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.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Baby's first bites: a randomized controlled trial to assess the effects of vegetable-exposure and sensitive feeding on vegetable acceptance, eating behavior and weight gain in infants and toddlers
    Veek, S.M.C. van der; Graaf, C. de; Vries, J.H.M. de; Jager, G. ; Vereijken, C.M.J.L. ; Weenen, H. ; Winden, N. van; Vliet, M.S. van; Schultink, J.M. ; Wild, V.W.T. de; Janssen, S. ; Mesman, J. - \ 2019
    BMC Pediatrics 19 (2019)1. - ISSN 1471-2431 - 1 p.
    Complementary feeding - Infant - Responsive feeding - Self-regulation of energy intake - Toddler - Vegetable exposure - Vegetables

    BACKGROUND: The start of complementary feeding in infancy plays an essential role in promoting healthy eating habits. Evidence shows that it is important what infants are offered during this first introduction of solid foods: e.g. starting exclusively with vegetables is more successful for vegetable acceptance than starting with fruits. How infants are introduced to solid foods also matters: if parents are sensitive and responsive to infant cues during feeding, this may promote self-regulation of energy intake and a healthy weight. However, the effectiveness of the what and the how of complementary feeding has never been experimentally tested in the same study. In the current project the what and how (and their combination) are tested in one study to determine their relative importance for fostering vegetable acceptance and self-regulation of energy intake in infants. METHODS: A four-arm randomized controlled trial (Baby's First Bites (BFB)) was designed for 240 first-time Dutch mothers and their infants, 60 per arm. In this trial, we compare the effectiveness of (a) a vegetable-exposure intervention focusing on the what in complementary feeding; (b) a sensitive feeding intervention focusing on the how in complementary feeding, (c) a combined intervention focusing on the what and how in complementary feeding; (d) an attention-control group. All mothers participate in five sessions spread over the first year of eating solid foods (child age 4-16 months). Primary outcomes are vegetable consumption, vegetable liking and self-regulation of energy intake. Secondary outcomes are child eating behaviors, child anthropometrics and maternal feeding behavior. Outcomes are assessed before, during and directly after the interventions (child age 18 months), and when children are 24 and 36 months old. DISCUSSION: The outcomes are expected to assess the impact of the interventions and provide new insights into the mechanisms underlying the development of vegetable acceptance, self-regulation and healthy eating patterns in infants and toddlers, as well as the prevention of overweight. The results may be used to improve current dietary advice given to parents of their young children on complementary feeding. TRIAL REGISTRATION: The trial was retrospectively registered during inclusion of participants at the Netherlands National Trial Register (identifier NTR6572 ) and at ClinicalTrials.gov ( NCT03348176 ). Protocol issue date: 1 April 2018; version number 1.

    Candidate gene for natural immune competence in chickens revealed through genome wide association study
    Visker, M.H.P.W. ; Berghof, T.V.L. ; Arts, J.A.J. ; Parmentier, H.K. ; Poel, J.J. van der; Vereijken, Addie ; Bovenhuis, H. - \ 2018
    In: Proceedings of the World Congress on Genetics Applied to Livestock Production. - WCGALP - 4 p.
