamental parameters, such as additive genetic variance or heritability. An implicit assumption of animal models...

    Authors: Stefanie Muff, Alina K. Niskanen, Dilan Saatoglu, Lukas F. Keller and Henrik Jensen

    Citation: Genetics Selection Evolution 2019 51:7

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  10. Content type: Research Article

    In pig and poultry breeding programs, the breeding goal is to improve crossbred (CB) performance, whereas selection in the purebred (PB) lines is often based on PB performance. Thus, response to selection may ...

    Authors: Pascal Duenk, Mario P. L. Calus, Yvonne C. J. Wientjes, Vivian P. Breen, John M. Henshall, Rachel Hawken and Piter Bijma

    Citation: Genetics Selection Evolution 2019 51:6

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  11. Content type: Short communication

    The identification of loci associated with resistance to mastitis or of the causative mutations may be helpful in breeding programs for dairy sheep as it is for cattle worldwide. Seven genomic regions that con...

    Authors: Claire Oget, Charlotte Allain, David Portes, Gilles Foucras, Alessandra Stella, Jean-Michel Astruc, Julien Sarry, Gwenola Tosser-Klopp and Rachel Rupp

    Citation: Genetics Selection Evolution 2019 51:5

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  12. Content type: Research Article

    Body weight (BW) at different ages are of increasing importance in dairy cattle breeding schemes, because of their strong correlation with energy efficiency traits, and their impact on cow health, longevity an...

    Authors: Tong Yin and Sven König

    Citation: Genetics Selection Evolution 2019 51:4

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  13. Content type: Research article

    Over many years, artificial selection has substantially improved milk production by cows. However, the genes that underlie milk production quantitative trait loci (QTL) remain relatively poorly characterised. ...

    Authors: Thomas J. Lopdell, Kathryn Tiplady, Christine Couldrey, Thomas J. J. Johnson, Michael Keehan, Stephen R. Davis, Bevin L. Harris, Richard J. Spelman, Russell G. Snell and Mathew D. Littlejohn

    Citation: Genetics Selection Evolution 2019 51:3

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  14. Content type: Research article

    Use of whole-genome sequence data (WGS) is expected to improve identification of quantitative trait loci (QTL). However, this requires imputation to WGS, often with a limited number of sequenced animals for th...

    Authors: Sanne van den Berg, Jérémie Vandenplas, Fred A. van Eeuwijk, Aniek C. Bouwman, Marcos S. Lopes and Roel F. Veerkamp

    Citation: Genetics Selection Evolution 2019 51:2

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  15. Content type: Research Article

    The use of whole-genome sequence (WGS) data for genomic prediction and association studies is highly desirable because the causal mutations should be present in the data. The sequencing of 935 sheep from a ran...

    Authors: Sunduimijid Bolormaa, Amanda J. Chamberlain, Majid Khansefid, Paul Stothard, Andrew A. Swan, Brett Mason, Claire P. Prowse-Wilkins, Naomi Duijvesteijn, Nasir Moghaddar, Julius H. van der Werf, Hans D. Daetwyler and Iona M. MacLeod

    Citation: Genetics Selection Evolution 2019 51:1

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  16. Content type: Research Article

    The size and type of ears are important conformation characteristics that distinguish pig breeds. A significant quantitative trait locus (QTL) for ear size has been identified on SSC5 (SSC for Sus scrofa chromoso...

    Authors: Congying Chen, Chenlong Liu, Xinwei Xiong, Shaoming Fang, Hui Yang, Zhiyan Zhang, Jun Ren, Yuanmei Guo and Lusheng Huang

    Citation: Genetics Selection Evolution 2018 50:72

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  17. Content type: Research Article

    Epistatic genomic relationship matrices for interactions of any-order can be constructed using the Hadamard products of orthogonal additive and dominance genomic relationship matrices and standardization based...

    Authors: Zulma G. Vitezica, Antonio Reverter, William Herring and Andres Legarra

    Citation: Genetics Selection Evolution 2018 50:71

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  18. Content type: Research Article

    Genome-wide marker data are used both in phenotypic genome-wide association studies (GWAS) and genome-wide prediction (GWP). Typically, such studies include high-dimensional data with thousands to millions of ...

    Authors: Patrik Waldmann

    Citation: Genetics Selection Evolution 2018 50:70

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  19. Content type: Research Article

    In this work, we investigated sequence variation, evolutionary constraint, and selection at the CD163 gene in pigs. A functional CD163 protein is required for infection by porcine reproductive and respiratory syn...

    Authors: Martin Johnsson, Roger Ros-Freixedes, Gregor Gorjanc, Matt A. Campbell, Sudhir Naswa, Kimberly Kelly, Jonathan Lightner, Steve Rounsley and John M. Hickey

    Citation: Genetics Selection Evolution 2018 50:69

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  20. Content type: Short communication

    Highly diversified in morphology and structure, feathers have evolved into various forms. Frizzle feathers, which result from a developmental defect of the feather, are observed in several domestic chicken bre...

    Authors: Jing Dong, Chuan He, Zhibing Wang, Yanqing Li, Shanshan Li, Lin Tao, Jiebo Chen, Donghua Li, Fenxia Yang, Naibin Li, Quan Zhang, Li Zhang, Guangqin Wang, Fisayo Akinyemi, He Meng and Bingwang Du

    Citation: Genetics Selection Evolution 2018 50:68

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  21. Content type: Research Article

    In this paper, we extend multi-locus iterative peeling to provide a computationally efficient method for calling, phasing, and imputing sequence data of any coverage in small or large pedigrees. Our method, ca...

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

    Citation: Genetics Selection Evolution 2018 50:67

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  22. Content type: Research Article

    Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives ...

    Authors: Andre L. S. Garcia, Brian Bosworth, Geoffrey Waldbieser, Ignacy Misztal, Shogo Tsuruta and Daniela A. L. Lourenco

    Citation: Genetics Selection Evolution 2018 50:66

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  23. Content type: Research Article

    Generally, populations differ in terms of environmental and genetic factors, which can create differences in allele substitution effects between populations. Therefore, a single genotype may have different add...

    Authors: Yvonne C. J. Wientjes, Mario P. L. Calus, Pascal Duenk and Piter Bijma

    Citation: Genetics Selection Evolution 2018 50:65

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  24. Content type: Research Article

    Inherent sources of error and bias that affect the quality of sequence data include index hopping and bias towards the reference allele. The impact of these artefacts is likely greater for low-coverage data th...

    Authors: Roger Ros-Freixedes, Mara Battagin, Martin Johnsson, Gregor Gorjanc, Alan J. Mileham, Steve D. Rounsley and John M. Hickey

    Citation: Genetics Selection Evolution 2018 50:64

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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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    The Correction to this article has been published in Genetics Selection Evolution 2019 51:11

  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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  48. 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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  49. 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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