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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Populatieanalyse Groninger Paard
Hoving, A.H. ; Vernooij, Kelly ; berg, Rozemarijn van den; Windig, Jack - \ 2015
Zeldzaam huisdier 40 (2015)4. - ISSN 0929-905X - p. 18 - 19.
paardenrassen - nederland - fokdoelen - groninger paard - populaties - genetica - inteelt - verwantschap - genenbanken - horse breeds - netherlands - breeding aims - groningen horse - populations - genetics - inbreeding - kinship - gene banks
We prijzen Nederlandse paardenrassen zoals het Groninger paard niet alleen omdat ze onderdeel van ons cultuurhistorisch erfgoed zijn maar ook vanwege hun veelzijdigheid en betrouwbare karakter. Helaas is de populatie klein. Dan is een goed doordacht fokbeleid nodig voor het behoud van genetische diversiteit en een gezonde populatie
Beelden van de Das in Nederland in Nederland 1900-2013: van ongedierte tot troeteldier?
Runhaar, Hens ; Runhaar, M. ; Vink, J. - \ 2015
De Levende Natuur 116 (2015)5. - ISSN 0024-1520 - p. 228 - 231.
meles meles - populations - wildlife conservation - wildlife management - attitudes - social change - human-animal relationships - populaties - wildbescherming - wildbeheer - sociale verandering - mens-dier relaties
Het herstel van de Nederlandse dassenpopulatie sinds 1980 is voor een belangrijk deel te verklaren uit een betere bescherming door o.a. de overheid, maar ook uit een andere omgang met de Das door boeren, jagers en bestuurders. Doel van dit artikel is om de beelden van de Das in de loop van de tijd te analyseren om daardoor inzicht te krijgen in de maatschappelijke kant van het herstel van de dassenpopulatie.
Linkage disequilibrium and genomic selection in pigs
Veroneze, R. - \ 2015
University. Promotor(en): Johan van Arendonk; S.E.F. Guimarães, co-promotor(en): John Bastiaansen. - Wageningen : Wageningen University - ISBN 9789462574151 - 142
varkens - verstoord koppelingsevenwicht - loci voor kwantitatief kenmerk - genomica - populaties - kruising - inteeltlijnen - fokwaarde - selectief fokken - genetica - pigs - linkage disequilibrium - quantitative trait loci - genomics - populations - crossbreds - inbred lines - breeding value - selective breeding - genetics

Securing a sufficiently large set of genotypes and phenotypes can be a limiting factor when implementing genomic selection. This limitation may be overcome by combining data from multiple populations or by using information of crossbred animals. The research described in this thesis characterized linkage disequilibrium (LD) patterns in different pig populations and evaluated whether the consistency of LD between populations allows us to make predictions about the performance of genomic selection when multiple populations are included in the prediction and/or validation datasets.

In chapter 2 I evaluated the persistence of LD and patterns of LD decay of pure and crossbred pig populations using real data that was representative of the crossbreeding structure of pig production. The persistence of phase between the crosses and their parental populations was high, indicating that similar marker effects might be expected across these populations. Across the purebred populations the persistence of phase was low therefore higher density panels should be used to have the same marker-QTL associations across these populations.

In chapter 3, the well-known nonlinear model developed by Sved (1971) was compared against a an alternative, loess regression, to describe LD decay. The loess regression model was found to be less influenced by the lack of residual normality, independence and homogeneity of variance than the nonlinear regression model. The loess regression model resulted in more reliable LD predictions and can be used to formally compare the LD decay curves between populations.

Chapter 4 showed the utility of different reference sets (across- and multi-population) for the prediction of genomic breeding values, as well as the potential of using crossbred performance in genomic prediction. None of the accuracies obtained using across-population, or multi-population genomic prediction, nor the accuracies obtained using crossbred data, followed the expectations based on LD that was described in chapter 2. I showed that across-population prediction accuracy was negligible even when the populations had common breeds in their genetic background. The variable accuracies of multi-population prediction and moderate accuracy of prediction of crossbred performance appeared to be a result of the differences in genetic architecture between pure populations and between purebred and crossbred animals.

In chapter 5, a methodology that uses information from genome wide association analyses in the genomic predictions was developed and evaluated. The aim in chapter 5 was to let the genomic prediction model use information from the genetic architecture in single- and multi-population genomic prediction. I showed that using weights based on GWAS results from a combined population did result in higher accuracies of GBLUP in single- as well as in multi-population predictions.

