Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Value of the Dutch Holstein Friesian germplasm collection to increase genetic variability and improve genetic merit
Doekes, H.P. ; Veerkamp, R.F. ; Bijma, P. ; Hiemstra, S.J. ; Windig, J. - \ 2018
Journal of Dairy Science 101 (2018)11. - ISSN 0022-0302 - p. 10022 - 10033.
conservation - dairy cow - gene bank collection - genetic diversity - genetic improvement

National gene bank collections for Holstein Friesian (HF) dairy cattle were set up in the 1990s. In this study, we assessed the value of bulls from the Dutch HF germplasm collection, also known as cryobank bulls, to increase genetic variability and improve genetic merit in the current bull population (bulls born in 2010–2015). Genetic variability was defined as 1 minus the mean genomic similarity (SIMSNP) or as 1 minus the mean pedigree-based kinship (fPED). Genetic merit was defined as the mean estimated breeding value for the total merit index or for 1 of 3 subindices (yield, fertility, and udder health). Using optimal contribution selection, we minimized relatedness (maximized variability) or maximized genetic merit at restricted levels of relatedness. We compared breeding schemes with only bulls from 2010 to 2015 with schemes in which cryobank bulls were also included. When we minimized relatedness, inclusion of genotyped cryobank bulls decreased mean SIMSNP by 0.7% and inclusion of both genotyped and nongenotyped cryobank bulls decreased mean fPED by 2.6% (in absolute terms). When we maximized merit at restricted levels of relatedness, inclusion of cryobank bulls provided additional merit at any level of mean SIMSNP or mean fPED except for the total merit index at high levels of mean SIMSNP. Additional merit from cryobank bulls depended on (1) the relative emphasis on genetic variability and (2) the selection criterion. Additional merit was higher when more emphasis was put on genetic variability. For fertility, for example, it was 1.74 SD at a mean SIMSNP restriction of 64.5% and 0.37 SD at a mean SIMSNP restriction of 67.5%. Additional merit was low to nonexistent for the total merit index and higher for the subindices, especially for fertility. At a mean SIMSNP of 64.5%, for example, it was 0.60 SD for the total merit index and 1.74 SD for fertility. In conclusion, Dutch HF cryobank bulls can be used to increase genetic variability and improve genetic merit in the current population, although their value is very limited when selecting for the current total merit index. Anticipating changes in the breeding goal in the future, the germplasm collection is a valuable resource for commercial breeding populations.

Genomic selection and inbreeding and kinship in Dutch-Flemish Holstein Friesian cattle
Doekes, H.P. ; Veerkamp, R.F. ; Bijma, P. ; Hiemstra, S.J. ; Ursinus, W.W. ; Beek, S. van der; Windig, J.J. - \ 2018
In: Proceedings of the 11th World Congress on Genetics Applied to Livestock Production. - - 5 p.
Since 2009, genomic selection (GS) has been widely applied in Holstein Friesian (HF) breeding programs. In this study, we evaluated how the introduction of GS in the Dutch-Flemish HF breeding program has affected inbreeding and kinship trends, using both pedigree-based and genomic measures. Rates of inbreeding and kinship for artificial insemination (AI) bulls increased with the introduction of GS, from 0.1-0.7% in 2003-2009 to 1.6-2.5% in 2009-2015. Rates of inbreeding and kinship for cows also increased with GS, although they were lower than for AI-bulls (i.e. 0.79-1.14% in 2009-2017). Levels of identical by state (IBS), which include relatedness due to both recent and distant common ancestors, increased faster than levels of identical by descent (IBD), which include only recent inbreeding and kinship. Accumulation of inbreeding varied substantially across the genome over time, with specific regions showing a striking increase in inbreeding since the introduction of GS. These findings emphasize the need for efficient genomic management of inbreeding in GS-schemes.
