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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Exploiting whole genome sequence variants in cattle breeding : Unraveling the distribution of genetic variants and role of rare variants in genomic evaluation
Zhang, Qianqian - \ 2017
University. Promotor(en): Henk Bovenhuis, co-promotor(en): G. Sahana; Mario Calus. - Wageningen : Wageningen University - ISBN 9788793643147 - 249
cattle - genomes - genetic variation - inbreeding - homozygosity - longevity - quantitative traits - animal breeding - animal genetics - rundvee - genomen - genetische variatie - inteelt - homozygotie - gebruiksduur - kwantitatieve kenmerken - dierveredeling - diergenetica

The availability of whole genome sequence data enables to better explore the genetic mechanisms underlying different quantitative traits that are targeted in animal breeding. This thesis presents different strategies and perspectives on utilization of whole genome sequence variants in cattle breeding. Using whole genome sequence variants, I show the genetic variation, recent and ancient inbreeding, and genome-wide pattern of introgression across the demographic and breeding history in different cattle populations. Using the latest genomic tools, I demonstrate that recent inbreeding can accurately be estimated by runs of homozygosity (ROH). This can further be utilized in breeding programs to control inbreeding in breeding programs. In chapter 2 and 4, by in-depth genomic analysis on whole genome sequence data, I demonstrate that the distribution of functional genetic variants in ROH regions and introgressed haplotypes was shaped by recent selective breeding in cattle populations. The contribution of whole genome sequence variants to the phenotypic variation partly depends on their allele frequencies. Common variants associated with different traits have been identified and explain a considerable proportion of the genetic variance. For example, common variants from whole genome sequence associated with longevity have been identified in chapter 5. However, the identified common variants cannot explain the full genetic variance, and rare variants might play an important role here. Rare variants may account for a large proportion of the whole genome sequence variants, but are often ignored in genomic evaluation, partly because of difficulty to identify associations between rare variants and phenotypes. I compared the powers of different gene-based association mapping methods that combine the rare variants within a gene using a simulation study. Those gene- based methods had a higher power for mapping rare variants compared with mixed linear models applying single marker tests that are commonly used for common variants. Moreover, I explored the role of rare and low-frequency variants in the variation of different complex traits and their impact on genomic prediction reliability. Rare and low-frequency variants contributed relatively more to variation for health-related traits than production traits, reflecting the potential of improving prediction reliability using rare and low-frequency variants for health-related traits. However, in practice, only marginal improvement was observed using selected rare and low-frequency variants when combined with 50k SNP genotype data on the reliability of genomic prediction for fertility, longevity and health traits. A simulation study did show that reliability of genomic prediction could be improved provided that causal rare and low-frequency variants affecting a trait are known.

The genetic background of bovine αs1- and αs2-casein phosphorylation
Fang, Zih-Hua - \ 2017
University. Promotor(en): E. Verrier; Henk Bovenhuis, co-promotor(en): P. Martin; Marleen Visker. - Wageningen : Wageningen University - ISBN 9789463438148 - 141
dairy cattle - alpha-s1-casein - alpha-s2-casein - phosphorylation - milk composition - milk proteins - genetic variation - genetic factors - animal genetics - melkvee - alfa-s-1-caseïne - alfa-s-2-caseïne - fosforylering - melksamenstelling - melkeiwitten - genetische variatie - genetische factoren - diergenetica

Phosphorylation of caseins (CN) is a crucial post-translational modification allowing caseins to aggregate as micelles. The formation and stability of casein micelles are important for transporting abundant minerals to the neonate and manufacturing of dairy products. Therefore, it is of great interest to explore variation in degrees of phosphorylation of caseins and study to what extent genetic and other factors contribute to this variation. This thesis aimed to investigate the genetic background of bovine milk protein composition with a focus on phosphorylation of αs1- and αs2-CN. Two studies were conducted to quantify phosphorylation levels of αs1- and αs2-CN: one in French Montbéliarde using liquid chromatography coupled with electrospray ionization mass spectrometry and the other in Dutch Holstein Friesian using capillary zone electrophoresis. In French Montbéliarde, in addition to the known isoforms αs1-CN-8P and-9P and αs2-CN-10P to -13P, three new phosphorylation isoforms were detected, namely αs2-CN-9P, αs2-CN-14P, and αs2-CN-15P. Relative concentrations of the phosphorylation isoforms varied considerably among cows. Phenotypic correlations showed that isoforms phosphorylated at higher degrees (αs1-CN-9P and αs2-CN-12P to -14P) correlated negatively with isoforms phosphorylated at lower degrees (αs1-CN-8P, αs2-CN-10P, and -11P). Furthermore, it was shown that αs1- and αs2-CN phosphorylation profiles changed across parity and lactation, and exploitable genetic variation for the phosphorylation degrees of αs1- and αs2-CN (defined as the proportion of higher-degree isoforms in αs1- and αs2-CN, respectively) exist. In Dutch Holstein Friesian, three αs2-CN isoforms, namely αs2-CN-10P to -12P, and the phosphorylation degrees of αs1- and αs2-CN were quantified. High intra-herd heritabilities were estimated for individual αs2-CN phosphorylation isoforms and the phosphorylation degrees of αs1- and αs2-CN (ranging from 0.54 to 0.89). This suggests that genetic factors contribute substantially to observed differences in αs1- and αs2-CN phosphorylation profiles. The highly positive correlation between the phosphorylation degrees of αs1- and αs2-CN (0.94) suggest that phosphorylation of αs1- and αs2-CN is related. Additionally, a total of 10 regions, distributed across Bos taurus autosomes (BTA) 1, 2, 6, 9, 11, 14, 15, 18, 24 and 28, were detected to be associated with individual αs1- and αs2-CN phosphorylation isoforms and their phosphorylation degrees. Regions on BTA1, 6, 11 and 14 were associated with multiple traits studied. Two quantitative trait loci (QTL) regions were detected on BTA1: one affecting αs2-CN production, and the other affecting αs1-CN PD and αs2-CN PD. The QTL region on BTA6 affected only individual αs2-CN isoforms. The QTL region on BTA11 and 14 affected relative concentrations of αs2-CN-10P and αs2-CN-11P, αs1-CN PD and αs2-CN PD. Results suggested that effects of identified genomic regions on αs1-CN PD and αs2-CN PD are probably due to changes in milk synthesis and phosphorus secretion in milk.

Comparative genomics and trait evolution in Cleomaceae, a model family for ancient polyploidy
Bergh, Erik van den - \ 2017
University. Promotor(en): Eric Schranz; Y. van de Peer. - Wageningen : Wageningen University - ISBN 9789463431705 - 106
capparaceae - genomics - polyploidy - evolution - genomes - reproductive traits - flowers - colour - glucosinolates - genetic variation - biosystematics - taxonomy - identification - genomica - polyploïdie - evolutie - genomen - voortplantingskenmerken - bloemen - kleur - glucosinolaten - genetische variatie - biosystematiek - taxonomie - identificatie

As more and more species have been sequenced, evidence has been piling up for a fascinating phenomenon that seems to occur in all plant lineages: paleopolyploidy. Polyploidy has historically been a much observed and studied trait, but until recently it was assumed that polyploids were evolutionary dead-ends due to their sterility. However, many studies since the 1990’s have challenged this notion by finding evidence for ancient genome duplications in many genomes of current species. This lead to the observation that all seed plants share at least one ancestral polyploidy event. Another polyploidy event has been proven to lie at the base of all angiosperms, further signifying the notion that ancient polyploidy is widespread and common. These findings have led to questions regarding the apparent disadvantages that can be observed in a first generation polyploid. If these disadvantages can be overcome however, duplication of a genome also presents an enormous potential for evolutionary novelty. Duplicated copies of genes are able to acquire changes that can lead to specialization of the duplicated pair into two functions (subfunctionalization) or the development of one copy towards an entirely new function (neofunctionalization).

Currently, most research towards polyploidy has focused on the economically and scientifically important Brassicaceae family containing the model plant Arabidopsis thaliana and many crops such as cabbage, rapeseed, broccoli and turnip. In this thesis, I lay the foundations for the expansion of this scope to the Cleomaceae, a widespread cosmopolitan plant family and a sister family of Brassicaceae. The species within Cleomaceae are diverse and exhibit many scientifically interesting traits. They are also in a perfect position phylogenetically to draw comparisons with the much more studied Brassicaceae. I describe the Cleomaceae and their relevance to polyploid research in more detail in the Introduction. I then describe the important first step towards setting up the genetic framework of this family with the sequencing of Tarenaya hassleriana in Chapter 1.