    Natural antibodies (NAb) are antibodies that are present in individuals without prior exposure to the antigen that they bind. In chickens, NAb have been associated with survival. Furthermore, genetic variation between chickens in NAb levels has been demonstrated. To improve our understanding of the genetic variation for NAb levels in chickens we performed a genome wide association study. A population of 1,628 White Leghorn chickens was investigated. Animals were phenotyped for NAb levels using the antigen keyhole limpet hemocyanin (KLH) as model. Animals were genotyped for 15,579 single nucleotide polymorphisms (SNP). Highly significant association between SNP and NAb levels was observed on chicken chromosome 4. A single SNP was identified as the most likely candidate for this association. Identification of this candidate SNP was based on further analysis with full genome sequence genotypes and on predicted consequences of associated SNP. This candidate SNP causes a phenylalanine to leucine amino acid change in one of the leucine rich repeats in toll-like receptor 1 family member A (TLR1A). Our results suggest an important role for TLR1A in relation to NAb levels in chickens. Further study should confirm the effect of the SNP in TLR1A on NAb levels and on the (natural) immune competence of chickens. Keywords: natural antibodies, toll-like receptor, TLR1A
    The genetic architecture of socially-affected traits : a GWAS for direct and indirect genetic effects on survival time in laying hens showing cannibalism
    Brinker, Tessa ; Bijma, Piter ; Vereijken, Addie ; Ellen, Esther D. - \ 2018
    Genetics, Selection, Evolution 50 (2018)1. - ISSN 0999-193X

    Background: Cannibalism is an important welfare problem in the layer industry. Cannibalism is a social behavior where individual survival is affected by direct genetic effects (DGE) and indirect genetic effects (IGE). Previous studies analysed repeated binomial survival, instead of survival time, which improved accuracies of breeding value predictions. Our study aimed at identifying SNPs associated with DGE and IGE for survival time, and comparing results from models that analyse survival time and repeated binomial survival. Methods: Survival data of three layer crosses (W1 * WA, W1 * WB, and W1 * WC) were used. Each individual had one survival time record and 13 monthly survival (0/1) records. Approximately 30,000 single nucleotide polymorphisms (SNPs) were included in the genome-wide association study (GWAS), using a linear mixed model for survival time, a linear mixed model and a generalized linear mixed model for repeated binomial survival (0/1). Backwards elimination was used to determine phenotypic and genetic variance explained by SNPs. Results: The same quantitative trait loci were identified with all models. A SNP associated with DGE was found in cross W1 * WA, with an allele substitution effect of 22 days. This SNP explained 3% of the phenotypic variance, and 36% of the total genetic variance. Four SNPs associated with DGE were found in cross W1 * WB, with effects ranging from 16 to 35 days. These SNPs explained 1 to 6% of the phenotypic variance and 9 to 44% of the total genetic variance. Our results suggest a link of DGE and IGE for survival time in layers with the gamma-aminobutyric acid (GABA) system, since a SNP located near a gene for a GABA receptor was associated with DGE and with IGE (not significant). Conclusions: This is one of the first large studies investigating the genetic architecture of a socially-affected trait. The power to detect SNP associations was relatively low and thus we expect that many effects on DGE and IGE remained undetected. Yet, GWAS results revealed SNPs with large DGE and a link of DGE and IGE for survival time in layers with the GABAergic system, which supports existing evidence for the involvement of GABA in the development of abnormal behaviors.

    A survey of functional genomic variation in domesticated chickens
    Derks, Martijn F.L. ; Megens, Hendrik Jan ; Bosse, Mirte ; Visscher, Jeroen ; Peeters, Katrijn ; Bink, Marco C.A.M. ; Vereijken, Addie ; Gross, Christian ; Ridder, Dick De; Reinders, Marcel J.T. ; Groenen, Martien A.M. - \ 2018
    Genetics, Selection, Evolution 50 (2018)1. - ISSN 0999-193X
    Background: Deleterious genetic variation can increase in frequency as a result of mutations, genetic drift, and genetic hitchhiking. Although individual effects are often small, the cumulative effect of deleterious genetic variation can impact population fitness substantially. In this study, we examined the genome of commercial purebred chicken lines for deleterious and functional variations, combining genotype and whole-genome sequence data. Results: We analysed over 22,000 animals that were genotyped on a 60 K SNP chip from four purebred lines (two white egg and two brown egg layer lines) and two crossbred lines. We identified 79 haplotypes that showed a significant deficit in homozygous carriers. This deficit was assumed to stem from haplotypes that potentially harbour lethal recessive variations. To identify potentially deleterious mutations, a catalogue of over 10 million variants was derived from 250 whole-genome sequenced animals from three purebred white-egg layer lines. Out of 4219 putative deleterious variants, 152 mutations were identified that likely induce embryonic lethality in the homozygous state. Inferred deleterious variation showed evidence of purifying selection and deleterious alleles were generally overrepresented in regions of low recombination. Finally, we found evidence that mutations, which were inferred to be evolutionally intolerant, likely have positive effects in commercial chicken populations. Conclusions: We present a comprehensive genomic perspective on deleterious and functional genetic variation in egg layer breeding lines, which are under intensive selection and characterized by a small effective population size. We show that deleterious variation is subject to purifying selection and that there is a positive relationship between recombination rate and purging efficiency. In addition, multiple putative functional coding variants were discovered in selective sweep regions, which are likely under positive selection. Together, this study provides a unique molecular perspective on functional and deleterious variation in commercial egg-laying chickens, which can enhance current genomic breeding practices to lower the frequency of undesirable variants in the population.
