178 results on '"ten Napel, J."'
Search Results
52. Genetic concepts to improve robustness of dairy cows
- Author
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ten Napel, J., Calus, M.P.L., Mulder, H.A., and Veerkamp, R.F.
- Subjects
Research ,WIAS ,Life Science ,Fokkerij en Genomica ,Animal Breeding and Genomics ,Wageningen Livestock Research ,Onderzoek - Published
- 2009
53. Betrouwbaar naar gezonde uiers: ontrafelen celgetalgegevens levert uiergezondheidsindex met 85 procent betrouwbaarheid
- Author
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de Haas, Y., de Jong, G., Lam, T.J.G.M., ten Napel, J., Ouweltjes, W., Sampimon, O.C., Veerkamp, R.F., and Windig, J.J.
- Subjects
dairy farming ,celgetal ,animal health ,somatic cell count ,breeding value ,dierveredeling ,koe-indexen ,animal breeding ,cow indexes ,diergezondheid ,melkkoeien ,udders ,melkveehouderij ,dairy cows ,uiers ,fokwaarde - Abstract
Fokken op uiergezondheid kan betrouwbaarder, zo luidt de conclusie van nieuw onderzoek. Door de celgetalgegevens dieper te analyseren ontstaat een index met 85 % betrouwbaarheid, vergelijkbaar met fokwaarden in de zo geroemde Scandinavische landen. Stieren zullen op z'n vroegst in april 2009 een vernieuwde fokwaarde krijgen
- Published
- 2008
54. Ruimere koe... lichter kalf
- Author
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ten Napel, J.
- Subjects
cattle husbandry ,geboorte ,parturition complications ,werkgroepen ,rundveehouderij ,keizersnede ,dierenwelzijn ,animal welfare ,beef cattle ,birth ,problem solving ,caesarean section ,bevallingscomplicaties ,vleesvee ,Wageningen Livestock Research ,working groups ,probleemoplossing - Abstract
Hoe buig je de cultuur van systematisch toepassen van een keizersnede om naar meer natuurlijke geboorten? Wageningen UR begeleidt dit proces door vleesveehouders in werkgroepen zelf te laten zoeken naar oplossingen
- Published
- 2008
55. Verbeteren van weerstand tegen mastitis via fokkerij
- Author
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de Haas, Y. and ten Napel, J.
- Subjects
Life Science ,ID - Dier en Omgeving ,Wageningen Livestock Research - Published
- 2008
56. The usefullness of breeding to decrease mastitis incidence
- Author
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de Haas, Y., de Jong, G., ten Napel, J., Ouweltjes, W., Sampimon, O.C., Veerkamp, R.F., and Windig, J.J.
- Subjects
Research ,Life Science ,ID - Dier en Omgeving ,Wageningen Livestock Research ,Onderzoek - Published
- 2008
57. Alternative use of somatic cells count in genetic selection for clinical mastitis
- Author
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de Haas, Y., ten Napel, J., Ouweltjes, W., and de Jong, G.
- Subjects
Research ,Life Science ,ID - Dier en Omgeving ,Wageningen Livestock Research ,Onderzoek - Published
- 2008
58. Improving selection on udder health by using different trait definitions of somatic cell count
- Author
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de Haas, Y., Bloemhof, S., Ouweltjes, W., ten Napel, J., and de Jong, G.
- Subjects
Research ,WIAS ,Life Science ,Fokkerij en Genomica ,Animal Breeding and Genomics ,ID - Dier en Omgeving ,Wageningen Livestock Research ,Onderzoek - Published
- 2008
59. Udder health and breeding
- Author
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de Haas, Y., de Jong, G., ten Napel, J., Ouweltjes, W., Sampimon, O.C., Veerkamp, R.F., and Windig, J.J.
- Subjects
Research ,Life Science ,ID - Dier en Omgeving ,Wageningen Livestock Research ,Onderzoek - Published
- 2008
60. Vervanging zeugenstapel vraagt om keuzes
- Author
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Lamers, J. and ten Napel, J.
- Subjects
biologische landbouw ,organic farming ,varkensfokkerij ,pigs ,biological production ,biologische productie ,pig breeding ,varkens ,Wageningen Livestock Research - Abstract
De vervanging van de biologische zeugenstapel vanuit de reguliere houderij staat onder druk. Biologische zeugenhouders zullen daarom een keuze moeten maken: kiezen ze ieder voor zich voor een rotatiekruising of meerwegkruising? Of kiest men samen voor een biologisch fokbedrijf of eigen aanfok met een biologische zeugenlijn? Om te komen tot zeugen met specifieke eigenschappen die passen bij de biologische houderij, is de inzet van alle zeugenhouders gewenst.
- Published
- 2008
61. Improvements in the Dutch udder Health index
- Author
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de Haas, Y., de Jong, G., Ouweltjes, W., ten Napel, J., and Windig, J.J.
- Subjects
Research ,Life Science ,ID - Dier en Omgeving ,Wageningen Livestock Research ,Onderzoek - Published
- 2008
62. Vertrouwen op de kracht van de koe
- Author
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ten Napel, J. and Veerkamp, R.F.
- Subjects
animal health ,breeding value ,inbreeding ,dierveredeling ,natural selection ,inteelt ,animal breeding ,diergezondheid ,farm management ,genetica ,melkkoeien ,melkproductie ,natuurlijke selectie ,dairy cows ,genetics ,agrarische bedrijfsvoering ,milk production ,fokwaarde - Abstract
Jarenlange selectie met de nadruk op melkproductie heeft de Nederlandse melkkoe kwetsbaar gemaakt. Als het even tegen zit komt ze sneller in de problemen dan voorheen, met als gevolg bijvoorbeeld mastitis en vruchtbaarheidsproblemen. Wageningen UR zoekt mogelijkheden om middels de fokkerij koeien weerbaarder en robuuster te maken
- Published
- 2008
63. Schadelijke piepschuimkever bondgenoot in strijd tegen vogelmijt
- Author
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ten Napel, J., Slingerland, R.M., and Groot Koerkamp, P.W.G.
