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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.

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Measuring stress-induced DNA methylation in apomictic Dandelions
Gurp, Thomas P. van - \ 2017
Wageningen University. Promotor(en): W.H. van der Putten, co-promotor(en): K.J.F. Verhoeven; A. Biere. - Wageningen : Wageningen University - ISBN 9789463436045 - 176
taraxacum officinale - epigenetics - dna methylation - inheritance - apomixis - environmental factors - taraxacum officinale - epigenetica - dna-methylering - overerving - apomixis - milieufactoren

The success or continuous existence of species requires continuous adaptation to changes in the environment to survive and contribute offspring to the next generation. Selection acts on the phenotype, which is in turn determined by the complex interplay of genetic, epigenetic and environmental variation. (Natural) selection leads to ‘survival of the fittest’ or best-adapted individuals to their local environment, ultimately determining which individuals contribute offspring to the next generation. Understanding the mechanisms by which epigenetic and genetic variation can arise and get passed on through generations determines our understanding of inheritance and evolution. Hitherto, the mechanistic understanding of genetics has shaped the scientific view of inheritance and evolution, leading to the gene-centered paradigm of Neo-Darwinism. However, recent studies indicate that besides genetic (DNA sequence) variation, epigenetic variation can also be transmitted between generations. Further studies on the properties and transgenerational dynamics of epigenetic variation are needed to enhance our understanding of heritability and evolution.

Epigenetic variation has distinct properties and different transgenerational dynamics compared to genetic variation. Epigenetic variation helps to regulate gene expression and determines the different cell types and function in eukaryotes. The main function of DNA methylation, an important part of the epigenetic code, is to prevent the spread of selfish genetic elements in the genome and to establish the different cellular profiles observed in multicellular organisms. One differentiating feature of epigenetic variation compared to genetic variation is that (specific) epigenetic variation can arise under the influence of stress. This can enable a trans-generational stress-response of organisms which can have a positive influence on the phenotype and (natural) selection on either the (enhanced level of) transgenerational phenotypic plasticity or the epigenetic variation itself, potentially influencing natural selection and ultimately evolution. Where genetic variation can be characterized as hard-inheritance, the inheritance of epigenetic variation is often referred to as ‘soft-inheritance’ due to the lower transgenerational stability and resetting that occurs in the intergenerational transfer of epigenetic variation. Epigenetic variation is also often dependent on, or a downstream consequence, of genetic variation, suggesting that it is (in part) determined by genetic variation.

Mechanistic studies in model species have contributed greatly to the understanding of the molecular mechanisms that control the dynamics of different epigenetic marks present in multicellular organisms. In plants, studies in the model plant Arabidopsis thaliana have resulted in deciphering the most important molecular mechanisms and actors, giving an ever-increasing insight into the dynamics of epigenetic regulation of cells and organisms. A key feature of model systems is the ability to ‘switch’ off certain genes or molecular pathways, for instance via the experimental use of mutants, enabling the study of their role in the heritability of epigenetic marks. DNA methylation is a well-studied epigenetic mark, which has shown high stability even in transgenerational experiments.

From the perspective of studying epigenetic variation, plants are particularly interesting for several reasons, most importantly: 1) The separation between soma and germline, the Weismann barrier, is less strict in plants compared to other eukaryotes, as in higher plants

germline cells are formed during floral development from somatic cells (which can occur throughout the life of the plant), whereas in most eukaryotes germline cell development is restricted to a defined point (early) in the organismal development. 2) The sessile nature of plants makes an adaptive plastic response to changing environments an important feature, a plant cannot just walk away when the going gets tough. 3) The transgenerational stability of DNA methylation is higher in plants compared to other eukaryotes such as mammals, in which epigenetic information is erased during germline reprogramming. These factors combined suggest that the potential importance of epigenetic variation in plants might be high.

In this thesis, I focus on studying DNA methylation in apomictic Dandelions, applying Next Generation Sequencing (NGS) approaches to the study of this non-model plant species. Apomictic dandelions produce seeds that are genetically identical to the ‘mother’ plant, which makes it easier to study the influence of epigenetic variation without confounding effects of genetic variation. Working with Next Generation Sequencing data is still relatively new and therefore not always optimized for specific types of analysis. I discovered a distinct error pattern in RNAseq data that indicated an artificial source of variation that could be traced back to the way the RNAseq libraries were constructed. The first publication of this thesis contains a technical analysis of such artefacts present in RNAseq data, suggesting that these errors are related to random hexamer mispriming during library construction (Chapter 2).

The main goal of my work is to better understand the role of epigenetic variation in adaptation and plasticity of plants. This role remains poorly understood. This is in part due to the lack of high-resolution techniques that allow for the detailed study of epigenetic marks such as DNA methylation in non-model organisms. Existing techniques for measuring DNA methylation such as methylation sensitive AFLPs offer only information on DNA methylation variation in an anonymous and limited fashion. The plummeting costs of sequencing techniques have enabled large-scale genotyping efforts (focusing on genetic variation only) for a wide variety of non-model organisms. Here, I extended this popular genotyping by sequencing technique, to allow for sequencing-based epigenotyping or epiGBS (chapter 3), which allows for measuring DNA methylation and genetic variation in hundreds of samples simultaneously. I have extensively validated the approach, providing evidence that with the right design, the accuracy of the DNA methylation measurements with epiGBS are as high as those with the gold standard Whole Genome Bisulfite Sequencing.

An important aim of my PhD research was to investigate the stability of (stress induced) DNA methylation variation in apomictic dandelions and the potential of phenotypic variation underpinned by DNA methylation variation to be subjected to selection. I therefore studied the transgenerational stability of both stress induced and natural DNA methylation variation in different genotypes of apomictic dandelions in a six-generation experiment, comparing DNA methylation patterns between generations and tracking changes in them (chapter 4) using epiGBS. I found clear but limited evidence for environmental induction of heritable DNA methylation changes after application of Jasmonic Acid. Furthermore, I found a significant negative relation between the similarity of DNA methylation patterns and intergenerational distance, indicating epigenetic divergence over generations. I conclude that DNA methylation in both CG and CHG (where H can be any nucleotide except for G) sequence context are heritable and that environmental perturbation can result in heritable DNA methylation changes which are however not widespread.