    Early and late feathering in Turkey and chicken : Same gene but different mutations
    Derks, Martijn F.L. ; Herrero-Medrano, Juan M. ; Crooijmans, Richard P.M.A. ; Vereijken, Addie ; Long, Julie A. ; Megens, Hendrik Jan ; Groenen, Martien A.M. - \ 2018
    Genetics, Selection, Evolution 50 (2018)1. - ISSN 0999-193X
    Background: Sex-linked slow (SF) and fast (FF) feathering rates at hatch have been widely used in poultry breeding for autosexing at hatch. In chicken, the sex-linked K (SF) and k+ (FF) alleles are responsible for the feathering rate phenotype. Allele K is dominant and a partial duplication of the prolactin receptor gene has been identified as the causal mutation. Interestingly, some domesticated Turkey lines exhibit similar slow- and fast-feathering phenotypes, but the underlying genetic components and causal mutation have never been investigated. In this study, our aim was to investigate the molecular basis of feathering rate at hatch in domestic Turkey. Results: We performed a sequence-based case-control association study and detected a genomic region on chromosome Z, which is statistically associated with rate of feathering at hatch in Turkey. We identified a 5-bp frameshift deletion in the prolactin receptor (PRLR) gene that is responsible for slow feathering at hatch. All female cases (SF Turkeys) were hemizygous for this deletion, while 188 controls (FF Turkeys) were hemizygous or homozygous for the reference allele. This frameshift mutation introduces a premature stop codon and six novel amino acids (AA), which results in a truncated PRLR protein that lacks 98 C-terminal AA. Conclusions: We present the causal mutation for feathering rate in Turkey that causes a partial C-terminal loss of the prolactin receptor, and this truncated PRLR protein is strikingly similar to the protein encoded by the slow feathering K allele in chicken.
    Genomic Region Containing Toll-Like Receptor Genes Has a Major Impact on Total IgM Antibodies Including KLH-Binding IgM Natural Antibodies in Chickens
    Berghof, T.V.L. ; Visker, M.H.P.W. ; Arts, J.A.J. ; Parmentier, H.K. ; Poel, J.J. van der; Vereijken, A.L.J. ; Bovenhuis, H. - \ 2018
    Frontiers in Immunology 8 (2018). - ISSN 1664-3224 - 14 p.
    Natural antibodies (NAb) are antigen binding antibodies present in individuals without a previous exposure to this antigen. Keyhole limpet hemocyanin (KLH)-binding NAb levels were previously associated with survival in chickens. This suggests that selective breeding for KLH-binding NAb may increase survival by means of improved general disease resistance. Genome-wide association studies (GWAS) were performed to identify genes underlying genetic variation in NAb levels. The studied population consisted of 1,628 adolescent layer chickens with observations for titers of KLH-binding NAb of the isotypes IgM, IgA, IgG, the total KLH-binding (IgT) NAb titers, total antibody concentrations of the isotypes IgM, IgA, IgG, and the total antibodies concentration in plasma. GWAS were performed using 57,636 single-nucleotide polymorphisms (SNP). One chromosomal region on chromosome 4 was associated with KLH-binding IgT NAb, and total IgM concentration, and especially with KLH-binding IgM NAb. The region of interest was fine mapped by imputing the region of the study population to whole genome sequence, and subsequently performing an association study using the imputed sequence variants. 16 candidate genes were identified, of which FAM114A1, Toll-like receptor 1 family member B (TLR1B), TLR1A, Krüppel-like factor 3 (KLF3) showed the strongest associations. SNP located in coding regions of the candidate genes were checked for predicted changes in protein functioning. One SNP (at 69,965,939 base pairs) received the maximum impact score from two independent prediction tools, which makes this SNP the most likely causal variant. This SNP is located in TLR1A, which suggests a fundamental role of TLR1A on regulation of IgM levels (i.e., KLH-binding IgM NAb, and total IgM concentration), or B cells biology, or both. This study contributes to increased understanding of (genetic) regulation of KLH-binding NAb levels, and total antibody concentrations.