In chapter 6 I placed my results in a broader context. I discussed about the theoretical and practical aspects of linkage disequilibrium in breeding and in the estimation of effective population size. I also discussed the application of genomic selection in a small population and in practical pig breeding, including the prospects of using whole genome sequence for genomic prediction.

Characterisation of cell-wall polysaccharides from mandarin segment membranes
Coll-Almela, L. ; Saura-Lopez, D. ; Laencina-Sanchez, J. ; Schols, H.A. ; Voragen, A.G.J. ; Ros-García, J.M. - \ 2015
Food Chemistry 175 (2015). - ISSN 0308-8146 - p. 36 - 42.
hairy ramified regions - cross-flow filtration - pectolytic enzyme - citrus-fruit - pectins - degradation - extraction - skin - rhamnogalacturonase - populations
In an attempt to develop a process of enzymatic peeling of mandarin segments suitable for use on an industrial scale, the cell wall fraction of the segment membrane of Satsuma mandarin fruits was extracted to obtain a chelating agent-soluble pectin fraction (ChSS), a dilute sodium hydroxide-soluble pectin fraction (DASS), a 1 M sodium hydroxide-soluble hemicellulose fraction (1MASS), a 4 M sodium hydroxide-soluble hemicellulose fraction (4MASS) and a cellulose-rich residue (3.1, 0.9, 0.4, 0.7 and 1.6% w/w of fresh membrane, respectively). The ChSS pectin consisted mainly of galacturonic acid followed by arabinose and galactose. The DASS fraction contained less galacturonic acid and more neutral sugars than ChSS. Eighty-nine percent of the galacturonic acid present in the segment membranes was recovered in the above two pectin fractions. The two hemicellulosic fractions consisted of two different molecular weight populations, which also differed in their sugar composition. Arabinose, xylose, mannose, galactose and glucose were the main sugar constituents of these hemicellulose fractions. In addition to an (arabino)xylan and a xyloglucan, the presence of an arabinogalactan is suggested by the sugar composition of both hemicelluloses. The pectin fractions were also characterised by their degradability by the pectic enzymes polygalacturonase, pectinmethylesterase and rhamnogalacturonan hydrolase. However the degree of degradation of the pectin fractions by enzymes differed, and the amount of the polymeric materials resistant to further degradation and the oligomeric products also differed. Using pectic enzymes it is possible to obtain peeled mandarin segments ready to eat or for canning.
Varied responses by yeast-like symbionts during virulence adaptation in a monophagous phloem-feeding insect
Ferrater, J.B. ; Naredo, A.I. ; Almazan, M.L.P. ; Jong, P.W. de; Dicke, M. ; Horgan, F.G. - \ 2015
Arthropod-Plant Interactions 9 (2015)3. - ISSN 1872-8855 - p. 215 - 224.
resistant rice varieties - nilaparvata-lugens homoptera - brown planthopper resistance - xylem ingestion - uric-acid - delphacidae - selection - populations - genes - aphid
This study examines the three-way interaction between symbionts, insect herbivores and their host plants during adaptation to resistant crop varieties. We conducted a long-term selection study (20 generations of continuous rearing) with a monophagous phloem-feeder, the brown planthopper [Nilaparvata lugens (Stål)], on several resistant rice (Oryza sativa L.) varieties. Planthopper fitness and the abundance of yeast-like symbionts (YLS) were monitored throughout the selection process. N. lugens populations collected from six regions in the Philippines adapted to the resistant varieties as noted by increasing body size and increased egg-laying. Adaptation was partially through physiological and behavioral changes apparent during feeding: Planthoppers on resistant plants had relatively high levels of xylem feeding compared with planthoppers on susceptible plants. YLS densities were highly dependent on the host rice variety. However, there were no consistent trends in YLS density during host plant switching and virulence adaptation: Compared to densities in planthoppers on the standard susceptible variety Taichung Native 1 (TN1), YLS densities were consistently higher on PTB33 (resistant), similar on IR62 (resistant) and IR65482 (moderately resistant) but lower on IR22 (susceptible). Furthermore, YLS densities often remained the same despite improved planthopper fitness over generations. Our results do not support the hypothesis that changes in YLS density mediate planthopper adaptation to resistant varieties. However, slight reductions in YLS densities toward the end of selection on TN1, IR22 and IR62 may indicate that YLS have lower functional significance where varieties and environmental conditions are constant between generations.
