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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    Population-level consequences of complementary sex determination in a solitary parasitoid
    Boer, J.G. de; Groenen, M.A.M. ; Pannebakker, B.A. ; Beukeboom, L.W. ; Kraus, R.H.S. - \ 2015
    BMC Evolutionary Biology 15 (2015). - ISSN 1471-2148 - 11 p.
    biological-control introduction - multilocus genotype data - wasp cotesia-glomerata - bee apis-mellifera - genetic-structure - linkage analysis - mating system - diploid males - determination mechanisms - ascertainment bias
    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
    Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine.
    Plomion, C. ; Chancerel, E. ; Endelman, J. ; Lamy, J.B. ; Mandrou, E. ; Lesur, I. ; Ehrenmann, F. ; Isik, F. ; Bink, M.C.A.M. ; Heerwaarden, J. van; Bouffier, L. - \ 2014
    BMC Genomics 15 (2014)1. - ISSN 1471-2164 - 17 p.
    multilocus genotype data - loblolly-pine - forest trees - cryptomeria-japonica - density-estimation - cloned population - breeding values - complex traits - consensus map - white spruce
    BACKGROUND: The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. RESULTS: Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (He) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of He across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. CONCLUSIONS: These results are a stepping stone for the development of strategies for studies in population genomics, association mapping and genomic prediction in this economical and ecologically important forest tree species.
    Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon
    Banaticla-Hilario, M.C.N. ; Berg, R.G. van den; Hamilton, N.R.S. ; McNally, K.L. - \ 2013
    Ecology and Evolution 3 (2013)9. - ISSN 2045-7758 - p. 3047 - 3062.
    asian wild-rice - multilocus genotype data - cultivated rice - population-structure - genetic-structure - phylogenetic analysis - evolutionary relationships - insertion-polymorphism - island populations - species cohesion
    Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by F-ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (H-E = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (H-E = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.
    Genetic diversity of Vietnamese domestic chicken populations as decision-making support for conservation strategies
    Pham, H.T.M. ; Berthouly-Salazar, C. ; Crooijmans, R.P.M.A. - \ 2013
    Animal Genetics 44 (2013)5. - ISSN 0268-9146 - p. 509 - 521.
    multilocus genotype data - breeds - program - microsatellites - construction - resources - inference - software - ecotypes - alleles
    The aims of this study were to assess the genetic diversity of 17 populations of Vietnamese local chickens (VNN) and one Red Jungle Fowl population, together with six chicken populations of Chinese origin (CNO), and to provide priorities supporting the conservation of genetic resources using 20 microsatellites. Consequently, the VNN populations exhibited a higher diversity than did CNO populations in terms of number of alleles but showed a slightly lower observed heterozygosity. The VNN populations showed in total seven private alleles, whereas no CNO private alleles were found. The expected heterozygosity of 0.576 in the VNN populations was higher than the observed heterozygosity of 0.490, leading to heterozygote deficiency within populations. This issue could be partly explained by the Wahlund effect due to fragmentation of several populations between chicken flocks. Molecular analysis of variance showed that most of genetic variation was found within VNN populations. The Bayesian clustering analysis showed that VNN and CNO chickens were separated into two distinct groups with little evidence for gene flow between them. Among the 24 populations, 13 were successfully assigned to their own cluster, whereas the structuring was not clear for the remaining 11 chicken populations. The contributions of 24 populations to the total genetic diversity were mostly consistent across two approaches, taking into account the within- and between-populations genetic diversity and allelic richness. The black H'mong, Lien Minh, Luong Phuong and Red Jungle Fowl were ranked with the highest priorities for conservation according to Caballero and Toro's and Petit's approaches. In conclusion, a national strategy needs to be set up for Vietnamese chicken populations, with three main components: conservation of high-priority breeds, within-breed management with animal exchanges between flocks to avoid Wahlund effect and monitoring of inbreeding rate.