In Chapter 2, I have studied the effects of polyploidy on the development of C4 photosynthesis by comparing the transcriptome of C3 photosynthesis based species Tarenaya hassleriana with the C4 based Gynandropsis gynandra. C4 photosynthesis is an elaboration of the more common C3 form of photosynthesis that concentrates CO2 in specific cells leading to decreased photorespiration by the RuBisCO and higher photosynthetic efficieny in low CO2 environments. I find that polyploidy has not led to sub- or neofunctionalization towards the development of this trait, but instead find evidence for another important phenomenon in postpolyploid evolution: the dosage balance hypothesis. This hypothesis states that genes which are dependent on specific dosage levels of their products will be maintained in duplicate; any change in their function would lead to dosage imbalance which would have deleterious effects on their pathway. We show that most genes involved in photosynthesis have returned to single copy in G. gynandra and that the changes leading to C4 have mostly taken place at the expression level confirming current assumptions on the development of this trait.

In Chapter 3, I have studied the effects of polyploidy on an important class of plant defence compounds: glucosinolates. These compounds, sometimes referred to as ‘mustard oils’, play an important role in the defence against herbivores and have radiated widely in Brassicaceae to form many different ‘flavors’ to deter specific herbivores. I show that in Cleomaceae many genes responsible for these compounds have benefited from the three rounds of polyploidy that T. hassleriana has undergone and that many duplicated genes have been retained. We also show that more than 75% is actively expressed in the plant, proving that the majority of these duplications has an active function in the plant.

Finally, in Chapter 4 I investigate a simple observation made during experiments with T. hassleriana in the greenhouse regarding the variation in flower colour between different individuals: some had pink flowers and some purple. Using LC-PDA mass spectrometry we find that the two colours are caused by different levels of two anthocyanin pigments, with cyanidin dominating in the purple flowers and pelargonidin being more abundant in pink flowers. Through sequence comparison and synteny analysis between A. thaliana and T. hassleriana we find the orthologs of the genes involved in this pathway. Using a Genotyping by Sequencing method on a cross between these two flower colours, we produce a collection of SNP markers on the reference genome. With these SNPs, we find two significant binary trait loci, one of which corresponds to the location of the F3’H ortholog which performs the conversion of a pelargonidin precursor to a cyanidin precursor.

In the General Conclusion, I combine all findings of the previous chapters and explain how they establish part of a larger species framework to study ancient polyploidy in angiosperms. I then put forth what these findings can mean for possible future research and the directions that are worth to be explored further.

Genetics of equine insect bite hypersensitivity and genetic diversity in horses
Shrestha, Merina - \ 2017
University. Promotor(en): Henk Bovenhuis; D.J. de Koning, co-promotor(en): Bart Ducro; A.M. Johansson. - Wageningen : Wageningen University - ISBN 9789463430166
paarden - equus - insectenbeten - overgevoeligheid - diergenetica - genetische diversiteit - genetische variatie - allergische reacties - horses - insect bites - hypersensitivity - animal genetics - genetic diversity - genetic variation - allergic reactions

Genetic variation contributing to the phenotypic variation was utilized in this thesis to understand the genetic background of a complex trait IBH, and to understand genetic diversity and relationships between various horse populations.

IBH is the most common skin allergic disorder in horses, caused by bites of midges, predominantly Culicoides species. It affects various horse breeds worldwide. With no effective treatment, IBH degrades horse health and causes economic loss. In this thesis, we used genome-wide SNPs to identify regions contributing to genetic variance of IBH susceptibility. We also investigated influence of increased number of horses and dense SNPs on identification of genomic regions associated to IBH susceptibility. Multiple genomic regions with small effects were observed in Studies I-III. Interesting genomic regions in the Icelandic horse population across the studies I and II, was observed on chromosomes 1, 7, 10, 15 and 17. The percentage of the genetic variance explained by top ten windows increased from 3.07% (Study I) to 6.56% (Study II). Novel genomic regions were identified when number of Icelandic horses was increased in Study II. Using dense SNPs on the Exmoor pony population we identified novel genomic regions, on chr 8, associated to IBH susceptibility, though with borderline significance.

In Study IV, pre-conceived understanding about evolutionary history of horse populations matched obtained results from investigation of genetic relationships within Dutch warmblood populations (pairwise mean FST ≤ 0.070), and within pony-like populations (pairwise mean FST ≤ 0.078). Horse populations with similar genetic background might share similar genetic components for IBH susceptibility. The Friesian horse population had lowest diversity (mean inbreeding coefficients: fi: 30.4%, fiROH= 22.2%) in Study IV and was genetically distinct (FST ranged from 0.13 to 0.17). This might be a result of a history of several population bottlenecks and selection on a closed breeding scheme. Low diversity in immunity related genes, observed in the Friesian horse population, might have led to increased prevalence of IBH. Similarly, low susceptibility of IBH in a warmblood population, KWPN sport horse population might be due to high genetic diversity ( =-6.9%). High genetic diversity in KWPN sport horse population might be a result of an open breeding scheme and interbreeding with other warmblood populations.

Super-performance in a palm species
Jansen, Merel - \ 2016
University. Promotor(en): Niels Anten; Pieter Zuidema, co-promotor(en): Frans Bongers; M. Martínez-Ramos. - Wageningen : Wageningen University - ISBN 9789462579996 - 193
chamaedorea elegans - understorey - tropical forests - spatial variation - leaves - growth - population ecology - defoliation - genetic variation - onderlaag - tropische bossen - ruimtelijke variatie - bladeren - groei - populatie-ecologie - ontbladering - genetische variatie

The world is changing rapidly due to anthropogenic disturbance. Effects include: global warming, massive pollution, a changed global nitrogen cycle, high rates of land-use change, and exotic species spread. This has a tremendous impact on both natural and agricultural systems. To understand these impacts, good understanding of ecological systems and underlying drivers is necessary. Ecological systems can be studied at different levels of aggregation. Different levels of aggregation influence each other and are also influenced by external drivers like the environment. The population level is of particular interest, because many important ecological processes occur at the population level, like evolution, extinction, and invasion. Ecologists are increasingly recognizing that population processes are strongly influenced by one level of aggregation lower, the individual level. Individual heterogeneity (i.e. differences between individuals in performance), determines many population processes including population growth rate. However, the exact relations between individual heterogeneity, the external drivers of it, and the population level are not always well understood. Furthermore, methods to analyze these relations are not always available.

Individual heterogeneity occurs at different temporal scales, ranging from short- to long-term performance differences between individuals, where short- and long-term refer to the expected lifespan of the species in question. Short-term differences between individuals are relatively easily identifiable and are common in almost all species. But long-term differences are much harder to determine especially for long-lived organisms. Long-term differences between individuals in reproduction have been identified for several animal species, and in growth for several tree species, but less is known about the existence of such differences in other life forms (e.g. palms, lianas or clonal plants). Quantifying the extent to which individuals differ is essential for understanding the influence of individual heterogeneity on population processes. Super-performing individuals (i.e. individuals that persistently grow faster and reproduce more than others), probably contribute more to the growth of the population and therefore to future generations. Future populations will, therefore, have the genetic characteristics of the super-performers. Which characteristics this will be, depends on the genetic and environmental drivers of super-performance. Full understanding of the influence of individual heterogeneity on population processes, therefore, requires knowledge of the underlying causes of individual heterogeneity.

For many species, it is known that spatial variation in environmental conditions can cause short-term performance differences between individuals, but it is often not clear if the same environmental factors that cause short-term performance differences are also the environmental factors that cause long-term performance differences. Furthermore, genetic variation is known to cause performance differences, but to what extent is not well studied in natural long-lived plant populations. Within-population genetic variation can be maintained in habitats that are characterized by strong temporal or spatial heterogeneity in environmental conditions if the performance of a genotype relative to others depends on the environment it experiences.