    Genomic region containing Toll-like receptor genes has a major effect on IgM (natural) antibodies in chickens
    Berghof, T.V.L. - \ 2017
    Powerpoint presentation of Tom V.L. Berghof, Marleen H.P.W. Visker, Joop A.J. Arts, Henk K. Parmentier, Jan J. van der Poel, Addie Vereijken, Henk Bovenhuis
    A genome-wide association of natural antibodies binding keyhole limpet hemocyanin in chickens reeals major QTL on chromosome 4 for IgM isotype
    Berghof, T.V.L. ; Parmentier, H.K. ; Arts, J.A.J. ; Hulzebosch, A.A. ; Poel, J.J. van der; Vereijken, Addie ; Visker, M.H.P.W. ; Bovenhuis, H. - \ 2017
    Estimation of total genetic effects for survival time in crossbred laying hens showing cannibalism, using pedigree or genomic information
    Brinker, T. ; Raymond, B. ; Bijma, P. ; Vereijken, A. ; Ellen, E.D. - \ 2017
    Journal of Animal Breeding and Genetics 134 (2017)1. - ISSN 0931-2668 - p. 60 - 68.
    BLUP - Laying hens - Social interactions - SsGBLUP - Total genetic effect

    Mortality of laying hens due to cannibalism is a major problem in the egg-laying industry. Survival depends on two genetic effects: the direct genetic effect of the individual itself (DGE) and the indirect genetic effects of its group mates (IGE). For hens housed in sire-family groups, DGE and IGE cannot be estimated using pedigree information, but the combined effect of DGE and IGE is estimated in the total breeding value (TBV). Genomic information provides information on actual genetic relationships between individuals and might be a tool to improve TBV accuracy. We investigated whether genomic information of the sire increased TBV accuracy compared with pedigree information, and we estimated genetic parameters for survival time. A sire model with pedigree information (BLUP) and a sire model with genomic information (ssGBLUP) were used. We used survival time records of 7290 crossbred offspring with intact beaks from four crosses. Cross-validation was used to compare the models. Using ssGBLUP did not improve TBV accuracy compared with BLUP which is probably due to the limited number of sires available per cross (~50). Genetic parameter estimates were similar for BLUP and ssGBLUP. For both BLUP and ssGBLUP, total heritable variance (T2), expressed as a proportion of phenotypic variance, ranged from 0.03 ± 0.04 to 0.25 ± 0.09. Further research is needed on breeding value estimation for socially affected traits measured on individuals kept in single-family groups.