    Genetic relationships in an international collection of Puccinia horiana isolates based on newly identified molecular markers and demonstration of recombination
    Backer, M. de; Bonants, P.J.M. ; Pedley, K.F. ; Maes, M. ; Roldan-Ruiz, I. ; Bockstaele, E. van; Heungens, K. ; Lee, T.A.J. van der - \ 2013
    Phytopathology 103 (2013)11. - ISSN 0031-949X - p. 1169 - 1179.
    chrysanthemum white rust - multilocus genotype data - single nucleotide polymorphisms - whole genome amplification - f-sp tritici - parentage analysis - computer-program - x morifolium - resistance - pathogens
    The obligate biotrophic pathogen Puccinia horiana is the causal agent of chrysanthemum white rust. Although P. horiana is a quarantine organism, it has been able to spread to most chrysanthemum-producing regions in the world since the 1960s; however, the transfer routes are largely obscure. An extremely low level of allelic diversity was observed in a geographically diverse set of eight isolates using complexity reduction of polymorphic sequences (CRoPS) technology. Only 184 of the 16,196 contigs (1.1%) showed one or more single-nucleotide polymorphisms (SNPs). Thirty-two SNPs and one simple-sequence repeat were translated into molecular markers and used to genotype 45 isolates originating from North and South America, Asia, and Europe. In most cases, phylogenetic clustering was related to geographic origin, indicating local establishment. The European isolates mostly grouped in two major populations that may relate to the two historic introductions previously reported. However, evidence of recent geographic transfer was also observed, including transfer events between Europe and South America and between Southeast Asia and Europe. In contrast with the presumed clonal propagation of this microcyclic rust, strong indications of marker recombination were observed, presumably as a result of anastomosis, karyogamy, and somatic meiosis. Recombination and transfer also explain the geographic dispersal of specific markers. A near-to-significant correlation between the genotypic data and previously obtained pathotype data was observed and one marker was associated with the most virulent pathotype group. In combination with a fast SNP detection method, the markers presented here will be helpful tools to further elucidate the transfer pathways and local survival of this pathogen
    Climate change and the spread of vector-borne diseases: using approximate Bayesian computation to compare invasion scenarios for the bluetongue virus vector Culicoides imicola in Italy
    Mardulyn, P. ; Goffredo, M. ; Conte, A. ; Hendrickx, G. ; Meiswinkel, R. ; Balenghien, T. ; Sghaier, S. ; Lohr, Y. ; Gilbert, M. - \ 2013
    Molecular Ecology 22 (2013)9. - ISSN 0962-1083 - p. 2456 - 2466.
    multilocus genotype data - chain monte-carlo - population-structure - mediterranean basin - entomological surveillance - statistical evaluation - expanding populations - genetic diversity - range expansion - history
    Bluetongue (BT) is a commonly cited example of a disease with a distribution believed to have recently expanded in response to global warming. The BT virus is transmitted to ruminants by biting midges of the genus Culicoides, and it has been hypothesized that the emergence of BT in Mediterranean Europe during the last two decades is a consequence of the recent colonization of the region by Culicoides imicola and linked to climate change. To better understand the mechanism responsible for the northward spread of BT, we tested the hypothesis of a recent colonization of Italy by C. imicola, by obtaining samples from more than 60 localities across Italy, Corsica, Southern France, and Northern Africa (the hypothesized source point for the recent invasion of C. imicola), and by genotyping them with 10 newly identified microsatellite loci. The patterns of genetic variation within and among the sampled populations were characterized and used in a rigorous approximate Bayesian computation framework to compare three competing historical hypotheses related to the arrival and establishment of C. imicola in Italy. The hypothesis of an ancient presence of the insect vector was strongly favoured by this analysis, with an associated P = 99%, suggesting that causes other than the northward range expansion of C. imicola may have supported the emergence of BT in southern Europe. Overall, this study illustrates the potential of molecular genetic markers for exploring the assumed link between climate change and the spread of diseases.