A prerequisite for epigenetic variation to contribute to adaptation is that epigenetic variants that affect the phenotype are heritable. To test whether an epigenetics-based selection response is possible, at least over the time course of a few generations, I selected early flowering for two subsequent generations in three genotypes of apomictic dandelions. This selection effort included lines that received a stress pre-treatment with either Jasmonic Acid or 5-azacytidine, to determine if stress-induced DNA methylation variation would increase the capacity to respond to selection. The selection experiment on flowering time (chapter 5) resulted in a shift in flowering time for all treatments in a young apomict, suggesting that natural and heritable epigenetic variation can underpin quantitative traits such as flowering time. I also found evidence for treatment induced (epi)genetic variation leading to a stronger selection response in one out of 3 genotypes. This suggests that stress- induced heritable epigenetic variation can lead to a selection response. Further study is however required to rule out genetic variants and to study the long-term stability of the variation selected upon.

Finally, in the General Discussion I summarize the findings, putting them in context with recently published studies. I reflect on the state of the field of ecological epigenetics and in what sense the epiGBS technique that I developed and other emerging techniques can contribute to a better understanding of the role of epigenetic variation in ecology and evolution. I reflect on the place of epiGBS compared to other techniques. I point out that with the growing evidence of the inadequacy and misinterpretation of MS-AFLP results a systematic review of such results by replicating the studies employing sequencing based techniques such as epiGBS instead of MS-AFLP is in order.

Building towards a multi-dimensional genetic architecture in Caenorhabditis elegans
Sterken, Mark G. - \ 2016
Wageningen University. Promotor(en): Jan Kammenga, co-promotor(en): Jaap Bakker; Gorben Pijlman. - Wageningen : Wageningen University - ISBN 9789462578692 - 167
caenorhabditis elegans - genetic models - introgression - genetic variation - quantitative trait loci - animal viruses - inheritance - rna interference - viral replication - gene expression - caenorhabditis elegans - genetische modellen - introgressie - genetische variatie - loci voor kwantitatief kenmerk - dierenvirussen - overerving - rna-interferentie - virusreplicatie - genexpressie

Trait variation within species is shaped by the genotype and the environment an individual is exposed to. Genomic information is inherited from the parents and forms the basis of the phenotype of an organism. The genetic variation between parents becomes differently distributed between their offspring, leading to trait variation in the offspring. Each trait can be affected by many genes, therefore the genetic architecture can be complex. In complex traits, multiple loci contribute to the ultimate trait value. However, complex traits are shaped not only by genetic variation but also by the environment and the interaction between genotype and environment. The interplay between genetic and environmental variation can affect the fitness of an organism.

Chapter 2 discusses how genotype and environment have shaped the phenotype of the nematode Caenorhabditis elegans, the model species used in this thesis, resulting in a laboratory adapted domesticized strain known as Bristol N2. Bristol N2 has been cultivated in the laboratory for over a decade, leading to the fixation of novel mutations in several genes that strongly affect its phenotype. Genotypic variation arisen by novel mutations in the genes npr-1, glb-5, and nath-10 was fixed in N2 due to the laboratory environment. The allelic variation in npr-1 affects the behaviour of this animal in an environment dependent manner, showcasing the interplay between genotype and environment. However, the altered behaviour warrants caution for interpretation of results obtained in the N2 strain.

The genotypic effects on trait variation can be large, and one of the more powerful population designs to study these effects are introgression lines. In chapter 3 the construction of a genome-wide introgression line (IL) panel between the N2 and the CB4856 strain is described. This panel contains loci of N2 introgressed in a homogeneous CB4856 background. It is demonstrated that together with CB4856-in-N2 ILs this new genome-wide introgression line library strongly facilitates the dissection of genetic interactions.

Chapter 4 and 5 investigate natural variation in infection with Orsay virus, a natural pathogen of the nematode C. elegans. In chapter 4 an assay is developed and tested on two wild-type strains (N2 and JU1580) and two mutant strains with mutations in the RNAi pathway. The development of the virus infection in the separate strains can be traced and the influence of genotype and age on the progression of the infection can be quantified. Furthermore, it is demonstrated that heritable RNAi plays a role in the viral load upon Orsay virus infection, an example of an epigenetically inherited environmental influence. In chapter 5 the assay is applied on an N2xCB4856 recombinant inbred line (RIL) population, after observing a lower viral load in CB4856 compared to N2. The RIL analysis resulted in the identification of two QTL on chromosome IV. These quantitative trait loci (QTL) were verified by CB4856-in-N2 ILs, but the IL analysis also indicated that there could be genetic interactions affecting the QTL. By a transcriptome analysis and a candidate gene search, the gene cul-6 was identified as a candidate underlying the allelic variation between the N2 and CB4856 strain.

Chapters 6 and 7 investigate the influence of genetic interactions and the environment on the genetic architecture of gene expression. In chapter 6 a N2xCB4856 RIL population was exposed to heat stress, leading to the identification of a trans-band on the top of chromosome IV. By analysis of candidate genes, cmk-1, egl-4, and eor-1 were implicated as contributing to the heat-stress induced transcriptional response affected by natural variation between N2 and CB4856. Furthermore, the genes with an expression-QTL on the trans-band were indicative of a stress response phenotype. By analysis of CB4856-in-N2 ILs, it was found that this locus leads to increased recovery from stress. In chapter 7 two-loci genetic interactions were mapped for gene expression in a N2xCB4856 RIL panel. These epistatic interactions were confirmed by measuring gene expression in a novel population of inbred line containing the full set of loci combinations. It was found that genetic interactions in gene expression can be identified by clustering and are pervasive. These genetically interacting loci affect evolutionary conserved genes.

In conclusion, this thesis unveils the mechanisms underlying the genetic architecture of complex traits in C. elegans resulting from genotype and interactions between genotype and environment. It provides tools to unravel these interactions in C. elegans, by providing the community with new resources such as the N2-in-CB4856 introgression lines. Although C. elegans has been a very powerful platform for quantitative trait dissection, we need to expand our mechanistic understanding of polygenic traits.

