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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Seascape genetics of a flatfish reveals local selection under high levels of gene flow
Diopere, Eveline ; Vandamme, Sara G. ; Habluetzel, Pascal I. ; Cariani, Alessia ; Houdt, Jeroen van; Rijnsdorp, A.D. ; Tinti, Fausto ; Volckaert, Filip A.M. ; Maes, Gregory E. - \ 2018
ICES Journal of Marine Science 75 (2018)2. - ISSN 1054-3139 - p. 675 - 689.
fish - isolation by distance - local adaptation - Northeast Atlantic Ocean - outlier locus - population genomics - SNP - sole
Local adaptation is often found to be in a delicate balance with gene flow in marine species with high dispersal potential. Genotyping with mapped transcriptome-derived markers and advanced seascape statistical analyses are proven tools to uncover the genomic basis of biologically relevant traits under environmental selection. Using a panel of 426 gene-linked single nucleotide polymorphisms (SNPs), we scanned 17 samples (n¼539) of sole (Solea solea L.) from the Northeast Atlantic Ocean and applied a node-based seascape analysis. Neutral loci confirmed a clear distinction between the North Sea–Baltic Sea transition zone and the other Eastern Atlantic samples. At a more subtle level,
the latter unit split in an English Channel and North Sea group, and a Bay of Biscay and Atlantic Iberian coast group. A fourth group, the Irish and Celtic Sea, was identified with 19 outlier loci. A pattern of isolation by distance (IBD) characterized the latitudinal distribution. Seascape analyses identified winter seawater temperature, food availability and coastal currents to explain a significant component of geographically distributed genetic variation, suggesting that these factors act as drivers of local adaptation. The evidence for local adaptation is in line with the current understanding on the impact of two key ecological factors, the life-history trait winter mortality and the behaviour of inshore/offshore spawning. We conclude that the subtle differentiation between two metapopulations (North Sea and Bay of Biscay) mirrors local adaptation.
At least three genomic regions with strong population differentiation point to locally divergent selection. Further functional characterization of these genomic regions should help with formulating adaptive management policies.
Admixture between released and wild game birds : a changing genetic landscape in European mallards (Anas platyrhynchos)
Söderquist, P. ; Elmberg, J. ; Gunnarsson, G. ; Thulin, C.G. ; Champagnon, J. ; Guillemain, M. ; Kreisinger, J. ; Prins, H.H.T. ; Crooijmans, R.P.M.A. ; Kraus, R.H.S. - \ 2017
European Journal of Wildlife Research 63 (2017)6. - ISSN 1612-4642
Cryptic introgression - Hand-reared - Hybridization - Restocking - SNP - Wildlife management
Disruption of naturally evolved spatial patterns of genetic variation and local adaptations is a growing concern in wildlife management and conservation. During the last decade, releases of native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but releases are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, is one of few terrestrial migratory vertebrates subjected to large-scale releases for hunting purposes. It is the most numerous and widespread duck in the world, yet each year more than three million farmed mallard ducklings are released into the wild in the European Union alone to increase the harvestable population. This study aimed to determine the genetic effects of such large-scale releases of a native species, specifically if wild and released farmed mallards differ genetically among subpopulations in Europe, if there are signs of admixture between the two groups, if the genetic structure of the wild mallard population has changed since large-scale releases began in the 1970s, and if the current data matches global patterns across the Northern hemisphere. We used Bayesian clustering (Structure software) and Discriminant Analysis of Principal Components (DAPC) to analyze the genetic structure of historical and present-day wild (n = 171 and n = 209, respectively) as well as farmed (n = 211) mallards from six European countries as inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed a clear genetic differentiation between wild and farmed mallards. Admixed individuals were found in the present-day wild population, implicating introgression of farmed genotypes into wild mallards despite low survival among released farmed mallards. Such cryptic introgression would alter the genetic composition of wild populations and may have unknown long-term consequences for conservation.
Genome-wide association mapping of flowering and ripening periods in apple
Urrestarazu, Jorge ; Muranty, Hélène ; Denancé, Caroline ; Leforestier, Diane ; Ravon, Elisa ; Guyader, Arnaud ; Guisnel, Rémi ; Feugey, Laurence ; Aubourg, Sébastien ; Celton, Jean Marc ; Daccord, Nicolas ; Dondini, Luca ; Gregori, Roberto ; Lateur, Marc ; Houben, Patrick ; Ordidge, Matthew ; Paprstein, Frantisek ; Sedlak, Jiri ; Nybom, Hilde ; Garkava-Gustavsson, Larisa ; Troggio, Michela ; Bianco, Luca ; Velasco, Riccardo ; Poncet, Charles ; Théron, Anthony ; Moriya, Shigeki ; Bink, Marco C.A.M. ; Laurens, François ; Tartarini, Stefano ; Durel, Charles Eric - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
Adaptive traits - Association genetics - Germplasm collection - GWAS - Malus × domestica Borkh - Microsynteny - Quantitative trait loci - SNP
Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.
Physical mapping of QTL for tuber yield, starch content and starch yield in tetraploid potato (Solanum tuberosum L.) by means of genome wide genotyping by sequencing and the 8.3 K SolCAP SNP array
Schönhals, Elske Maria ; Ding, Jia ; Ritter, Enrique ; Caldas Paulo, Joao ; Cara, Nicolás ; Tacke, Ekhard ; Hofferbert, Hans Reinhard ; Lübeck, Jens ; Strahwald, Josef ; Gebhardt, Christiane - \ 2017
BMC Genomics 18 (2017)1. - ISSN 1471-2164
Candidate gene - Complex trait - Genome wide genotyping - GWAS - Potato (Solanum tuberosum) - SNP - Starch content - Tuber - Yield
Background: Tuber yield and starch content of the cultivated potato are complex traits of decisive importance for breeding improved varieties. Natural variation of tuber yield and starch content depends on the environment and on multiple, mostly unknown genetic factors. Dissection and molecular identification of the genes and their natural allelic variants controlling these complex traits will lead to the development of diagnostic DNA-based markers, by which precision and efficiency of selection can be increased (precision breeding). Results: Three case-control populations were assembled from tetraploid potato cultivars based on maximizing the differences between high and low tuber yield (TY), starch content (TSC) and starch yield (TSY, arithmetic product of TY and TSC). The case-control populations were genotyped by restriction-site associated DNA sequencing (RADseq) and the 8.3 k SolCAP SNP genotyping array. The allele frequencies of single nucleotide polymorphisms (SNPs) were compared between cases and controls. RADseq identified, depending on data filtering criteria, between 6664 and 450 genes with one or more differential SNPs for one, two or all three traits. Differential SNPs in 275 genes were detected using the SolCAP array. A genome wide association study using the SolCAP array on an independent, unselected population identified SNPs associated with tuber starch content in 117 genes. Physical mapping of the genes containing differential or associated SNPs, and comparisons between the two genome wide genotyping methods and two different populations identified genome segments on all twelve potato chromosomes harboring one or more quantitative trait loci (QTL) for TY, TSC and TSY. Conclusions: Several hundred genes control tuber yield and starch content in potato. They are unequally distributed on all potato chromosomes, forming clusters between 0.5-4 Mbp width. The largest fraction of these genes had unknown function, followed by genes with putative signalling and regulatory functions. The genetic control of tuber yield and starch content is interlinked. Most differential SNPs affecting both traits had antagonistic effects: The allele increasing TY decreased TSC and vice versa. Exceptions were 89 SNP alleles which had synergistic effects on TY, TSC and TSY. These and the corresponding genes are primary targets for developing diagnostic markers.
Genetic structure of a QTL hotspot on chromosome 2 in sweet cherry indicates positive selection for favorable haplotypes
Cai, Lichun ; Voorrips, Roeland E. ; Weg, Eric van de; Peace, Cameron ; Iezzoni, Amy - \ 2017
Molecular Breeding 37 (2017)7. - ISSN 1380-3743 - 10 p.
Haplotype - Prunus avium - QTL hotspot - SNP