    Diverse spore rains and limited local mixing shaped fern genetic diversity in a recent habitat colonized by long-distance dispersal
    Groot, G.A. de; During, H.J. ; Ansell, S.W. ; Schneider, H. ; Wubs, E.R.J. ; Maas, J.W. ; Korpelainen, H. ; Erkens, R.H.J. - \ 2012
    Annals of Botany 109 (2012)5. - ISSN 0305-7364 - p. 965 - 978.
    multilocus genotype data - population-structure - postagricultural forests - reproductive-biology - microsatellite data - homosporous ferns - differentiation - pteridophyta - inference - software
    Background and Aims: Populations established by long-distance colonization are expected to show low levels of genetic variation per population, but strong genetic differentiation among populations. Whether isolated populations indeed show this genetic signature of isolation depends on the amount and diversity of diaspores arriving by long-distance dispersal, and time since colonization. For ferns, however, reliable estimates of long-distance dispersal rates remain largely unknown, and previous studies on fern population genetics often sampled older or non-isolated populations. Young populations in recent, disjunct habitats form a useful study system to improve our understanding of the genetic impact of long-distance dispersal. Methods: Microsatellite markers were used to analyse the amount and distribution of genetic diversity in young populations of four widespread calcicole ferns (Asplenium scolopendrium, diploid; Asplenium trichomanes subsp. quadrivalens, tetraploid; Polystichum setiferum, diploid; and Polystichum aculeatum, tetraploid), which are rare in The Netherlands but established multiple populations in a forest (the Kuinderbos) on recently reclaimed Dutch polder land following long-distance dispersal. Reference samples from populations throughout Europe were used to assess how much of the existing variation was already present in the Kuinderbos. Key Results: A large part of the Dutch and European genetic diversity in all four species was already found in the Kuinderbos. This diversity was strongly partitioned among populations. Most populations showed low genetic variation and high inbreeding coefficients, and were assigned to single, unique gene pools in cluster analyses. Evidence for interpopulational gene flow was low, except for the most abundant species. Conclusions: The results show that all four species, diploids as well as polyploids, were capable of frequent long-distance colonization via single-spore establishment. This indicates that even isolated habitats receive dense and diverse spore rains, including genotypes capable of self-fertilization. Limited gene flow may conserve the genetic signature of multiple long-distance colonization events for several decades
    Population Analysis of the Fusarium graminearum Species Complex from Wheat in China Show a Shift to More Aggressive Isolates
    Zhang, H. ; Lee, T.A.J. van der; Waalwijk, C. ; Chen, W. ; Xu, Jin ; Xu, Jingsheng ; Zhang, Y. ; Feng, J. - \ 2012
    PLoS ONE 7 (2012)2. - ISSN 1932-6203 - 13 p.
    head blight pathogen - multilocus genotype data - genealogical concordance - mycotoxin chemotypes - genetic diversity - gibberella-zeae - eastern china - f-asiaticum - clade - scab
    A large number of Fusarium isolates was collected from blighted wheat spikes originating from 175 sampling sites, covering 15 provinces in China. Species and trichothecene chemotype determination by multilocus genotyping (MLGT) indicated that F. graminearum s. str. with the 15-acetyl deoxynivalenol (15ADON) chemotype and F. asiaticum with either the nivalenol (NIV) or the 3-acetyl deoxynivalenol (3ADON) chemotype were the dominant causal agents. Bayesian model-based clustering with allele data obtained with 12 variable number of tandem repeats (VNTR) markers, detected three genetic clusters that also show distinct chemotypes. High levels of population genetic differentiation and low levels of effective number of migrants were observed between these three clusters. Additional genotypic analyses revealed that F. graminearum s. str. and F. asiaticum are sympatric. In addition, composition analysis of these clusters indicated a biased gene flow from 3ADON to NIV producers in F. asiaticum. In phenotypic analyses, F. asiaticum that produce 3ADON revealed significant advantages over F. asiaticum that produce NIV in pathogenicity, growth rate, fecundity, conidial length, trichothecene accumulation and resistance to benzimidazole. These results suggest that natural selection drives the spread of a more vigorous, more toxigenic pathogen population which also shows higher levels of fungicide resistance