Genome-wide characterization of selection signatures and runs of homozygosity in Ugandan goat breeds
Onzima, Robert B. ; Upadhyay, Maulik R. ; Doekes, Harmen P. ; Brito, Luiz F. ; Bosse, Mirte ; Kanis, Egbert ; Groenen, Martien A.M. ; Crooijmans, Richard P.M.A. - \ 2018
Frontiers in Genetics 9 (2018). - ISSN 1664-8021
Adaptation - Candidate genes - Capra hircus - Genetic diversity - Genomic inbreeding - Homozygosity - Selective sweeps

Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, FROH, based on runs of homozygosity (ROH), in six Ugandan goat breeds: Boer (n = 13), and the indigenous breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29), and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all breeds, based on marker-specific fixation index (FST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signaling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g., IL10RB and IL23A), growth and fatty acid composition (e.g., FGF9 and IGF1), and thermo-tolerance (e.g., MTOR and MAPK3). The study revealed little overlap between breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g., GJB2 and GJA3) were also identified. Furthermore, analysis of ROH in indigenous goat breeds showed very low levels of genomic inbreeding (with the mean FROH per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean FROH = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these goat breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan goat breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.

Limits to genetic rescue by outcross in pedigree dogs
Windig, J.J. ; Doekes, H.P. - \ 2018
Journal of Animal Breeding and Genetics 135 (2018)3. - ISSN 0931-2668 - p. 238 - 248.
conservation genetics - dogs - genetic defects

Outcrossing should reduce inbreeding levels and associated negative effects in highly inbred populations. In this study, we investigated the effectiveness of different outcrossing schemes using computer simulations. The inbreeding rate estimated for a 25-year period of 2.1% per generation in a highly inbred dog breed reduced to 1.8% when a single litter was produced by an outcross without backcrosses. To reduce the inbreeding rate below 1%, more than eight of the 14 litters born yearly in the recipient breed had to be outcrossed. However, outcrossing in pedigree dogs is usually followed by backcrossing and generally involves one or a few litters. Backcrossing reduced the effect of outcrossing considerably. When two litters were produced by an outcross followed by one generation of backcross, the inbreeding rate was 2.0% per generation. Continuously outcrossing was more effective than a single or a few outcrosses. When each newborn litter during 25 years had a 5% chance of being produced by an outcross, the inbreeding rate reduced to −0.2%. To investigate the possibility that new alleles were introduced from the donor population into the recipient population, the fate of different type of alleles (varying from completely lethal to beneficial) before and after an outcross was investigated by first simulating 80 years of natural selection prior to the outcross and then different types of outcross. Because natural selection reduced the frequency of lethal alleles before outcrossing, the introduction of a lethal allele that was segregating in the donor breed but not in the recipient breed occurred rarely. Introduction of slightly detrimental alleles or neutral alleles occurred more frequently. In conclusion, outcrossing only had a limited short-term effect unless repeated continuously. Nevertheless, it may help to buy time in which the population structure can be changed so that the effective population size increases.

Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein-Friesian breeding program from 1986 to 2015
Doekes, Harmen P. ; Veerkamp, Roel F. ; Bijma, Piter ; Hiemstra, Sipke J. ; Windig, Jack J. - \ 2018
Genetics, Selection, Evolution 50 (2018)1. - ISSN 0999-193X

Background: 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 composition (around 2000) and the implementation of genomic selection (GS; around 2010). These changes are expected to have influenced genetic diversity trends. Our aim was to evaluate genome-wide and region-specific diversity in HF artificial insemination (AI) bulls in the Dutch-Flemish breeding program from 1986 to 2015. Methods: Pedigree and genotype data (~ 75.5 k) of 6280 AI-bulls were used to estimate rates of genome-wide inbreeding and kinship and corresponding effective population sizes. Region-specific inbreeding trends were evaluated using regions of homozygosity (ROH). Changes in observed allele frequencies were compared to those expected under pure drift to identify putative regions under selection. We also investigated the direction of changes in allele frequency over time. Results: Effective population size estimates for the 1986-2015 period ranged from 69 to 102. Two major breakpoints were observed in genome-wide inbreeding and kinship trends. Around 2000, inbreeding and kinship levels temporarily dropped. From 2010 onwards, they steeply increased, with pedigree-based, ROH-based and marker-based inbreeding rates as high as 1.8, 2.1 and 2.8% per generation, respectively. Accumulation of inbreeding varied substantially across the genome. A considerable fraction of markers showed changes in allele frequency that were greater than expected under pure drift. Putative selected regions harboured many quantitative trait loci (QTL) associated to a wide range of traits. In consecutive 5-year periods, allele frequencies changed more often in the same direction than in opposite directions, except when comparing the 1996-2000 and 2001-2005 periods. Conclusions: Genome-wide and region-specific diversity trends reflect major changes in the Dutch-Flemish HF breeding program. Introduction of OCS and the shift in breeding goal were followed by a drop in inbreeding and kinship and a shift in the direction of changes in allele frequency. After introduction of GS, rates of inbreeding and kinship increased substantially while allele frequencies continued to change in the same direction as before GS. These results provide insight in the effect of breeding practices on genomic diversity and emphasize the need for efficient management of genetic diversity in GS schemes.