    A genome-wide association study of natural antibodies binding keyhole limpet hemocyanin in chickens reveals major QTL on chromosome 4 for IgM isotype
    Berghof, T.V.L. ; Parmentier, H.K. ; Arts, J.A.J. ; Hulzebosch, A.A. ; Poel, J.J. van der; Vereijken, Addie ; Visker, M.H.P.W. ; Bovenhuis, H. - \ 2016
    Genomic prediction of survival time in a population of brown laying hens showing cannibalistic behavior
    Alemu, Setegn W. ; Calus, Mario P.L. ; Muir, William M. ; Peeters, Katrijn ; Vereijken, Addie ; Bijma, Piter - \ 2016
    Genetics, Selection, Evolution 48 (2016)1. - ISSN 0999-193X

    Background: Mortality due to cannibalism causes both economic and welfare problems in laying hens. To limit mortality due to cannibalism, laying hens are often beak-trimmed, which is undesirable for animal welfare reasons. Genetic selection is an alternative strategy to increase survival and is more efficient by taking heritable variation that originates from social interactions into account, which are modelled as the so-called indirect genetic effects (IGE). Despite the considerable heritable variation in survival time due to IGE, genetic improvement of survival time in laying hens is still challenging because the detected heritable variation of the trait with IGE is still limited, ranging from 0.06 to 0.26, and individuals that are still alive at the end of the recording period are censored. Furthermore, survival time records are available late in life and only on females. To cope with these challenges, we tested the hypothesis that genomic prediction increases the accuracy of estimated breeding values (EBV) compared to parental average EBV, and increases response to selection for survival time compared to a traditional breeding scheme. We tested this hypothesis in two lines of brown layers with intact beaks, which show cannibalism, and also the hypothesis that the rate of inbreeding per year is lower for genomic selection than for the traditional breeding scheme. Results and discussion: The standard deviation of genomic prediction EBV for survival time was around 22 days for both lines, indicating good prospects for selection against mortality in laying hens with intact beaks. Genomic prediction increased the accuracy of the EBV by 35 and 32 % compared to the parent average EBV for the two lines. At the current reference population size, predicted response to selection was 91 % higher when using genomic selection than with the traditional breeding scheme, as a result of a shorter generation interval in males and greater accuracy of selection in females. The predicted rate of inbreeding per generation with truncation selection was substantially lower for genomic selection than for the traditional breeding scheme for both lines. Conclusions: Genomic selection for socially affected traits is a promising tool for the improvement of survival time in laying hens with intact beaks.

    Risk/Benefit Communication about Food—A Systematic Review of the Literature
    Frewer, L.J. ; Fischer, A.R.H. ; Brennan, M. ; Bánáti, D. ; Lion, R. ; Meertens, R.M. ; Rowe, G. ; Siegrist, M. ; Verbeke, W. ; Vereijken, C.M.J.L. - \ 2016
    Critical Reviews in Food Science and Nutrition 56 (2016)10. - ISSN 1040-8398 - p. 1728 - 1745.
    benefit communication - food hazard - food safety - risk communication - Risk perception - trust

    A systematic review relevant to the following research questions was conducted (1) the extent to which different theoretical frameworks have been applied to food risk/benefit communication and (2) the impact such food risk/benefit communication interventions have had on related risk/benefit attitudes and behaviors. Fifty four papers were identified. The analysis revealed that (primarily European or US) research interest has been relatively recent. Certain food issues were of greater interest to researchers than others, perhaps reflecting the occurrence of a crisis, or policy concern. Three broad themes relevant to the development of best practice in risk (benefit) communication were identified: the characteristics of the target population; the contents of the information; and the characteristics of the information sources. Within these themes, independent and dependent variables differed considerably. Overall, acute risk (benefit) communication will require advances in communication process whereas chronic communication needs to identify audience requirements. Both citizen's risk/benefit perceptions and (if relevant) related behaviors need to be taken into account, and recommendations for behavioral change need to be concrete and actionable. The application of theoretical frameworks to the study of risk (benefit) communication was infrequent, and developing predictive models of effective risk (benefit) communication may be contingent on improved theoretical perspectives.

    Accuracy of genomic prediction using imputed whole-genome sequence data in white layers
    Heidaritabar, M. ; Calus, M.P.L. ; Megens, H.J. ; Vereijken, A. ; Groenen, M.A.M. ; Bastiaansen, J.W.M. - \ 2016
    Journal of Animal Breeding and Genetics (2016). - ISSN 0931-2668 - p. 167 - 179.