Super-performing individuals possibly play an important role in the resistance and resilience of populations to disturbance (i.e. maintaining and recovering population growth rate under stress), because super-performers potentially contribute more to the recovery of the population. However, this depends on the relative tolerance to disturbance of super-performers compared to under-performers. A positive relation between performance and tolerance would make super-performers more important, while a negative relation would make them less important. Many types of disturbances entail leaf loss and tolerance to leaf loss is associated with performance being larger than what one would assume based on the amount of leaf area loss. Tolerance can be achieved by compensating for leaf loss in terms of growth rate, which entails either allocating more new assimilates to leaves, allocating new assimilates more efficiently to leaf area (i.e. by increasing specific leaf area), or growing faster with existing leaf area (i.e. by increasing net assimilation rate). Genetic variation in tolerance and compensatory responses would allow populations to adapt to changes in disturbance events that entail leaf loss.

Individual heterogeneity could also have implications for management. Plant and animal populations are managed at many different levels ranging from harvest from natural populations to modern agricultural practices. When harvesting from natural populations, it might be beneficial to spare the individuals that are most important for future production. Individuals could be spared, either because they contribute most to population growth, because they are tolerant to harvesting (which is relevant when only part of a plant is harvested), or when they start producing less or lower quality product. The productivity of natural populations could also be increased by actively promoting those environmental conditions and genotypes that allow for high productivity, which is the basis of agriculture and common practice in forest management. To determine how this can best be done, knowledge of the causes of individual heterogeneity is necessary.

The general aim of this thesis is to identify and quantify the mechanisms that determine individual heterogeneity and to determine how this heterogeneity, in turn, affects population level processes. This aim was divided into four main questions that I addressed: (1) To what extent do individuals differ in performance? (2) What causes individual heterogeneity in performance? (3) What are the demographic consequences of individual heterogeneity? (4) Can individual differences be used to improve the management of populations? To answer these questions, we used the tropical forest understorey palm Chamaedorea elegans as a study system, of which the leaves are an important non-timber forest product that is being used in the floral industry worldwide. We collected demographic data, measured spatial variation in environmental conditions, and applied a defoliation treatment to simulate leaf harvesting, in a natural population in Chiapas, Mexico. Furthermore, we grew seedlings from different mothers from our study population in the greenhouses of Wageningen University, where we also applied a defoliation treatment.

In Chapter 2 we quantified the extent to which individuals differ in long-term growth rate, and analyzed the importance of fast growers for population growth. We reconstructed growth histories from internodes and showed that growth differences between individuals are very large and persistent in our study population. This led to large variation in life growth trajectories, with individuals of the same age varying strongly in size. This shows that not only in canopy trees but also in species in the light limited understorey growth differences can be very large. Past growth rate was found to be a very good predictor of current performance (i.e. growth and reproduction). Using an Integral Projection Model (i.e. a type of demographic model) that was based on size and past growth rate, we showed that fast-growing individuals are much more important for population growth than others: the 50% fastest growing individuals contributed almost two times as much to population growth as the 50% slowest growing individuals.

In Chapter 3 we analyzed the extent to which observed long-term growth differences can be caused by environmental heterogeneity. Short-term variation in performance was mainly driven by light availability, while soil variables and leaf damage had smaller effects, and spatial heterogeneity in light availability and soil pH were autocorrelated over time. Using individual-based simulation models, we analyzed the extent to which spatial environmental heterogeneity could explain observed long-term variation in growth, and showed that this could largely be explained if the temporal persistence of light availability and soil pH was taken into account. We also estimated long-term inter-individual variation in reproduction to be very large. We further analyzed the importance of temporal persistence in environmental variation for long-term performance differences, by analyzing the whole range of values of environmental persistence, and the strength of the effect of the environmental heterogeneity on short-term performance. We showed that long-term performance differences become large when either the strength of the effect of the environmental factor on short-term performance is large, or when the spatial variation in the environmental factor is persistent over time. This shows that an environmental factor that in a short-term study might have been dismissed as unimportant for long-term performance variation, might, in reality, contribute strongly.

In Chapter 4 we tested for genetic variation in growth potential, tolerance to leaf loss, compensatory growth responses, and if growth potential and tolerance were genetically correlated in our study population. We quantified compensatory responses with an iterative growth model that takes into account the timing of leaf loss. Genetic variation in growth potential was large, and plants compensated strongly for leaf loss, but genetic variation in tolerance and compensatory growth responses was very limited. Growth performances in defoliated and undefoliated conditions were positively genetically correlated (i.e. the same genotypes perform relatively well compared to others, both with and without the stress of leaf loss). The high genetic variation in growth potential and the positive correlation between treatments suggests that the existence of super-performing individuals in our study population likely has (at least in part) a genetic basis. These super-performing individuals, that grow fast even under the stress of leaf loss, possibly contribute disproportionately to population resistance and resilience to disturbance. The low genetic variation in tolerance and compensatory responses, however, suggests that populations might have limited ability to adapt to changes in disturbance regimes that entail increases in leaf loss. Furthermore, the high genetic variation in growth potential could potentially be used in management practices like enrichment planting.

In Chapter 5 we explore the potential of using individual heterogeneity to design smarter harvest schemes, by sparing individuals that contribute most to future productivity. We tested if fast and slow growers, and small and large individuals, responded differently to leaf loss in terms of vital rates, but found only very limited evidence for this. Using Integral Projection Models that were based on stem length and past growth rate, we simulated leaf harvest over a period of 20 years, in several scenarios of sparing individuals, which we compared to “Business as usual” (i.e. no individuals being spared, BAU). Sparing individuals that are most important for population growth, was beneficial for population size (and could, therefore, reduce extinction risk), increased annual leaf harvest at the end of the simulation period, but cumulated leaf harvest over 20 years was much lower compared to BAU. Sparing individuals that produced leaves of non-commercial size (i.e. <25cm), therefore allowing them to recover, also resulted in a lower total leaf harvest over 20 years. However, a much higher harvest (a three-fold increase) was found when only leaves of commercial size were considered. These results show that it is possible to increase yield quality and sustainability (in terms of population size) of harvesting practices, by making use of individual heterogeneity. The analytical and modeling methods that we present are applicable to any natural system from which either whole individuals, or parts of individuals, are harvested, and provide an extra tool that could be considered by managers and harvest practitioners to optimize harvest practices.

In conclusion, in this thesis, I showed that in a long-lived understorey palm growth differences are very large and persistent (Chapter 2) and that it is likely that long-term differences in reproduction are also very large (Chapter 3). I also showed that spatial heterogeneity in environmental conditions can to a large extent explain these differences and that when evaluating the environmental drivers of individual heterogeneity, it is important to take the persistence of spatial variation into account (Chapter 3). Individual heterogeneity also is partly genetically determined. I showed that genetic variation in growth potential to be large (Chapter 4), and that fast growers keep on growing fast under the stress of leaf loss (Chapters 4,5). Therefore it is likely that genetic variation contributes to long-term differences between individuals. Genetic variation for tolerance and compensatory responses was estimated to be low (Chapter 4), suggesting that the adaptive potential of our study population to changes in disturbance events that entail leaf loss might be low. I also showed that super-performing individuals are much more important for the growth of the population (Chapter 2) and that individuals that are important for future production could be used to improve the management of natural populations (Chapter 5).

This study provides improved insight into the extent of individual heterogeneity in a long-lived plant species and its environmental and genetic drivers, and clearly shows the importance of individual heterogeneity and its drivers for population processes and management practices. It also presents methods on how persistent performance differences between individuals can be incorporated into demographic tools, how these can be used to analyze individual contributions to population dynamics, to extrapolate short-term to long–term environmental effects, and to analyze smart harvesting scenarios that take differences between individuals into account. These results indicate that individual heterogeneity, underlying environmental and genetic drivers, and population processes are all related. Therefore, when evaluating the effect of environmental change on population processes, and in the design of management schemes, it is important to keep these relations in mind. The methodological tools that we presented provide a means of doing this.

Building towards a multi-dimensional genetic architecture in Caenorhabditis elegans
Sterken, Mark G. - \ 2016
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 - 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.