A genomic region of particular interest for sweet cherry (Prunus avium L.) breeding is a quantitative trait locus (QTL) “hotspot” on chromosome 2. QTLs for fruit size, firmness, sweetness, and flowering time are reported to map to this region. An understanding of genetic diversity, allele sources, linkage relationships, and historical recombinations is critical to enable the combining of favorable alleles at multiple loci. The objectives of this study were to characterize, visualize, and interpret the genetic structure of this previously identified QTL hotspot within North American sweet cherry breeding germplasm, using a pedigree-based haploblocking approach. Across the 29.4 cM (6.3 Mbp) region defined by single nucleotide polymorphism (SNP) information from the RosBREED cherry 6K SNP array v1, a total of 12 recombination events falling into six inter-marker regions were traced within the pedigree of elite and wild germplasm (n = 55). These recombinations defined five haploblocks containing 5–15 markers and exhibiting 7–11 haplotypes each. Over the entire QTL hotspot, 30 extended haplotypes were identified for which parental gametes could be determined. When the haploblocks and their haplotypes were used to explore genetic diversity, ancestry, and recombination patterns, and then integrated with previous QTL results for fruit size, the results indicated that favorable alleles at this QTL hotspot are under positive selection in breeding. The genetic framework provided by a haploblock approach and knowledge of haplotype-level diversity sets the stage for assigning breeding utility to these haplotypes.