    Biological information - Causal mutations - Genomic prediction accuracy - Imputation - Whole-genome sequence

    There is an increasing interest in using whole-genome sequence data in genomic selection breeding programmes. Prediction of breeding values is expected to be more accurate when whole-genome sequence is used, because the causal mutations are assumed to be in the data. We performed genomic prediction for the number of eggs in white layers using imputed whole-genome resequence data including ~4.6 million SNPs. The prediction accuracies based on sequence data were compared with the accuracies from the 60 K SNP panel. Predictions were based on genomic best linear unbiased prediction (GBLUP) as well as a Bayesian variable selection model (BayesC). Moreover, the prediction accuracy from using different types of variants (synonymous, non-synonymous and non-coding SNPs) was evaluated. Genomic prediction using the 60 K SNP panel resulted in a prediction accuracy of 0.74 when GBLUP was applied. With sequence data, there was a small increase (~1%) in prediction accuracy over the 60 K genotypes. With both 60 K SNP panel and sequence data, GBLUP slightly outperformed BayesC in predicting the breeding values. Selection of SNPs more likely to affect the phenotype (i.e. non-synonymous SNPs) did not improve the accuracy of genomic prediction. The fact that sequence data were based on imputation from a small number of sequenced animals may have limited the potential to improve the prediction accuracy. A small reference population (n = 1004) and possible exclusion of many causal SNPs during quality control can be other possible reasons for limited benefit of sequence data. We expect, however, that the limited improvement is because the 60 K SNP panel was already sufficiently dense to accurately determine the relationships between animals in our data.

    Preliminary evaluation of the feasibility of using geospatial information to refine soil fertility recommendations
    Kempen, B. ; Vereijken, P.F.G. ; Keizer, L.C.P. ; Ruiperez Gonzalez, M. ; Bindraban, P.S. ; Wendt, J. - \ 2015
    Washington D.C. : VFRC
    Rooting area and drinker affect dunging behaviour of organic pics
    Vermeer, H.M. ; Altena, H. ; Vereijken, P.F.G. ; Bracke, M.B.M. - \ 2015
    Applied Animal Behaviour Science 165 (2015). - ISSN 0168-1591 - p. 66 - 71.
    Hygiene is a common problem on outdoor runs of growing organic pigs. Manure and urine are mainly excreted outdoors and tend to spread all over the run. Reducing the soiled surface area may be beneficial to animal welfare, hygiene, ammonia emissions and labour, not only in organic but also in conventional systems. The objective was to reduce the soiled surface area in the pen and to make the outdoor run more attractive for pigs. Introduction of a rooting area and drinker in the outdoor run was tested in a 2 × 2 factorial design. In total, four replicates were studied in a room with two rows of four pens containing 14 pigs each. More pigs went outdoors in pens with rooting area access than in pens without a rooting area (11.2 vs. 8.5%, P = 0.003). This was due to more pigs entering the rooting area and an adjacent slatted floor. Addition of a drinker did not attract more pigs outdoors (P = 0.53). The rooting area improved the cleanliness of the whole pen (P < 0.001). However, in some cases the rooting area was also used as a dunging area. The area around the additional outdoor drinker was cleaner, but on the whole, pens were dirtier (P = 0.011). Introduction of an outdoor drinker resulted in more indoor pen fouling, especially around the indoor drinker (P < 0.001). An outdoor rooting area makes the outdoor run more attractive for pigs and reduces the dunging area. This study contributes to the knowledge base on how to reduce the dunging surface in pens for organic pigs
    Accuracy of genomic prediction using whole genome sequence data in White egg layer chickens
    Heidaritabar, M. ; Calus, M.P.L. ; Megens, H.J.W.C. ; Groenen, M.A.M. ; Vereijken, A. ; Bastiaansen, J.W.M. - \ 2015
    In: Book of Abstracts 66th Annual Meeting of the EAAP. - Wageningen Academic Publishers - p. 246 - 246.