Epigenetic inheritance in apomictic dandelions : stress-induced and heritable modifications in DNA methylation and small RNA
Preite, V. - \ 2016
Wageningen University. Promotor(en): Wim van der Putten, co-promotor(en): K.J.F. Verhoeven. - Wageningen : Wageningen University - ISBN 9789462578715 - 152
taraxacum officinale - epigenetics - inheritance - apomixis - dna methylation - rna - heritability - stress - taraxacum officinale - epigenetica - overerving - apomixis - dna-methylering - rna - heritability - stress

Epigenetic variation, such as changes in DNA methylations, regulatory small RNAs (sRNAs) and chromatin modifications can be induced by environmental stress. There is increasing information that such induced epigenetic modifications can be transmitted to offspring, potentially mediating adaptive transgenerational responses to environmental changes. However, it is unclear if this phenomenon is common and relevant for adaptation under natural conditions. My thesis study aimed to examine epigenetic inheritance in common and widespread apomictic dandelions (Taraxacum officinale Wig.). Due to their asexual reproduction mode by producing clonal seeds offspring from seeds are genetically uniform and thus suitable to investigate epigenetic effects that are not confounded with genetic variation.

I exposed apomictic dandelion lineages to drought and salicylic acid (SA) stress, which induces plant defense responses following pathogen attack, and found effects on patterns of DNA methylation up to two stress-free offspring generations after exposure. However, a heritable stress signal was not present in all tests and was stress- and lineage-dependent. Drought stress triggered a weak and lineage-dependent signal that was lost again in the second offspring generation. SA treatment revealed a stress-related increased rate of DNA methylation changes in the two offspring generations, but no stress signal was found in the stressed generation itself. I also observed changes in small RNA production due the drought and SA stress experienced two generations ago. These transgenerational sRNA effects showed association with gene functions related to grandparental drought and SA stress, which suggests functional relevance of the transgenerational effects.

I used a reciprocal transplantation field experiment to investigate whether exposing dandelions to natural field stresses also triggers DNA methylation changes. The experiment revealed evidence of adaptive divergence between the populations, suggesting that non-native habitats are experienced as more stressful. However, under these field conditions no induction-based DNA methylation changes were found that persisted into offspring.

By using AFLP and MS-AFLP screening of natural apomictic dandelion populations across a north-south transect in Europe I examined if natural, heritable DNA methylation variation reflects underlying genetic variation, or if it shows patterns that are not predictable from underlying genetics. I found that a large part of heritable DNA methylation differentiation along the north-south transect was correlated with genetic differentiation. However, a fraction of differentiation in heritable DNA methylation was independent from genetic variation. This suggests a potential of epigenetics to play an evolutionary role independently, at least to some extent, from underlying genetics. Overall, I found indications of epigenetic inheritance in apomictic dandelions. Whether epigenetic variation would result in adaptive phenotypic variation in nature and whether it would persist long enough to play a relevant role in adaptation remains unclear and requires further study.