Genome-wide association study unravels the genetic control of the apple volatilome and its interplay with fruit texture
Farneti, Brian ; Guardo, Mario Di; Khomenko, Iuliia ; Cappellin, Luca ; Biasioli, Franco ; Velasco, Riccardo ; Costa, Fabrizio - \ 2017
Journal of Experimental Botany 68 (2017)7. - ISSN 0022-0957 - p. 1467 - 1478.
Ester - Fruit texture - Functional principal component analysis - GWAS - Multiple factor analysis - Phenylpropene - PTR-ToF-MS - SNP - VOCs - Volatilome

Fruit quality represents a fundamental factor guiding consumers' preferences. Among apple quality traits, volatile organic compounds and texture features play a major role. Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-ToF-MS), coupled with an artificial chewing device, was used to profile the entire apple volatilome of 162 apple accessions, while the fruit texture was dissected with a TAXT-AED texture analyzer. The array of volatile compounds was classed into seven major groups and used in a genome-wide association analysis carried out with 9142 single nucleotide polymorphisms (SNPs). Marker-trait associations were identified on seven chromosomes co-locating with important candidate genes for aroma, such as MdAAT1 and MdIGS. The integration of volatilome and fruit texture data conducted with a multiple factor analysis unraveled contrasting behavior, underlying opposite regulation of the two fruit quality aspects. The association analysis using the first two principal components identified two QTLs located on chromosomes 10 and 2, respectively. The distinction of the apple accessions on the basis of the allelic configuration of two functional markers, MdPG1 and MdACO1, shed light on the type of interplay existing between fruit texture and the production of volatile organic compounds. c The Author 2017.

Deciphering the genetic control of fruit texture in apple by multiple family-based analysis and genome-wide association
Guardo, Mario Di; Bink, Marco C.A.M. ; Guerra, Walter ; Letschka, Thomas ; Lozano, Lidia ; Busatto, Nicola ; Poles, Lara ; Tadiello, Alice ; Bianco, Luca ; Visser, Richard G.F. ; Weg, Eric van de; Costa, Fabrizio - \ 2017
Journal of Experimental Botany 68 (2017)7. - ISSN 0022-0957 - p. 1451 - 1466.
Apple - Bayesian statistics - Fruit texture - Genome-wide association study (GWAS) - High-resolution phenotyping - Pedigree-based analysis (PBA) - RT-qPCR - SNP

Fruit texture is a complex feature composed of mechanical and acoustic properties relying on the modifications occurring in the cell wall throughout fruit development and ripening. Apple is characterized by a large variation in fruit texture behavior that directly impacts both the consumer's appreciation and post-harvest performance. To decipher the genetic control of fruit texture comprehensively, two complementing quantitative trait locus (QTL) mapping approaches were employed. The first was represented by a pedigree-based analysis (PBA) carried out on six full-sib pedigreed families, while the second was a genome-wide association study (GWAS) performed on a collection of 233 apple accessions. Both plant materials were genotyped with a 20K single nucleotide polymorphism (SNP) array and phenotyped with a sophisticated high-resolution texture analyzer. The overall QTL results indicated the fundamental role of chromosome 10 in controlling the mechanical properties, while chromosomes 2 and 14 were more associated with the acoustic response. The latter QTL, moreover, showed a consistent relationship between the QTL-estimated genotypes and the acoustic performance assessed among seedlings. The in silico annotation of these intervals revealed interesting candidate genes potentially involved in fruit texture regulation, as suggested by the gene expression profile. The joint integration of these approaches sheds light on the specific control of fruit texture, enabling important genetic information to assist in the selection of valuable fruit quality apple varieties.