    Genome-wide association studies for Agronomical Traits in a world wide Spring Barley Collection
    Pasam, R.K. ; Sharma, R. ; Malosetti, M. ; Eeuwijk, F.A. van; Haseneyer, G. ; Kilian, B. ; Graner, A. - \ 2012
    BMC Plant Biology 12 (2012). - ISSN 1471-2229
    multilocus genotype data - hordeum-vulgare l. - linkage disequilibrium - population-structure - complex traits - flowering time - qtl analysis - missing heritability - haplotype structure - genetic diversity
    Background Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for the detection and fine mapping of quantitative trait loci (QTL) underlying complex agronomic traits. In this study we explored the genetic basis of variation for the traits heading date, plant height, thousand grain weight, starch content and crude protein content in a diverse collection of 224 spring barleys of worldwide origin. The whole panel was genotyped with a customized oligonucleotide pool assay containing 1536 SNPs using Illumina's GoldenGate technology resulting in 957 successful SNPs covering all chromosomes. The morphological trait "row type" (two-rowed spike vs. six-rowed spike) was used to confirm the high level of selectivity and sensitivity of the approach. This study describes the detection of QTL for the above mentioned agronomic traits by GWAS. Results Population structure in the panel was investigated by various methods and six subgroups that are mainly based on their spike morphology and region of origin. We explored the patterns of linkage disequilibrium (LD) among the whole panel for all seven barley chromosomes. Average LD was observed to decay below a critical level (r2-value 0.2) within a map distance of 5-10 cM. Phenotypic variation within the panel was reasonably large for all the traits. The heritabilities calculated for each trait over multi-environment experiments ranged between 0.90-0.95. Different statistical models were tested to control spurious LD caused by population structure and to calculate the P-value of marker-trait associations. Using a mixed linear model with kinship for controlling spurious LD effects, we found a total of 171 significant marker trait associations, which delineate into 107 QTL regions. Across all traits these can be grouped into 57 novel QTL and 50 QTL that are congruent with previously mapped QTL positions. Conclusions Our results demonstrate that the described diverse barley panel can be efficiently used for GWAS of various quantitative traits, provided that population structure is appropriately taken into account. The observed significant marker trait associations provide a refined insight into the genetic architecture of important agronomic traits in barley. However, individual QTL account only for a small portion of phenotypic variation, which may be due to insufficient marker coverage and/or the elimination of rare alleles prior to analysis. The fact that the combined SNP effects fall short of explaining the complete phenotypic variance may support the hypothesis that the expression of a quantitative trait is caused by a large number of very small effects that escape detection. Notwithstanding these limitations, the integration of GWAS with biparental linkage mapping and an ever increasing body of genomic sequence information will facilitate the systematic isolation of agronomically important genes and subsequent analysis of their allelic diversity
    New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties
    Cornille, A. ; Gladieux, P. ; Smulders, M.J.M. ; Roldán-Ruiz, I. ; Laurens, F. ; Cam, B. le; Nersesyan, A. ; Clavel, J. ; Olonova, M. ; Feugey, L. ; Gabrielyan, I. ; Zhang, Xiu-Guo ; Tenaillon, M.I. ; Giraud, T. - \ 2012
    Plos Genetics 8 (2012)5. - ISSN 1553-7404
    appels - malus domestica - domesticatie - voorouders - wilde verwanten - genetische bronnen van plantensoorten - genetische diversiteit - apples - malus domestica - domestication - ancestors - wild relatives - plant genetic resources - genetic diversity - approximate bayesian computation - multilocus genotype data - allele frequency data - sylvestris l. mill. - population-structure - microsatellite markers - molecular-genetics - spondias-purpurea - genus malus - fruit tree
    The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species.
    Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks
    Kraus, R.H.S. ; Kerstens, H.H.D. ; Hooft, W.F. van; Megens, H.J.W.C. ; Elmberg, J. ; Tsvey, A. ; Sartakov, D. ; Soloviev, S.A. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. ; Ydenberg, R.C. ; Prins, H.H.T. - \ 2012
    BMC Evolutionary Biology 12 (2012). - ISSN 1471-2148 - 10 p.
    mallards anas-platyrhynchos - multilocus genotype data - linkage disequilibrium - population-structure - phylogenetic-relationships - hybridization patterns - finite population - miocene climate - waterfowl aves - average number
    The study of speciation and maintenance of species barriers is at the core of evolutionary biology. During speciation the genome of one population becomes separated from other populations of the same species, which may lead to genomic incompatibility with time. This separation is complete when no fertile offspring is produced from inter-population matings, which is the basis of the biological species concept. Birds, in particular ducks, are recognised as a challenging and illustrative group of higher vertebrates for speciation studies. There are many sympatric and ecologically similar duck species, among which fertile hybrids occur relatively frequently in nature, yet these species remain distinct
    A Bayesian analysis of gene flow from crops to their wild relatives: cultivated (Lactuca sativa L.) and prickly lettuce (L. serriola L.) and the recent expansion of L. serriola in Europe
    Uwimana, B. ; Andrea, L. D'; Felber, F. ; Hooftman, D.A.P. ; Nijs, H.C.M. den; Smulders, M.J.M. ; Visser, R.G.F. ; Wiel, C.C.M. van de - \ 2012
    Molecular Ecology 21 (2012)11. - ISSN 0962-1083 - p. 2640 - 2654.
    genetically-modified crops - multilocus genotype data - populus-nigra l. - population-structure - sect lactuca - situ conservation - hybridization - asteraceae - hybrids - spp.
    Interspecific gene flow can lead to the formation of hybrid populations that have a competitive advantage over the parental populations, even for hybrids from a cross between crops and wild relatives. Wild prickly lettuce (Lactuca serriola) has recently expanded in Europe and hybridization with the related crop species (cultivated lettuce, L. sativa) has been hypothesized as one of the mechanisms behind this expansion. In a basically selfing species, such as lettuce, assessing hybridization in natural populations may not be straightforward. Therefore, we analysed a uniquely large data set of plants genotyped with SSR (simple sequence repeat) markers with two programs for Bayesian population genetic analysis, STRUCTURE and NewHybrids. The data set comprised 7738 plants, including a complete genebank collection, which provided a wide coverage of cultivated germplasm and a fair coverage of wild accessions, and a set of wild populations recently sampled across Europe. STRUCTURE analysis inferred the occurrence of hybrids at a level of 7% across Europe. NewHybrids indicated these hybrids to be advanced selfed generations of a hybridization event or of one backcross after such an event, which is according to expectations for a basically selfing species. These advanced selfed generations could not be detected effectively with crop-specific alleles. In the northern part of Europe, where the expansion of L. serriola took place, the fewest putative hybrids were found. Therefore, we conclude that other mechanisms than crop/wild gene flow, such as an increase in disturbed habitats and/or climate warming, are more likely explanations for this expansion.
    Population structure revealed by different marker types (SSR or DArT) has an impact on the results of genome-wide association mapping in European barley cultivars
    Matthies, I.E. ; Hintum, T.J.L. van; Weise, S. ; Röder, M.S. - \ 2012
    Molecular Breeding 30 (2012)2. - ISSN 1380-3743 - p. 951 - 966.
    different germplasm groups - multilocus genotype data - doubled-haploid progeny - simple sequence repeats - malting-quality - linkage disequilibrium - genetic diversity - qtl analysis - yield components - spring barley
    Diversity arrays technology (DArT) and simple sequence repeat (SSR) markers were applied to investigate population structure, extent of linkage disequilibrium and genetic diversity (kinship) on a genome-wide level in European barley (Hordeum vulgare L.) cultivars. A set of 183 varieties could be clearly distinguished into spring and winter types and was classified into five subgroups based on 253 DArT or 22 SSR markers. Despite the fact, that the same number of groups was revealed by both marker types, it could be shown that this grouping was more distinct for the SSRs than the DArTs, when assigned to a Q-matrix by STRUCTURE. This was supported by the findings from principal coordinate analysis, where the SSRs showed a better resolution according to seasonal habit and row number than the DArTs. A considerable influence on the rate of significant associations with malting and kernel quality parameters was revealed by different marker types in this genome-wide association study using general and mixed linear models considering population structure. Fewer spurious associations were observed when population structure was based on SSR rather than on DArT markers. We therefore conclude that it is advisable to use independent marker datasets for calculating population structure and for performing the association analysis.