- Subjects
mites ,integrated pest management ,insectenbestrijding ,mijten ,insect control ,plagen veroorzaakt door geleedpotigen ,geïntegreerde bestrijding ,geïntegreerde plagenbestrijding ,mijtenbestrijding ,alphitobius diaperinus ,ATV Farm Technology ,poultry farming ,mite control ,integrated control ,pluimveehouderij ,Wageningen Livestock Research ,arthropod pests - Abstract
Pluimveehouders van de Scharrelclub Veluwe merkten een positieve kant op van de schadelijke piepschuimkever: bij een groeiende populatie neemt de overlast van de vogelmijt af. Zij vroegen Wageningen UR te onderzoeken hoe de piepschuimkever kan worden ingezet bij de vogelmijtbestrijding
- Published
- 2007
64. Monitoring van bloedluispopulatie op praktijkbedrijven; buis met stokje zeer geschikt voor bewustwording
- Author
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van Emous, R.A. and ten Napel, J.
- Subjects
pluimveeziekten ,poultry farming ,animal disease prevention ,poultry ,pluimvee ,pluimveehouderij ,poultry diseases ,dierziektepreventie - Abstract
Bloedluis wordt vaak in een laat stadium ontdekt door pluimveehouders. Als dan de behandeling moet worden gestart is het erg moeilijk om een effectieve behandeling in te zetten. Animal Sciences Group met een methode ontwikkeld, waarmee op tijd duidelijk kan worden vastgesteld wanneer pluimvee bloedluis heeft
- Published
- 2007
65. Slapeloze nachten van de bloedluis : netwerk 'Scharrelnetwerk Veluwe'
- Author
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ten Napel, J.
- Subjects
eriosoma ,networking ,biological control ,cooperation ,biologische bestrijding ,farm management ,free range husbandry ,pluimveeziekten ,poultry farming ,netwerken (activiteit) ,pluimveehouderij ,samenwerking ,agrarische bedrijfsvoering ,scharrelhouderij ,poultry diseases - Abstract
Het netwerk voor scharrelkippenhouders 'Scharrelnetwerk Veluwe' boog zich over de bloedluis, maar moest veel hobbels nemen om deze onbekende plaag onder de aandacht te brengen bij de gehele sector en kennis te vinden over biologische bestrijding ervan
- Published
- 2007
66. Bloedluis in beeld : Netwerk: Scharrel netwerk Veluwe
- Author
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ten Napel, J.
- Subjects
disease control ,knowledge ,animal disease prevention ,biological control ,biologische bestrijding ,ziektebestrijding ,free range husbandry ,dierziektepreventie ,pluimveeziekten ,poultry farming ,networks ,pluimveehouderij ,scharrelhouderij ,poultry diseases ,kennis ,Wageningen Livestock Research ,netwerken - Abstract
n het najaar van 2005 dienden drie pluimveehouders uit de Scharrelstudieclub Veluwe een aanvraag in voor ondersteuning vanuit het programma Netwerken in de Veehouderij. Ze zaten behoorlijk met de handen in het haar omdat bloedluis (vogelmijt) steeds meer een onbeheersbaar probleem aan het worden was. Het netwerk van de grond krijgen bleek een lastig probleem en is ook niet echt gelukt. Het bloedluisprobleem duidelijker op de kaart zetten is wel gelukt. Een kant en klare oplossing is er echter nog niet
- Published
- 2006
67. High-health varkenshouderij in Nederland: kans of illusie?
- Author
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ten Napel, J.
- Subjects
animal health ,varkenshouderij ,agrarische bedrijfsvoering ,diergezondheid ,farm management ,international comparisons ,questionnaires ,pig farming ,vragenlijsten ,Wageningen Livestock Research ,internationale vergelijkingen - Abstract
Het doel van dit onderzoek was om een idee te krijgen van de relevantie van high-health varkenshouderij voor Nederland, op basis van ervaringen in Nederland en vergelijkbare andere landen. In totaal zijn 17 mensen, die via hun werk te maken hebben met high-health varkenshouderij, benaderd met een vragenlijst. Deze mensen zijn werkzaam in 6 landen en de professionele groepen 'werkzaam op high-health varkensbedrijven', 'onafhankelijk veterinair deskundige' en 'wetenschappelijk betrokken' waren in gelijke mate vertegenwoordigd. Er zijn geen harde cijfers over de prevalentie van high-health varkenshouderij
- Published
- 2006
68. Utilising intrinsic robustness in agricultural production systems
- Author
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ten Napel, J., Bianchi, F.J.J.A., and Bestman, M.W.P.
- Subjects
landbouwproductie ,PE&RC ,sustainability ,duurzame landbouw ,sustainable agriculture ,agrarische productiesystemen ,biologische landbouw ,duurzaamheid (sustainability) ,organic farming ,agricultural production ,Leerstoelgroep Gewas- en onkruidecologie ,Crop and Weed Ecology ,agricultural production systems ,Wageningen Livestock Research - Abstract
This paper explores the potential of utilising robust crops and livestock for improving sustainability of agriculture. Two approaches for dealing with unwanted fluctuations that may influence agricultural production, such as diseases and pests, are discussed. The prevailing approach, which we call the ‘Control Model’, is to protect crops and livestock from disturbances as much as possible, to regain balance with monitoring and intervention and to look for add-on solutions only. There are a number of problems associated with the Control Model, including reduced animal welfare, environmental pollution and low public support. An alternative approach, which we call the ‘Adaptation Model’, is based on reducing the consequences of disturbances rather than taking disturbances out
- Published
- 2006
69. Semen in straws
- Author
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Woelders, H. and ten Napel, J.
- Subjects
ID - Dier en Omgeving - Published
- 2005
70. Genetic relationships among production traits and rebreeding performance
- Author
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ten Napel, J. and Johnson, R.K.