Optimised evaluation and management of genome-wide and region-specific genetic diversity in livestock
Doekes, Harmen - \ 2017
Optimised evaluation and management of genome-wide and region-specific genetic diversity in livestock
Doekes, Harmen - \ 2017
Genetische analyse van de Stabij
Doekes, H.P. ; Oldenbroek, J.K. ; Windig, J.J. - \ 2016
Zeldzaam huisdier 41 (2016)1. - ISSN 0929-905X - p. 18 - 19.
zeldzame rassen - genetische analyse - hondenrassen - friese stabij - dierveredeling - rare breeds - genetic analysis - dog breeds - frisian stabyhoun - animal breeding
De Stabij is een van de negen oorspronkelijke Nederlandse hondenrassen die een belangrijke rol vervullen in het Fairfok-programma van de Raad van Beheer voor de Kynologie. De SZH ondersteunt dat programma door de rasverenigingen van kennis en advies te voorzien en heeft met het CGN een genetische analyse gemaakt van het Stabijras.
Genetische analyse van het Markiesje
Doekes, H.P. ; Oldenbroek, J.K. ; Windig, J.J. - \ 2016
Zeldzaam huisdier 41 (2016)2. - ISSN 0929-905X - p. 20 - 21.
hondenrassen - zeldzame rassen - genetische analyse - dierveredeling - stamboeken - dog breeds - rare breeds - genetic analysis - animal breeding - herdbooks
Het Markiesje is een van de negen oorspronkelijke Nederlandse hondenrassen. Het vervult een belangrijke rol in het Fairfok-programma. De SZH ondersteunt dat programma door de rasverenigingen van kennis en advies te voorzien.
Hydrate sodium calcium aluminosilicate does not reduce rumen lipopolysacharide concentrations in cows
Pilachai, R. ; Schonewille, J.T. ; Thamrongyoswittayakul, C. ; Aiumlamai, S. ; Wachirapakorn, C. ; Everts, H. ; Vlaeminck, B. ; Doekes, G. ; Hendriks, W.H. - \ 2014
Animal Feed Science and Technology 191 (2014). - ISSN 0377-8401 - p. 111 - 115.
subacute ruminal acidosis - dairy-cows - inflammatory response - in-vitro - lipopolysaccharide - smectite - triggers - system - milk
The efficacy of hydrate sodium calcium aluminosilicate (HSCAS) to reduce the concentrations of free lipopolysaccharide (LPS) in rumen fluid of cows was investigated. Six, rumen-fistulated crossbred Holstein, non-pregnant, dry cows were randomly assigned to three experimental rations in a study with a replicated 3 × 3 Latin square design with 28-d periods. During the first 20 days of each experimental period, cows were offered concentrate (5.4 kg dry matter; DM) without HSCAS and rice straw ad libitum. On day 21, cows were fasted for 12 h prior to commencement of a 7-d measurement period during which time cows were offered concentrate (10.5 kg DM) containing either 0, 5 or 10 g/kg of HSCAS and 1.5 kg DM rice straw. Rumen fluid was collected on days 1, 3 and 7 during the measurement period for analysis of pH, LPS and volatile fatty acids (VFA). Supplemental HSCAS did not affect the pH or the concentrations of total and individual VFA in the ruminal fluid. Mean postprandial rumen pH was reduced to values below 5.6 at all times. Rumen LPS concentrations significantly increased from day 1 to 7 during each measurement period with values ranging from 4489 to 104,000 EU/mL but they were not significantly affected by supplemental HSCAS.