    Anchovy population expansion in the North Sea
    Petitgas, P. ; Alheit, J. ; Peck, A. ; Raab, K.E. ; Irigoien, X. ; Huret, M. ; Kooij, J. van; Pohlmann, T. ; Wagner, C. ; Zarraonaindia, I. ; Dickey-Collas, M. - \ 2012
    Marine Ecology Progress Series 444 (2012). - ISSN 0171-8630 - p. 1 - 13.
    engraulis-encrasicolus l. - multilocus genotype data - european anchovy - climate-change - fish populations - regime shifts - pelagic fish - wadden sea - atlantic - biscay
    The abundance and spatial occupation of European anchovy Engraulis encrasicolus have increased in the North Sea since the mid-1990s. We use a cross-disciplinary approach combining genetics, transport modelling, survey time series analyses and physical oceanographic modelling to investigate 3 ­hypotheses on the reasons for this change. Evidence from connectivity studies suggests that the population of North Sea anchovy is separate from that in the Bay of Biscay. The recruitment pulses observed in survey data fit a life cycle which includes spawning in early summer and larval development in late summer. This also supports the concept of population expansion originating from local remnant population(s). In terms of growth physiology, suitable thermal windows have expanded, making conditions more favourable for life cycle closure and population persistence/productivity. In addition to the increased frequency of warm summers, which favour larvae and juvenile growth, the decrease in the number of severe winters is also likely to improve overwinter survival. Overall, the evidence supports the hypothesis that the increase in anchovy abundance originated from the improved productivity of existing populations. This increase was associated with an expansion in thermal habitats and is probably not due to a northward shift in the distribution of southern conspecifics.
    Genome wide association analyses for drought tolerance related traits in barley (Hordeum vulgare L.)
    Varshney, R.K. ; Paulo, M.J. ; Grando, S. ; Eeuwijk, F.A. van; Keizer, L.C.P. ; Guo, P. ; Ceccarelli, S. ; Kilian, A. ; Baum, M. ; Graner, A. - \ 2012
    Field Crops Research 126 (2012). - ISSN 0378-4290 - p. 171 - 180.
    multilocus genotype data - triticum-aestivum l. - ab-qtl analysis - linkage disequilibrium - population-structure - agronomic traits - spring barley - mapping population - allele frequencies - yield components
    Genome wide association (GWA) analysis of yield, yield components, developmental, physiological and anatomical traits was conducted for a barley germplasm collection consisting of 185 cultivated (Hordeum vulgare L.) and 38 wild (Hordeum spontaneum L.) genotypes, originating from 30 countries of four continents. Phenotypic evaluations were performed at a dry (Breda) and wet (Tel Hadya) location in Syria. Genome wide association study was done with 816 markers comprised of 710 diversity array technology (DArT), 61 single nucleotide polymorphism (SNP) and 45 microsatellite or simple sequence repeat (SSR) markers. Diversity analysis revealed 5 groups of germplasm, related to origin (Middle East, North Africa), structural information (two-rows), and domestication (wild versus domesticated). Linkage disequilibrium (LD) decayed after 3 cM with a few exceptions at 10 and 15 cM. Although a few QTLs were identified that differed between the dry and wet site, these QTLs explained low phenotypic variation and could not unequivocally be related to drought tolerance when compared to earlier linkage mapping based QTL analysis studies. Therefore, GWA analysis seems to be not very effective for identification of major QTLs for complex traits like drought tolerance in highly structured germplasm collections
    Identification of high utility SNPs for population assignment and traceability purposes in the pig using high-throughput sequencing
    Ramos, A.M. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Schook, L.B. ; Groenen, M.A.M. - \ 2011
    Animal Genetics 42 (2011)6. - ISSN 0268-9146 - p. 613 - 620.