- Subjects
ID-Lelystad, Instituut voor Dierhouderij en Diergezondheid ,Reproduction ,ID Lelystad, Institute for Animal Science and Health ,WIAS ,Fokkerij en Genomica ,Pigs ,Growth ,Animal Breeding and Genomics ,Selection - Published
- 1997
71. Genetic aspects of intervals from weaning to estrus in swine
- Author
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ten Napel, J., Agricultural University, E.W. Brascamp, and J.K. Oldenbroek
- Subjects
calving interval ,weaning ,tussenkalftijd ,spenen ,WIAS ,pigs ,Fokkerij en Genomica ,oestrus ,Animal Breeding and Genomics ,varkens - Abstract
Genetic variation in interval from weaning to estrus, and genetic relationships with traits commonly under selection were studied using data from an eight-generation selection experiment on a short interval from weaning to estrus, and data from an American breeding company. From the biological background and the distribution of data it appears that interval from weaning to estrus is either normal or prolonged. Selection for a short interval reduced the average interval by reducing the incidence of prolonged intervals only. Sows on units of the breeding company studied with a prolonged interval had consistently more favorable estimated breeding values for backfat and growth rate, than sows with a normal interval. Analysis of data from the selection experiment did not confirm this. Model studies showed that extending the number of traits under selection with a 0/1 trait, representing normal and prolonged intervals, gives the highest response ineach of the traits under selection.
- Published
- 1996
72. A human nose scoring system for boar taint and its relationship with androstenone and skatole
- Author
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Mathur, P.K., primary, ten Napel, J., additional, Bloemhof, S., additional, Heres, L., additional, Knol, E.F., additional, and Mulder, H.A., additional
- Published
- 2012
- Full Text
- View/download PDF
73. Adaptive response to Eimeria acervulina in rearing hens is affected by suboptimal incubation temperature and heat exposure in later life
- Author
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Walstra, I., primary, ten Napel, J., additional, Kemp, B., additional, and van den Brand, H., additional
- Published
- 2012
- Full Text
- View/download PDF
74. A biological approach to examine genetic variation in weaning-to-oestrus interval in first-litter sows based on a review
- Author
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ten Napel, J., Kemp, B., Luiting, P., and de Vries, A.G.
- Subjects
ID-Lelystad, Instituut voor Dierhouderij en Diergezondheid ,Postweaning oestrus ,Reproduction ,ID Lelystad, Institute for Animal Science and Health ,Sow ,WIAS ,Veehouderij ,Fokkerij en Genomica ,Genetic variation ,Animal Husbandry ,Animal Breeding and Genomics - Published
- 1995
75. Breeding replacement gilts for organic pig herds
- Author
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Leenhouwers, J.I., primary, Ten Napel, J., additional, Hanenberg, E.H.A.T., additional, and Merks, J.W.M., additional
- Published
- 2011
- Full Text
- View/download PDF
76. Temperature manipulation during layer chick embryogenesis
- Author
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Walstra, I., primary, ten Napel, J., additional, Kemp, B., additional, and van den Brand, H., additional
- Published
- 2010
- Full Text
- View/download PDF
77. Combining somatic cell count traits for optimal selection against mastitis
- Author
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Windig, J.J., primary, Ouweltjes, W., additional, ten Napel, J., additional, de Jong, G., additional, Veerkamp, R.F., additional, and De Haas, Y., additional
- Published
- 2010
- Full Text
- View/download PDF
78. Early life experiences affect the adaptive capacity of rearing hens during infectious challenges
- Author
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Walstra, I., primary, ten Napel, J., additional, Kemp, B., additional, Schipper, H., additional, and van den Brand, H., additional
- Published
- 2010
- Full Text
- View/download PDF
79. Characterization of distributions of somatic cell counts
- Author
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ten Napel, J., primary, de Haas, Y., additional, de Jong, G., additional, Lam, T.J.G.M., additional, Ouweltjes, W., additional, and Windig, J.J., additional
- Published
- 2009
- Full Text
- View/download PDF
80. The Use of Data from Sampling for Bacteriology for Genetic Selection Against Clinical Mastitis
- Author
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Ouweltjes, W., primary, Windig, J.J., additional, de Jong, G., additional, Lam, T.J.G.M., additional, ten Napel, J., additional, and de Haas, Y., additional
- Published
- 2008
- Full Text
- View/download PDF
81. Robustness in dairy cattle
- Author
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Veerkamp, R.F., primary, Calus, M.P.L., additional, Beerda, B., additional, and Ten Napel, J., additional
- Published
- 2007
- Full Text
- View/download PDF
82. Genetics of pig health and immunity
- Author
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ten Napel, J.
- Subjects
Life Science ,General Medicine ,ID - Dier en Omgeving - Abstract
Infectious diseases have great impact on the margin per pig sold and the animal’s welfare. The common veterinary approach to illness is to deal with the pathogen and ideally eliminate the pathogen from the herd. This approach reduces the probability of an outbreak, but increases the consequences of an outbreak, should it occur. A complicating matter is that an increasing number of parasites and pathogens have become resistant to antibiotics or anthelmintics. The objective of this paper is to draw attention to the pig’s ability to deal effectively with pathogens after natural exposure, with particular emphasis on genetic improvement. The terms used in this paper are defined as in Knap and Bishop (2000).
- Published
- 2005
83. Genetics of the interval from weaning to estrus in first-litter sows: correlated responses.
- Author
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ten Napel, J, primary, Meuwissen, T H, additional, Johnson, R K, additional, and Brascamp, E W, additional
- Published
- 1998
- Full Text
- View/download PDF
84. Effect of treating dairy cows of three breeds with recombinantly derived bovine somatotropin for three years
- Author
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Oldenbroek, J.K., primary, Garssen, G.J., additional, ten Napel, J., additional, Verplanke, J.C., additional, Brown, A.C.G., additional, and Jonker, L.J., additional
- Published
- 1991
- Full Text
- View/download PDF
85. Ultrastructure of developing subgingival plaque in beagle dogs.
- Author
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ten Napel, J. H., Theilade, J., Matsson, L., and Attström, R.