Epigenetic Basis of Morphological Variation and Phenotypic Plasticity in Arabidopsis thaliana
Kooke, R. ; Johannes, F. ; Wardenaar, R. ; Becker, F.F.M. ; Etcheverry, M. ; Colot, V. ; Vreugdenhil, D. ; Keurentjes, J.J.B. - \ 2015
The Plant Cell 27 (2015)2. - ISSN 1040-4651 - p. 337 - 348.
quantitative trait loci - dna methylation - transcription factor - qtl analysis - population - plant - inheritance - stability - evolution - performance
Epigenetics is receiving growing attention in the plant science community. Epigenetic modifications are thought to play a particularly important role in fluctuating environments. It is hypothesized that epigenetics contributes to plant phenotypic plasticity because epigenetic modifications, in contrast to DNA sequence variation, are more likely to be reversible. The population of decrease in DNA methylation 1-2 (ddm1-2)-derived epigenetic recombinant inbred lines (epiRILs) in Arabidopsis thaliana is well suited for studying this hypothesis, as DNA methylation differences are maximized and DNA sequence variation is minimized. Here, we report on the extensive heritable epigenetic variation in plant growth and morphology in neutral and saline conditions detected among the epiRILs. Plant performance, in terms of branching and leaf area, was both reduced and enhanced by different quantitative trait loci (QTLs) in the ddm1-2 inherited epigenotypes. The variation in plasticity associated significantly with certain genomic regions in which the ddm1-2 inherited epigenotypes caused an increased sensitivity to environmental changes, probably due to impaired genetic regulation in the epiRILs. Many of the QTLs for morphology and plasticity overlapped, suggesting major pleiotropic effects. These findings indicate that epigenetics contributes substantially to variation in plant growth, morphology, and plasticity, especially under stress conditions
Production of interspecific Campanula hybrids by ovule culture: exploring the effecto of ovule isolation time
Röper, A.C. ; Lütken, H. ; Christensen, B. ; Boutilier, K.A. ; Petersen, K.K. ; Müller, R. - \ 2015
Euphytica 203 (2015). - ISSN 0014-2336 - p. 643 - 657.
embryo rescue - inbreeding depression - breeding system - hybridization - incompatibility - trifolium - inheritance - phylogeny - endosperm - crosses
The Campanula genus comprises several economically important ornamental plants species.Wide hybridisation is a method to increase phenotypic variability, but is limited due to interspecies hybridisation barriers.In this study we investigated whether ovule culture could be used to increase the success rate of interspecific hybridisation between C. portenschlagiana 9 C. poscharskyana and C. medium 9 C. formanekiana. The effect of different ovule isolation times on ovule germination in vitro was examined. In general, the number of collectible ovules and ovule germination was low. Interspecific hybrids between C. medium and C. formanekiana exhibited an increased number of viable ovules with later isolation time, but with different ovule germination rates. A parent-of-origin effect on both the number of collectible ovules and ovule germination was observed for C. medium 9 C. formanekiana. Histological analysis of embryo and endosperm development in collectible ovules isolated at different time points from interspecific crosses showed that the vast majority of ovules did not contain an embryo. When present, embryo development only progressed with ovule collection time in the C. medium and C. formanekiana crosses. The occurrence of miscoloured seedlings in interspecific crosses indicated incompatibilities between the parental lines that could not be prevented by reciprocal crossing. The low number of collectible ovules and germination rates might be inhibited due to fertilisation barriers.With this study, a protocol for ovule culture was established and the usefulness of ovule culture to obtain interspecific hybrids of selected Campanula species was demonstrated
Prevalence and co-occurrence of hip dysplasia and elbow dysplasia in Dutch pure-bred dogs
Lavrijsen, I.C.M. ; Heuven, H.C.M. ; Meij, B.P. ; Theyse, L.F.H. ; Nap, R.C. ; Leegwater, P.A.J. ; Hazewinkel, H.A.W. - \ 2014
Preventive Veterinary Medicine 114 (2014)2. - ISSN 0167-5877 - p. 114 - 122.
german-shepherd dogs - uk labrador retrievers - bernese mountain dog - canine hip - control program - cost-analysis - inheritance - osteochondrosis - heritability - breeds
Hip as well as elbow dysplasia (HD, ED) are developmental disorders leading to malformation of their respective joints. For a long time both disorders have been scored and targeted for improvement using selective breeding in several Dutch dog populations. In this paper all scores for both HD and ED, given to pure bred dogs in the Netherlands from 2002 to 2010, were analyzed. Heritabilities and correlations between HD and ED were calculated for the 4 most frequently scored breeds. Heritabilities ranged from 0.0 to 0.37 for HD related traits (FCI-score, osteoarthritis, congruity, shape and laxity (Norberg angle); FCI: Federation Cynologique Internationale) and from 0.0 to 0.39 for ED related traits (IEWG score, osteoarthritis, sclerosis and indentation; IEWG: International Elbow Working Group). HD related traits showed high genetic and residual correlations among each other but were only to a minor extent correlated with ED related traits, which also showed high correlations among each other. Genetic correlations were higher than residual correlations. Phenotypic and genetic trends since 2001 for the four most scored breeds were slightly positive but decreasing overtime, indicating that selection over the past decade has not been effective. (C) 2014 Published by Elsevier B.V.
Mapping in the era of sequencing: high density genotyping and its application for mapping TYLCV resistance in Solanum pimpinellifolium
Viquez-Zamora, M. ; Caro Rios, C.M. ; Finkers, H.J. ; Tikunov, Y.M. ; Bovy, A.G. ; Visser, R.G.F. ; Bai, Y. ; Heusden, A.W. van - \ 2014
BMC Genomics 15 (2014). - ISSN 1471-2164 - 10 p.
leaf-curl-virus - recombinant inbred lines - mass-spectrometry - lycopersicon-pimpinellifolium - tomato - infection - genes - metabolomics - inheritance - population
Background A RIL population between Solanum lycopersicum cv. Moneymaker and S. pimpinellifolium G1.1554 was genotyped with a custom made SNP array. Additionally, a subset of the lines was genotyped by sequencing (GBS). Results A total of 1974 polymorphic SNPs were selected to develop a linkage map of 715 unique genetic loci. We generated plots for visualizing the recombination patterns of the population relating physical and genetic positions along the genome. This linkage map was used to identify two QTLs for TYLCV resistance which contained favourable alleles derived from S. pimpinellifolium. Further GBS was used to saturate regions of interest, and the mapping resolution of the two QTLs was improved. The analysis showed highest significance on Chromosome 11 close to the region of 51.3 Mb (qTy-p11) and another on Chromosome 3 near 46.5 Mb (qTy-p3). Furthermore, we explored the population using untargeted metabolic profiling, and the most significant differences between susceptible and resistant plants were mainly associated with sucrose and flavonoid glycosides. Conclusions The SNP information obtained from an array allowed a first QTL screening of our RIL population. With additional SNP data of a RILs subset, obtained through GBS, we were able to perform an in silico mapping improvement to further confirm regions associated with our trait of interest. With the combination of different¿~¿omics platforms we provide valuable insight into the genetics of S. pimpinellifolium-derived TYLCV resistance.
Indirect genetic effects and inbreeding: consequences of BLUP selection for socially affected traits on rate of inbreeding.
Khaw, H.L. ; Ponzoni, R.W. ; Bijma, P. - \ 2014
Genetics, Selection, Evolution 46 (2014). - ISSN 0999-193X - 8 p.
tilapia oreochromis-niloticus - multilevel selection - biological groups - fish welfare - populations - gain - parameters - inheritance - aquaculture - prediction
Background Social interactions often occur among living organisms, including aquatic animals. There is empirical evidence showing that social interactions may genetically affect phenotypes of individuals and their group mates. In this context, the heritable effect of an individual on the phenotype of another individual is known as an Indirect Genetic Effect (IGE). Selection for socially affected traits may increase response to artificial selection, but also affect rate of inbreeding. Methods A simulation study was conducted to examine the effect of Best Linear Unbiased Prediction (BLUP) selection for socially affected traits on the rate of inbreeding. A base scenario without IGE and three alternative scenarios with different magnitudes of IGE were simulated. In each generation, 25 sires and 50 dams were mated, producing eight progeny per dam. The population was selected for 20 generations using BLUP. Individuals were randomly assigned to groups of eight members in each generation, with two families per group, each contributing four individuals. “Heritabilities” (for both direct and indirect genetic effects) were equal to 0.1, 0.3 or 0.5, and direct–indirect genetic correlations were -0.8, -0.4, 0, 0.4, or 0.8. The rate of inbreeding was calculated from generation 10 to 20. Results For the base scenario, the rates of inbreeding were 4.09, 2.80 and 1.95% for “heritabilities” of 0.1, 0.3 and 0.5, respectively. Overall, rates of inbreeding for the three scenarios with IGE ranged from 2.21 to 5.76% and were greater than for the base scenarios. The results show that social interaction within groups of two families increases the resemblance between estimated breeding values of relatives, which, in turn, increases the rate of inbreeding. Conclusion BLUP selection for socially affected traits increased the rate of inbreeding. To maintain inbreeding at an acceptable rate, a selection algorithm that restricts the increase in mean kinship, such as optimum contribution selection, is required.
Missing heritability and soft inheritance of morphology and metabolism in Arabidopsis
Kooke, R. - \ 2014
Wageningen University. Promotor(en): Harro Bouwmeester; Joost Keurentjes, co-promotor(en): Dick Vreugdenhil. - Wageningen University : Wageningen University - ISBN 9789462570412 - 283
arabidopsis - heritability - overerving - plantenmorfologie - metabolisme - plantenfysiologie - genetica - epigenetica - genetische variatie - arabidopsis - heritability - inheritance - plant morphology - metabolism - plant physiology - genetics - epigenetics - genetic variation

The plant phenotype is shaped by complex interactions between its genotype and the environment. Although the genotype is stable and determined by the genomic sequence, plants are able to respond flexibly to changes in environmental conditions by orchestrated signal transduction pathways. The genomic sequence may change with each generation through chromosome rearrangements, meiotic recombination and spontaneous mutations. Through natural selection on these randomly induced changes, genotypes become adapted to their local environment. Because different genotypes adapt to different environments, natural variation within species expands in time and gives rise to a wide variety of genotypes and phenotypes. The genetic architecture that specifies the phenotype can be investigated by analyzing different genotypes in the same environment and associate the phenotypic variation with molecular markers that discriminate the genotypes. Recent advances in next-generation sequencing technology enabled the fast sequencing of entire genomes, and in Arabidopsisthalianaalone, more than 1000 different genotypes have been fully resequenced. The sequencing allows the association of phenotypic variation with large numbers of single nucleotide polymorphisms (SNPs) that greatly enhance resolution in genome-wide association studies (GWAS).