An evolutionary and functional genomics study of Noccaea caerulescens, a heavy metal hyperaccumulating plant species
Wang, Y. - \ 2016
University. Promotor(en): Maarten Koornneef, co-promotor(en): Mark Aarts. - Wageningen : Wageningen University - ISBN 9789462578562 - 190 p.
brassicaceae - genomics - hyperaccumulator plants - heavy metals - genes - genetic variation - genomica - hyperaccumulerende planten - zware metalen - genen - genetische variatie

Noccaea caerulescens is the only known Zn/Cd/Ni hyperaccumulator. The Ganges accession (2n = 14) has an, yet unpublished, genome size of ~319 Mb, with 29,712 predicted genes representing 15,874 gene families. This species is distributed mainly in Europe. Three ecotypes can be distinguished: two metallicolous ecotypes, resident to serpentine soil (Ni enriched) and calamine soil (Zn/Cd enriched), and a non-metallicolous ecotype, growing on regular, non-metalliferous soils. The physiological differences that underlie variation in heavy metal accumulation and tolerance are well-understood, and the molecular basis of hyperaccumulation and tolerance has been explored by transcript profiling in the presence of metals and by comparative transcriptome analysis using N. caerulescens and non-hyperaccumulators such as Arabidopsis thaliana. The genetic variation which emerged during the evolution of metal hyperaccumulation has not yet been investigated. The work described in this thesis considers the identification of genetic variation under selection for Zn/Cd hyperaccumulation and tolerance by next generation resequencing of the wild metallicolous (calamine) and non-metallicolous populations and the generation of a mutant N. caerulescens library for functional analysis. The regulation of flowering time was also investigated, using early flowering mutants selected from the mutant library.

Targets and tools for optimizing lignocellulosic biomass quality of miscanthus
Weijde, R.T. van der - \ 2016
University. Promotor(en): Richard Visser, co-promotor(en): Luisa Trindade; Oene Dolstra. - Wageningen : Wageningen University - ISBN 9789462578388 - 231 p.
miscanthus - bioethanol - biomass - biofuels - lignocellulose - fuel crops - plant breeding - cell walls - cell wall components - genetic diversity - genetic variation - biomass conversion - biobased economy - biomassa - biobrandstoffen - brandstofgewassen - plantenveredeling - celwanden - celwandstoffen - genetische diversiteit - genetische variatie - biomassaconversie

Miscanthus is a perennial energy grass characterized by a high productivity and resource-use efficiency, making it an ideal biomass feedstock for the production of cellulosic biofuels and a wide range of other biobased value-chains. However, the large-scale commercialization of converting biomass into cellulosic biofuel is hindered by our inability to efficiently deconstruct the plant cell wall. The plant cell wall is a complex and dynamic structure and its components are extensively cross-linked into an unyielding matrix. The production of biofuel depends on the extraction, hydrolysis and fermentation of cell wall polysaccharides, which currently requires energetically and chemically intensive processing operations that negatively affect the economic viability and sustainability of the industry. To address this challenge it is envisioned that the bioenergy feedstocks can be compositionally tailored to increase the accessibility and extractability of cell wall polysaccharides, which would allow a more efficient conversion of biomass into biofuel under milder processing conditions.

Extensive phenotypic and genetic diversity in cell wall composition and conversion efficiency was observed in different miscanthus species, including M. sinensis, M. sacchariflorus and interspecific hybrids between these two species. In multiple experiments a twofold increase in the release of fermentable sugars was observed in ‘high quality’ accessions compared to ‘low quality’ accessions. The exhaustive characterization of eight highly diverse M. sinensis genotypes revealed novel and distinct breeding targets for different bioenergy conversion routes. The key traits that contributed favourably to the conversion efficiency of biomass into biofuel were a high content of hemicellulosic polysaccharides, extensive cross-linking of hemicellulosic polysaccharides (revealed by a high content of trans-ferulic acids and a high ratio of arabinose-to-xylose), a low lignin content and extensive incorporation of para-coumaric acid into the lignin polymer.

Lignin is widely recognized as one of the key factors conveying recalcitrance against enzymatic deconstruction of the cell wall. The incorporation of para-coumaric acid into the lignin polymer is hypothesized to make lignin more easily degradable during alkaline pretreatment, one of the most widely applied processing methods that is used to pretreat biomass prior to enzymatic hydrolysis. Previous studies have shown that reducing lignin content is often implicated in reduced resistance of plants to lodging. We hypothesize that extensively cross-linked hemicellulosic polysaccharides may fulfil a similar function in supporting cell wall structural rigidity and increasing the content of hemicellulosic polysaccharides may be a way to reduce lignin content without adversely affecting cell wall rigidity. This strategy can be used to improve biomass quality for biobased applications, as hemicellulosic polysaccharides are more easily degradable during industrial processing than lignin. Furthermore, hemicellulosic polysaccharides adhere to cellulose, which negatively affects the level of cellulose crystallinity. Crystalline cellulose is harder to degrade than its more amorphous form. Therefore the reduction of cellulose crystallinity is another mechanism through which increasing the content of hemicellulosic polysaccharides positively contributes to cell wall degradability. These results provided new insights into the traits that may be targeted to improve the quality of lignocellulose feedstocks.

However, evaluation of complex biochemical traits for selection purposes is hindered by the fact that their accurate quantification is a costly, lengthy and laborious procedure. To overcome these limitations an accurate and high-throughput method was developed based on near-infrared spectroscopy. Through extensive calibration we developed accurate prediction models for a wide range of biomass quality characteristics, which may be readily implemented as a phenotyping tool for selection purposes.

Additionally, progress through breeding may substantially be improved by marker-assisted selection, which will reduce the need for the evaluation of genotype performance in multi-year field trials. To this end, a biparental M. sinensis mapping population of 186 individuals was developed and genotyped using a genotyping-by-sequencing approach. A total of 564 short-sequence markers were used to construct a new M. sinensis genetic map. Cell wall composition and conversion efficiency were observed to be highly heritable and quantitatively inherited properties. This is the first genetic study in miscanthus to map quantitative trait loci (QTLs) for biomass quality properties and is a first step towards the application of marker-assisted selection for biomass quality properties.

Through the evaluation of a diverse set of miscanthus genotypes in multiple locations we demonstrated that in addition to genotypic variation, growing conditions may have a substantial influence on cell wall composition and conversion efficiency. While further research is needed to identify which specific environmental parameters are responsible for the observed effects, these results clearly indicate that the environmental influence on biomass quality needs to be taken into account in order to match genotype, location and end-use of miscanthus as a lignocellulose feedstock. Moreover, significant genotype-by-environment interaction effects were observed for cell wall composition and conversion efficiency, indicating variation in environmental sensitivity across genotypes. Although the magnitude of the genotypic differences was small in comparison to genotype and environmental main effects, this affected the ranking of accession across environments. Stability analysis indicated some stable accessions performed relatively across diverse locations.

In addition to trialing miscanthus in diverse locations, we also evaluated miscanthus biomass quality under drought conditions for a number of reasons: 1) drought stress is linked to a differential expression of cell wall biosynthesis genes, 2) incidence of drought events is increasing due to climate change, 3) irrigation is likely to be uneconomical during the cultivation of miscanthus and 4) miscanthus has many characteristics that make it a crop with a good potential for cultivation on marginal soils, where abiotic stresses such as drought may prevail. Drought stress was shown to result in a large reduction in cell wall and cellulose content and a substantial increase in hemicellulosic polysaccharides and cellulose conversion rates. We hypothesized that the reduction in cellulose content was due to an increase in the production of osmolytes, which are well-known for their role in plant protection against drought. The results indicated that drought stress had a positive effect on the cell wall degradability of miscanthus biomass.

Overall the compendium of knowledge generated within the framework of this thesis provided insights into the variation in biomass quality properties in miscanthus, increased our understanding of the molecular, genetic and environmental factors influencing its conversion efficiency into biofuel and provided tools to exploit these factors to expand the use of miscanthus as a lignocellulose feedstock.

