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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Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds
Onzima, R.B. ; Upadhyay, M.R. ; Mukiibi, R. ; Kanis, E. ; Groenen, M.A.M. ; Crooijmans, R.P.M.A. - \ 2018
Animal Genetics 49 (2018)1. - ISSN 0268-9146 - p. 59 - 70.
breed composition - breed diversity - Capra hircus - heterozygosity - indigenous goats - population genetics
Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO) and expected (HE) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes.
Data from: Distinguishing migration events of different timing for wild boar in the Balkans
Alexandri, Panoraia ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Groenen, M. ; Goedbloed, D.J. ; Herrero Medrano, J.M. ; Rund, L.A. ; Schook, Lawrence B. ; Chatzinikos, Evangelos ; Triantaphyllidis, Costas ; Triantafyllidis, Alexander - \ 2016
SNPs - population genetics - recent migration - genetic diversity - mammal - microsatellites - Sus scrofa
Aim: We compared the power of different nuclear markers to investigate genetic structure of southern Balkan wild boar. We distinguished between historic events, such as isolation in different refugia during glacial periods, from recent demographic processes, such as naturally occurring expansions. Location: Southern Balkans/Greece. Methods: We sampled 555 wild boars from 20 different locations in southern Balkans/Greece. All individuals were analysed with 10 microsatellites and a subgroup of 91 with 49,508 single nucleotide polymorphisms (SNPs). Patterns of genetic structure and demographic processes were assessed with Bayesian clustering, linkage disequilibrium and past effective population size estimation analysis. Results: Both microsatellite and SNP data analyses detected genetic structure caused by historic events and support the existence of three groups in the studied area. A hybrid zone between two of the groups was also detected. We also showed that genome-wide SNP data analysis can identify recent events in bottlenecked populations. Main conclusions: We inferred the three groups diverged ~50,000–10,000 yr bp when populations contracted to different refugia. Our findings strengthened the evidence that the southern Balkan area was a glacial refugium including further local smaller refugia. Genome-wide genotyping inferred a recent population expansion that can mimic a ‘refugium within refugium’ scenario. It seems that microsatellite data tend to overestimate genetic structure when genetic drift happens in bottlenecked populations over a short distance. Therefore, genome-wide SNPs are more powerful at inferring phylogeography in natural populations, resolving inconsistencies from mitochondrial and microsatellite data sets.
Data from: Molecular biogeography of prickly lettuce (Lactuca serriola L.) shows traces of recent range expansion
Andrea, L. D'; Meirmans, Patrick ; Wiel, C.C.M. van de; Guadagnuolo, Roberto ; Treuren, R. van; Kozlowski, Gregor ; Nijs, Hans den; Felber, F. - \ 2016
biogeography - microsatellites - chloroplast PCR-RFLP - population genetics - global change - population structure - phylogeography
Microsatellite data in GenePop format for Lactuca serriola in Europe
The fine-scale genetic structure of the malaria vectors Anopheles funestus and Anopheles gambiae (Diptera: Culicidae) in the north-eastern part of Tanzania
Gélin, P. ; Magalon, H. ; Drakeley, C. ; Maxwell, C. ; Magesa, S. ; Takken, W. ; Boëte, C. - \ 2016
International Journal of Tropical Insect Science 36 (2016)4. - ISSN 1742-7584 - p. 161 - 170.
altitude - Anopheles funestus - Anopheles gambiae - malaria - microsatellite - population genetics - Tanzania - 016-3966

Understanding the impact of altitude and ecological heterogeneity at a fine scale on the populations of malaria vectors is essential to better understand and anticipate eventual epidemiological changes. It could help to evaluate the spread of alleles conferring resistance to insecticides and also determine any increased entomological risk of transmission in highlands due to global warming. We used microsatellite markers to measure the effect of altitude and distance on the population genetic structure of Anopheles funestus and Anopheles gambiae s.s. in the Muheza area in the north-eastern part of Tanzania (seven loci for each species). Our analysis reveals strong gene flow between the different populations of An. funestus from lowland and highland areas, as well as between populations of An. gambiae sampled in the lowland area. These results highlight for An. funestus the absence of a significant spatial subpopulation structuring at small-scale, despite a steep ecological and altitudinal cline. Our findings are important in the understanding of the possible spread of alleles conferring insecticide resistance through mosquito populations. Such information is essential for vector control programmes to avoid the rapid spread and fixation of resistance in mosquito populations.