GWAS on human diseases suffer from missing heritability that is most likely caused by the genetic architecture of the disease traits. Many variants of small effect or rare variants most likely determine a large part of the genetic variation and these variants are difficult to identify in GWAS due to lack of statistical power. In plants, several GWAS have been performed and they have identified previously validated genes and genes involved in monogenic disease resistance, but elucidating quantitative traits such as many agronomic important traits might be problematic in plants as well. Chapter 2 describes a GWA study in which quantitative morphological traits, such as leaf area, flowering time and branching were examined in 350 accessions of Arabidopsis for association with about 200,000 SNPs. The morphological traits showed extensive variation and were highly heritable, but GWA mapping could not identify the genetic variants that explain the heritability. Therefore, missing heritability was addressed using genomic selection models and these models confirmed the quantitative complex architecture of the morphological traits. Based upon these results, the heritability was assumed to be hidden below the significance threshold, and indeed lowering the significance threshold enabled the identification of many candidate genes that have been implicated to play a role in the phenotype directly or indirectly, in previous studies. One candidate gene was studied in more detail; natural variants of ACS11, an ethylene biosynthesis gene, associated significantly with the petiole to leaf length ratio. ACS11is indeed expressed in petioles and ectopically supplied ethylene abolished the difference in the phenotype of natural variants at this locus, strongly suggesting that ACS11is involved in the regulation of petiole growth.

However, lowering the significance threshold also increases the number of false-positive associations, non-causal alleles that co-segregate with the trait values. Because regulation of the morphological traits occurs at multiple intermediate levels, increased certainty on the associations can be obtained by performing GWA mapping on the intermediate levels from genotype to phenotype such as gene expression, and protein and metabolite content. Chapter 3 describes a literature survey into the multi-dimensional regulation of metabolic networks that are regulated by inputs from the clock, the communication between cells and between source and sink tissues, and the environment. The metabolic status of the plant can be seen as the final product of the interaction with the environment, and as such, it can serve as a blueprint for growth and development. Chapter 4 describes the abundant variation in enzyme activities and metabolites involved in primary carbon and nitrogen metabolism. The metabolite and enzyme activity data were analyzed together with plant biomass data, and many pleiotropic regulators were identified with opposite effects on primary metabolism and biomass formation. Natural variants in two stress-responsive genes were oppositely associated with biomass and many enzymes and metabolites involved in primary metabolism, suggesting that higher enzyme activities and higher levels of sugars and proteins might be needed to support plant resistance to stress at the expense of growth.

Some studies indicated that epigenetic variation, independent of the genetic SNPs, may contribute to missing heritability. Epigenetic inheritance is defined as the inheritance of phenotypic variation to future generations without changes in DNA sequence. Epigenetic variation is caused by variation in chromatin marks such as DNA methylation, histone modifications and small RNAs. Recently, a recombinant inbred line (RIL) population was developed in Arabidopsis where the chromosomes are differentially methylated in lines with an otherwise isogenic background by crossing wild-type Col-0 with a hypomethylated ddm1-2mutant. Chapter 5 describes the epigenetic regulation of morphology and phenotypic plasticity by studying morphological variation in 99 epiRILs under control and saline conditions. The morphology and plasticity trait values were associated with differentially methylated regions (DMRs) that were used as molecular markers in QTL mapping. Many QTLs for various morphological traits and phenotypic plasticity parameters co-located, suggesting pleiotropic epigenetic regulation of growth, morphology and plasticity. Furthermore, methylation variation in the promoter of a salt-tolerance gene, HIGH-AFFINITY K+TRANSPORTER1 (HKT1)associated significantly with leaf area, especially under saline conditions.

To gain more insight into the epigenetic regulation of plant growth and morphology, chapter 6 describes the epigenetic regulation of secondary metabolite levels in leaves and flowers and studies the relationship with the morphological traits determined in chapter 5. Many of the QTLs that were found for growth and morphology overlapped with the QTLs for metabolic traits, and suggest pleiotropic regulation. Furthermore, subsets of the metabolites correlated well with the morphological traits and might thus be regulated by the same loci. The majority of metabolite QTLs was detected for glucosinolates and flavonoids in the flowers, and methylation variation was observed for some of the biosynthetic pathway genes of these compounds when comparing Col-0 and ddm1-2, which indicates a role for epigenetic regulation of these biosynthesis pathways.

Although stable, natural epialleles have been found in plant species and the environment can induce hypo- and hypermethylation of DNA, it remains elusive whether environmentally-induced epigenetic changes can be inherited to subsequent generations, independent of genetic variation. Chapter 7 describes the transgenerational inheritance of phenotypic variation in progeny derived from a common Arabidopsis founder line. The progeny of stressed parents and grandparents showed variation in morphological traits, metabolite accumulation and gene expression. For example, many salt-responsive genes were up-regulated in progeny of salt-stressed grandparents. The responses to biotic (methyljasmonate) and abiotic (salt) stress differed strongly and this suggests that different environments can cause different transgenerational responses. Because all lines are derived from a single ancestor, epigenetic variation and not DNA variation is most likely causal for the phenotypic variation. Further studies are, however, needed to provide conclusive evidence for transgenerational inheritance.

Chapter 8 provides a synthesis of the work and discusses the GWA studies in the light of missing heritability, genetic architecture and the verification of candidate genes. The work on epigenetic regulation of phenotypic plasticity, morphology and metabolism is discussed in relation to Lamarckian soft inheritance that gained new enthusiasm after some recent discoveries in the field of epigenetics. And finally, the metabolomics work is discussed in the light of the growth-defense hypothesis that states that investments in defense occur at the expense of growth.