Plant responses to multiple herbivory : phenotypic changes and their ecological consequences
Li, Yehua - \ 2016
University. Promotor(en): Marcel Dicke, co-promotor(en): Rieta Gols. - Wageningen : Wageningen University - ISBN 9789462578043 - 165
brassica oleracea - brevicoryne brassicae - aphidoidea - caterpillars - insect pests - pest resistance - defence mechanisms - phenotypes - insect plant relations - parasitoids - natural enemies - herbivore induced plant volatiles - plant-herbivore interactions - genetic variation - rupsen - insectenplagen - plaagresistentie - verdedigingsmechanismen - fenotypen - insect-plant relaties - parasitoïden - natuurlijke vijanden - herbivoor-geinduceerde plantengeuren - plant-herbivoor relaties - genetische variatie

This thesis explores whether aphid-infestation interferes with the plant response to chewing herbivores and whether this impacts performance and behaviour of individual chewing insect herbivores and their natural enemies, as well as the entire insect community. I investigated this using three wild cabbage populations (Brassica oleracea) that are known to differ in inducible secondary chemistry, to reveal whether patterns were consistent.

A literature review on recent developments in the field of plant interactions with multiple herbivores (Chapter 2) addressed how plant traits mediate interactions with various species of the associated insect community and their dynamics. In addition, the mechanisms underlying phenotypic changes in response to different herbivores were discussed from the expression of defence-related genes, phytohormones and secondary metabolites in plants to their effects on the performance and behaviour of individual insects as well as the entire insect community. In Chapter 3, I investigated the effects of early-season infestation by the aphid Brevicoryne brassicae on the composition and dynamics of the entire insect community throughout the season in a garden experiment replicated in two consecutive years. Aphid infestation in the early season only affected a subset of the community, i.e. the natural enemies of aphids, but not the chewing herbivores and their natural enemies. Moreover, the effects were only significant in the first half (June & July), but waned in the second half of the season (August & September). The effect of aphid infestation on the community of natural enemies also varied among the cabbage populations. Chapter 4 investigated the effects of aphid infestation on plant direct defences against chewing herbivores in laboratory experiments by comparing the performance of chewing herbivores and their parasitoids on aphid-infested and aphid-free plants. The performance of the specialist herbivore Plutella xylostella and its parasitoid Diadegma semiclausum was better on plants infested with aphids than on aphid-free plants, whereas the performance of the generalist herbivore Mamestra brassicae and its parasitoid Microplitis mediator was not affected by aphid infestation. These results suggest that aphid induced changes in plant traits may differentially affect the performance of leaf-chewing herbivore species attacking the same host plant, and also varied among the cabbage populations. Chapter 5 examined the effects of B. brassicae aphid infestation on plant indirect defences against chewing herbivores. In a two-choice olfactometer bioassay, preference behaviour for volatiles emitted by plants infested with hosts alone and those emitted by plants infested with aphids and hosts was compared for D. semiclausum and M mediator, larval endoparasitoids of caterpillars of P. xylostella and M. brassicae, respectively. In addition, the headspace volatiles emitted by host-infested and dually-infested plants were collected and analyzed. Co-infestation with aphids differentially affected volatile-mediated foraging behaviour of the two parasitoid species in an infestation period-dependent manner. Diadegma semiclausum preferred dually infested plants over host-infested plants when aphids infested the plants for a short time period, i.e. 7 days, but the volatile preference of D. semiclausum was reversed when aphid infestation was extended to 14 days. In contrast, M. mediator consistently preferred volatiles emitted by the dually-infested plants over those emitted by host-infested plants. The patterns of preference behaviour of the two wasp species were consistent across the three cabbage populations. Interestingly, the emission rate of most volatile compounds was reduced in plants dually-infested with caterpillars and aphids compared to singly-infested with caterpillars. This study showed that aphid infestation increased plant indirect defences against caterpillars, but depended on the aphid infestation period and specific caterpillar-parasitoid association. We hypothesized a negative interference of aphid infestation on plant defences against chewing herbivores based on previously reported SA-JA antagonism. In Chapter 6, we assessed the activation of SA and JA signaling pathways in plants infested by both aphids (B. brassicae) and various caterpillar species (P. xylostella, M. brassicae and Pieris brassicae) in different time sequences by quantifying transcription levels of the SA- and JA-responsive marker genes, PR-1 and LOX respectively. The results did not provide support for SA-JA antagonism. Compared to single infestation with each of the herbivore species, dual infestation with aphid and caterpillars had no interactive effects on the transcription levels of the SA- and JA-responsive maker genes, regardless of the temporal sequence of aphid and caterpillar attack, or the identity of the attacking caterpillar species.

The findings of this thesis contribute to our understanding of plant responses to herbivory by insect species belonging to different feeding guilds and their ecological effects on other associated community members. Aphid infestation may interfere with plant direct and indirect defences against leaf-chewing herbivores at the individual species level, but the effects are species-specific and also depend on the infestation period of aphids. Early-season aphid infestation may further affect the composition of the insect community, but the effect is smaller influencing only a subset of the community compared to early infestation by chewing herbivores. The molecular mechanism underlying plant responses to both phloem-feeding and leaf-chewing herbivores are complex and require the investigation of a range of genes involved in JA- and SA-mediated defence signal transduction. Plant interact with multiple herbivores at different levels of biological organization ranging from the subcellular level to the individual and the community level, and an integrated multidisciplinary approach is required to investigate plant-insect interactions.

Natural genetic variation for regulation of photosynthesis response to light in Arabidopsis thaliana
Rooijen, R. van - \ 2016
University. Promotor(en): Maarten Koornneef, co-promotor(en): Mark Aarts; Jeremy Harbinson. - Wageningen : Wageningen University - ISBN 9789462578203 - 235 p.
arabidopsis thaliana - photosynthesis - genetic variation - light - efficiency - fotosynthese - genetische variatie - licht - efficiëntie

The efficiency of photosynthesis results from the composition and organization of the plant’s internal structural components as well as the capability of response to environmental fluctuations. This thesis aims at identifying the genetic loci that are regulating the (sub-) processes in photosynthetic acclimation to increased irradiance levels, in order to obtain the genetic information useful to breed for photosynthetic performance. It uses genome wide association studies (GWAS) to reveal which genetic loci are being exploited in nature for keeping good photosynthetic performances in natural conditions. Phenotypic variation among natural accessions in photosynthetic light use efficiency response to increased growth irradiance is related to its variation in genetics in order to identify the associated genetic loci. In Chapter 2 is described which light environment reveals most natural variation in photosynthetic performance and for which photosynthetic parameter this is. It shows different Arabidopsis accessions display different photosynthetic responses to various light environments, well relatable to genetic differences. A candidate gene list for the direct response to increased growth irradiance was revealed after performing genome wide association analysis. Chapter 3 elaborates on the genome wide association results by visualizing the dynamics of the associated genetic loci over the time course of the photosynthetic response to increased irradiance. It shows it is possible to simplify the complexity of photosynthetic physiology as well as the genetic analysis in such way to confirm the causal genes underlying the associated loci, by confirming this for the YELLOW SEEDLING 1 (YS1) gene, a gene encoding a Pentatrico-Peptide-Repeat (PPR) protein involved in RNA editing of plastid-encoded genes essential for photosystems I and II. Genetic variation for any trait can be on the transcriptional level or on the functional level. In Chapter 4, the gene regulation in three Arabidopsis accessions with contrasting photosynthesis efficiency responses to increased irradiance is studied. These differences in photosynthesis efficiency are associated to differences in activation extents of heat responsive genes as well as to differences in the presence of a gene activation pathway acting on membrane lipid remodelling, suggested to maintain balanced cellular phosphate concentrations. Chapter 5 confirms the significance of maintaining balanced cellular phosphate concentrations for photosynthesis efficiency responses to increased irradiance. It describes how genome wide association mapping and linkage mapping combine to reveal genetic epistatic interactions between PHOSPHATIDIC ACID PHOPSPHOHYDROLASE 2 (PAH2, phosphate metabolism gene) and ASPARAGINE SYNTHETASE 2 (ASN2, nitrogen metabolism gene), both acting in the delivery of orthophosphate in the chloroplast. In conclusion this thesis contributes new insights into the physiological and molecular pathways underlying photosynthesis responses to increased growth irradiances.