Detektion von Labortierallergenen mit einem semi-quantitativen Schnelltest
Zahradnik, E. ; Koets, M. ; Tolba, R. ; Sander, I. ; Amerongen, A. van; Doekes, G. ; Renström, A. ; Brüning, T. ; Raulf-Heimsoth, M. - \ 2007
Atemwegs- und Lungkrankheiten 33 (2007)8. - ISSN 0341-3055 - p. 314 - 315.
Semiquantitative Schnelltestmethode für den Nachweis von Labortierallergenen am Arbeitsplatz
Raulf-Heimsoth, M. ; Zahradnik, E. ; Koets, M. ; Tolba, R. ; Sander, I. ; Amerongen, A. van; Doekes, G. ; Renström, A. ; Brüning, T. - \ 2006
Arbeitsmedizin, Sozialmedizin, Umweltmedizin: Zeitschrift fuer Praxis, Klinik, Forschung, Begutachtung 41 (2006)3. - ISSN 0944-6052 - p. 136 - 136.
Rapid detection of fungal alpha-amylase in the work environment with a lateral flow immunoassay
Bogdanovic, J. ; Koets, M. ; Sander, I. ; Wouters, I. ; Meijster, T. ; Heederik, D.J.J. ; Amerongen, A. van; Doekes, G. - \ 2006
Journal of Allergy and Clinical Immunology 118 (2006)5. - ISSN 0091-6749 - p. 1157 - 1163.
bakery workers - baking industry - allergens - sensitization - antibodies - antigen - dust - hiv
Background Occupational allergen exposure assessment usually requires airborne dust sampling at the worksite followed by dust extraction and enzyme immunoassay (EIA) analysis at the laboratory. Use of semiquantitative lateral flow immunoassays (LFIAs) may allow a more rapid detection procedure with direct on-site demonstration of a bioallergen exposure hazard. Objective In a field study, we evaluated a recently developed LFIA for fungal alpha-amylase, an important bakery allergen. Methods Airborne and surface dust (wipe) samples and samples from flours and baking additives used at the workplace were collected in 5 industrial bakeries and tested in the LFIA for fungal amylase. For comparison, amylase was measured in sample eluates with the reference EIA method. Results Sensitivity of the LFIA was 1 to 10 ng/mL, and of EIA, 25 pg/mL. In LFIA, most flour samples, 84% of wipe samples, 26% of personal airborne dust, and none of the 26 ambient air dust samples produced a visible reaction. Wipe samples from dough-making areas and flour samples gave the strongest reactions. All extracts with >5 ng allergen per milliliter showed a positive LFIA reaction. Conclusion The LFIA for fungal amylase is an easy and rapid method to demonstrate the allergen directly at the worksite in less than 10 to 20 minutes. Similar LFIA methods may be used for other occupational allergens in other work environments. Clinical implications Lateral flow immunoassays for occupational allergens may be of great value in occupational hygiene surveys to demonstrate directly to workers and supervisors the hazards of work-related bioallergen exposure.
A rapid lateral flow immunoassay for the detection of fungal alpha-amylase at the workplace
Koets, M. ; Sander, I. ; Bogdanovic, J. ; Doekes, G. ; Amerongen, A. van - \ 2006
Journal of Environmental Monitoring 8 (2006)9. - ISSN 1464-0325 - p. 942 - 946.