A heritable antiviral RNAi response limits Orsay virus infection in Caenorhabditis elegans N2
Sterken, M.G. ; Snoek, L.B. ; Bosman, K.J. ; Daamen, J. ; Riksen, J.A.G. ; Bakker, J. ; Pijlman, G.P. ; Kammenga, J.E. - \ 2014
PLoS ONE 9 (2014)2. - ISSN 1932-6203
c. elegans - gene-expression - interference - requirements - inheritance - environment - diversity - pathways - genotype - immunity
Orsay virus (OrV) is the first virus known to be able to complete a full infection cycle in the model nematode species Caenorhabditis elegans. OrV is transmitted horizontally and its infection is limited by antiviral RNA interference (RNAi). However, we have no insight into the kinetics of OrV replication in C. elegans. We developed an assay that infects worms in liquid, allowing precise monitoring of the infection. The assay revealed a dual role for the RNAi response in limiting Orsay virus infection in C. elegans. Firstly, it limits the progression of the initial infection at the step of recognition of dsRNA. Secondly, it provides an inherited protection against infection in the offspring. This establishes the heritable RNAi response as anti-viral mechanism during OrV infections in C. elegans. Our results further illustrate that the inheritance of the anti-viral response is important in controlling the infection in the canonical wild type Bristol N2. The OrV replication kinetics were established throughout the worm life-cycle, setting a standard for further quantitative assays with the OrV-C. elegans infection model.
On the asymmetry of mating in natural populations of the mushroom fungus Schizophyllum commune
Nieuwenhuis, B.P.S. ; Nieuwhof, S. ; Aanen, D.K. - \ 2013
Fungal Genetics and Biology 56 (2013). - ISSN 1087-1845 - p. 25 - 32.
cut beech logs - incompatibility factors - nuclear migration - heterobasidion-annosum - mitochondrial genome - buller phenomenon - genetic-structure - dna - inheritance - selection
Before a mycelium of a mushroom-forming basidiomycete develops mushrooms, the monokaryotic mycelium needs to become fertilized. Although the mechanistic details of mating in mushrooms have been studied thoroughly in laboratory research, very little is known on mating patterns in nature. In this study, we performed fine-scale analyses of three populations of Schizophyllum commune from their natural substrate (i.e. dead beech branches). From the three branches, 24, 12, and 24 fruiting bodies were isolated and for each mushroom, the origins of its nuclei and cytoplasm were reconstructed using DNA markers. Nuclear genotypes were determined using sequencing data and mating types, and mitochondrial haplotypes using SNP markers. From these combined data we reconstructed colonization and mating patterns of the mycelia. On each branch, we found multiple dikaryons (3, 3, and 8, respectively); in two instances one nuclear haplotype was shared between two dikaryons and in two other cases a nuclear haplotype was shared between three dikaryons. Each dikaryon always had a single mitochondrial haplotype. These findings indicate that mating usually is not symmetrical and that a monokaryon is most likely fertilized by a small monokaryon, a spore or a dikaryon. Sharing of nuclear haplotype between different dikaryons resulted either from multiple fertilizations of a single monokaryon, if the dikaryons had identical mitochondrial haplotypes, or, if the dikaryons had different mitochondria] haplotypes, most likely from secondary matings between a monokaryon and a dikaryon (Buller phenomenon). We conclude that mating in S. commune between same-sized monokaryons with reciprocal migration, as generally described in textbooks, is rare in nature. We discuss the implications of non-symmetric mating for basidiomycete evolution. (C) 2013 Elsevier Inc. All rights reserved.
Multilevel selection with kin and non-kin groups, experimental results with japanese quail (coturnix japonica)
Muir, W.M. ; Bijma, P. ; Schinckel, A. - \ 2013
Evolution 67 (2013)6. - ISSN 0014-3820 - p. 1598 - 1606.
genetical evolution - small populations - connected world - adaptation - tribolium - differentiation - inheritance - covariance - transgenes - components
An experiment was conducted comparing multilevel selection in Japanese quail for 43 days weight and survival with birds housed in either kin (K) or random (R) groups. Multilevel selection significantly reduced mortality (6.6% K vs. 8.5% R) and increased weight (1.30 g/MG K vs. 0.13 g/MG R) resulting in response an order of magnitude greater with Kin than Random. Thus, multilevel selection was effective in reducing detrimental social interactions, which contributed to improved weight gain. The observed rates of response did not differ significantly from expected, demonstrating that current theory is adequate to explain multilevel selection response. Based on estimated genetic parameters, group selection would always be superior to any other combination of multilevel selection. Further, near optimal results could be attained using multilevel selection if 20% of the weight was on the group component regardless of group composition. Thus, in nature the conditions for multilevel selection to be effective in bringing about social change maybe common. In terms of a sustainability of breeding programs, multilevel selection is easy to implement and is expected to give near optimal responses with reduced rates of inbreeding as compared to group selection, the only requirement is that animals be housed in kin groups.
Epigenetic changes and transposon reactivation in Thai rice hybrids. Molecular Breeding
Kantama, L. ; Junbuathong, S. ; Sakulkoo, J. ; Jong, J.H.S.G.M. de; Apisitwanich, S. - \ 2013
Molecular Breeding 31 (2013)4. - ISSN 1380-3743 - p. 815 - 827.
cytosine methylation - dna methylation - elements mites - genome - retrotransposons - hybridization - markers - inheritance - activation - expression
Inter- or intraspecific hybridization is the first step in transferring exogenous traits to the germplasm of a recipient crop. One of the complicating factors is the occurrence of epigenetic modifications of the hybrids, which in turn can change their gene expression and phenotype. In this study we present an analysis of epigenome changes in rice hybrids that were obtained by crossing rice cultivars, most of them of indica type and Thai origin. Comparing amplified fragment length polymorphism (AFLP) fingerprints of twenty-four cultivars, we calculated Nei’s indexes for measuring genetic relationships. Epigenetic changes in their hybrids were established using methylation-sensitive AFLP fingerprinting and transposon display of the rice transposable elements (TEs) Stowaway Os-1 and Mashu, leading to the question whether the relationship between parental genomes is a predictor of epigenome changes, TE reactivation and changes in TE methylation. Our study now reveals that the genetic relationship between the parents and DNA methylation changes in their hybrids is not significantly correlated. Moreover, genetic distance correlates only weakly with Mashu reactivation, whereas it does not correlate with Stowaway Os-1 reactivation. Our observations also suggest that epigenome changes in the hybrids are localized events affecting specific chromosomal regions and transposons rather than affecting the genomic methylation landscape as a whole. The weak correlation between genetic distance and Mashu methylation and reactivation points at only limited influence of genetic background on the epigenetic status of the transposon. Our study further demonstrates that hybridizations between and among specific japonica and indica cultivars induce both genomic DNA methylation and reactivation/methylation change in the Stowaway Os-1 and Mashu transposons. The observed epigenetic changes seem to affect the transposons in a clear manner, partly driven by stochastic processes, which may account for a broader phenotypic plasticity of the hybrids. A better understanding of the epigenome changes leading to such transposon activation can lead to the development of novel tools for more variability in future rice breeding
