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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    Revised calculation of Kalinowski's ancestral and new inbreeding coefficients
    Doekes, Harmen P. ; Curik, Ino ; Nagy, István ; Farkas, János ; Kövér, György ; Windig, Jack J. - \ 2020
    Diversity 12 (2020)4. - ISSN 1424-2818
    Ancestral inbreeding - Gene dropping - Inbreeding depression - New inbreeding - Purging

    To test for the presence of purging in populations, the classical pedigree-based inbreeding coefficient (F) can be decomposed into Kalinowski's ancestral (FANC) and new (FNEW) inbreeding coefficients. The FANC and FNEW can be calculated by a stochastic approach known as gene dropping. However, the only publicly available algorithm for the calculation of FANC and FNEW, implemented in GRain v 2.1 (and also incorporated in the PEDIG software package), has produced biased estimates. The FANC was systematically underestimated and consequently, FNEW was overestimated. To illustrate this bias, we calculated FANC and FNEW by hand for simple example pedigrees. We revised the GRain program so that it now provides unbiased estimates. Correlations between the biased and unbiased estimates of FANC and FNEW, obtained for example data sets of Hungarian Pannon White rabbits (22,781 individuals) and Dutch Holstein Friesian cattle (37,061 individuals), were high, i.e., >0.96. Although the magnitude of bias appeared to be small, results from studies based on biased estimates should be interpreted with caution. The revised GRain program (v 2.2) is now available online and can be used to calculate unbiased estimates of FANC and FNEW.

    Value of gene bank material for the commercial breeding population of Dutch Holstein Friesian cattle
    Windig, J.J. ; Doekes, H.P. ; Veerkamp, R.F. ; Bijma, P. ; Hiemstra, S.J. - \ 2019
    In: Value of gene bank material for the commercial breeding population of Dutch Holstein Friesian cattle. - Wageningen : Wageningen Academic Publishers (Book of Abstracts ) - ISBN 9789086863396 - p. 368 - 368.
    Not all inbreeding is depressing
    Doekes, H.P. ; Veerkamp, R.F. ; Bijma, P. ; Hiemstra, S.J. ; Jong, Gerben de; Windig, J.J. - \ 2019
    In: Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. - Wageningen : Wageningen Academic Publishers (Book of Abstracts ) - ISBN 9789086863396 - p. 142 - 142.
    Inbreeding decreases animal performance (inbreeding depression), but not all inbreeding is expected to be equally harmful. Inbreeding on recent ancestors is expected to be more harmful than inbreeding on more ancient ancestors, because of purging. Purging is the removal of deleterious recessive alleles over time by selection. We investigated the effects of recent and ancient inbreeding on yield, fertility and udder health of 38,792 Holstein Friesian first-parity cows, using linear mixed models. Pedigree data were used to compute traditional inbreeding (FPED) and genotype data were used to identify regions of homozygosity (ROH) and compute ROH-based inbreeding (FROH). Inbreeding depression was apparent, e.g. a 1% increase in FROH was associated with a decrease in 305-d milk yield of 36.3 kg (SE=2.4), an increase in calving interval of 0.48 days (SE=0.15) and an increase in mean somatic cell score in day 150 to 400 of 0.86 units (SE=0.28). Distinguishing recent from ancient inbreeding gave mixed results. For example, only very long ROHs (which indicate recent inbreeding) signicantly increased calving interval, whereas both long and short ROH decreased protein yield. When FPED was split into new and ancestral components, based on whether alleles were identical by descent for the first time or not, there was clear evidence of purging. For example, a 1% increase in new inbreeding was associated with a 2.2 kg (SE=0.4) decrease in protein yield, compared to a 0.9 kg (SE=0.8) increase for ancestral inbreeding. The mixed results may be partly due to difficulties in estimating ancient inbreeding. Distant ancestors are less well registered, and short ROHs may be less reliable than long ROHs. Furthermore, purging may have acted on some, but not all alleles. To conclude, there is purging in the population, but purging effects are only partly rejected by the difference in inbreeding depression due to recent and ancient inbreeding.
    Characterization of genetic diversity conserved in the gene bank for dutch cattle breeds
    Breukelen, Anouk E. van; Doekes, Harmen P. ; Windig, Jack J. ; Oldenbroek, Kor - \ 2019
    Diversity 11 (2019)12. - ISSN 1424-2818 - p. 1 - 13.
    Cattle - Conservation - Cryobank - Genetic variation

    In this study, we characterized genetic diversity in the gene bank for Dutch native cattle breeds. A total of 715 bulls from seven native breeds and a sample of 165 Holstein Friesian bulls were included. Genotype data were used to calculate genetic similarities. Based on these similarities, most breeds were clearly differentiated, except for two breeds (Deep Red and Improved Red and White) that have recently been derived from the MRY breed, and for the Dutch Friesian and Dutch Friesian Red, which have frequently exchanged bulls. Optimal contribution selection (OCS) was used to construct core sets of bulls with a minimized similarity. The composition of the gene bank appeared to be partly optimized in the semen collection process, i.e., the mean similarity within breeds based on the current number of straws per bull was 0.32% to 1.49% lower than when each bull would have contributed equally. Mean similarity could be further reduced within core sets by 0.34% to 2.79% using OCS. Material not needed for the core sets can be made available for supporting in situ populations and for research. Our findings provide insight in genetic diversity in Dutch cattle breeds and help to prioritize material in gene banking.