    nucleotide polymorphism discovery - multilocus genotype data - reduced representation - breed assignment - markers - genome - cattle - technology - inference - assay
    The objectives of this study were to develop breed-specific single nucleotide polymorphisms (SNPs) in five pig breeds sequenced with Illumina's Genome Analyzer and to investigate their usefulness for breed assignment purposes. DNA pools were prepared for Duroc, Landrace, Large White, Pietrain and Wild Boar. The total number of animals used for sequencing was 153. SNP discovery was performed by aligning the filtered reads against Build 7 of the pig genome. A total of 313,964 high confidence SNPs were identified and analysed for the presence of breed-specific SNPs (defined in this context as SNPs for which one of the alleles was detected in only one breed). There were 29,146 putative breed-specific SNPs identified, of which 4441 were included in the PorcineSNP60 beadchip. Upon re-examining the genotypes obtained using the beadchip, 193 SNPs were confirmed as being breed specific. These 193 SNPs were subsequently used to assign an additional 490 individuals from the same breeds, using the sequenced individuals as reference populations. In total, four breed assignment tests were performed. Results showed that for all methods tested 99% of the animals were correctly assigned, with an average probability of assignment of at least 99.2%, indicating the high utility of breed-specific markers for breed assignment and traceability. This study provides a blueprint for the way next-generation sequencing technologies can be used for the identification of breed-specific SNPs, as well as evidence that these SNPs may be a powerful tool for breed assignment and traceability of animal products to their breeds of origin.
    Substantial molecular variation and low genetic structure in Kenya’s black rhinoceros: implications for conservation
    Muya, S.M. ; Bruford, M.W. ; Muigai, A.W.T. ; Osiemo, Z.B. ; Mwachiro, E. ; Ouma, B.O. ; Goossens, B. - \ 2011
    Conservation Genetics 12 (2011)6. - ISSN 1566-0621 - p. 1575 - 1588.
    mitochondrial control region - multilocus genotype data - diceros-bicornis - population-structure - microsatellite loci - dna variation - f-statistics - diversity - software - cheetah
    Kenya’s black rhinoceros population declined by more than 98% from 20,000 individuals in the 1970s to around 400 individuals in 1990 due to the effects of poaching, at which time the surviving individuals were isolated in a series of demographically inviable subpopulations. An initial management exercise translocated the survivors into four high security sanctuaries to control poaching and enhance breeding, and this measure successfully arrested the decline. Subsequently, new sanctuaries were established and the metapopulation size reached 650 animals by 2008. However, translocations and the current management strategy that partitions the metapopulation into ‘montane’ and ‘lowland’ rhinoceros may have substantial consequences at the population level and their impact on population genetic diversity has not been investigated. In this study, 12 of the 16 extant subpopulations were analysed using 408 bp of mitochondrial control region sequence (n = 170) and nine microsatellite loci (n = 145). Both markers detected moderate to high genetic diversity (h = 0.78 ± 0.027, n = 170; HO = 0.70 ± 0.087, n = 145) consistent with previous studies on Diceros bicornis michaeli. However, mtDNA and nDNA diversity varied substantially between subpopulations. The results suggest that the Masai Mara is more differentiated, inbred and isolated than other subpopulations. It also suggests that there are neither distinct montane and lowland groups nor other detectable historical barriers to gene flow. Instead the large majority of genetic diversity was partitioned at the level of individuals; highlighting the need to conserve as many individuals as possible. Future translocations should consider the genetic profile of individuals and the demographic history of both the donor and recipient subpopulations.
    Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?
    Odong, T.L. ; Heerwaarden, J. van; Jansen, J. ; Hintum, T.J.L. van; Eeuwijk, F.A. van - \ 2011
    Theoretical and Applied Genetics 123 (2011)2. - ISSN 0040-5752 - p. 195 - 205.
    multilocus genotype data - genome-wide association - forming core subsets - population-structure - data set - linkage disequilibrium - f-statistics - number - inference - diversity
    Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies.