Genetische monitoring van de Nederlandse otterpopulatie : ontwikkeling van populatieomvang en genetische status 2014/2015
Kuiters, A.T. ; Groot, G.A. de; Lammertsma, D.R. ; Jansman, H.A.H. ; Bovenschen, J. - \ 2016
Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-technical report 62) - 30 p.
lutra lutra - otters - populatiegenetica - inteelt - mortaliteit - monitoring - nederland - population genetics - inbreeding - mortality - netherlands
Jaarlijks wordt de Nederlandse otterpopulatie genetisch gemonitord in opdracht van het Ministerie van
Economische Zaken. Daarmee wordt een vinger aan de pols gehouden wat betreft de ontwikkeling van de
genetische status van de populatie. Deze vorm van monitoring, waarbij gebruik wordt gemaakt van DNA
geïsoleerd uit uitwerpselen en doodvondsten, maakt het tevens mogelijk veranderingen in de ruimtelijke
verspreiding en de populatieomvang te volgen. De monitoringsronde van 2014/2015 laat zien dat de
populatie verder is gegroeid naar ca. 160 individuen. Op populatieniveau lijkt geen verder verlies aan
genetische variatie te zijn opgetreden. De genetische variatie binnen individuen is evenmin verder
afgenomen in tegenstelling tot voorafgaande jaren. Onderdeel van deze monitoring is ook autopsie van dode
otters, waarbij wordt gekeken naar de doodsoorzaak en de belangrijkste lichaamskenmerken. Verkeer is
verreweg de belangrijkste doodsoorzaak. Locaties waar otters worden doodgereden, worden geregistreerd
en bijgehouden in een database. Deze informatie is belangrijk voor het veiliger maken van knelpuntlocaties
om zo het aantal verkeersslachtoffers te beperken. Het aantal verkeersslachtoffers neemt nog ieder jaar toe,
waarbij de toename evenredig is aan de toename in de populatieomvang
Population-level consequences of complementary sex determination in a solitary parasitoid
Boer, J.G. de; Groenen, M. ; Pannebakker, B.A. ; Beukeboom, L.W. ; Kraus, Robert - \ 2015
population genetics - whole genome sequencing - SNPcomplementary sex determination - inbreeding - biological control
Background: Sex determination mechanisms are known to be evolutionarily labile but the factors driving transitions in sex determination mechanisms are poorly understood. All insects of the Hymenoptera are haplodiploid, with males normally developing from unfertilized haploid eggs. Under complementary sex determination (CSD), diploid males can be produced from fertilized eggs that are homozygous at the sex locus. Diploid males have near-zero fitness and thus represent a genetic load, which is especially severe under inbreeding. Here, we study mating structure and sex determination in the parasitoid Cotesia vestalis to investigate what may have driven the evolution of two complementary sex determination loci in this species. Results: We genotyped Cotesia vestalis females collected from eight fields in four townships in Western Taiwan. 98 SNP markers were developed by aligning Illumina sequence reads of pooled DNA of eight different females against a de novo assembled genome of C. vestalis. This proved to be an efficient method for this non-model species and provides a resource for future use in related species. We found significant genetic differentiation within the sampled population but variation could not be attributed to sampling locations by AMOVA. Non-random mating was detected, with 8.1% of matings between siblings. Diploid males, detected by flow cytometry, were produced at a rate of 1.4% among diploids. Conclusions: We think that the low rate of diploid male production is best explained by a CSD system with two independent sex loci, supporting laboratory findings on the same species. Fitness costs of diploid males in C. vestalis are high because diploid males can mate with females and produce infertile triploid offspring. This severe fitness cost of diploid males combined with non-random mating may have resulted in evolution from single locus CSD to CSD with two independent loci.