    There is an increasing interest in using whole genome sequence data in genomic selection breeding programs. Prediction of breeding values is expected to be more accurate when whole genome sequence is used, since the causal mutations are assumed to be in the data. We report genomic prediction for number of eggs in White egg layer chickens using whole genome re-sequence data including more than 4.5 million SNPs. We compared the prediction accuracies based on sequence data with accuracies from the 60k SNP chip data. We applied Genomic Best Linear Unbiased Prediction (GBLUP) and BayesC prediction. Moreover, we evaluated the prediction accuracy using different types of variants (Synonymous, non-synonymous and non-coding SNPs). Genomic prediction using 60k, resulted in prediction accuracy of 0.74 when GBLUP was applied. With sequence data, there was a small increase (~1%) in prediction accuracy over the 60k genotypes. With both 60k and sequence data, GBLUP slightly outperformed BayesC in predicting the breeding values. Selection of SNPs more likely to affect the phenotype (i.e. non-synonymous SNPs) did not improve accuracy of genomic prediction. The small number of sequenced animals in this study, which affects the accuracy of imputed sequence data, may have limited the potential to improve the prediction accuracy. We expect, however, that the limited improvement is because the 60k SNPs are sufficient to accurately determine the relationships between animals.
    Accuracy of imputation using the most common sires as reference population in layer chickens
    Heidaritabar, M. ; Calus, M.P.L. ; Vereijken, A. ; Groenen, M.A.M. ; Bastiaansen, J.W.M. - \ 2015
    BMC Genetics 16 (2015). - ISSN 1471-2156 - 14 p.
    Genotype imputation has become a standard practice in modern genetic research to increase genome coverage and improve the accuracy of genomic selection (GS) and genome-wide association studies (GWAS). We assessed accuracies of imputing 60K genotype data from lower density single nucleotide polymorphism (SNP) panels using a small set of the most common sires in a population of 2140 white layer chickens. Several factors affecting imputation accuracy were investigated, including the size of the reference population, the level of the relationship between the reference and validation populations, and minor allele frequency (MAF) of the SNP being imputed. Results The accuracy of imputation was assessed with different scenarios using 22 and 62 carefully selected reference animals (Ref 22 and Ref 62 ). Animal-specific imputation accuracy corrected for gene content was moderate on average (~ 0.80) in most scenarios and low in the 3K to 60K scenario. Maximum average accuracies were 0.90 and 0.93 for the most favourable scenario for Ref 22 and Ref 62 respectively, when SNPs were masked independent of their MAF. SNPs with low MAF were more difficult to impute, and the larger reference population considerably improved the imputation accuracy for these rare SNPs. When Ref 22 was used for imputation, the average imputation accuracy decreased by 0.04 when validation population was two instead of one generation away from the reference and increased again by 0.05 when validation was three generations away. Selecting the reference animals from the most common sires, compared with random animals from the population, considerably improved imputation accuracy for low MAF SNPs, but gave only limited improvement for other MAF classes. The allelic R 2 measure from Beagle software was found to be a good predictor of imputation reliability (correlation¿~¿0.8) when the density of validation panel was very low (3K) and the MAF of the SNP and the size of the reference population were not extremely small. Conclusions Even with a very small number of animals in the reference population, reasonable accuracy of imputation can be achieved. Selecting a set of the most common sires, rather than selecting random animals for the reference population, improves the imputation accuracy of rare alleles, which may be a benefit when imputing with whole genome re-sequencing data.
    Ervaringen met HNT bij Kwekerij Vereijken (tomaten)
    Raaphorst, M.G.M. - \ 2015
    Kas als Energiebron
    A small number of key ancestors provides high imputation accuracy in layer chicken
    Heidaritabar, M. ; Vereijken, A. ; Calus, M.P.L. ; Groenen, M. ; Bastiaansen, J.W.M. - \ 2014
    Accuracy of Genomic Breeding Values Predicted Within and Across Breeds in Pig Populations
    Hidalgo, A.M. ; Bastiaansen, J.W.M. ; Lopes, M.S. ; Harlizius, B. ; Groenen, M. ; Koning, D.J. de; Vereijken, A. ; Windig, J.J. - \ 2014
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