Worms under stress: unravelling genetic complex traits through perturbation

M. Rodriguez Sanchez

Research output: Thesisinternal PhD, WU

Abstract

The genetic architecture of an organism could be considered ‘the most amazing piece of engineering’ existing in nature. Looking from a certain distance, the genetic complexity of an organism could be described as an immense jigsaw puzzle. As in a real jigsaw, the connection between two pieces will suggest or bring us to the third one and so on. The genetic responses to perturbation reveal interactions between many alleles of which effects are not that noticeable under optimal conditions.

In the general introduction of this thesis (chapter 1), the reader can find a brief overview of the model organismCaenorhabditis elegans and how this nematode has increasingly taken a crucial position in relevant biological studies over the last few decades. Moreover, the outline of this thesis is extensively described in this section.

My thesis brings together examples of perturbation in C. elegans at three different levels: phenotypic perturbation, as a result of genetic variation in Recombinant Inbred Lines (RILs), genetic perturbation, performed by genome combinations (RILs), introgressed fragments of exogenous genome in introgression lines (ILs) and induced mutations, and environmental perturbation (i.e. heat stress conditions). We have combined these perturbations in order to increase the potential of these tools in investigating genetic variation in C. elegans. Our RILs and ILs are combinations of two of the most divergent genomes of C. elegans strains these are Bristol N2 and CB4856 (Hawaii).

The translation of this knowledge to research in human disease is of great interest since many complex diseases are regulated by small effect genes that occur during stress or aging. This thesis expounds how C. elegans has gained a prominent position as a model organism for studying the genetic of complex disease pathways. Here I have presented different studies and concluded that environmental stress perturbation experiments in C. elegans represents a crucial implement in the way to increase our understanding of the genetics of human diseases such as Huntington’s disease, Parkinson’s disease, Alzheimer’s disease or cancer. We performed an exhaustive analysis of the current experiments and new insights that used C. elegans as a model organism for complex human diseases. This thesis contains a detailed study where we analyze the past, discuss about the present and suggest new possibilities for the future of C. elegans as a model organism (chapter 2).

The experimental sections of the thesis consist of quantitative genetic analyses of genomic regions associated with phenotypic variations observed under a certain perturbation. We use genotypic and phenotypic data measured in our RILs and ILs together with QTL mapping techniques to estimate the position of candidate loci, which are associated with a phenotypic variation.

In C. elegans, β-catenin genebar-1plays an important role in vulva development whereas in humans it plays an important role in cancer progression.In our study in bar-1 mutant RILs, we constructed different combinations of two genomes in C. elegans strains. The lack of β-catenin was included to the combination of the two genomes. These mutant RILs point us to the presence of polymorphic modifiers of vulva development in C. elegans and pave the way towards the development of a new tool to uncover cryptic variation in two genetic variants (chapter 3).

To gain insight into the subtle effects of natural variants and more concretely into the genetics of heat-shock recovery, we exposed RILs to heat-stress. We investigated here the hormesis effects on life span and offspring, and described associated loci in C. elegans (chapter 4). Our observations showed that there is natural variation in hormesis effects on life span for heat-shock.

As a combination of environmental and genetic perturbation, we studied the effects of heat stress in C. elegans combined with ILs (chapter 5). We demonstrate the importance of the chromosome IV and a concrete locus in heat stress response. In order to identify the role of a locus distal to chromosomeIV, we selected a set of ILs containing a fragment of CB4856 (Hawaii) genome introgressed in a N2 (Bristol) background around this candidate locus previously described in other studies. We studied gene expression in normal and heat stress conditions by quantitative RT-PCR. Through this study we are able to confirm the role of the locus distal to chromosome IV in heat stress response.

In the general discussion (chapter 6) I discuss the final results of the thesis and put them into the perspective of the current progresses in genetics studies of C. elegans and how stress response is associated with variations in pathways and thus in cellular and molecular process in health and/or disease.  

Overall this thesis demonstrates at least a part of the incredible potential of C. elegans as a complex genetic model using quantitative genetic analyses, which complement more established forward genetic screens.

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • Bakker, Jaap, Promotor
  • Kammenga, Jan, Co-promotor
Award date14 Mar 2014
Place of PublicationWageningen
Publisher
Print ISBNs9789461738516
Publication statusPublished - 2014

Fingerprint

inbred lines
heat stress
introgression
loci
genome
human diseases
organisms
vulva
quantitative genetics
Hawaii
phenotypic variation
chromosomes
mutants
genetic variation
neoplasms
modifiers (genes)
human development
Parkinson disease
Alzheimer disease
mutagenesis

Keywords

  • caenorhabditis elegans
  • genetics
  • animal models
  • stress
  • heat stress
  • stress response
  • genetic variation