- Subjects
- *
DENTAL plaque , *DENTAL deposits , *DENTAL hygiene , *BACTERIAL diseases , *PERIODONTICS , *PERIODONTAL disease - Abstract
The aim of this study was to describe the ultrastructure of developing subgingival plaque. In 6 beagle dogs, healthy gingiva prevailed after a pre-experimental period of intensive plaque control. At the start of the experimental, all oral hygiene measures were withdrawn. Biopsies comprising buccal gingiva and adjacent dental tissues were obtained from premolars and molars on days 0. 4. 7, 21. and 28 and processed for electron microscopy. Sections of day 0 exhibited a junctional epithelium in close contact with the tooth and absence of subgingival aggregations of bacteria on the tooth surface. For each of the subsequent periods studied. some sections did not exhibit subgingival plaque. In the remaining sections with subgingival plaque. almost all bacteria appeared in aggregates attached to the tooth surface. The number of bacteria at the orifice of the gingival sulcus increased with time. Further apically, the micro-organisms formed either a continuous layer of even thickness or, more frequentlty. discrete microcolonies along the tooth surface. The bacteria comprised practically entirely Gram-negative cocci, rods or spirochetes. The latter were present either mixed with the other types it the discrete microcolonies or constituted the bulk of the continuous layer of plaque. In the apical part of the subgingival plaque, a shift from Gram-negative cocci and rod during the earls stages of gingival inflammation, to a predominance of spirochetes in later stages was noted. The study shows that in dogs, starting from a plaque- and gingivitis-free baseline, a predominantly Gram-negative subgingival flora may form within a few days alter withdrawal of all oral hygiene measures and that a shift in the bacterial composition of the subgingival plaque rakes place during a 4-week period of no oral hygiene. [ABSTRACT FROM AUTHOR]
- Published
- 1985
- Full Text
- View/download PDF
86. Identification of a Thermostatic Expansion Valve
- Author
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Broersen, P.M.T. and ten Napel, J.
- Abstract
A thermostatic expansion valve controls the liquid flow to the evaporator of a compression refrigerating system. This system has an undesirable oscillating behaviour in efficient operating points. The stability critically depends on the numerical values of some unknown parameters of the valve. These parameters are estimated with a closed form weighted least squares technique, applied to the fourier coefficients of output and a binary multifrequency input signal. The accuracy of the estimated parameters is improved by a new and simple method to determine weights for the residuals experimentally. The weights are also used in the parameter covariance matrix on which an order estimation criterion is based.
- Published
- 1982
- Full Text
- View/download PDF
87. Mogelijkheden voor selektie op kalfsvlees- en stierevleesproduktie-eigenschappen bij zwartbont melkvee = Possibilities to select on veal and beef production in black and white dairy cattle
- Author
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ten Napel, J., Dijkstra, J., and Laurijsen, H.A.J.
- Subjects
meat production ,melkveerassen ,selectie ,vleesproductie ,selection ,Research Institute for Animal Husbandry ,dairy breeds ,Instituut voor Veeteeltkundig Onderzoek - Abstract
In de periode 1980 tot '86 werd er een nakomelingenonderzoek uitgevoerd van 38 zwartbonte proefstieren die de eigenprestatietoets hadden ondergaan. De nakomelingen werden gemest als vleeskalf of als vleesstier. Het doel van de proef was de genetische relatie te onderzoeken tussen de eigenprestatie van jonge proefstieren onder opfokomstandigheden en de prestaties van de nakomelingen onder mesterijomstandigheden. Daarbij lag in deze proef de nadruk op de genetische verbanden met slachtkwaliteit. Vanwege de beperkte technische en financiele mogelijkheden werd gebruik gemaakt van stieren met een extreem hoge of lage bevleesdheid, waarbij het verband via een regressieberekening werd bepaald. Er zijn in totaal gegevens van 532 vleeskalveren en 621 vleesstieren gebruikt
- Published
- 1987
88. Alternative Somatic Cell Count Traits as Mastitis Indicators for Genetic Selection.
- Author
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De Haas, Y., Ouweltjes, W., Ten Napel, J., Windig, J. J., and De Jong, G.
- Subjects
- *
SOMATIC cells , *MASTITIS , *GENETICS , *COWS , *LACTATION - Abstract
The aim of this study was to define alternative traits of somatic cell count (SCC) that can be used to decrease genetic susceptibility to clinical and subclinical mastitis (CM and SCM, respectively). Three kinds of SCC traits were evaluated: 1) lactation-averages of SCC, 2) traits derived from the proportion of test-day SCC above 150,000 cells/mL, and 3) patterns of peaks in SCC. Genetic parameters for these SCC traits and their genetic correlation with CM and SCM were estimated; CM and SCM were scored as binary traits. Two data sets (A and B) depending on CM recording were available. After editing, subset A contained 28,688 lactations from 21,673 cows in 394 herds. Subset B contained 56,726 lactations of 30,145 cows in 272 herds. Variance components for sire and permanent animal effects were estimated. Estimated heritabilities for all mastitis traits were around 0.03. Heritabilities for SCC traits ranged from 0.01 for patterns of peaks in SCC to 0.13 for lactation-average SCC. Genetic correlations between SCC traits and CM or SCM ranged from 0.55 to 0.93 for CM and from 0.55 to 0.98 for SCM. High genetic correlations were estimated between CM and SCC averaged over 250 d in milk (0.87), and between SCM and presence of test-day SCC >150,000 cells/mL (0.98) in subset A. In subset B, a high genetic correlation was estimated between CM and an SCC peak with a quick recovery (0.93) and between SCM and SCC averaged between 151 and 400 d (0.95). Partial genetic correlations were calculated to investigate the additional information of the alternative SCC traits, compared with lactation-average SCC. They showed that some traits remain informative for CM and others for SCM. Therefore, use of information from a combination of different SCC traits may be more successful in improving overall udder health than the traditional single SCC measure. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
89. Prediction of additive genetic variances of descendants for complex families based on Mendelian sampling variances.
- Author
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Niehoff TAM, Ten Napel J, and Calus MPL
- Abstract
The ability to predict the outcome of selection and mating decisions enables breeders to make strategically better selection decisions. To improve genetic progress, those individuals need to be selected whose offspring can be expected to show high genetic variance next to high breeding values. Previously published approaches enable to predict the variance of descendants of two future generations for up to 4 founding haplotypes, or 2 outbred individuals, based on phased genotypes, allele effects and recombination frequencies. The purpose of this study was to develop a general approach for the analytical calculation of the genetic variance in any future generation. The core development is an equation for the prediction of the variance of double haploid lines, under the assumption of no selection and negligible drift, stemming from an arbitrary number of founder haplotypes. This double haploid variance can be decomposed into gametic Mendelian sampling variances (MSV) of ancestors of the double haploid lines allowing usage for non-double haploid genotypes which enables application in animal breeding programs as well as in plant breeding programs. Together with the breeding values of the founders, the gametic MSV may be used in new selection criteria. We present our idea of such a criterion that describes the genetic level of selected individuals in four generations. Since breeding programs do select, the assumption made for predicting variances is clearly violated which decreases the accuracy of predicted gametic MSV caused by changes in allele frequency and linkage disequilibrium. Despite violating the assumption, we found high predictive correlations of our criterion to the true genetic level which was obtained by means of simulation for the "corn" and "cattle" genome models tested in this study (0.90 and 0.97). In practice, the genotype phases, genetic map and allele effects all need to be estimated meaning inaccuracies in their estimation will lead to inaccurate variance prediction. Investigation of variance prediction accuracy when input parameters are estimated was not part of this study., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)
- Published
- 2024
- Full Text
- View/download PDF
90. Improving selection decisions with mating information by accounting for Mendelian sampling variances looking two generations ahead.