Genetische monitoring van de Nederlandse otterpopulatie 2013/2014 : ontwikkeling van populatieomvang en populatiegenetische status
Kuiters, A.T. ; Groot, G.A. de; Lammertsma, D.R. ; Jansman, H.A.H. ; Bovenschen, J. - \ 2015
Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2624) - 39
lutra lutra - otters - fauna - populatiedichtheid - populatiegenetica - inteelt - mortaliteit - dna - monitoring - friesland - noordwest-overijssel - drenthe - population density - population genetics - inbreeding - mortality
Jaarlijks wordt in opdracht van het ministerie van Economische Zaken de Nederlandse otterpopulatie genetisch gemonitord. Daarmee wordt een vinger aan de pols gehouden wat betreft de ontwikkeling van de genetische status van de populatie. Deze vorm van monitoring, gebaseerd op DNA-profielen op basis van DNA geïsoleerd uit verse spraints (uitwerpselen), maakt het tevens mogelijk veranderingen in de ruimtelijke verspreiding en de populatieomvang van jaar tot jaar te volgen. De monitoringsronde van 2013/2014 laat zien dat de populatie verder is gegroeid naar een aantal van ca. 140 individuen. Echter, de genetische variatie binnen individuen is sterker afgenomen vergeleken met voorafgaande jaren. Onderdeel van deze monitoring is ook autopsie van dode otters, waarbij wordt gekeken naar de doodsoorzaak en de belangrijkste lichaamskenmerken. Knelpuntlocaties waar otters worden doodgereden worden in beeld gebracht. Er is een sterke toename van het jaarlijkse aantal verkeersslachtoffers. Deze lijkt gelijke tred te houden met de toename van de populatieomvang.
Population genetics and disease ecology of European wild boar
Goedbloed, D.J. - \ 2013
University. Promotor(en): Herbert Prins; Ron Ydenberg, co-promotor(en): Pim van Hooft. - S.l. : s.n. - ISBN 9789461737236 - 123
wilde varkens - sus scrofa - infectieziekten - populatiegenetica - ecologie - mycoplasma hyopneumoniae - varkenscircovirus-1 - ziekteoverdracht - fauna - noordwest-europa - wild pigs - infectious diseases - population genetics - ecology - porcine circovirus-1 - disease transmission - northwestern europe
Welke factoren beïnvloeden de frequentie van de ziekten in wilde populaties? Het promotieonderzoek van Daniel Goedbloed beoordeelde de invloed van demografische, genetische en omgevingsfactoren op de frequentie van twee infectieziekten in Noordwest-Europese wilde zwijnen populaties.
Advies voor genetisch beheer van de Bonte Bentheimen populatie in Nederland
Windig, J.J. ; Hoving, A.H. - \ 2013
Wageningen : Centre for genetic resources (CGN) (CGN rapport 28) - 16
varkens - beren (varkens) - kunstmatige inseminatie - fokkerijmethoden - dierveredeling - populatiegenetica - genetische bronnen van diersoorten - varkensrassen - zeldzame rassen - pigs - boars - artificial insemination - animal breeding methods - animal breeding - population genetics - animal genetic resources - pig breeds - rare breeds
De Bonte Bentheimer heeft in Nederland een kleine populatieomvang. In kleine rassen kan inteelt voor grote problemen zorgen en dus is een goed fokbeleid nodig om een te sterke inteelttoename te voorkomen.