Sex-specific effects of natural and sexual selection on the evolution of life span and ageing in Drosophila simulans
Archer, C.R. ; Duffy, E. ; Hosken, D.J. ; Mokkonen, M. ; Okada, K. ; Oku, K. ; Sharma, M.D. ; Hunt, J. - \ 2015
Functional Ecology 29 (2015)4. - ISSN 0269-8463 - p. 562 - 569.
extrinsic mortality - oxidative stress - female fitness - history traits - male-sterility - seed beetle - senescence - melanogaster - age - populations
1. Variation in the strength of age-dependent natural selection shapes differences in ageing rates across species and populations. Likewise, sexual selection can promote divergent patterns of senescence across the sexes. However, the effects of these processes on the evolution of ageing have largely been considered independently, and interactions between them are poorly understood. 2. We use experimental evolution to investigate how natural and sexual selection affect life span and ageing in Drosophila simulans. 3. Replicate populations were evolved under lifetime monogamy (relaxed sexual selection) or lifetime polyandry (elevated sexual selection) and at one of two temperatures, 25 °C (relaxed natural selection) or 27 °C (enhanced natural selection), in a fully factorial design. We measured longevity in 150 individually housed flies taken from each of three replicate populations per selection regime. 4. We found that natural and sexual selection affected the evolution of life span via sex-specific effects on different ageing parameters (ageing rate vs. baseline mortality): natural selection reduced the rate of ageing in both sexes but increased male baseline mortality, while sexual selection elevated baseline mortality in both sexes but particularly in males. 5. This means that sexual and natural selection interacted to reduce male life span but acted on female life span by independently affecting particular ageing parameters. Sex-specific effects of sexual and natural selection may help explain the diverse patterns of ageing seen in nature but complicate predictions about how ageing and life span evolve across the sexes.
Quantification of transmission of foot-and-mouth disease virus caused by an environment contaminated with secretions and excretions from infected calves
Bravo De Rueda, C. ; Jong, M. de; Eblé, P.L. ; Dekker, A. - \ 2015
Veterinary Research 46 (2015). - ISSN 0928-4249
between-pen transmission - classical swine-fever - vaccinated pigs - actinobacillus-pleuropneumoniae - influenza-viruses - dairy-cows - inactivation - campylobacter - formaldehyde - populations
Foot-and-mouth disease virus (FMDV) infected animals can contaminate the environment with their secretions and excretions. To quantify the contribution of a contaminated environment to the transmission of FMDV, this study used calves that were not vaccinated and calves that were vaccinated 1 week prior to inoculation with the virus in direct and indirect contact experiments. In direct contact experiments, contact calves were exposed to inoculated calves in the same room. In indirect contact experiments, contact calves were housed in rooms that previously had held inoculated calves for three days (either from 0 to 3 or from 3 to 6 days post inoculation). Secretions and excretions from all calves were tested for the presence of FMDV by virus isolation; the results were used to quantify FMDV transmission. This was done using a generalized linear model based on a 2 route (2R, i.e. direct contact and environment) SIR model that included information on FMDV survival in the environment. The study shows that roughly 44% of transmission occurs via the environment, as indicated by the reproduction ratio ^R0 2R environment that equalled 2.0, whereas the sum of ^R0 2R contact and ^R0 2R environment equalled 4.6. Because vaccination 1 week prior to inoculation of the calves conferred protective immunity against FMDV infection, no transmission rate parameters could be estimated from the experiments with vaccinated calves. We conclude that a contaminated environment contributes considerably to the transmission of FMDV therefore that hygiene measures can play a crucial role in FMD control.
Early-season crop colonization by parasitoids is associated with native vegetation, but is spatially and temporally erratic
Bianchi, F.J.J.A. ; Walters, B.J. ; Hove, A.L.T. ; Cunningham, S.A. ; Werf, W. van der; Douma, J.C. ; Schellhorn, N.A. - \ 2015
Agriculture, Ecosystems and Environment 207 (2015). - ISSN 0167-8809 - p. 10 - 16.