    Nederlandse genenbank voor landbouwhuisdieren: waardevolle bron voor de fokkerij
    Schurink, A. ; Hulsegge, B. ; Windig, J.J. ; Hoving, A.H. ; Doekes, H.P. ; Hiemstra, S.J. - \ 2019
    - p. 1 - 1.
    Fokdoelen en fokwaarden: hoe kies je een passende stier voor je bedrijf?
    Breukelen, Anouk van; Doekes, H.P. ; Hoving, A.H. ; Sluis, M. van der; Poppe, H.W.M. - \ 2019
    Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle
    Doekes, Harmen P. ; Veerkamp, Roel F. ; Bijma, Piter ; Jong, Gerben de; Hiemstra, Sipke J. ; Windig, Jack J. - \ 2019
    Genetics, Selection, Evolution 51 (2019)1. - ISSN 0999-193X - 16 p.

    BACKGROUND: Inbreeding decreases animal performance (inbreeding depression), but not all inbreeding is expected to be equally harmful. Recent inbreeding is expected to be more harmful than ancient inbreeding, because selection decreases the frequency of deleterious alleles over time. Selection efficiency is increased by inbreeding, a process called purging. Our objective was to investigate effects of recent and ancient inbreeding on yield, fertility and udder health traits in Dutch Holstein-Friesian cows. METHODS: In total, 38,792 first-parity cows were included. Pedigree inbreeding ([Formula: see text]) was computed and 75 k genotype data were used to compute genomic inbreeding, among others based on regions of homozygosity (ROH) in the genome ([Formula: see text]). RESULTS: Inbreeding depression was observed, e.g. a 1% increase in [Formula: see text] was associated with a 36.3 kg (SE = 2.4) decrease in 305-day milk yield, a 0.48 day (SE = 0.15) increase in calving interval and a 0.86 unit (SE = 0.28) increase in somatic cell score for day 150 through to 400. These effects equalled - 0.45, 0.12 and 0.05% of the trait means, respectively. When [Formula: see text] was split into generation-based components, inbreeding on recent generations was more harmful than inbreeding on more distant generations for yield traits. When [Formula: see text] was split into new and ancestral components, based on whether alleles were identical-by-descent for the first time or not, new inbreeding was more harmful than ancestral inbreeding, especially for yield traits. For example, a 1% increase in new inbreeding was associated with a 2.42 kg (SE = 0.41) decrease in 305-day fat yield, compared to a 0.03 kg (SE = 0.71) increase for ancestral inbreeding. There were no clear differences between effects of long ROH (recent inbreeding) and short ROH (ancient inbreeding). CONCLUSIONS: Inbreeding depression was observed for yield, fertility and udder health traits. For yield traits and based on pedigree, inbreeding on recent generations was more harmful than inbreeding on distant generations and there was evidence of purging. Across all traits, long and short ROH contributed to inbreeding depression. In future work, inbreeding depression and purging should be assessed in more detail at the genomic level, using higher density information and genomic time series.

    High inbreeding rates in Dutch Holstein Friesian breeding program since start genomic selection
    Doekes, Harmen - \ 2018

    Breeding programs for livestock breeds are constantly adjusted. Researchers of Wageningen University & Research have investigated how major changes in the breeding program of Dutch Holstein-Friesian dairy cattle have affected inbreeding and genetic diversity trends.

    Hoge inteelttoename in Holstein Friesian fokprogramma sinds begin genomic selection
    Doekes, Harmen - \ 2018

    Fokprogramma’s voor landbouwhuisdierrassen veranderen continue. Onderzoekers van Wageningen University & Research bestudeerden hoe recente ontwikkelingen in het Nederlandse Holstein Friesian fokprogramma en veranderingen in inteelt en genetische diversiteit samenhangen.

    Assessing the value of the Dutch Holstein-Friesian germplasm collection
    Doekes, H.P. ; Veerkamp, R.F. ; Bijma, P. ; Hiemstra, S.J. ; Windig, J.J. - \ 2018
    New insights into the value of Dutch gene bank for cattle breeds
    Doekes, Harmen - \ 2018

    The Dutch gene bank collection for cattle breeds was set up in 1993 and is managed by the Centre for Genetic Resources, the Netherlands (CGN) of Wageningen University & Research. The collection consists of genetic material (semen) of rare Dutch cattle breeds, as well as a representative sample of the breeding programs of Holstein Friesian (HF) and Meuse-Rhine-Yssel (MRY) of the last decennia. Researchers of Wageningen University & Research showed that the stored material of HF and MRY is valuable for conservation of genetic diversity and potentially for future genetic improvement if substantial changes in breeding goal occur.

    Nieuwe inzichten in de waarde van Nederlandse genenbank voor runderrassen
    Doekes, Harmen - \ 2018

    De Nederlandse genenbankcollectie voor runderrassen bestaat sinds 1993 en wordt beheerd door het Centrum voor Genetische Bronnen, Nederland (CGN) van Wageningen University & Research. De collectie bevat genetisch materiaal (sperma) van zeldzame Nederlandse rassen, alsmede een dwarsdoorsnede van de Nederlandse fokpopulaties voor Holstein Friesian (HF) en Maas-Rijn-IJssel (MRIJ) van de afgelopen decennia. Onderzoekers van Wageningen University & Research lieten zien dat het opgeslagen materiaal voor HF en MRIJ waardevol is voor behoud van genetische diversiteit en bij eventuele sterke veranderingen van het fokdoel.

    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 Livestock Genomics 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
    IMAGE
    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.
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