Genetica van wilde zwijnen in Limburg en Noord-Brabant : verspreiding, herkomst en verwantschap
Jansman, H.A.H. ; Hofmeester, T.R. ; Groot, G.A. de; Laros, I. ; Bovenschen, J. ; Speelman, M. ; Hout, J.J. van der; Casaer, J. ; Breyne, P. ; Koelewijn, H.P. - \ 2013
Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2404) - 62
sus scrofa - wilde varkens - populatiedynamica - populatiegenetica - genetica - migratie - limburg - noord-brabant - fauna - wild pigs - population dynamics - population genetics - genetics - migration
In Limburg komen op verschillende plaatsen buiten het officiële leefgebied De Meinweg wilde zwijnen voor. De aantallen in deze zogenaamde nulstandsgebieden nemen toe, en ook in Noord-Brabant worden in toenemende mate wilde zwijnen gesignaleerd. In opdracht van de provincies Limburg en Noord-Brabant voerde Alterra een genetisch onderzoek uit naar de populatiestructuur en herkomst van de wilde zwijnen in Limburg en Noord-Brabant. Het onderzoek laat zien dat sprake is van een aantal afzonderlijke populaties met een unieke genetische samenstelling. Door gunstigere omstandigheden weten de populaties van wilde zwijnen in Noordwest Europa in aantal en verspreidingsgebied toe te nemen. Genetisch kon dan ook vastgesteld worden dan in de meeste gevallen de nieuwe populaties ontstaan zijn uit de naburige bestaande populaties. In enkele gevallen kan sprake zijn geweest van een (gedeeltelijke) onnatuurlijke oorsprong door ontsnappingen uit gevangenschap of illegale herintroducties. De genetische variatie in de populaties is redelijk, maar laag vergeleken met het buitenland. Onder de huidige omstandigheden lijkt de uitwisseling tussen deze jonge populaties echter voldoende om de variatie in de toekomst op z'n minst in stand te houden.
Genetische tools voor natuurbeheer: van het lab naar de praktijk
Groot, G.A. de; Laros, I. - \ 2013
Vakblad Natuur Bos Landschap 10 (2013)4. - ISSN 1572-7610 - p. 4 - 7.
natuurbeheer - genetische diversiteit - populatiegenetica - populatie-ecologie - nature management - genetic diversity - population genetics - population ecology
Genetische technieken worden nog altijd maar mondjesmaat gebruikt in het natuurbeheer en -beleid. Dit is deels het gevolg van een imagoprobleem: in het verleden waren deze technieken prijzig, en de toepassingsmogelijkheden beperkt. De moleculaire ecologie staat echter niet stil en nieuwe ontwikkelingen volgen elkaar in hoog tempo op. Gevestigde technieken hebben hun concrete waarde voor beleidsvorming en praktisch populatiebeheer inmiddels bewezen, en werden prijstechnisch steeds interessanter. Nieuwe technieken bieden een efficïënt alternatief voor conventionele inventarisaties. Tijd voor een update.
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.
Genetic diversity and population structure of cucumber (Cucumis sativus L.)
Lv, J. ; Qi, J. ; Shi, Q. ; Shen, D. ; Zhang, S. ; Shao, G. ; Li, H. ; Sun, Z. ; Weng, Y. ; Shang, Y. ; Gu, X. ; Li, X. ; Zhu, X. ; Zhang, J. ; Treuren, R. van; Dooijeweert, W. van; Zhang, Z. ; Huang, S. - \ 2012
PLoS One 7 (2012)10. - ISSN 1932-6203 - 9
genetische diversiteit - cucumis sativus - komkommers - populatiegenetica - genenbanken - dna-fingerprinting - germplasm - genetische merkers - vruchtgroenten - groenten - genetic diversity - cucumbers - population genetics - gene banks - dna fingerprinting - genetic markers - fruit vegetables - vegetables - genome - map
Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.