terebrans hymenoptera-ichneumonidae - managing ecosystem services - biological-control - bemisia-tabaci - pest-control - agricultural landscapes - habitats - biodiversity - populations - arthropods
Semi-natural habitats in agricultural landscapes may support parasitoid populations that provide biocontrol services by suppressing populations of crop pests, but little is known about the spatial pattern and variability of these services at different levels of scale. Here we investigate the rarely studied phenomenon of early-season crop colonization by parasitoids and the relationship with the surrounding landscape. We assessed parasitism of whiteflies by placing whitefly infested cotton seedlings in remnant vegetation, arable land 25–125 m from remnant vegetation, and arable land further than 400 m from remnant vegetation. Twelve to twenty sentinel plants were exposed in a 25 × 25 m grid pattern in plots in each habitat. The experiment was conducted at 18 locations across two landscapes and repeated three times in a 2-week period in 2007 and 2008. Parasitism was observed during the first three days after the introduction of the whitefly infested seedlings and was in all cases caused by Encarsia spp. The mean number of parasitized whitefly per plant was 0.106 ± 0.025 and was highest on cotton plants placed in remnant vegetation, declining with increasing distance from remnant vegetation. A regression model with land use and meteorological variables received more statistical support from the data than models with only landscape and time period as factors. Parasitism levels were influenced by the proportion of remnant vegetation, grassland, as well as wind, temperature, dew point temperature and year. Early-season colonization of whitefly infested seedlings by parasitoids was erratic and characterized by large spatial (inter-plant and inter-plot) and temporal variation. Our study confirms that remnant vegetation function as reservoirs for parasitoids and that parasitoids can penetrate arable fields beyond 125 m within 3 days. However, variation in the occurrence of parasitism makes it difficult to predict parasitoid colonization at a specific place and time. Therefore, field-based scouting for pests and parasitoids is necessary, even in landscapes with a high biocontrol potential.
Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856
Thompson, O.A. ; Snoek, L.B. ; Nijveen, H. ; Sterken, M.G. ; Volkers, R.J.M. ; Brenchley, R. ; Hof, A. van 't; Bevers, R.P.J. ; Cossins, A.R. ; Yanai, I. ; Hajnal, A. ; Schmid, T. ; Perkins, J.D. ; Spencer, D. ; Kruglyak, L. ; Andersen, E.C. ; Moerman, D.G. ; Hillier, L.W. ; Kammenga, J.E. ; Waterston, R.H. - \ 2015
Genetics 200 (2015)3. - ISSN 0016-6731 - p. 975 - 989.
natural variation data - c. elegans - arabidopsis-thaliana - gene - polymorphism - populations - diversity - nematodes - dna - evolutionary
The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that result in a total of 3.3 megabasepairs (Mb) of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, that have a greatly elevated SNV density, ranging from 2% to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.
The hybrid nature of pig genomes : unraveling the mosaic haplotype structure in wild and commercial Sus scrofa populations
Bosse, M. - \ 2015
University. Promotor(en): Martien Groenen, co-promotor(en): Hendrik-Jan Megens; Ole Madsen. - Wageningen : Wageningen University - ISBN 9789462573000 - 253
dieren - varkens - dierveredeling - genomen - hybridisatie - sus scrofa - haplotypen - genomica - populaties - genetische variatie - animals - pigs - animal breeding - genomes - hybridization - haplotypes - genomics - populations - genetic variation - cum laude
cum laude graduation
Length-and weight-dependent clearance rates of juvenile mussels (Mytilus edulis) on various planktonic prey items
Jacobs, P. ; Troost, K. ; Riegman, R. ; Meer, J. van der - \ 2015
Helgolander Marine Research 69 (2015)1. - ISSN 1438-387X - p. 101 - 112.
suspension-feeding bivalves - filtration-rate - particle retention - physiological energetics - food concentration - condition index - wadden sea - body size - zooplankton - populations
Filtration capacity and feeding behaviour has been intensely studied for adult mussels (Mytilus edulis), but less information is available for juvenile mussels (1.5–25 mm,
The effect of rare alleles on estimated genomic relationships from whole genome sequence data
Eynard, S.E. ; Windig, J.J. ; Leroy, G. ; Binsbergen, R. van; Calus, M.P.L. - \ 2015
BMC Genetics 16 (2015). - ISSN 1471-2156 - 24 p.
information - pedigree - conservation - populations - prediction - accuracy - cattle - coefficients - improvement - challenges
Relationships between individuals and inbreeding coefficients are commonly used for breeding decisions, but may be affected by the type of data used for their estimation. The proportion of variants with low Minor Allele Frequency (MAF) is larger in whole genome sequence (WGS) data compared to Single Nucleotide Polymorphism (SNP) chips. Therefore, WGS data provide true relationships between individuals and may influence breeding decisions and prioritisation for conservation of genetic diversity in livestock. This study identifies differences between relationships and inbreeding coefficients estimated using pedigree, SNP or WGS data for 118 Holstein bulls from the 1000 Bull genomes project. To determine the impact of rare alleles on the estimates we compared three scenarios of MAF restrictions: variants with a MAF higher than 5%, variants with a MAF higher than 1% and variants with a MAF between 1% and 5%. Results We observed significant differences between estimated relationships and, although less significantly, inbreeding coefficients from pedigree, SNP or WGS data, and between MAF restriction scenarios. Computed correlations between pedigree and genomic relationships, within groups with similar relationships, ranged from negative to moderate for both estimated relationships and inbreeding coefficients, but were high between estimates from SNP and WGS (0.49 to 0.99). Estimated relationships from genomic information exhibited higher variation than from pedigree. Inbreeding coefficients analysis showed that more complete pedigree records lead to higher correlation between inbreeding coefficients from pedigree and genomic data. Finally, estimates and correlations between additive genetic (A) and genomic (G) relationship matrices were lower, and variances of the relationships were larger when accounting for allele frequencies than without accounting for allele frequencies. Conclusions Using pedigree data or genomic information, and including or excluding variants with a MAF below 5% showed significant differences in relationship and inbreeding coefficient estimates. Estimated relationships and inbreeding coefficients are the basis for selection decisions. Therefore, it can be expected that using WGS instead of SNP can affect selection decision. Inclusion of rare variants will give access to the variation they carry, which is of interest for conservation of genetic diversity.