Genetic mapping and QTL analysis of Botrytis resistance in Gerbera hybrida
Fu, Yiqian ; Silfhout, Alex van; Shahin, Arwa ; Egberts, Ronny ; Beers, Martin ; Velde, Ans van der; Houten, Adrie van; Tuyl, Jaap M. van; Visser, Richard G.F. ; Arens, Paul - \ 2017
Molecular Breeding 37 (2017)2. - ISSN 1380-3743
Gerbera grey mould - Linkage group - QTL mapping - SNP
Gerbera hybrida is an economically important cut flower. In the production and transportation of gerbera with unavoidable periods of high relative humidity, grey mould occurs and results in losses in quality and quantity of flowers. Considering the limitations of chemical use in greenhouses and the impossibility to use these chemicals in auction or after sale, breeding for resistant gerbera cultivars is considered as the best practical approach. In this study, we developed two segregating F1 populations (called S and F). Four parental linkage maps were constructed using common and parental specific SNP markers developed from expressed sequence tag sequencing. Parental genetic maps, containing 30, 29, 27 and 28 linkage groups and a consensus map covering 24 of the 25 expected chromosomes, could be constructed. After evaluation of Botrytis disease severity using three different tests, whole inflorescence, bottom (of disc florets) and ray floret, quantitative trait locus (QTL) mapping was performed using the four individual parental maps. A total of 20 QTLs (including one identical QTL for whole inflorescence and bottom tests) were identified in the parental maps of the two populations. The number of QTLs found and the explained variance of most QTLs detected reflect the complex mechanism of Botrytis disease response.
Data from: Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle
Upadhyay, M.R. ; Chen, W. ; Lenstra, J.A. ; Goderie, C.R.J. ; Machugh, D.E. ; Park, S.D.E. ; Magee, D.A. ; Matassino, D. ; Ciani, F. ; Megens, H.J.W.C. ; Arendonk, J.A.M. van; Groenen, M. - \ 2016
aurochs - primitive cattle - SNP - gene flow - runs of homozygosity
This file contains the information for 777,962 markers genotyped in 143 samples using the Illumina BovineHD BeadChip. The vcf file contains the aurochs genotypes, which corresponds to SNP positions in Illumina BovineHD Beadchip.
Ancient split of major genetic lineages of European Black Pine : evidence from chloroplast DNA
Naydenov, Krassimir D. ; Naydenov, Michel K. ; Alexandrov, Alexander ; Vasilevski, Kole ; Gyuleva, Veselka ; Matevski, Vlado ; Nikolic, Biljana ; Goudiaby, Venceslas ; Bogunic, Faruk ; Paitaridou, Despina ; Christou, Andreas ; Goia, Irina ; Carcaillet, Christopher ; Alcantara, Adrian Escudero ; Ture, Cengiz ; Gulcu, Suleyman ; Peruzzi, Lorenzo ; Kamary, Salim ; Bojovic, Srdjan ; Hinkov, Georgi ; Tsarev, Anatoly - \ 2016
Tree Genetics and Genomes 12 (2016)4. - ISSN 1614-2942
Chloroplast DNA - Phylogeography - Pinus nigra - Population structure - SNP - SSR