- Author
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Niehoff TAM, Ten Napel J, Bijma P, Pook T, Wientjes YCJ, Hegedűs B, and Calus MPL
- Subjects
- Animals, Breeding methods, Female, Male, Selective Breeding, Quantitative Trait Loci, Models, Genetic, Selection, Genetic
- Abstract
Background: Breeding programs are judged by the genetic level of animals that are used to disseminate genetic progress. These animals are typically the best ones of the population. To maximise the genetic level of very good animals in the next generation, parents that are more likely to produce top performing offspring need to be selected. The ability of individuals to produce high-performing progeny differs because of differences in their breeding values and gametic variances. Differences in gametic variances among individuals are caused by differences in heterozygosity and linkage. The use of the gametic Mendelian sampling variance has been proposed before, for use in the usefulness criterion or Index5, and in this work, we extend existing approaches by not only considering the gametic Mendelian sampling variance of individuals, but also of their potential offspring. Thus, the criteria developed in this study plan one additional generation ahead. For simplicity, we assumed that the true quantitative trait loci (QTL) effects, genetic map and the haplotypes of all animals are known., Results: In this study, we propose a new selection criterion, ExpBVSelGrOff, which describes the genetic level of selected grand-offspring that are produced by selected offspring of a particular mating. We compare our criterion with other published criteria in a stochastic simulation of an ongoing breeding program for 21 generations for proof of concept. ExpBVSelGrOff performed better than all other tested criteria, like the usefulness criterion or Index5 which have been proposed in the literature, without compromising short-term gains. After only five generations, when selection is strong (1%), selection based on ExpBVSelGrOff achieved 5.8% more commercial genetic gain and retained 25% more genetic variance without compromising inbreeding rate compared to selection based only on breeding values., Conclusions: Our proposed selection criterion offers a new tool to accelerate genetic progress for contemporary genomic breeding programs. It retains more genetic variance than previously published criteria that plan less far ahead. Considering future gametic Mendelian sampling variances in the selection process also seems promising for maintaining more genetic variance., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
91. Accelerated matrix-vector multiplications for matrices involving genotype covariates with applications in genomic prediction.
- Author
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Freudenberg A, Vandenplas J, Schlather M, Pook T, Evans R, and Ten Napel J
- Abstract
In the last decade, a number of methods have been suggested to deal with large amounts of genetic data in genomic predictions. Yet, steadily growing population sizes and the suboptimal use of computational resources are pushing the practical application of these approaches to their limits. As an extension to the C/CUDA library miraculix , we have developed tailored solutions for the computation of genotype matrix multiplications which is a critical bottleneck in the empirical evaluation of many statistical models. We demonstrate the benefits of our solutions at the example of single-step models which make repeated use of this kind of multiplication. Targeting modern Nvidia
® GPUs as well as a broad range of CPU architectures, our implementation significantly reduces the time required for the estimation of breeding values in large population sizes. miraculix is released under the Apache 2.0 license and is freely available at https://github.com/alexfreudenberg/miraculix., Competing Interests: MiXBLUP is developed and marketed by the Animal Breeding and Genomics group at Wageningen UR Livestock Research, of which JV, TP, and JT are employees. The cattle data used in this study is proprietary and the intellectual property of the Irish Cattle Breeding Federation, at which RE is an employee. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Freudenberg, Vandenplas, Schlather, Pook, Evans and Ten Napel.)- Published
- 2023
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92. Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population.
- Author
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Bonifazi R, Calus MPL, Ten Napel J, Veerkamp RF, Biffani S, Cassandro M, Savoia S, and Vandenplas J
- Subjects
- Cattle, Animals, Male, Pedigree, Genotype, Phenotype, Reference Values, Genomics
- Abstract
Background: International evaluations combine data from different countries allowing breeders to have access to larger panels of elite bulls and to increase the accuracy of estimated breeding values (EBV). However, international and national evaluations can use different sources of information to compute EBV (EBV
INT and EBVNAT , respectively), leading to differences between them. Choosing one of these EBV results in losing the information that is contained only in the discarded EBV. Our objectives were to define and validate a procedure to integrate publishable sires' EBVINT and their associated reliabilities computed from pedigree-based or single-step international beef cattle evaluations into national evaluations to obtain "blended" EBV. The Italian (ITA) pedigree-based national evaluation was used as a case study to validate the integration procedure., Methods: Publishable sires' international information, i.e. EBVINT and their associated reliabilities, was included in the national evaluation as pseudo-records. Data were available for 444,199 individual age-adjusted weaning weights of Limousin cattle from eight countries and 17,607 genotypes from four countries (ITA excluded). To mimic differences between international and national evaluations, international evaluations included phenotypes (and genotypes) of animals born prior to January 2019, while national evaluations included ITA phenotypes of animals born until April 2019. International evaluations using all available information were considered as reference scenarios. Publishable sires were divided into three groups: sires with ≥ 15, < 15 and no recorded offspring in ITA., Results: Overall, for these three groups, integrating either pedigree-based or single-step international information into national pedigree-based evaluations improved the similarity of the blended EBV with the reference EBV compared to national evaluations without integration. For instance, the correlation with the reference EBV for direct (maternal) EBV went from 0.61 (0.79) for a national evaluation without integration to 0.97 (0.88) when integrating single-step international information, on average across all groups of publishable sires., Conclusions: Our proposed one-animal-at-a-time integration procedure yields blended EBV that are in close agreement with full international EBV for all groups of animals analysed. The procedure can be directly applied by countries since it does not rely on specific software and is computationally inexpensive, allowing straightforward integration of publishable sires' EBVINT from pedigree-based or single-step based international beef cattle evaluations into national evaluations., (© 2023. The Author(s).)- Published
- 2023
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93. Efficient large-scale single-step evaluations and indirect genomic prediction of genotyped selection candidates.