Detection of induced mutations in CaFAD2 genes by next generation sequencing leading to the production of improved oil composition in Crambe abyssinica
Cheng, J. ; Salentijn, E.M.J. ; Huang Bangquan, ; Denneboom, C. ; Dechesne, A.C. ; Krens, F.A. ; Visser, R.G.F. ; Loo, E.N. van - \ 2015
Plant Biotechnology Journal 13 (2015)4. - ISSN 1467-7644 - p. 471 - 481.
induced point mutations - crop improvement - reverse genetics - oleic-acid - functional genomics - fad2 gene - discovery - arabidopsis - populations - cloning
Crambe abyssinica is a hexaploid oil crop for industrial applications. An increase of erucic acid (C22:1) and reduction of polyunsaturated fatty acid (PUFA) contents in crambe oil is a valuable improvement. An increase in oleic acid (C18:1), a reduction in PUFA and possibly an increase in C22:1 can be obtained by down-regulating the expression of fatty acid desaturase2 genes (CaFAD2), which code for the enzyme that converts C18:1 into C18:2. We conducted EMS-mutagenesis in crambe, followed by Illumina sequencing, to screen mutations in three expressed CaFAD2 genes. Two novel analysis strategies were used to detect mutation sites. In the first strategy, mutation detection targeted specific sequence motifs. In the second strategy, every nucleotide position in a CaFAD2 fragment was tested for the presence of mutations. Seventeen novel mutations were detected in 1100 one-dimensional pools (11 000 individuals) in three expressed CaFAD2 genes, including non-sense mutations and mis-sense mutations in CaFAD2-C1, -C2 and -C3. The homozygous non-sense mutants for CaFAD2-C3 resulted in a 25% higher content of C18:1 and 25% lower content of PUFA compared to the wild type. The mis-sense mutations only led to small changes in oil composition. Concluding, targeted mutation detection using NGS in a polyploid was successfully applied and it was found that a non-sense mutation in even a single CaFAD2 gene can lead to changes in crambe oil composition. Stacking the mutations in different CaFAD2 may gain additional changes in C18:1 and PUFA contents.
Inbreeding depression and purging in a haplodiplois: gender-related effects
Tien, N.S.H. ; Sabelis, M.W. ; Egas, M. - \ 2015
Heredity 114 (2015). - ISSN 0018-067X - p. 327 - 332.
x-linked genes - female fecundity - load - populations - selection - genetics - mite - extinction
Compared with diploid species, haplodiploids suffer less inbreeding depression because male haploidy imposes purifying selection on recessive deleterious alleles. However, alleles of genes only expressed in the diploid females are protected in heterozygous individuals. This leads to the prediction that haplodiploids suffer more from inbreeding effects on life-history traits controlled by genes with female-limited expression. To test this, we used a wild population of the haplodiploid mite Tetranychus urticae. First, negative effects of inbreeding were investigated by comparing maturation rate, juvenile survival, oviposition rate and longevity between lines created by three generations of either outbreeding or mother-son inbreeding. Second, purging through inbreeding was investigated by comparing the intensity of inbreeding depression between outbred families with known inbreeding/outbreeding mating histories. Negative effects of inbreeding and evidence for purging were found for the female trait oviposition rate, but not for juvenile survival and longevity. Both male and female maturation rate were negatively affected by inbreeding, most likely due to maternal effects because inbred offspring of outbred mothers was not affected. These results support the hypothesis that, in haplodiploids inbreeding effects and genetic variation due to deleterious recessive alleles may depend on gender.