Herkomst en migratie van Nederlandse edelherten en wilde zwijnen : een basiskaart van de genetische patronen in Nederland en omgeving
Groot, G.A. de; Spek, G.J. ; Bovenschen, J. ; Laros, I. ; Meel, Tom van; Jansman, H.A.H. - \ 2016
Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2724) - 71 p.
cervus elaphus - sus scrofa - migration - genetic variation - wildlife conservation - netherlands - migratie - genetische variatie - wildbescherming - nederland
De laatste jaren worden in toenemende mate incidentele waarnemingen van edelherten en wilde zwijnen buiten de toegewezen leefgebieden gedaan. De vraag is vervolgens of dit om natuurlijke immigratie vanuit (niet-omrasterde) leefgebieden in binnen- of buitenland gaat en waar ze dan vandaan zijn gekomen, of dat het een ontsnapt of losgelaten dier betreft. Om deze vraag in de toekomst in voorkomende gevallen effectief te kunnen beantwoorden, stelde Alterra in opdracht van BIJ12 – Faunafonds en Vereniging Het Edelhert een landelijke genetische referentiedatabase op van de zwijnen- en edelhertenpopulaties in Nederland en nabijgelegen populaties in België en Duitsland. In dit rapport worden de mogelijkheden van deze databases voor herkomstbepalingen nader onderzocht. Tevens geeft dit onderzoek, op basis van de verkregen databases, een overzicht van de genetische vitaliteit van de Nederlandse populaties van beide soorten met betrekking tot diversiteit, inteeltrisico’s en uitwisselingsmogelijkheden.
Conservation genetics of the frankincense tree
Bekele, A.A. - \ 2016
University. Promotor(en): Frans Bongers, co-promotor(en): Rene Smulders; K. Tesfaye Geletu. - Wageningen : Wageningen University - ISBN 9789462576865 - 158 p.
boswellia - genomes - dna sequencing - tropical forests - genetic diversity - genetic variation - genetics - forest management - plant breeding - genomen - dna-sequencing - tropische bossen - genetische diversiteit - genetische variatie - genetica - bosbedrijfsvoering - plantenveredeling

Boswellia papyrifera is an important tree species of the extensive Combretum-Terminalia dry tropical forests and woodlands in Africa. The species produces a frankincense which is internationally traded because of its value as ingredient in cosmetic, detergent, food flavor and perfumes productions, and because of its extensive use as incense during religious and cultural ceremonies in many parts of the world. The forests in which B. papyrifera grows are increasingly overexploited at the expense of the economic benefit and the wealth of ecological services they provide. Populations of B. papyrifera have declined in size and are increasingly fragmented. Regeneration has been blocked for the last 50 years in most areas and adult productive trees are dying. Projections showed a 90% loss of B. papyrifera trees in the coming 50 years and a 50% loss of frankincense production in 15 years time.

This study addressed the conservation genetics of B. papyrifera. Forty six microsatellite (SSR) markers were developed for this species, and these genetic markers were applied to characterize the genetic diversity pattern of 12 B. papyrifera populations in Ethiopia. Next to this, also the generational change in genetic diversity and the within-population genetic structure (FSGS) of two cohort groups (adults and seedlings) were studied in two populations from Western Ethiopia. In these populations seedlings and saplings were found and natural regeneration still takes place, a discovery that is important for the conservation of the species.

Despite the threats the populations are experiencing, ample genetic variation was present in the adult trees of the populations, including the most degraded populations. Low levels of population differentiation and isolation-by-distance patterns were detected. Populations could be grouped into four genetic clusters: the North eastern (NE), Western (W), North western (NW) and Northern (N) part of Ethiopia. The clusters corresponded to environmentally different conditions in terms of temperature, rainfall and soil conditions. We detected a low FSGS and found that individuals are significantly related up to a distance of 60-130 m.

Conservation of the B. papyrifera populations is urgently needed. The regeneration bottlenecks in most existing populations are an urgent prevailing problem that needs to be solved to ensure the continuity of the genetic diversity, species survival and sustainable production of frankincense. Local communities living in and around the forests should be involved in the use and management of the forests. In situ conservation activities will promote gene flow among fragmented populations and scattered remnant trees, so that the existing level of genetic diversity may be preserved. Geographical distance among populations is the main factor to be considered in sampling for ex situ conservation. A minimum of four conservation sites for B. papyrifera is recommended, representing each of the genetic clusters. Based on the findings of FSGS analyses, seed collection for ex situ conservation and plantation programmes should come from trees at least 100 m, but preferably 150 m apart.

Genetic variation in plant chemistry : consequences for plant-insect interactions
Geem, Moniek van - \ 2016
University. Promotor(en): Wim van der Putten; J.A. Harvey, co-promotor(en): Rieta Gols. - Wageningen : Wageningen University - ISBN 9789462576681 - 141 p.
phytochemistry - plant composition - genetic variation - insect plant relations - interactions - defence mechanisms - soil biology - fytochemie - plantensamenstelling - genetische variatie - insect-plant relaties - interacties - verdedigingsmechanismen - bodembiologie

Plants form the basis of many food webs and are consumed by a wide variety of organisms, including herbivorous insects. Over the course of evolution, plants have evolved mechanisms to defend themselves against herbivory, whereas herbivorous insects have evolved counter-mechanisms to overcome these defences (a.k.a. co-evolutionary arms races). Plant-insect interactions are not restricted to plants and their herbivores (bi-trophic interactions), but also involve natural enemies of the herbivores such as parasitoids and predators (tri-trophic interactions). Plant quality can affect the quality of the host or prey for parasitoids and predators, respectively. In addition, other plant traits are important in providing shelter, alternative food sources, or chemical cues that can be used for host/prey location. Moreover, as plants reside in both soil and air, they mediate interactions between organisms above- and belowground through changes in plant quality. Plant quality is determined by secondary metabolites and morphological traits that may negatively affect the performance of insects, as well as by primary metabolites that plants produce in order to grow, develop and reproduce, which also provide essential nutrients for insects.

Natural plant populations often exhibit genetic variation in various plant traits that include, amongst others, primary and secondary chemistry. Genetic variation in plant defence traits, such as the production of secondary metabolites, can be under selection pressure from a suite of biotic and abiotic factors that vary in space and time. Herbivorous insects may encounter a wide range of plant metabolites because the total concentrations of primary and secondary metabolites and the concentrations of individual compounds vary between genetically different plants. Also as a consequence of genetic variation, plants can respond differently to herbivory in terms of induced defence chemistry and re-allocation of metabolites.

The main aim of this thesis was to study how genetic variation in plant chemistry affects (multi)trophic interactions between wild cabbage plants and associated insects, both above- and belowground. As a model system I used five naturally occurring populations of wild cabbage (Brassica oleracea) located in the Dorset area in the UK. These populations have been shown to genetically differ in their defence chemistry profiles even though they are located in relatively close proximity to each other. Wild cabbages belong to the Brassicaceae, a plant family that is characterized by the production of glucosinolates, a group of secondary metabolites. Together with the enzyme myrosinase they form the chemical defence system of Brassicaceous plants including wild cabbage. Glucosinolates and myrosinases are stored separately in plant tissues but upon tissue damage they come into contact with each other upon which the glucosinolates are hydrolysed into potentially toxic break down products. The wild cabbage populations used in this thesis differ in their total glucosinolate concentrations as well as in the expression of individual glucosinolates.

In chapter 1 I describe plant-insect interactions in a multi-trophic framework, including both the above- and belowground compartments. Genetic variation in plant traits is introduced as the main topic of this thesis, and I present the main aim and outline of my work.

In chapter 2 I discuss how aboveground-belowground interactions influence the evolution and maintenance of genetic variation in plant defence chemistry. I review literature on AG-BG interactions as selection pressures for genetic variation, discuss hypotheses about plant mediation of AG-BG interactions, identify gaps in our knowledge such as the influence of spatial-temporal variation in AG-BG interactions, and in the end present new data on genetic variation in secondary chemistry of wild cabbage and related species.

The co-evolutionary arms race between plants and insects has resulted in adaptations in herbivores to cope with plant defence traits. Some insect herbivore species concentrate or sequester secondary metabolites from their food plant and use them in defence against their own enemies. In chapter 3 I studied whether sequestration of glucosinolates by a specialist herbivore is an effective defence mechanism against a generalist predatory bug. I used the sequestering herbivore Athalia rosae as one prey species, and the non-sequestering herbivore Pieris rapae as the control prey species. I compared the performance of the predatory stink bug Podisus maculiventris on these two prey species. As an extra factor, the two prey species were each reared on three different wild cabbage populations to test if plant population would have an effect on the predator through the sequestering herbivore. I found no consistent effect of plant population on the performance of the predator, and prey species only marginally affected its performance. Based on the results I suggest that in some trophic interactions sequestration is not an effective defence mechanism but merely an alternative way of harmlessly dealing with plant secondary metabolites.