The role of Mallard (Anas platyrhynchos) in the spread of avian influenza: genomics, population genetics, and flyways
Kraus, R.H.S. - \ 2011
University. Promotor(en): Herbert Prins; Ron Ydenberg, co-promotor(en): Pim van Hooft. - [S.l.] : S.n. - ISBN 9789461730282 - 143
aviaire influenzavirussen - aviaire influenza - anas platyrhynchos - ziekteoverdracht - vogeltrek - genomica - populatiegenetica - evolutionaire genetica - zoögeografie - bioveiligheid - ziekteoverzichten - epidemiologie - avian influenza viruses - avian influenza - disease transmission - bird migration - genomics - population genetics - evolutionary genetics - zoogeography - biosafety - disease surveys - epidemiology

Birds, in particular poultry and ducks, are a source of many infectious diseases, such as those caused by influenza viruses. These viruses are a threat not only to the birds themselves but also to poultry farming and human health, as forms that can infect humans are known to have evolved. It is believed that migratory birds in general play an important role in the global spread of avian influenza (AI). However, it is still debated how large this role precisely is and whether other modes of spread may be more important. The mallard (Anas platyrhynchos) is the world’s most abundant and well-studied waterfowl species. Besides being an important game and agricultural species, it is also a flagship species in wetland conservation and restoration. Waterfowl (Anseriformes: Anatidae) and especially ducks currently are the focal bird group in long distance dispersal of Avian Influenza in the wild, and the mallard has been identified as the most likely species to transport this virus.

In my thesis I report aspects of the biology of this important host species of AI by molecular ecological means. As molecular marker system I established a genome-wide set of more than 100,000 SNPs of which I developed a subset of 384 SNPs into an assay to genotype about 1,000 ducks. This subset was employed to study the evolutionary history and speciation processes in the Anas genus. Further investigations into the world-wide mallard population structure on a species level were based not only on this set of 384 SNPs but also on mitochondrial DNA sequences. Last but not last, I investigated an option of AI sampling and detection from duck faeces by technology that is safe from a biohazard perspective, and solves transportation issues related to cold chains.

The main results of my thesis include the development of a generally applicable improved analysis pipeline to develop genome-wide SNP sets for non-model organisms. Further, my results show that, from a migration system perspective, mallard flyways/populations can hardly be delineated from a biological point of view. Detailed phylogenetic, population genetic and coalescent analyses of a data set of samples spanning the whole northern hemisphere leads me to conclude that the only firm population boundaries that I can draw are between Eurasia and North America, within which panmixia is almost achieved. Mallards’ and other Anas-ducks’ whole continental to global distribution brings them together in sympatry. I can show that a combination of sympatric distribution, conflicting genetically determined and learned mate recognition mechanisms, and genomic compatibility between species helps to explain the long-standing puzzle of waterfowl hybridisation and introgression of genes from one duck species into another. Besides obvious management implications I propose that this fact can be part of the explanation why ducks are so well adaptable and successful, as well as why they show extraordinary abilities to withstand AI infections, or its consequences for health status.

Genetic variation in the chicken genome: insights in selection
Elferink, M.G. - \ 2011
University. Promotor(en): Martien Groenen, co-promotor(en): Richard Crooijmans. - [S.l.] : S.n. - ISBN 9789085859208 - 162
pluimvee - dierveredeling - genomen - populatiegenetica - genen - rassen (dieren) - genetische kartering - genetische variatie - selectie - poultry - animal breeding - genomes - population genetics - genes - breeds - genetic mapping - genetic variation - selection

The chicken currently provides more than a quarter of the meat and nearly all eggs produced worldwide. For future improvements in production traits and animal welfare as well as to address future consumer demands it is necessary to understand the etiology and biology underlying production traits and diseases. The primary aim of the research described in this thesis was to investigate the utility of several molecular approaches to identify causative variants underlying a variety of traits in the chicken.
The general introduction in chapter 1 provides an overview of the domestication history of the chicken - with a particular focus on commercial chicken breeds - and describes the importance to identify causative variants underlying production traits and diseases. Furthermore, several different molecular techniques and methods are introduced that are being used to detect causative variants underlying monogenic and polygenic traits.