- Author
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Vandenplas J, Ten Napel J, Darbaghshahi SN, Evans R, Calus MPL, Veerkamp R, Cromie A, Mäntysaari EA, and Strandén I
- Subjects
- Animals, Cattle genetics, Genotype, Genomics, Phenotype, Pedigree, Models, Genetic, Genome
- Abstract
Background: Single-step genomic best linear unbiased prediction (ssGBLUP) models allow the combination of genomic, pedigree, and phenotypic data into a single model, which is computationally challenging for large genotyped populations. In practice, genotypes of animals without their own phenotype and progeny, so-called genotyped selection candidates, can become available after genomic breeding values have been estimated by ssGBLUP. In some breeding programmes, genomic estimated breeding values (GEBV) for these animals should be known shortly after obtaining genotype information but recomputing GEBV using the full ssGBLUP takes too much time. In this study, first we compare two equivalent formulations of ssGBLUP models, i.e. one that is based on the Woodbury matrix identity applied to the inverse of the genomic relationship matrix, and one that is based on marker equations. Second, we present computationally-fast approaches to indirectly compute GEBV for genotyped selection candidates, without the need to do the full ssGBLUP evaluation., Results: The indirect approaches use information from the latest ssGBLUP evaluation and rely on the decomposition of GEBV into its components. The two equivalent ssGBLUP models and indirect approaches were tested on a six-trait calving difficulty model using Irish dairy and beef cattle data that include 2.6 million genotyped animals of which about 500,000 were considered as genotyped selection candidates. When using the same computational approaches, the solving phase of the two equivalent ssGBLUP models showed similar requirements for memory and time per iteration. The computational differences between them were due to the preprocessing phase of the genomic information. Regarding the indirect approaches, compared to GEBV obtained from single-step evaluations including all genotypes, indirect GEBV had correlations higher than 0.99 for all traits while showing little dispersion and level bias., Conclusions: In conclusion, ssGBLUP predictions for the genotyped selection candidates were accurately approximated using the presented indirect approaches, which are more memory efficient and computationally fast, compared to solving a full ssGBLUP evaluation. Thus, indirect approaches can be used even on a weekly basis to estimate GEBV for newly genotyped animals, while the full single-step evaluation is done only a few times within a year., (© 2023. The Author(s).)
- Published
- 2023
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94. Differences across herds with different dairy breeds in daily milk yield based proxies for resilience.
- Author
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Adriaens I, Bonekamp G, Ten Napel J, Kamphuis C, and De Haas Y
- Abstract
Global sustainability issues such as climate change, biodiversity loss and food security require food systems to become more resource efficient and better embedded in the local environment. This needs a transition towards more diverse, circular and low-input dairy farming systems with animals best suited to the specific environmental conditions. When varying environmental challenges are posed to animals, cows need to become resilient to disturbances they face. This resilience of dairy cows for disturbances can be quantified using sensor features and resilience indicators derived from daily milk yield records. The aim of this study was to explore milk yield based sensor features and resilience indicators for different cattle groups according to their breeds and herds. To this end, we calculated 40 different features to describe the dynamics and variability in milk production of first parity dairy cows. After correction for milk production level, we found that various aspects of the milk yield dynamics, milk yield variability and perturbation characteristics indeed differed across herds and breeds. On farms with a lower breed proportion of Holstein Friesian across cows, there was more variability in the milk yield, but perturbations were less severe upon critical disturbances. Non-Holstein Friesian breeds had a more stable milk production with less (severe) perturbations. These differences can be attributed to differences in genetics, environments, or both. This study demonstrates the potential to use milk yield sensor features and resilience indicators as a tool to quantify how cows cope with more dynamic production conditions and select animals for features that best suit a farms' breeding goal and specific environment., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Adriaens, Bonekamp, Ten Napel, Kamphuis and De Haas.)
- Published
- 2023
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95. Impact of genomic preselection on subsequent ssGBLUP evaluation of preselected animals for scarcely recorded feed intake in pigs.
- Author
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Jibrila I, Ten Napel J, Vandenplas J, Bergsma R, Veerkamp RF, and Calus MPL
- Subjects
- Animals, Swine genetics, Retrospective Studies, Genotype, Phenotype, Eating genetics, Pedigree, Models, Genetic, Genome, Genomics methods
- Abstract
We have previously shown that single-step genomic best linear unbiased prediction (ssGBLUP) estimates breeding values of genomically preselected animals without preselection bias for widely recorded traits, that is traits recorded for the majority of animals in the breeding population. This study investigated the impact of genomic preselection (GPS) on accuracy and bias in ssGBLUP evaluation of genomically preselected animals for a scarcely recorded trait, that is a trait recorded for only a small proportion of the animals, which generally has a lower prediction accuracy than widely recorded traits, mainly due to having a much smaller number of phenotypes available. We used data from a commercial pig breeding program, considering feed intake as a scarcely recorded target trait, being available for ~30% of the animals with phenotypes for any trait, and average daily gain, backfat thickness and loin depth as widely recorded predictor traits, being available for >95% of the animals with phenotypes for any trait. The data contained the routine GPS implemented by commercial animal breeding programs, and we retrospectively implemented two scenarios with additional layers of GPS by discarding pedigree, genotypes and phenotypes of animals without progeny. The ssGBLUP evaluation following GPS used records only from the target trait, only from the predictor traits, or both. Accuracy for feed intake did not differ statistically across GPS scenarios, although it tended to decrease with more intense GPS. The accuracy had average values of 0.37, 0.44, and 0.45 across all GPS scenarios when, respectively, records from only the target trait, only the predictor traits, or both were used in the ssGBLUP evaluation. Considerable deflation of the genomic breeding values for feed intake was observed in the most stringent GPS scenario, due to the variance components being underestimated as a result of the limited amount of strongly preselected data. As long as (co)variance components were unbiased, no or only marginal bias was observed. These results for accuracy and bias were observed whether records of the scarcely recorded target trait, of the predictor traits, or both were used in the ssGBLUP evaluation. Our results show that for the scarcely recorded feed intake in pigs, ssGBLUP is able to estimate breeding values of preselected animals without preselection bias, similarly as previously observed for widely recorded traits., (© 2023 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.)