Identification of seed-related QTL in Brassica rapa
Bagheri, H. ; Pino del Carpio, D. ; Hanhart, C.J. ; Bonnema, A.B. ; Keurentjes, J.J.B. ; Aarts, M.G.M. - \ 2013
Spanish Journal of Agricultural Research 11 (2013)4. - ISSN 1695-971X - p. 1085 - 1093.
quantitative trait loci - genetic-linkage map - campestris l - turnip rape - flowering time - oilseed rape - oil content - color - inheritance - napus
To reveal the genetic variation, and loci involved, for a range of seed-related traits, a new F2 mapping population was developed by crossing Brassica rapa ssp. parachinensis L58 (CaiXin) with B. rapa ssp. trilocularis R-o-18 (spring oil seed), both rapid flowering and self-compatible. A linkage map was constructed using 97 AFLPs and 21 SSRs, covering a map distance of 757 cM with an average resolution of 6.4 cM, and 13 quantitative trait loci (QTL) were detected for nine traits. A strong seed colour QTL (LOD 26) co-localized with QTL for seed size (LOD 7), seed weight (LOD 4.6), seed oil content (LOD 6.6), number of siliques (LOD 3) and number of seeds per silique (LOD 3). There was only a significant positive correlation between seed colour and seed oil content in the yellow coloured classes. Seed coat colour and seed size were controlled by the maternal plant genotype. Plants with more siliques tended to have more, but smaller, seeds and higher seed oil content. Seed colour and seed oil content appeared to be controlled by two closely linked loci in repulsion phase. Thus, it may not always be advantageous to select for yellow-seededness when breeding for high seed oil content in Brassicas.
Genetic consequences of breaking migratory traditions in barnacle geese Branta leucopsis
Jonker, R.M. ; Kraus, R.H.S. ; Zhang, Q. ; Hooft, W.F. van; Larsson, K. ; Jeugd, H.P. van der; Kurvers, R.H.J.M. ; Wieren, S.E. van; Loonen, M.J.J.E. ; Crooijmans, R.P.M.A. ; Ydenberg, R.C. ; Groenen, M.A.M. ; Prins, H.H.T. - \ 2013
Molecular Ecology 22 (2013)23. - ISSN 0962-1083 - p. 5835 - 5847.
parental care - canada geese - evolution - bird - population - differentiation - direction - connectivity - relatedness - inheritance
Cultural transmission of migratory traditions enables species to deal with their environment based on experiences from earlier generations. Also, it allows a more adequate and rapid response to rapidly changing environments. When individuals break with their migratory traditions new population structures can emerge that may affect gene flow. Recently, the migratory traditions of the Barnacle Goose Branta leucopsis changed, and new populations differing in migratory distance emerged. Here, we investigate the population genetic structure of the Barnacle Goose to evaluate the consequences of altered migratory traditions. We used a set of 358 Single Nucleotide Polymorphisms (SNP) markers to genotype 418 individuals from breeding populations in Greenland, Spitsbergen, Russia, Sweden and the Netherlands, the latter two being newly emerged populations. We used Discriminant Analysis of Principal Components, FST , linkage disequilibrium and a comparison of gene flow models using migrate-n to show that there is significant population structure, but that relatively many pairs of SNPs are in linkage disequilibrium, suggesting recent admixture between these populations. Despite the assumed traditions of migration within populations we also show that genetic exchange occurs between all populations. The newly established non-migratory population in the Netherlands is characterized by high emigration into other populations which suggests more exploratory behaviour, possibly as a result of shortened parental care. These results suggest that migratory traditions in populations are subject to change in geese and that such changes have population genetic consequences. We argue that the emergence of non-migration likely resulted from developmental plasticity.
Genetic correlations between lactation performance and growing-finishing traits in pigs
Bergsma, R. ; Mathur, P.K. ; Kanis, E. ; Verstegen, M.W.A. ; Knol, E.F. ; Arendonk, J.A.M. van - \ 2013
Journal of Animal Science 91 (2013)8. - ISSN 0021-8812 - p. 3601 - 3611.
feed-intake - multilevel selection - body development - sows - parameters - growth - inheritance - components - efficiency - energy
Genetic selection for increased litter size of sows increases the risk of a large negative energy balance during lactation. Furthermore, the feed intake capacity of the lactating sows might be reduced due to the simultaneous selection for greater feed efficiency during the growth phase when sows were actually reared as finishers but later on selected for breeding. There is a need to improve lactation performance of sows and continue selection for feed efficiency of grower-finishers in commercial breeding. Therefore, this study was conducted to estimate genetic correlations between growing-finishing traits and lactation performance traits. An additional objective was to study the impact of including additive social effects in the animal model on genetic correlation estimates. Analyses were performed on a population of 1,149 commercial crossbred sows with repeated observations on lactation performance traits and their 7,723 grower-finisher offspring. The genetic correlation between daily BW gain of grower-finishers and starting BW of lactating sows was positive (rg = 0.24; P <0.05). The correlation between off-test backfat of grower-finishers and fat mass of lactating sows was also positive (rg = 0.53; P <0.05). The genetic regulation of feed intake from the beginning of lactation seems to differ from the genetic regulation of feed intake during the growing-finishing period, as the correlation between these 2 traits was low (rg = +0.23; P <0.05). Feed efficiency during growing-finishing and lactation phases showed similar tendencies as the genetic correlation between residual feed intake of the grower-finisher and lactation efficiency of sows was –0.51 (P <0.05). Taking heritable social effects into account for daily BW gain and feed intake did not affect the genetic correlation estimates, either within growing-finishing traits or between growing-finishing traits and lactation performance traits. It was concluded that in the absence of antagonistic genetic correlations, selection for growing-finishing traits in dam lines could be combined with selection for lactation performance traits.