The European Black Pine (Pinus nigra Arn.) has a long and complex history. Genetic distance and frequency analyses identified three differentiated genetic groups, which corresponded to three wide geographical areas: Westerns Mediterranean, Balkan Peninsula and Asia Minor. These groups shared common ancestors (14.75 and 10.72 Ma). The most recent splits occurred after the Messinian Salinity Crisis (4.37 Ma) and the Early–Middle Pleistocene Transitions (0.93 Ma). The posterior ancestral population size (Na) is 260,000–265,000 individuals. Each pool is further fragmented, with evidence of a phylogeographic structure (Nst > Gst) typically observed in some natural populations from the Western Mediterranean region and the Balkan Peninsula. The laboratory analysis was performed by fragment analysis—i.e. electrophoretic sizing of polymerase chain reaction fragments, combined with the sequencing analysis of 33 % of all individuals as a control. Intense sampling of chloroplast DNA polymorphisms (3154 individuals and 13 markers: SNPs and SSRs) over the full area of the species’ natural distribution indicated moderate among-population variability (Gst(nc) ≤ 0.177) in various parts of its range. These results indicate that the natural populations have long migration histories that differ from one another and that they have been strongly phylogeographically affected by complex patterns of isolation, speciation and fragmentation. Long and varying climatic fluctuations in the region of the principal genetic group have been the probable cause of different forest community associations with different successional patterns resulting in interglacial refugia vs. macro long-term refugia.

PediHaplotyper : software for consistent assignment of marker haplotypes in pedigrees
Voorrips, Roeland E. ; Bink, Marco C.A.M. ; Kruisselbrink, Johannes W. ; Koehorst-van Putten, Herma J.J. ; Weg, Eric van de - \ 2016
Molecular Breeding 36 (2016). - ISSN 1380-3743
Haploblock - Haplotyping - Pedigree - SNP

In the study of large outbred pedigrees with many founders, individual bi-allelic markers, such as SNP markers, carry little information. After phasing the marker genotypes, multi-allelic loci consisting of groups of closely linked markers can be identified, which are called “haploblocks”. Here, we describe PediHaplotyper, an R package capable of assigning consistent alleles to such haploblocks, allowing for missing and incorrect SNP data. These haploblock genotypes are much easier to interpret by the human investigator than the original SNP data and also allow more efficient QTL analyses that require less memory and computation time.

Genomic prediction of growth in pigs based on a model including additive and dominance effects
Lopes, M.S. ; Bastiaansen, J.W.M. ; Janss, L. ; Knol, E.F. ; Bovenhuis, H. - \ 2016
Journal of Animal Breeding and Genetics (2016). - ISSN 0931-2668 - p. 180 - 186.
Phenotype prediction - SNP - Variance component

Independent of whether prediction is based on pedigree or genomic information, the focus of animal breeders has been on additive genetic effects or 'breeding values'. However, when predicting phenotypes rather than breeding values of an animal, models that account for both additive and dominance effects might be more accurate. Our aim with this study was to compare the accuracy of predicting phenotypes using a model that accounts for only additive effects (MA) and a model that accounts for both additive and dominance effects simultaneously (MAD). Lifetime daily gain (DG) was evaluated in three pig populations (1424 Pietrain, 2023 Landrace, and 2157 Large White). Animals were genotyped using the Illumina SNP60K Beadchip and assigned to either a training data set to estimate the genetic parameters and SNP effects, or to a validation data set to assess the prediction accuracy. Models MA and MAD applied random regression on SNP genotypes and were implemented in the program Bayz. The additive heritability of DG across the three populations and the two models was very similar at approximately 0.26. The proportion of phenotypic variance explained by dominance effects ranged from 0.04 (Large White) to 0.11 (Pietrain), indicating that importance of dominance might be breed-specific. Prediction accuracies were higher when predicting phenotypes using total genetic values (sum of breeding values and dominance deviations) from the MAD model compared to using breeding values from both MA and MAD models. The highest increase in accuracy (from 0.195 to 0.222) was observed in the Pietrain, and the lowest in Large White (from 0.354 to 0.359). Predicting phenotypes using total genetic values instead of breeding values in purebred data improved prediction accuracy and reduced the bias of genomic predictions. Additional benefit of the method is expected when applied to predict crossbred phenotypes, where dominance levels are expected to be higher.