- Published
- 2023
- Full Text
- View/download PDF
96. International single-step SNPBLUP beef cattle evaluations for Limousin weaning weight.
- Author
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Bonifazi R, Calus MPL, Ten Napel J, Veerkamp RF, Michenet A, Savoia S, Cromie A, and Vandenplas J
- Subjects
- Animals, Cattle genetics, Genome, Genotype, Pedigree, Phenotype, Weaning, Models, Genetic, Polymorphism, Single Nucleotide
- Abstract
Background: Compared to national evaluations, international collaboration projects further improve accuracies of estimated breeding values (EBV) by building larger reference populations or performing a joint evaluation using data (or proxy of them) from different countries. Genomic selection is increasingly adopted in beef cattle, but, to date, the benefits of including genomic information in international evaluations have not been explored. Our objective was to develop an international beef cattle single-step genomic evaluation and investigate its impact on the accuracy and bias of genomic evaluations compared to current pedigree-based evaluations., Methods: Weaning weight records were available for 331,593 animals from seven European countries. The pedigree included 519,740 animals. After imputation and quality control, 17,607 genotypes at a density of 57,899 single nucleotide polymorphisms (SNPs) from four countries were available. We implemented two international scenarios where countries were modelled as different correlated traits: an international genomic single-step SNP best linear unbiased prediction (SNPBLUP) evaluation (ssSNPBLUP
INT ) and an international pedigree-based BLUP evaluation (PBLUPINT ). Two national scenarios were implemented for pedigree and genomic evaluations using only nationally submitted phenotypes and genotypes. Accuracies, level and dispersion bias of EBV of animals born from 2014 onwards, and increases in population accuracies were estimated using the linear regression method., Results: On average across countries, 39 and 17% of sires and maternal-grand-sires with recorded (grand-)offspring across two countries were genotyped. ssSNPBLUPINT showed the highest accuracies of EBV and, compared to PBLUPINT , led to increases in population accuracy of 13.7% for direct EBV, and 25.8% for maternal EBV, on average across countries. Increases in population accuracies when moving from national scenarios to ssSNPBLUPINT were observed for all countries. Overall, ssSNPBLUPINT level and dispersion bias remained similar or slightly reduced compared to PBLUPINT and national scenarios., Conclusions: International single-step SNPBLUP evaluations are feasible and lead to higher population accuracies for both large and small countries compared to current international pedigree-based evaluations and national evaluations. These results are likely related to the larger multi-country reference population and the inclusion of phenotypes from relatives recorded in other countries via single-step international evaluations. The proposed international single-step approach can be applied to other traits and breeds., (© 2022. The Author(s).)- Published
- 2022
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97. Impact of genomic preselection on subsequent genetic evaluations with ssGBLUP using real data from pigs.
- Author
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Jibrila I, Vandenplas J, Ten Napel J, Bergsma R, Veerkamp RF, and Calus MPL
- Subjects
- Animals, Bias, Genomics methods, Phenotype, Swine genetics, Genome, Models, Genetic
- Abstract
Background: Empirically assessing the impact of preselection on genetic evaluation of preselected animals requires comparing scenarios that take different approaches into account, including scenarios without preselection. However, preselection is almost always performed in animal breeding programs, so it is difficult to have a dataset without preselection. Hence, most studies on preselection have used simulated datasets, and have concluded that genomic estimated breeding values (GEBV) from subsequent single-step genomic best linear unbiased prediction (ssGBLUP) evaluations are unbiased. The aim of this study was to investigate the impact of genomic preselection (GPS) on accuracy and bias in subsequent ssGBLUP evaluations, using data from a commercial pig breeding program., Methods: We used data on average daily gain during performance testing, average daily gain throughout life, backfat thickness, and loin depth from one sire line and one dam line of pigs. As these traits have different weights in the breeding goals of the two lines, we analyzed the lines separately. For each line, we implemented a reference GPS scenario that kept all available data, against which the next two scenarios were compared. We then implemented two other scenarios with additional layers of GPS by removing all animals without progeny either (i) only in the validation generation, or (ii) in all generations. We conducted subsequent ssGBLUP evaluations for each GPS scenario, using all the data remaining after implementing the GPS scenario. Accuracy and bias were computed by comparing GEBV against progeny yield deviations of validation animals., Results: Results for all traits and in both lines showed a marginal loss in accuracy due to the additional layers of GPS. Average accuracies across all GPS scenarios in the two lines were 0.39, 0.47, 0.56, and 0.60, for average daily gain during performance testing and throughout life, backfat thickness, and loin depth, respectively. Biases were largely absent, and when present, did not differ greatly between the GPS scenarios., Conclusions: We conclude that the impact of preselection on accuracy and bias in subsequent ssGBLUP evaluations of selection candidates in pigs is generally minimal. We expect this conclusion to apply for other animal breeding programs as well, since preselection of any type or intensity generally has the same effect in animal breeding programs., (© 2022. The Author(s).)
- Published
- 2022
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98. The impact of direct-maternal genetic correlations on international beef cattle evaluations for Limousin weaning weight.