Genetic Variation and Combining Ability Analysis of Bruising Sensitivity in Agaricus bisporus
Gao, W. ; Baars, J.J.P. ; Dolstra, O. ; Visser, R.G.F. ; Sonnenberg, A.S.M. - \ 2013
PLoS ONE 8 (2013)10. - ISSN 1932-6203
schizophyllum-commune - growth-rate - inheritance - populations - improvement - mushrooms - selection - yield
Advanced button mushroom cultivars that are less sensitive to mechanical bruising are required by the mushroom industry, where automated harvesting still cannot be used for the fresh mushroom market. The genetic variation in bruising sensitivity (BS) of Agaricus bisporus was studied through an incomplete set of diallel crosses to get insight in the heritability of BS and the combining ability of the parental lines used and, in this way, to estimate their breeding value. To this end nineteen homokaryotic lines recovered from wild strains and cultivars were inter-crossed in a diallel scheme. Fifty-one successful hybrids were grown under controlled conditions, and the BS of these hybrids was assessed. BS was shown to be a trait with a very high heritability. The results also showed that brown hybrids were generally less sensitive to bruising than white hybrids. The diallel scheme allowed to estimate the general combining ability (GCA) for each homokaryotic parental line and to estimate the specific combining ability (SCA) of each hybrid. The line with the lowest GCA is seen as the most attractive donor for improving resistance to bruising. The line gave rise to hybrids sensitive to bruising having the highest GCA value. The highest negative SCA possibly indicates heterosis effects for resistance to bruising. This study provides a foundation for estimating breeding value of parental lines to further study the genetic factors underlying bruising sensitivity and other quality-related traits, and to select potential parental lines for further heterosis breeding. The approach of studying combining ability in a diallel scheme was used for the first time in button mushroom breeding. Citation: Gao W, Baars JJP, Dolstra O, Visser RGF, Sonnenberg ASM (2013) G
De vererving van het witrikpatroon en de variatie daaarin
Schoon, M. ; Oldenbroek, J.K. ; Oijen, M. van - \ 2013
Zeldzaam huisdier 38 (2013)3. - ISSN 0929-905X - p. 18 - 19.
witrik - rundveerassen - zeldzame rassen - diergenetica - dierveredeling - kleur - overerving - coloursides white back - cattle breeds - rare breeds - animal genetics - animal breeding - colour - inheritance
In een afstudeeropdracht voor van Hall Larenstein is de vererving van de witrikkleur bij runderen bestudeerd en is de vraag beantwoord waarom er zoveel kleurpatronen zijn binnen deze kleurslag.
AFLP-based population structure analysis as a means to validate the complex taxonomy of dogroses (Rosa section Caninae)
Riek, J. de; Cock, K. de; Smulders, M.J.M. ; Nybom, H. - \ 2013
Molecular Phylogenetics and Evolution 67 (2013)3. - ISSN 1055-7903 - p. 547 - 559.
genus rosa - skewed distribution - microsatellite dna - molecular markers - sugar-beet - differentiation - inheritance - diversity - rosoideae - generose
Within the genus Rosa numerous species have been described. Circumscription of the dogrose section Caninae is straightforward, but the delineation of species and subsections within this section is less clear, partly due to hybridisation between species. We have investigated the extent to which DNA marker-based information of wild populations corroborates present-day dogrose taxonomy and hypotheses about the origination of taxa. Sampling was conducted in a transect across Europe, collecting over 900 specimens of all encountered dogrose taxa. For comparison, we also included more than 200 samples of species belonging to other sections. Two lines of statistical analyses were used to investigate the genetic structure based on AFLP data: 1) an unstructured model with principal coordinate analysis and hierarchical clustering, and 2) a model with a superimposed taxonomic structure based on analysis of genetic diversity using a novel approach combining assignment tests with canonical discriminant analysis. Support was found for five of the seven subsections, whereas R. balsamica apparently belongs to subsection Caninae thus omitting the need for recognizing subsection Tomentellae. For R. stylosa, a hybridogenic origin with a non-dogrose section member has been suggested, and it can be treated either as a separate subsection or within subsection Caninae. Within the subsection Rubigineae, a species cluster with low support for the taxa R. micrantha, R. rubiginosa and the putatively hybridogenous R. gremlii was identified. Similarly, several species in the subsection Caninae overlapped considerably, and are best regarded as one common species complex. This population genetic approach provides a general method to validate the taxonomic system in complex and polyploid taxa.
Differences in acidity of apples are probably mainly caused by a malic acid transporter gene on LG16
Khan, S.A. ; Beekwilder, J. ; Schaart, J.G. ; Mumm, R. ; Soriano, J.M. ; Jacobsen, E. ; Schouten, H.J. - \ 2013
Tree Genetics and Genomes 9 (2013)2. - ISSN 1614-2942 - p. 475 - 487.
malus-pumila mill. - phenolic-compounds - aluminum tolerance - malate transporter - organic-acids - amino-acids - arabidopsis - metabolism - fruits - inheritance
Acidity has profound effects on the taste of apples (Malus × domestica). Malic acid is the predominant organic acid in apples. Differences in malic acid content are caused by differences in accumulation of malic acid in the vacuole. This accumulation may be caused by a gene that is responsible for transport of malic acid from the cytosol into the vacuole. Here, we provide evidence that a malic acid transporter gene at the top of chromosome 16 caused significant differences in malic acid concentration and pH of apples. The pH of apples in a segregating F1 population was mapped and at the pH locus (named henceforth Ma locus for malic acid), two putative malic acid transporter genes were detected. These genes show high homology to AtALMT genes that code for malate channel proteins located in vacuolar membrane in Arabidopsis. The expression of one of the candidate genes (Ma1) cosegregated clearly with malic acid content. The inheritance of at least one dominant allele of this gene sufficed for an increased expression level that likely caused the observed threefold increase of the malic acid concentration and the reduction of the pH from 4 to 3 in mature apples, compared to the presence of the recessive, lowly expressed allele only. Our results show that differences in fruit acidity were probably caused by differences in expression levels of alleles of a malic acid transporter gene.
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