Linkage maps are essential for linkage analysis, important to study recombination rates and recombination hotspots within the genome and can assist in the sequence assembly of genomes. In chapter 2 we describe the construction of a new high-resolution linkage map of the chicken genome based on two chicken populations with a total of 1619 individuals. The two populations used are a purebred broiler line and a broiler x broiler cross. This high resolution allowed accurate identification of recombination hotspots in the chicken genome, including sex specific recombination. Furthermore, to improve the current reference genome (WASHUC2), 613 unmapped markers were included in the genome-wide assay that included a total of 17,790 SNPs. The resulting linkage map comprises 13,340 SNPs, of which 360 had not been assigned to a known chromosome on chicken genome build WASHUC2. The resulting linkage map is composed of 31 linkage groups, with a total length of 3,054 cM for the sex-average map of the combined population. Regional differences in recombination hotspots between the two mapping populations were observed for several chromosomes near the telomere of the p arm. The sex-specific analysis revealed that these regional differences were mainly caused by female-specific recombination hotspots in the broiler × broiler cross.
In chapter 3 we describe the molecular characterization of the locus causing the late feathering phenotype; a monogenic trait in chicken that results in a delayed emergence of flight feathers at hatch. The late feathering phenotype is beneficial to breeders as it can be used for sex typing at hatch. The locus has, therefore, been extensively used in diverse commercial chicken breeds. However, a retrovirus closely linked to the late feathering allele causes a negative pleiotropic effect on egg production and causes viral infections. Within this chapter we describe the identification of a 180 kb tandem duplication in the late feathering allele using a quantitative PCR approach. The tandem duplication results in the partial duplication of two genes; the prolactin receptor and the gene encoding sperm flagellar protein 2. Sequence analysis revealed that the duplication is identical in broiler, white egg-layer, and brown egg-layer lines. This information was also used to design a molecular test to detect this duplication, particularly in heterozygous individuals.
The recent advances in massive parallel sequencing technologies have enabled rapid and cost-effective detection of all genetic variants within genomes. The detection of all genetic variants within a genome has further increased our ability to identify causative variants underlying quantitative trait loci (QTL). In chapter 4, we combined a genome-wide association study with whole-genome resequencing to identify causative variants underlying the pulmonary hypertension syndrome (PHS), a polygenic trait in chicken. PHS is a metabolic disease that has been linked to intense selection on growth rate and feed conversion ratio of modern broilers (meat-type chicken). PHS has become one of the most frequent causes of mortality within the broiler industry and leads to substantial economic losses and reduced animal welfare. In total, 18 QTL regions were identified in the genome-wide association study. In order to detect causative variants underlying these QTL regions, we sequenced the genomes of twelve individuals. To maximize the detection of causative variants we selected the individuals based on extreme phenotypes for PHS. Within 8 QTL regions we identified a total of 10 genes that contain at least one variant that is predicted to affect protein function. Moreover, 7.62 million SNPs were detected within the twelve animals compared to the reference genome. These markers can be used in the development of future genome-wide assays.
Genomic regions that have undergone selection should contain loci that influence important phenotypic traits and will, therefore, include causative variant(s) that could aid in further future improvement of production traits and disease resistance. In chapter 5, we applied hitch-hiking mapping to make a broad assessment of the effects of selection histories in domesticated chicken. Towards this end, we sampled commercial chickens representing all major breeding goals from multiple breeding companies. In addition, we sampled non-commercial chicken diversity by sampling almost all recognized traditional Dutch breeds and a representative sample of breeds from China. The broad sample of 67 commercial and non-commercial breeds were assessed for signatures of selection in the genome using information of 57,636 SNPs that were genotyped on pooled DNA samples. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations. The detection of regions of putative selection resulted in the identification of several candidate genes that could aid in further improvement of production traits and disease resistance.
Finally, the general discussion in chapter 6 describes the main findings of this thesis. In this chapter recommendations are given for the best strategies to detect causative variants underlying monogenic or polygenic traits. All strategies can benefit substantially from the recent developments in massive parallel sequencing, although the high costs of this method currently prevent large scale studies. In order to perform powerful and cost-effective studies, several strategies are discussed that combine massive parallel sequencing with other existing methods and techniques. Furthermore, the limitations of the different strategies are addressed, as well as the improvements needed in the near future to identify causative variants underlying a variety of traits in, but not limited to, the chicken.