In addition to aboveground plant-insect interactions, belowground interactions were considered as well. To test whether the performance of the belowground specialist herbivore Delia radicum, of which the larvae feed on root tissues, was influenced by population-related variation in defence chemistry, I reared this species on the five wild cabbage populations (chapter 4). Chemical analyses of root tissues revealed that there were differences amongst the populations in plant primary (amino acids and sugars) and secondary (glucosinolates) chemistry, but this did not affect the performance of the root herbivore, suggesting that D. radicum is well adapted to a wide range of total concentrations and concentrations of individual metabolites.

Whereas in chapters 3 and 4 I only focused on one compartment (aboveground and belowground respectively), in chapter 5 I included both compartments in one experiment. I studied the effect of belowground herbivory by larvae of the root fly D. radicum on the performance of an aboveground multi-trophic food chain, and whether this effect differed among three wild cabbage populations. I found that belowground herbivory differentially affected the performances of a specialist aboveground herbivore, the diamondback moth Plutella xylostella, and its parasitoid, Cotesia vestalis, with the parasitoid being more affected than the herbivore. Their performance also differed between the wild cabbage populations, often in interaction with the presence/absence of the belowground herbivore. For both the above- and belowground herbivore I found correlations between performance and plant chemistry, which differed between the insect species and also between males and females.

In chapter 6 I discuss the results of my experiments in relation to other studies. I finish with a general conclusion about my work and provide some ideas for future studies that could contribute to our knowledge in the field of (multi)trophic above-belowground interactions with regard to genetic variation in plant chemistry.

In my thesis I show that genetic variation in plant chemistry can affect the outcome of above-belowground plant-insect interactions. Herbivores and higher trophic levels were differently affected by the wild cabbage populations, and this difference was also influenced by the location of herbivory (i.e. aboveground or belowground). In both chapter 4 and chapter 5 I found no strong, unidirectional links between plant chemistry and insect performance, suggesting that other metabolites may have played a role in the observed differential effects of the wild cabbage populations. I also show that sequestration of plant allelochemicals in some herbivores is an alternative way of harmlessly dealing with plant secondary metabolites instead of an effective defence mechanism against predators (chapter 3).

Genomic selection in egg-laying chickens
Heidaritabar, M. - \ 2016
University. Promotor(en): Martien Groenen, co-promotor(en): John Bastiaansen. - Wageningen : Wageningen University - ISBN 9789462576704 - 220 p.
hens - genomics - genetic variation - selective breeding - quantitative traits - breeding value - animal genetics - animal breeding - hennen - genomica - genetische variatie - selectief fokken - kwantitatieve kenmerken - fokwaarde - diergenetica - dierveredeling

Abstract

Heidaritabar, M. (2016). Genomic selection in egg-laying chickens. PhD thesis, Wageningen University, the Netherlands

In recent years, prediction of genetic values with DNA markers, or genomic selection (GS), has become a very intense field of research. Many initial studies on GS have focused on the accuracy of predicting the genetic values with different genomic prediction methods. In this thesis, I assessed several aspects of GS. I started with evaluating results of GS against results of traditional pedigree-based selection (BLUP) in data from a selection experiment that applied both methods side by side. The impact of traditional selection and GS on the overall genome variation as well as the overlap between regions selected by GS and the genomic regions predicted to affect the traits were assessed. The impact of selection on genome variation was assessed by measuring changes in allele frequencies that allowed the identification of regions in the genome where changes must be due to selection. These frequency changes were shown to be larger than what could be expected from random fluctuations, indicating that selection is really affecting the allele frequencies and that this effect is stronger in GS compared with BLUP. Next, concordance was tested between the selected regions and regions that affect the traits, as detected by a genome-wide association study. Results showed a low concordance overall between the associated regions and the selected regions. However, markers in associated regions did show larger changes in allele frequencies compared with the average changes across the genome. The selection experiment was performed using a medium density of DNA markers (60K). I subsequently explored the potential benefits of whole-genome sequence data for GS by comparing prediction accuracy from imputed sequence data with the accuracy obtained from the 60K genotypes. Before sequencing, the selection of key animals that should be sequenced to maximize imputation accuracy was assessed with the original 60K genotypes. The accuracy of genotype imputation from lower density panels using a small number of selected key animals as reference was compared with a scenario where random animals were used as the reference population. Even with a very small number of animals as reference, reasonable imputation accuracy could be obtained. Moreover, selecting key animals as reference considerably improved imputation accuracy of rare alleles compared with a set of random reference animals. While imputation from a small reference set was successful, imputation to whole-genome sequence data hardly improved genomic prediction accuracy compared with the predictions based on 60K genotypes. Using only those markers from the whole-genome sequence that are more likely to affect the phenotype was expected to remove noise from the data, but resulted in slightly lower prediction accuracy compared with the complete genome sequence. Finally, I evaluated the inclusion of dominance effects besides additive effects in GS models. The proportion of variance due to additive and dominance effects were estimated for egg production and egg quality traits of a purebred line of layers. The proportion of dominance variance to the total phenotypic variance ranged from 0 to 0.05 across traits. Also, the impact of fitting dominance besides additive effects on prediction accuracy was investigated, but was not found to improve accuracy of genomic prediction of breeding values.

Breeding against infectious diseases in animals
Rashidi, H. - \ 2016
University. Promotor(en): Johan van Arendonk, co-promotor(en): Herman Mulder; P.K. Mathur. - Wageningen University - ISBN 9789462576452 - 179 p.
livestock - infectious diseases - animal breeding - selective breeding - disease resistance - tolerance - genetic variation - breeding value - genetic correlation - traits - genomics - animal genetics - vee - infectieziekten - dierveredeling - selectief fokken - ziekteresistentie - tolerantie - genetische variatie - fokwaarde - genetische correlatie - kenmerken - genomica - diergenetica

Infectious diseases in farm animals are of major concern because of animal welfare, production costs, and public health. Farms undergo huge economic losses due to infectious disease. The costs of infections in farm animals are mainly due to production losses, treatment of infected animals, and disease control strategies. Control strategies, however, are not always successful. Selective breeding for the animals that can mount a defence against infection could therefore be a promising approach. Defensive ability of an animal has two main mechanisms: resistance (ability to control the pathogen burden) and tolerance (ability to maintain performance when pathogen burden increases). When it is difficult to distinguish between resistance and tolerance, defensive ability is measured as resilience that is the ability to maintain performance during a disease outbreak regardless of pathogen burden. Studies have focused on the genetics of resistance and resilience with little known about the genetics of tolerance and its relationship with resistance and resilience. The objectives of this thesis were to: 1) estimate the genetic variation in resistance, tolerance, and resilience to infection in order to assess the amenability of these traits for selective breeding in farm animals, 2) estimate the genetic correlation between resistance, tolerance and resilience and 3) detect genomic regions associated with resistance, tolerance, and resilience.

In chapter 2, we studied the variation among sows in response to porcine reproductive and respiratory syndrome (PRRS). First a statistical method was developed to detect PRRS outbreaks based on reproduction records of sows. The method showed a high sensitivity (78%) for disease phases. Then the variation of sows in response to PRRS was quantified using 2 models on the traits number of piglets born alive (NBA) and number of piglets born dead (LOSS): 1) bivariate model considering the trait in healthy and disease phases as different traits, and 2) reaction norm model modelling the response of sows as a linear regression of the trait on herd-year-week estimates of NBA. Trait correlations between healthy and disease phases deviated from unity (0.57±0.13 – 0.87±0.18). The repeatabilities ranged from 0.07±0.027 to 0.16±0.005. The reaction norm model had higher predictive ability in disease phase compared to the bivariate model.