- Author
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Bonifazi R, Vandenplas J, Ten Napel J, Veerkamp RF, and Calus MPL
- Subjects
- Animals, Body Weight, Cattle genetics, Linear Models, Phenotype, Reproducibility of Results, Weaning, Models, Genetic
- Abstract
In beef cattle maternally influenced traits, estimates of direct-maternal genetic correlations (rdm) are usually reported to be negative. In international evaluations, rdm can differ both within countries (rdm_WC) and between countries (rdm_BC). The rdm_BC are difficult to estimate and are assumed to be zero in the current model for international beef cattle evaluations (Interbeef). Our objective was to investigate re-ranking of international estimated breeding values (IEBVs) in international beef cattle evaluations between models that either used estimated values for rdm or assumed them to be 0. Age-adjusted weaning weights and pedigree data were available for Limousin beef cattle from ten European countries. International EBVs were obtained using a multi-trait animal model with countries modeled as different traits. We compared IEBVs from a model that uses estimated rdm_BC (ranging between -0.14 and +0.14) and rdm_WC (between -0.33 and +0.40) with IEBVs obtained either from the current model that assumes rdm_BC to be 0, or from an alternative model that assumes both rdm_BC and rdm_WC to be 0. Direct and maternal IEBVs were compared across those three scenarios for different groups of animals. The ratio of population accuracies from the linear regression method was used to further investigate the impact of rdm on international evaluations, for both the whole set of animals in the evaluation and the domestic ones. Ignoring rdm_BC, i.e., replacing estimated values with 0, resulted in no (rank correlations > 0.99) or limited (between 0.98 and 0.99) re-ranking for direct and maternal IEBVs, respectively. Both rdm_BC and rdm_WC had less impact on direct IEBVs than on maternal IEBVs. Re-ranking of maternal IEBVs decreased with increasing reliability. Ignoring rdm_BC resulted in no re-ranking for sires with IEBVs that might be exchanged across countries and limited re-ranking for the top 100 sires. Using estimated rdm_BC values instead of considering them to be 0 resulted in null to limited increases in population accuracy. Ignoring both rdm_BC and rdm_WC resulted in considerable re-ranking of animals' IEBVs in all groups of animals evaluated. This study showed the limited impact of the current practice of ignoring rdm_BC in international evaluations for Limousin weaning weight, most likely because the estimated rdm_BC was close to 0. We expect that these conclusions can be extended to other traits that have reported rdm values in the range of rdm_WC values for weaning weight in Limousin., (© The Author(s) 2021. Published by Oxford University Press on behalf of the American Society of Animal Science.)
- Published
- 2021
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- View/download PDF
99. Avoiding preselection bias in subsequent single-step genomic BLUP evaluations of genomically preselected animals.
- Author
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Jibrila I, Vandenplas J, Ten Napel J, Veerkamp RF, and Calus MPL
- Subjects
- Animals, Female, Genomics, Genotype, Male, Models, Genetic, Pedigree, Phenotype, Genome
- Abstract
In animal breeding, parents of the next generation are usually selected in multiple stages, and the initial stages of this selection are called preselection. Preselection reduces the information available for subsequent evaluation of preselected animals and this sometimes leads to bias. The objective of this study was to establish the minimum information required to subsequently evaluate genomically preselected animals without bias arising from preselection, with single-step genomic best linear unbiased prediction (ssGBLUP). We simulated a nucleus of a breeding program in which a recent population of 15 generations was produced. In each generation, parents of the next generation were selected in a single-stage selection based on pedigree BLUP. However, in generation 15, 10% of male and 15% of female offspring were preselected on their genomic estimated breeding values (GEBV). These GEBV were estimated using ssGBLUP, including the pedigree of all animals in generations 0-15, genotypes of all animals in generations 13-15 and phenotypes of all animals in generations 11-14. In subsequent ssGBLUP evaluation of these preselected animals, genotypes and phenotypes from various groups of animals were excluded one after another. We found that GEBV of the preselected animals were only estimated without preselection bias when genotypes and phenotypes of all animals in generations 13 and 14 and of the preselected animals were included in the subsequent evaluation. We also found that genotypes of the animals discarded at preselection only helped in reducing preselection bias in GEBV of their preselected sibs when genotypes of their parents were absent or excluded from the subsequent evaluation. We concluded that to prevent preselection bias in subsequent ssGBLUP evaluation of genomically preselected animals, information representative of the reference data used in the evaluation at preselection and genotypes and phenotypes of the preselected animals are needed in the subsequent evaluation., (© 2020 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.)
- Published
- 2021
- Full Text
- View/download PDF
100. Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals.
- Author
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Jibrila I, Ten Napel J, Vandenplas J, Veerkamp RF, and Calus MPL
- Subjects
- Animals, Female, Male, Pedigree, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait, Heritable, Selection, Genetic, Breeding methods, Livestock genetics, Poultry genetics
- Abstract
Background: Preselection of candidates, hereafter referred to as preselection, is a common practice in breeding programs. Preselection can cause bias and accuracy loss in subsequent pedigree-based best linear unbiased prediction (PBLUP). However, the impact of preselection on subsequent single-step genomic BLUP (ssGBLUP) is not completely clear yet. Therefore, in this study, we investigated, across different heritabilities, the impact of intensity and type of preselection on subsequent ssGBLUP evaluation of preselected animals., Methods: We simulated a nucleus of a breeding programme, in which a recent population of 15 generations was produced with PBLUP-based selection. In generation 15 of this recent population, the parents of the next generation were preselected using several preselection scenarios. These scenarios were combinations of three intensities of preselection (no, high or very high preselection) and three types of preselection (genomic, parental average or random), across three heritabilities (0.5, 0.3 or 0.1). Following each preselection scenario, a subsequent evaluation was performed using ssGBLUP by excluding all the information from the preculled animals, and these genetic evaluations were compared in terms of accuracy and bias for the preselected animals, and in terms of realized genetic gain., Results: Type of preselection affected selection accuracy at both preselection and subsequent evaluation stages. While preselection accuracy decreased, accuracy in the subsequent ssGBLUP evaluation increased, from genomic to parent average to random preselection scenarios. Bias was always negligible. Genetic gain decreased from genomic to parent average to random preselection scenarios. Genetic gain also decreased with increasing intensity of preselection, but only by a maximum of 0.1 additive genetic standard deviation from no to very high genomic preselection scenarios., Conclusions: Using ssGBLUP in subsequent evaluations prevents preselection bias, irrespective of intensity and type of preselection, and heritability. With GPS, in addition to reducing the phenotyping effort considerably, the use of ssGBLUP in subsequent evaluations realizes only a slightly lower genetic gain than that realized without preselection. This is especially the case for traits that are expensive to measure (e.g. feed intake of individual broiler chickens), and traits for which phenotypes can only be measured at advanced stages of life (e.g. litter size in pigs).
- Published
- 2020
- Full Text
- View/download PDF
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