    What's in a name; Genetic structure in Solanum section Petota studied using population-genetic tools
    Jacobs, M.M.J. ; Smulders, M.J.M. ; Berg, R.G. van den; Vosman, B. - \ 2011
    BMC Evolutionary Biology 11 (2011). - ISSN 1471-2148 - 20 p.
    fragment length polymorphism - multilocus genotype data - brevicaule complex solanaceae - wild potato - species boundaries - aflp markers - phylogenetic-relationships - series megistacroloba - berthaultii hawkes - morphological data
    Background - The taxonomy and systematic relationships among species of Solanum section Petota are complicated and the section seems overclassified. Many of the presumed (sub)species from South America are very similar and they are able to exchange genetic material. We applied a population genetic approach to evaluate support for subgroups within this material, using AFLP data. Our approach is based on the following assumptions: (i) accessions that may exchange genetic material can be analyzed as if they are part of one gene pool, and (ii) genetic differentiation among species is expected to be higher than within species. Results - A dataset of 566 South-American accessions (encompassing 89 species and subspecies) was analyzed in two steps. First, with the program STRUCTURE 2.2 in an 'unsupervised' procedure, individual accessions were assigned to inferred clusters based on genetic similarity. The results showed that the South American members of section Petota could be arranged in 16 clusters of various size and composition. Next, the accessions within the clusters were grouped by maximizing the partitioning of genetic diversity among subgroups (i.e., maximizing Fst values) for all available individuals of the accessions (2767 genotypes). This two-step approach produced an optimal partitioning into 44 groups. Some of the species clustered as genetically distinct groups, either on their own, or combined with one or more other species. However, accessions of other species were distributed over more than one cluster, and did not form genetically distinct units. Conclusions - We could not find any support for 43 species (almost half of our dataset). For 28 species some level of support could be found varying from good to weak. For 18 species no conclusions could be drawn as the number of accessions included in our dataset was too low. These molecular data should be combined with data from morphological surveys, with geographical distribution data, and with information from crossing experiments to identify natural units at the species level. However, the data do indicate which taxa or combinations of taxa are clearly supported by a distinct set of molecular marker data, leaving other taxa unsupported. Therefore, the approach taken provides a general method to evaluate the taxonomic system in any species complex for which molecular data are available.
    Comparative methods for association studies: a case study on metabolite variation in a Brassica rapa core collection
    Pino del Carpio, D. ; Basnet, R.K. ; Vos, C.H. de; Maliepaard, C.A. ; Paulo, M.J. ; Bonnema, A.B. - \ 2011
    PLoS ONE 6 (2011)5. - ISSN 1932-6203
    multilocus genotype data - genome-wide association - population-structure - random forests - linkage disequilibrium - flowering time - inference - classification - resistance - traits
    Background Association mapping is a statistical approach combining phenotypic traits and genetic diversity in natural populations with the goal of correlating the variation present at phenotypic and allelic levels. It is essential to separate the true effect of genetic variation from other confounding factors, such as adaptation to different uses and geographical locations. The rapid availability of large datasets makes it necessary to explore statistical methods that can be computationally less intensive and more flexible for data exploration. Methodology/Principal Findings A core collection of 168 Brassica rapa accessions of different morphotypes and origins was explored to find genetic association between markers and metabolites: tocopherols, carotenoids, chlorophylls and folate. A widely used linear model with modifications to account for population structure and kinship was followed for association mapping. In addition, a machine learning algorithm called Random Forest (RF) was used as a comparison. Comparison of results across methods resulted in the selection of a set of significant markers as promising candidates for further work. This set of markers associated to the metabolites can potentially be applied for the selection of genotypes with elevated levels of these metabolites. Conclusions/Significance The incorporation of the kinship correction into the association model did not reduce the number of significantly associated markers. However incorporation of the STRUCTURE correction (Q matrix) in the linear regression model greatly reduced the number of significantly associated markers. Additionally, our results demonstrate that RF is an interesting complementary method with added value in association studies in plants, which is illustrated by the overlap in markers identified using RF and a linear mixed model with correction for kinship and population structure. Several markers that were selected in RF and in the models with correction for kinship, but not for population structure, were also identified as QTLs in two bi-parental DH populations.
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