The laboratory domestication of Caenorhabditis elegans
Sterken, M.G. ; Snoek, L.B. ; Kammenga, J.E. ; Andersen, E.C. - \ 2015
Trends in Genetics 31 (2015)6. - ISSN 0168-9525 - p. 224 - 231.
life-history traits - c. elegans - natural variation - social-behavior - npr-1 - genetics - yeast - environment - populations - diversity
Model organisms are of great importance to our understanding of basic biology and to making advances in biomedical research. However, the influence of laboratory cultivation on these organisms is underappreciated, and especially how that environment can affect research outcomes. Recent experiments led to insights into how the widely used laboratory reference strain of the nematode Caenorhabditis elegans compares with natural strains. Here we describe potential selective pressures that led to the fixation of laboratory-derived alleles for the genes npr1, glb-5, and nath-10. These alleles influence a large number of traits, resulting in behaviors that affect experimental interpretations. Furthermore, strong phenotypic effects caused by these laboratory-derived alleles hinder the discovery of natural alleles. We highlight strategies to reduce the influence of laboratory-derived alleles and to harness the full power of C. elegans.
Unravelling the genetics of iron status in African populations : candidate gene association studies
Gichohi-Wainaina, W.N. - \ 2015
University. Promotor(en): Michael Zimmermann; Edith Feskens, co-promotor(en): Alida Melse-Boonstra; G.W. Towers. - Wageningen : Wageningen University - ISBN 9789462572102 - 198
ijzergebrekanemie - voeding - genetische factoren - eiwitten - volksgezondheid - voeding en gezondheid - populaties - afrika - iron deficiency anaemia - nutrition - genetic factors - proteins - public health - nutrition and health - populations - africa

Abstract

Background: Investigating the manner in which genetic and environmental factors interact to increase susceptibility to iron deficiency, has the potential to impact on strategies to overcome iron deficiency as well as the development of biomarkers to monitor iron status in populations. Single nucleotide polymorphisms or genetic variants that may affect the composition and hence the functionality of proteins involved in iron metabolism have been the subject of recent genetic association studies. However, these investigations have not yet been carried out in African populations that differ genetically from populations of European ancestry and which bear the highest burden of iron deficiency. The overall aim of this thesis was to investigate the genetics of iron status in African populations using a candidate gene approach.

Methods: In order to evaluate the association between identified TMPRSS6 gene variants and iron status we conducted a systematic review with meta-analyses. We primarily searched the literature using the HuGE Navigator, Pubmed and Scopus databases for primarily genome wide association studies. Fixed effects meta-analysis was used to obtain summary estimates. Associations between reported variants and iron status as well as gene-gene and variant interactions that influence iron status were investigated in a female black South African cohort (n=686; range 32–86 years) which were part of the Prospective Urban and Rural Epidemiology (PURE) study. Concentrations of haemoglobin, serum ferritin, serum transferrin receptor and body iron stores were determined. Thirty SNPs were genotyped and passed all quality criteria. To investigate whether previously identified associations in populations of European ancestry are replicated in populations of African ancestry, we conducted candidate gene association studies. Twenty iron status-associated variants in 628 Kenyans, 609 Tanzanians, 608 South Africans and 228 African Americans were genotyped and associations investigated using haemoglobin and serum ferritin as outcome measures. Finally, we assessed the effect of TNF-α allele variants (TNF‒1031, TNF‒308) on malaria rates, the severity of malaria as indicated by haemoglobin concentrations at the time of presentation with febrile episodes and the association between Plasmodium infection and haemoglobin concentration in symptomless parasite carriers. We used data from a placebo-controlled trial which consisted of 612 Tanzanian children aged 6–60 months. Cox regression models were used in the primary analysis to account for multiple episodes per child.