inhalable dust - exposure - sensitization - bakeries - allergens - symptoms - workers
Fungal alpha-amylase is a flour supplement which is added to improve the quality of bakery products. Various studies have shown that exposure to this enzyme is an important risk factor for the development of bakers allergy and this allergy is reported to be one of the most frequent causes of occupational asthma. A rapid assay was developed to monitor exposure to occupational allergens directly at the workplace. The sensitivity of the developed assay is 0.32 ng amylase mL¿1 in a buffer system with the commercially available alpha-amylase preparation Fungamyl 1600S as the standard. Initial validation tests (n = 33) were performed with airborne and settled dust from an industrial bakery. The new lateral flow immunoassay detected amylase in 22 of the 26 samples regarded as positive in an enzyme immunoassay, and was negative for all seven enzyme immunoassay-negative samples, while the four lateral flow immunoassay-negative/enzyme immunoassay-positive samples all had levels below 2 ng mL¿1. The sensitivity of 2 ng mL¿1 of the amylase lateral flow immunoassay is sufficient for first screening purposes and, therefore, this simple and rapid assay may allow direct on-site demonstration of work-related hazards of bio-allergen exposure. This would be particularly useful in occupational hygiene practice, especially in traditional or small-scale bakeries which lack the technological skills for testing the exposure to respiratory allergens
Nachweis von arbeitsplatzbezogenen Aeroallergenen : Einsatz einer semi-quantitativen Schnelltestmethode
Zahradnik, E. ; Koets, M. ; Sander, I. ; Tolba, R. ; Amerongen, A. van; Doekes, G. ; Renström, A. ; Brüning, T. ; Raulf-Heimsoth, M. - \ 2006
Gefahrstoffe : Reinhaltung der Luft 66 (2006)3. - ISSN 0949-8036 - p. 120 - 124.
Workplace-related allergen exposure is an important risk factor for the development of occupational allergy and asthma. New allergen specific semi-quantitative tests, Lateral Flow Immuno Assays (LFIAs), have been developed for the detection of occupational allergen exposure directly at the workplaces. These tests are quick and simple to perform, the results are visible within minutes and easily interpretable. In this article, the principle of LFIA is described and the practical application of the immunoassays for mouse and rat urinary allergens in a laboratory animal facility is presented. The results show that the sensitivity of the rapid tests is sufficient for the detection of small amounts of allergen in extracts from deposited dust. Thus they can help to reveal the allergen sources and to develop preventive and interventional measures. Furthermore, the LFIAs are especially suited for the direct on-site demonstration of allergen contaminations to staff members and, therefore, useful in occupational hygiene practice. This method is also a feasible screening system before starting extensive measurements of airborne allergens.
Boeren voor Natuur op Twickel; plan eerste fase
Stortelder, A.H.F. ; Buizer, I.M. ; Corporaal, A. ; Doekes, E.R. ; Ekamper, T. ; Hesselnk, K. ; Kwak, R.G.M. ; Schrijver, R.A.M. ; Vries, C. de - \ 2005
Wageningen : Alterra (Alterra-rapport 1055) - 199 p.
Verspreiding van organisch stof rond de mengvoederbedrijven in Doetinchem : oriëntatiemeting organisch stof
Doekes, G. ; Loon, J. van; Spithoven, J. - \ 2001
Wageningen : Wetenschapswinkel (Adviesbrief / Wetenschapswinkel 164) - 35
verontreiniging - geluidshinder - luchtverontreiniging - stof - meelindustrie - nederland - ademhaling - fysiologie - gelderland - pollution - noise pollution - air pollution - dust - milling industry - netherlands - respiration - physiology
The effect of smoking on cytokine release after exposure to organic dust components in a whole blood assay
Sigsgaard, T. ; Maarl, E. van der; Bak, N. ; Bonefels-Jorgensen, E.C. ; Omland, O. ; Doekes, G. - \ 1999
In: Proceedings of the 23rd Cotton and Other Organic Dusts Research Conference, Beltwide Cotton Conferences, Orlando,Florida.USA, 3-7 Jan, 1999. - Memphis : National Cotton Council of America, 1999 - p. 197 - 200.
Effect of 50- and 100-mg vitamin E supplements on cellular immune function in noninstitutionalized elderly persons
Pallast, E.G. ; Schouten, E.G. ; Waart, F.G. de; Fonk, H.C. ; Doekes, G. ; Blomberg, B.M. von; Kok, F.J. - \ 1999
American Journal of Clinical Nutrition 69 (1999). - ISSN 0002-9165 - p. 1273 - 1281.
Exposure-response relations of alpha-amylase sensitisation in British bakeries and flour mills
Nieuwenhuijsen, M.J. ; Heederik, D.J.J. ; Doekes, G. ; Venables, K.M. ; Newman Taylor, A.J. - \ 1999
Occupational and Environmental Medicine 56 (1999). - ISSN 1351-0711 - p. 197 - 201.
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