Estimating genetic diversity across the neutral genome with the use of dense marker maps
Engelsma, K.A. ; Calus, M.P.L. ; Bijma, P. ; Windig, J.J. - \ 2010
Genetics, Selection, Evolution 42 (2010). - ISSN 0999-193X - 10
populatiegenetica - computersimulatie - genetische diversiteit - merkergenen - population genetics - computer simulation - genetic diversity - marker genes - linkage disequilibrium - prediction - selection - conservation - populations - haplotypes
Background With the advent of high throughput DNA typing, dense marker maps have become available to investigate genetic diversity on specific regions of the genome. The aim of this paper was to compare two marker based estimates of the genetic diversity in specific genomic regions lying in between markers: IBD-based genetic diversity and heterozygosity. Methods A computer simulated population was set up with individuals containing a single 1-Morgan chromosome and 1665 SNP markers and from this one, an additional population was produced with a lower marker density i.e. 166 SNP markers. For each marker interval based on adjacent markers, the genetic diversity was estimated either by IBD probabilities or heterozygosity. Estimates were compared to each other and to the true genetic diversity. The latter was calculated for a marker in the middle of each marker interval that was not used to estimate genetic diversity. Results The simulated population had an average minor allele frequency of 0.28 and an LD (r2) of 0.26, comparable to those of real livestock populations. Genetic diversities estimated by IBD probabilities and by heterozygosity were positively correlated, and correlations with the true genetic diversity were quite similar for the simulated population with a high marker density, both for specific regions (r = 0.19-0.20) and large regions (r = 0.61-0.64) over the genome. For the population with a lower marker density, the correlation with the true genetic diversity turned out to be higher for the IBD-based genetic diversity. Conclusions Genetic diversities of ungenotyped regions of the genome (i.e. between markers) estimated by IBD-based methods and heterozygosity give similar results for the simulated population with a high marker density. However, for a population with a lower marker density, the IBD-based method gives a better prediction, since variation and recombination between markers are missed with heterozygosity.
Levels of inbreeding in group mating captive broodstock populations of Common sole, (Solea solea), inferred from parental relatedness and contribution
Blonk, R.J.W. ; Komen, J. ; Kamstra, A. ; Crooijmans, R.P.M.A. ; Arendonk, J.A.M. van - \ 2009
Aquaculture 289 (2009)1-2. - ISSN 0044-8486 - p. 26 - 31.
vissen - tong (vis) - voortplanting - natuurlijke paring - populatiegenetica - nageslacht - inteelt - kuitschieten - afstamming - heterozygotie - genetische diversiteit - genetische bronnen - fishes - dover soles - reproduction - natural mating - population genetics - progeny - inbreeding - spawning - parentage - heterozygosity - genetic diversity - genetic resources - cod gadus-morhua - fish breeding programs - dover sole - spawning aggregations - scophthalmus-maximus - reproductive success - genetic-variation - mass selection - dna markers - senegalensis
In this paper, we estimate levels of inbreeding with parental relatedness and contribution inferred from microsatellites in groups of Common sole that reproduce by natural mating. We present results on spawning patterns during one entire reproductive season of wild Common sole, Solea solea, kept in two broodstock groups (28 animals in broodstock A; 20 animals in broodstock B) under semi-natural conditions. Batches of eggs were collected daily and incubated separately. First, we performed a parentage analysis on parents and samples of 24 newly hatched larvae from all batches, using 10 polymorphic microsatellite markers. As expected, contribution of parents to offspring was highly skewed. In both broodstocks, five or less parental pairs produced more than half of the total progeny. Natural spawning and unequal contributions of parents to offspring resulted in significant deviations from Hardy–Weinberg equilibria. Furthermore, few alleles were lost and levels of heterozygosity in offspring population increased. Next, we calculated relatedness between parents that mated successfully based on estimates of molecular similarity. Mean coefficients of coancestry in offspring were determined using parental relatedness and contributions. Levels of coancestry in progeny were substantially high. These results show that due to different parental contributions, natural mating in groups can result in significant inbreeding in future generations despite of limited loss of alleles and high levels of heterozygosity in first generation progeny. This shows that using loss of alleles and levels of heterozygosity alone can be misleading for estimation of genetic diversity.