Results: In our systematic review we included eleven studies on Caucasian populations, four on Asian populations and one study on an African-American population. Differences in minor allele frequencies (MAF) of 8 TMPRSS6 SNPs (rs855791, rs4820268, rs2111833, rs1421312, rs228921, rs228918, rs228919 and rs575620) across ethnic groups were observed; with the MAF of rs855791 being significantly higher in Asian populations than in Caucasians (0.55 vs 0.42). In the meta-analysis, the A allele of rs855791 was associated with lower haemoglobin and ferritin concentrations in all populations. This allele was also associated with increased serum transferrin receptor and transferrin concentrations. We observed similar associations for the G allele in rs4820268. In general, minor allele frequencies (MAF) from females in the PURE population were lower compared to those of males and females of European ancestry populations in the 1000 Genomes Project. In the TF gene, the SNP rs1799852 was associated with decreased serum ferritin (p=0.01) and body iron concentrations (p=0.03) and increased serum transferrin receptor (sTfR) concentrations (P=0.004), while rs3811647 was associated with transferrin receptor and body iron (both P=0.03) in a U-shaped manner. The chromosome 6 SNP allele combination (AAA) consisting of rs1799964 and rs1800629 both in TNF α and rs2071592 in NFKBIL1 was associated with higher odds for low serum ferritin concentrations (serum ferritin<15µg/L; OR:1.86 (95%-CI, 1.23-2.79)). The chromosome 22 SNP allele combination (GG) consisting of rs228918 and rs228921 in the TMPRSS6 gene was associated with lower odds for increased sTfR concentrations (sTfR>8.3mg/L; OR:0.79 (95%-CI,0.63-0.98). We successfully replicated reported significant associations with lowered haemoglobin concentrations for two loci in TMPRSS6 namely rs2413450 and rs4820268 and with increased haemoglobin concentrations for one locus in TF (rs3811658) when analysing the four populations of African ancestry. When ferritin was considered as an outcome measure, we replicated associations with increased ferritin concentrations in two loci namely, rs228918 in TMPRSS6 and rs1525892 in TF. No other significant associations were determined. Malaria rates were higher in Tanzanian children with the TNF‒1031CC genotype (rs1799964) compared to the AA genotype (crude hazard ratio (HR), 95%CI: 1.41 [1.01‒1.97], adjusted HR 1.31 [0.97‒1.76]y) but were lower in those with the TNF‒308AA genotype (rs1800629) (adjusted HR 0.13 [0.02‒0.63]) compared to those harbouring the wild type homozygous genotype.

Conclusions: This thesis demonstrates previously observed associations between TMPRSS6 gene variants and haemoglobin concentrations in European ancestry populations are replicated in African populations. Replication of results in other loci previously associated with iron status in European ancestry populations was not achieved. Additionally, minor allele frequencies of single nucleotide polymorphisms associated with iron status are generally higher in European ancestry cohorts compared to those of African ancestry populations. The lack of association of reported variants may indicate that novel loci are responsible for the heritability of iron status in African populations. We have additionally observed that TNF α variants increase malaria severity. Malaria is a major cause of iron deficiency in malaria endemic areas. Our finding emphasizes that to alleviate iron deficiency in malaria endemic areas prevention and treatment of malaria is necessary. This thesis highlights the need to conduct genetic association studies in African populations where iron deficiency is of utmost public health significance. In addition, investigations into the genetics of iron status are bound to contribute towards the development of biomarkers that are useful in the determination of iron status in areas of high inflammation burden.

Genomic sequencing and microsatellite marker development for Boswellia papyrifera, an economically important but threatened tree native to dry tropical forests
Addisalem, A.B. ; Esselink, G. ; Bongers, F. ; Smulders, M.J.M. - \ 2015
AoB Plants 7 (2015). - ISSN 2041-2851 - 11 p.
populus-nigra l. - conservation genetics - frankincense - populations - ethiopia - database - plants - reads - tool - dna
Microsatellite (or simple sequence repeat, SSR) markers are highly informative DNA markers often used in conservation genetic research. Next-generation sequencing enables efficient development of large numbers of SSR markers at lower costs. Boswellia papyrifera is an economically important tree species used for frankincense production, an aromatic resinous gum exudate from bark. It grows in dry tropical forests in Africa and is threatened by a lack of rejuvenation. To help guide conservation efforts for this endangered species, we conducted an analysis of its genomic DNA sequences using Illumina paired-end sequencing. The genome size was estimated at 705 Mb per haploid genome. The reads contained one microsatellite repeat per 5.7 kb. Based on a subset of these repeats, we developed 46 polymorphic SSR markers that amplified 2-12 alleles in 10 genotypes. This set included 30 trinucleotide repeat markers, four tetranucleotide repeat markers, six pentanucleotide markers and six hexanucleotide repeat markers. Several markers were cross-transferable to Boswellia pirrotae and B. popoviana. In addition, retrotransposons were identified, the reads were assembled and several contigs were identified with similarity to genes of the terpene and terpenoid backbone synthesis pathways, which form the major constituents of the bark resin.