Identification of candidate genes involved in Witches' broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil
Royaert, Stefan ; Jansen, J. ; Silva, Daniela Viana da; Jesus Branco, Samuel Martins de; Livingstone, Donald S. ; Mustiga, Guiliana ; Marelli, Jean Philippe ; Araújo, Ioná Santos ; Corrêa, Ronan Xavier ; Motamayor, Juan Carlos - \ 2016
BMC Genomics 17 (2016). - ISSN 1471-2164 - 16 p.
Candidate genes - Genetic linkage map - Marker-trait associations - SNP - Theobroma cacao L - Witches' broom disease

Background: Witches' broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm. Results: We developed a dense genetic linkage map with a length of 852.8 cM that contains 3,526 SNPs and is based on the MP01 mapping population, which counts 459 trees from a cross between the resistant 'TSH 1188' and the tolerant 'CCN 51' at the Mars Center for Cocoa Science in Barro Preto, Bahia, Brazil. Seven quantitative trait loci (QTL) that are associated with WBD were identified on five different chromosomes using a multi-trait QTL analysis for outbreeders. Phasing of the haplotypes at the major QTL region on chromosome IX on a diversity panel of genotypes clearly indicates that the major resistance locus comes from a well-known source of WBD resistance, the clone 'SCAVINA 6'. Various potential candidate genes identified within all QTL may be involved in different steps leading to disease resistance. Preliminary expression data indicate that at least three of these candidate genes may play a role during the first 12 h after infection, with clear differences between 'CCN 51' and 'TSH 1188'. Conclusions: We combined the information from a large mapping population with very distinct parents that segregate for WBD, a dense set of mapped markers, rigorous phenotyping capabilities and the availability of a sequenced genome to identify several genomic regions that are involved in WBD resistance. We also identified a novel source of resistance that most likely comes from the 'CCN 51' parent. Thanks to the large population size of the MP01 population, we were able to pick up QTL and markers with relatively small effects that can contribute to the creation and selection of more tolerant/resistant plant material.

First step in using molecular data for microbial food safety risk assessment; hazard identification of Escherichia coli O157 : H7 by coupling genomic data with in vitro adherence to human epithelial cells
Pielaat, Annemarie ; Boer, M.P. ; Wijnands, Lucas M. ; Hoek, A.H.A.M. van; Bouw, El ; Barker, G.C. ; Teunis, P.F.M. ; Aarts, Henk J.M. ; Franz, Eelco - \ 2015
International Journal of Food Microbiology 213 (2015). - ISSN 0168-1605 - p. 130 - 138.
GWAS - Microbiology - Risk assessment - SNP - STEC

The potential for using whole genome sequencing (WGS) data in microbiological risk assessment (MRA) has been discussed on several occasions since the beginning of this century. Still, the proposed heuristic approaches have never been applied in a practical framework. This is due to the non-trivial problem of mapping microbial information consisting of thousands of loci onto a probabilistic scale for risks. The paradigm change for MRA involves translation of multidimensional microbial genotypic information to much reduced (integrated) phenotypic information and onwards to a single measure of human risk (i.e. probability of illness).In this paper a first approach in methodology development is described for the application of WGS data in MRA; this is supported by a practical example. That is, combining genetic data (single nucleotide polymorphisms; SNPs) for Shiga toxin-producing Escherichia coli (STEC) O157 with phenotypic data (in vitro adherence to epithelial cells as a proxy for virulence) leads to hazard identification in a Genome Wide Association Study (GWAS).This application revealed practical implications when using SNP data for MRA. These can be summarized by considering the following main issues: optimum sample size for valid inference on population level, correction for population structure, quantification and calibration of results, reproducibility of the analysis, links with epidemiological data, anchoring and integration of results into a systems biology approach for the translation of molecular studies to human health risk.Future developments in genetic data analysis for MRA should aim at resolving the mapping problem of processing genetic sequences to come to a quantitative description of risk. The development of a clustering scheme focusing on biologically relevant information of the microbe involved would be a useful approach in molecular data reduction for risk assessment.

Data from: Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations
Goedbloed, D.J. ; Megens, H.J.W.C. ; Hooft, W.F. van; Herrero-Medrano, J. ; Lutz, W. ; Alexandri, P. ; Crooijmans, R.P.M.A. ; Groenen, M. ; Wieren, S.E. van; Ydenberg, R.C. ; Prins, H.H.T. - \ 2012
hybridisation - mammals - population genetics - empirical - SNP - Sus scrofa
Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele frequency spectrum analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP analysis is a promising tool to quantify recent hybridization in free-living populations.
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