Genetic conservation of endangered animal populations
Oliehoek, P.A. - \ 2009
University. Promotor(en): Johan van Arendonk, co-promotor(en): Piter Bijma. - [S.l.] : S.n. - ISBN 9789085853503 - 113
dieren - genetische diversiteit - inteelt - bedreigde soorten - bedreigde rassen - stamboom - populatiegenetica - populaties - conservering - ex-situ conservering - animals - genetic diversity - inbreeding - endangered species - endangered breeds - pedigree - population genetics - populations - conservation - ex situ conservation
Genetic factors in metapopulation survival : introduction to a PhD-project
Cobben, M.M.P. ; Arens, P.F.P. ; Verboom, J. ; Smulders, M.J.M. - \ 2008
habitats - populatiegenetica - demografie - distributie - conservering - genetische diversiteit - klimaatverandering - simulatiemodellen - metapopulaties - ecologische hoofdstructuur - population genetics - demography - distribution - conservation - genetic diversity - climatic change - simulation models - metapopulations - ecological network
Short introduction to a PhD project. Which factors determine the level and distribution of genetic diversity in fragmented populations, and how are these affected by increased temperature and weather variability? METAPHOR, a stochastic, spatially explicit, individual-based simulation model for demography of fragmented populations, will be extended with a genetic module to explore these research questions
Effects of population size on virus evolution: a baculovirus perspective
Zwart, M.P. - \ 2008
University. Promotor(en): Just Vlak, co-promotor(en): Wopke van der Werf; Arjan de Visser. - S.l. : S.n. - ISBN 9789085049920 - 140
baculovirus - populatiegenetica - autographa californica - insectenvirussen - virusziekten - infectie - polymerase-kettingreactie - evolutie - waarschijnlijkheidsmodellen - genotypen - dna-virussen - virus-gastheer interacties - population genetics - insect viruses - viral diseases - infection - polymerase chain reaction - evolution - probabilistic models - genotypes - dna viruses - virus-host interactions
This thesis explores the population genetics of the baculovirus infection process and the consequences for virus evolution. Using Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) and lepidopteran insect larvae as a model system, we attempt to characterize (1) elemental virus-host and virus-virus interactions pertinent to virus invasion and disease of the host, focussing largely on the number of virus individuals invading a host insect and including the first strong experimental evidence that a single virion can cause disease in a host animal, and (2) the interactions that can occur between virus genotypes during the process of diseasing the host, specifically competition.
The development of two technologies was necessary to address these questions. First, a method for generating clonal baculovirus populations containing molecular tag sequences was devised: insect larvae were transfected with full-length baculovirus genomic DNA modified to allow replication in Escherichia coli (bacmids). Second, a quantitative real-time PCR (qPCR) based assay was developed to measure the frequency of a baculovirus genotype in a mixed population.
In order to estimate the number of pathogen individuals invading the host and causing death, a basic probabilistic model that links this number to host survival was developed and experimentally tested. This model is based on the independent action hypothesis (IAH): the notion that (1) every pathogen individual has a fixed probability of invading the host, (2) if a pathogen individual invades the host this will irrevocably lead to host death, and (3) that pathogen individuals act independently. Here the model was specifically developed to predict how often hosts are invaded by two pathogen genotypes, when being challenged by a pathogen population consisting of two genotypes. Model predictions were tested using two near-identical bacmid-derived virus genotypes, larvae of three host species, and the qPCR assay. IAH model predictions were confirmed in early instar (L3) larvae of permissive host species (Spodoptera exigua and Trichoplusia ni). This strongly suggests that in these instances it is the action of one invading virion which leads to host death. Model predictions did not hold for late instar larvae (L5) of permissive host species and both early and late larvae of a semi-permissive species (Mamestra brassicae), which show greater resistance to AcMNPV. In these instances there was a too high frequency of invasions with both genotypes, suggesting that more virions had invaded these larvae to cause disease than predicted by IAH.
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