In chapter 3 we studied 1) the genetic variation in resistance and tolerance of sheep to gastrointestinal nematode infection and 2) the genetic correlation between resistance and tolerance. Sire models on faecal nematode egg count (FEC), IgA, and pepsinogen were used to study the genetic variation in resistance. Heritability for resistance traits ranged from 0.19±0.10 to 0.59±0.20. A random regression model was used to study the reaction norm of sheep body weight on FEC as an estimate of tolerance to nematode infection. We observed a significant genetic variance in tolerance (P<0.05). Finally a bivariate model was used to study the genetic correlation between resistance and tolerance. We observed a negative genetic correlation (-0.63±0.25) between resistance and tolerance.

In chapter 4, we studied the response to selection in resistance and tolerance when using estimated breeding values for resilience. We used Monte Carlo simulation to generate 100 half-sib families with known breeding values for resistance (pathogen burden) and tolerance. We used selection index theory to predict response to selection for resistance and tolerance: 1) when pathogen burden is known and selection is based on true breeding values for resistance and tolerance and 2) when pathogen burden is unknown and selection is based on estimated breeding values for resilience. Using EBV for resilience in absence of records for pathogen burden resulted in favourable responses in resistance and tolerance to infections, with more emphasis on tolerance than on resistance. However, more genetic gain in resistance and tolerance could be achieved when pathogen burden was known.

In chapter 5 we studied genomics regions associated with resistance, resilience, and tolerance to PRRS. Resistance was modelled as sire effect on area under the PRRS viremia curve up to 14 days post infection (AUC14). Resilience was modelled as sire effects on daily growth of pigs up to 28 days post infection (ADG28). Tolerance was modelled as the sire effect on the regression of ADG28 on AUC14. We identified a major genomics region on chromosome 4 associated with resistance and resilience to PRRS. We also identified genomics regions on chromosome 1 associated with tolerance to PRRS.

In the general discussion (chapter 6) I discussed: 1) response to infection as a special case of genotype by environment interaction, 2) random regression model as a statistical tool for studying response to disease, 3) advantages and requirements of random regression models, and 4) selective breeding of farm animals for resistance, tolerance, and resilience to infections. I concluded that random regression is a powerful approach to estimate response to infection in animals. If the adequate amount of data is available random regression model could estimate breeding values of animals more accurately compared to other models. I also concluded that before including resistance and tolerance into breeding programs, breeders should make sure about the added values of including these traits on genetic progress. Selective breeding for resilience could be a pragmatic approach to simultaneously improve resistance and tolerance.

Selectie en genetische variatie in een fokprogramma
Oldenbroek, Kor ; Maurice - Van Eijndhoven, Myrthe - \ 2015
Zeldzaam huisdier 40 (2015)4. - ISSN 0929-905X - p. 14 - 17.
dierveredeling - veredelingsprogramma's - genetische variatie - selectie - zeldzame rassen - heritability - inteelt - verwantschap - groninger paard - animal breeding - breeding programmes - genetic variation - selection - rare breeds - inbreeding - kinship - groningen horse
In drie voorgaande artikelen in deze serie zijn achtereenvolgens het fokdoel, de registratie van gegevens en de basisprincipes van de erfelijkheid besproken. In dit laatste artikel wordt het belang van genetische variatie en de selectie van ouderdieren besproken. Twee belangrijke elementen in het fokprogramma van een zeldzaam ras.
Natural genetic variation in Arabidopsis thaliana photosynthesis
Flood, P.J. - \ 2015
University. Promotor(en): Maarten Koornneef, co-promotor(en): Mark Aarts; Jeremy Harbinson. - Wageningen : Wageningen University - ISBN 9789462575004 - 278
arabidopsis thaliana - genetische variatie - fotosynthese - genomen - chlorofyl - fenotypen - genetic variation - photosynthesis - genomes - chlorophyll - phenotypes

Oxygenic photosynthesis is the gateway of the sun’s energy into the biosphere, it is where light becomes life. Genetic variation is the fuel of evolution, without it natural selection is powerless and adaptation impossible. In this thesis I have set out to study a relatively unexplored field which sits at the intersection of these two topics, namely natural genetic variation in plant photosynthesis. To begin I reviewed the available literature (Chapter 2), from this it became clear that the main bottleneck restricting progress was the lack of high-throughput phenotyping platforms for photosynthesis. To address this an automated high-throughput chlorophyll fluorescence phenotyping system was developed, which could measure 1440 plants in less than an hour for ΦPSII, a measure of photosynthetic efficiency (Chapter 3). Using this phenotyping platform I screened five populations of Arabidopsis thaliana. Three of these populations resulted from bi-parental crosses and segregated for only two genomes, using these I conducted family mapping (Chapter 4). The final two populations were composed of natural, field collected, accessions and were analysed using a genome wide association approach (Chapter 5). The family mapping approach had greater statistical power due to within population replication and the genome wide association approach had higher mapping resolution due to historical recombination. Both approaches were used to identify genomic regions (loci) which were responsible for some of the variation in photosynthesis observed. The number and average effect of these loci was used to infer the genetic architecture of photosynthesis as a highly complex polygenic trait for which there are many loci of very small effect. In addition to screening these large populations a smaller subset of 18 lines was assayed for natural variation in phosphorylation of photosystem II (PSII) proteins in response to changing light (Chapter 6). This exploratory study indicated that this process shows considerable variation and may be important for adaptation of the photosynthetic apparatus to photosynthetic extremes. The genetic mapping studies just described, focus exclusively on genetic variation in the nuclear genome, whilst this contains the majority of the plants genetic information there is also a store of genetic information in the chloroplast and mitochondria. These genetic repositories contain genes which are essential for photosynthesis and energy metabolism. Any variation in these genes could have a large impact on photosynthesis. To study natural variation in these genomes I developed a new population of reciprocal nuclear-organellar hybrids (cybrids) which could be used to study the effect of genetic variation in organelles whilst controlling for nuclear genetic variation (Chapter 7). Preliminary results indicate that this resource will be of great use in disentangling natural genetic variation in nucleo-organelle interactions. Finally I looked at one chloroplast encoded photosynthetic mutation in more detail (Chapter 8). This mutation had evolved in response to herbicide application and had spread along British railways. When studying this population of resistant plants I found empirical evidence for organelle mediated nuclear genetic hitchhiking. This is a previously undescribed evolutionary phenomenon and is likely to be quite common. In conclusion there is an abundance of genetic variation in photosynthesis which can be used to improve the trait for agriculture and provide insights into novel evolutionary phenomena in the field.

Plantenveredeling Domesticatie en voedselzekerheid
Jacobsen, Evert - \ 2015
plant breeding - varieties - domestication - plant breeding methods - genetic variation - food crops - genetic resources - resistance breeding - food security
The hybrid nature of pig genomes : unraveling the mosaic haplotype structure in wild and commercial Sus scrofa populations
Bosse, M. - \ 2015
University. Promotor(en): Martien Groenen, co-promotor(en): Hendrik-Jan Megens; Ole Madsen. - Wageningen : Wageningen University - ISBN 9789462573000 - 253
dieren - varkens - dierveredeling - genomen - hybridisatie - sus scrofa - haplotypen - genomica - populaties - genetische variatie - animals - pigs - animal breeding - genomes - hybridization - haplotypes - genomics - populations - genetic variation - cum laude
cum laude graduation
Vaak scrapieresistentie bij Nederlandse Toggenburgers
Hoving-Bolink, A.H. ; Windig, J.J. ; Koekoek, A. ; Hoekstra, H. ; Oldenbroek, J.K. ; Langeveld, J. - \ 2015
Zeldzaam huisdier 40 (2015)1. - ISSN 0929-905X - p. 20 - 21.
rassen (dieren) - geitenrassen - zeldzame rassen - genetische variatie - scrapie - ziekteresistentie - nederlandse toggenburgergeit - geitenziekten - dierveredeling - toegepast onderzoek - breeds - goat breeds - rare breeds - genetic variation - disease resistance - dutch toggenburg - goat diseases - animal breeding - applied research
Zeldzame Nederlandse rassen zijn niet alleen onderdeel van ons cultureel erfgoed, maar hebben soms ook een verrassende genetische variant. Zo is sinds een paar jaar bekend dat er een allel bestaat dat bescherming biedt tegen scrapie. In onderzoek van Wageningen UR met de geitensector blijkt dat het relatief kleine ras de Nederlandse Toggenburger veel dieren kent met het scrapieresistentie allel.
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