Host plant resistance towards the cabbage whitefly in Brassica oleracea and its wild relatives
Pelgrom, K.T.B. ; Broekgaarden, C. ; Voorrips, R.E. ; Bas, N. ; Visser, R.G.F. ; Vosman, B.J. - \ 2015
Euphytica 202 (2015)2. - ISSN 0014-2336 - p. 297 - 306.
aleyrodes-proletella homoptera - glucosinolate polymorphism - insect-resistance - cultivars - populations - fruticulosa - tomato - tabaci
The cabbage whitefly (Aleyrodes proletella) is a phloem-feeding insect that is a serious problem in Brassica oleracea crops like Brussels sprouts, kale and savoy cabbage. In order to develop whitefly-resistant varieties it is essential to identify effective sources of resistance. In this study, we screened a large collection of 432 accessions, including wild material and landraces of Brassica oleracea as well as crop wild relatives, to determine whitefly performance in a no-choice field experiment. Putatively resistant accessions were further tested under greenhouse conditions. Resistant accessions were identified among B. oleracea var. capitata (cabbage) landraces and in the species B. villosa, B. incana and B. montana. Whereas resistance in cabbage is only expressed in plants of at least 12 weeks old, some wild relatives were already starting to express resistance at 6 weeks. This could open up possibilities for breeding cabbages that are resistant at a young(er) plant age. Our research also shows again the importance of crop wild relatives for finding pest resistances.
Plant diversity and identity effects on predatory nematodes and their prey
Kostenko, O. ; Duyts, H. ; Grootemaat, S. ; Deyn, G.B. de; Bezemer, T.M. - \ 2015
Ecology and Evolution 5 (2015)4. - ISSN 2045-7758 - p. 836 - 847.
entomopathogenic nematodes - biological-control - biodiversity experiment - parasitic nematodes - food-web - soil - communities - grasslands - steinernema - populations
There is considerable evidence that both plant diversity and plant identity can influence the level of predation and predator abundance aboveground. However, how the level of predation in the soil and the abundance of predatory soil fauna are related to plant diversity and identity remains largely unknown. In a biodiversity field experiment, we examined the effects of plant diversity and identity on the infectivity of entomopathogenic nematodes (EPNs, Heterorhabditis and Steinernema spp.), which prey on soil arthropods, and abundance of carnivorous non-EPNs, which are predators of other nematode groups. To obtain a comprehensive view of the potential prey/food availability, we also quantified the abundance of soil insects and nonpredatory nematodes and the root biomass in the experimental plots. We used structural equation modeling (SEM) to investigate possible pathways by which plant diversity and identity may affect EPN infectivity and the abundance of carnivorous non-EPNs. Heterorhabditis spp. infectivity and the abundance of carnivorous non-EPNs were not directly related to plant diversity or the proportion of legumes, grasses and forbs in the plant community. However, Steinernema spp. infectivity was higher in monocultures of Festuca rubra and Trifolium pratense than in monocultures of the other six plant species. SEM revealed that legumes positively affected Steinernema infectivity, whereas plant diversity indirectly affected the infectivity of Heterorhabditis EPNs via effects on the abundance of soil insects. The abundance of prey (soil insects and root-feeding, bacterivorous, and fungivorous nematodes) increased with higher plant diversity. The abundance of prey nematodes was also positively affected by legumes. These plant community effects could not be explained by changes in root biomass. Our results show that plant diversity and identity effects on belowground biota (particularly soil nematode community) can differ between organisms that belong to the same feeding guild and that generalizations about plant diversity effects on soil organisms should be made with great caution.
Dutch hedgehogs Erinaceus europaeus are nowadays mainly found in urban areas, possibly due to the negative Effects of badgers Meles meles
Poel, J. van de; Dekker, J.J.A. ; Langevelde, F. van - \ 2015
Wildlife Biology 21 (2015)1. - ISSN 0909-6396 - p. 51 - 55.
abundance - populations - roads - odor
In several west European countries, the distribution of hedgehogs Erinaceus europaeus is declining. In the UK, predation by the European badger Meles meles is considered to be the main death cause of hedgehogs. In the Netherlands, badger density is rising, which suggests the same cause for the decline. As landscape and land use largely diff er between the UK and the Netherlands, we investigated the relationship between the distribution of badgers and hedgehogs in the Netherlands. Th erefore, we used the presence of badgers and hedgehogs recorded in the period 2007 – 2010 in grid cells of 1 km 2 , together with environmental variables, i.e. land-use types and soil types, to describe the habitat of both species. Although the distribution of badgers in the Netherlands is still limited, we found indeed a negative eff ect of badger presence on hedgehog presence. We also found a positive eff ect of urban area, recreational land use and roads on hedgehog presence, whereas these types had a negative eff ect on badger presence. Our study suggests that hedgehogs in the Netherlands are nowadays found close to human occupation, possibly due to the negative eff ect of badgers. Th ese results contribute to understanding of the declining distribution of hedgehogs in western Europe.
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