Cite this

Rodriguez Sanchez, M. (2014). Worms under stress: unravelling genetic complex traits through perturbation. Wageningen: Wageningen University.
Rodriguez Sanchez, M.. / Worms under stress: unravelling genetic complex traits through perturbation. Wageningen : Wageningen University, 2014. 124 p.
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abstract = "The genetic architecture of an organism could be considered ‘the most amazing piece of engineering’ existing in nature. Looking from a certain distance, the genetic complexity of an organism could be described as an immense jigsaw puzzle. As in a real jigsaw, the connection between two pieces will suggest or bring us to the third one and so on. The genetic responses to perturbation reveal interactions between many alleles of which effects are not that noticeable under optimal conditions. In the general introduction of this thesis (chapter 1), the reader can find a brief overview of the model organismCaenorhabditis elegans and how this nematode has increasingly taken a crucial position in relevant biological studies over the last few decades. Moreover, the outline of this thesis is extensively described in this section. My thesis brings together examples of perturbation in C. elegans at three different levels: phenotypic perturbation, as a result of genetic variation in Recombinant Inbred Lines (RILs), genetic perturbation, performed by genome combinations (RILs), introgressed fragments of exogenous genome in introgression lines (ILs) and induced mutations, and environmental perturbation (i.e. heat stress conditions). We have combined these perturbations in order to increase the potential of these tools in investigating genetic variation in C. elegans. Our RILs and ILs are combinations of two of the most divergent genomes of C. elegans strains these are Bristol N2 and CB4856 (Hawaii). The translation of this knowledge to research in human disease is of great interest since many complex diseases are regulated by small effect genes that occur during stress or aging. This thesis expounds how C. elegans has gained a prominent position as a model organism for studying the genetic of complex disease pathways. Here I have presented different studies and concluded that environmental stress perturbation experiments in C. elegans represents a crucial implement in the way to increase our understanding of the genetics of human diseases such as Huntington’s disease, Parkinson’s disease, Alzheimer’s disease or cancer. We performed an exhaustive analysis of the current experiments and new insights that used C. elegans as a model organism for complex human diseases. This thesis contains a detailed study where we analyze the past, discuss about the present and suggest new possibilities for the future of C. elegans as a model organism (chapter 2). The experimental sections of the thesis consist of quantitative genetic analyses of genomic regions associated with phenotypic variations observed under a certain perturbation. We use genotypic and phenotypic data measured in our RILs and ILs together with QTL mapping techniques to estimate the position of candidate loci, which are associated with a phenotypic variation. In C. elegans, β-catenin genebar-1plays an important role in vulva development whereas in humans it plays an important role in cancer progression.In our study in bar-1 mutant RILs, we constructed different combinations of two genomes in C. elegans strains. The lack of β-catenin was included to the combination of the two genomes. These mutant RILs point us to the presence of polymorphic modifiers of vulva development in C. elegans and pave the way towards the development of a new tool to uncover cryptic variation in two genetic variants (chapter 3). To gain insight into the subtle effects of natural variants and more concretely into the genetics of heat-shock recovery, we exposed RILs to heat-stress. We investigated here the hormesis effects on life span and offspring, and described associated loci in C. elegans (chapter 4). Our observations showed that there is natural variation in hormesis effects on life span for heat-shock. As a combination of environmental and genetic perturbation, we studied the effects of heat stress in C. elegans combined with ILs (chapter 5). We demonstrate the importance of the chromosome IV and a concrete locus in heat stress response. In order to identify the role of a locus distal to chromosomeIV, we selected a set of ILs containing a fragment of CB4856 (Hawaii) genome introgressed in a N2 (Bristol) background around this candidate locus previously described in other studies. We studied gene expression in normal and heat stress conditions by quantitative RT-PCR. Through this study we are able to confirm the role of the locus distal to chromosome IV in heat stress response. In the general discussion (chapter 6) I discuss the final results of the thesis and put them into the perspective of the current progresses in genetics studies of C. elegans and how stress response is associated with variations in pathways and thus in cellular and molecular process in health and/or disease.   Overall this thesis demonstrates at least a part of the incredible potential of C. elegans as a complex genetic model using quantitative genetic analyses, which complement more established forward genetic screens.",
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Rodriguez Sanchez, M 2014, 'Worms under stress: unravelling genetic complex traits through perturbation', Doctor of Philosophy, Wageningen University, Wageningen.

Worms under stress: unravelling genetic complex traits through perturbation. / Rodriguez Sanchez, M.

Wageningen : Wageningen University, 2014. 124 p.

Research output: Thesisinternal PhD, WU

TY - THES

T1 - Worms under stress: unravelling genetic complex traits through perturbation

AU - Rodriguez Sanchez, M.

N1 - WU thesis 5701

PY - 2014

Y1 - 2014

N2 - The genetic architecture of an organism could be considered ‘the most amazing piece of engineering’ existing in nature. Looking from a certain distance, the genetic complexity of an organism could be described as an immense jigsaw puzzle. As in a real jigsaw, the connection between two pieces will suggest or bring us to the third one and so on. The genetic responses to perturbation reveal interactions between many alleles of which effects are not that noticeable under optimal conditions. In the general introduction of this thesis (chapter 1), the reader can find a brief overview of the model organismCaenorhabditis elegans and how this nematode has increasingly taken a crucial position in relevant biological studies over the last few decades. Moreover, the outline of this thesis is extensively described in this section. My thesis brings together examples of perturbation in C. elegans at three different levels: phenotypic perturbation, as a result of genetic variation in Recombinant Inbred Lines (RILs), genetic perturbation, performed by genome combinations (RILs), introgressed fragments of exogenous genome in introgression lines (ILs) and induced mutations, and environmental perturbation (i.e. heat stress conditions). We have combined these perturbations in order to increase the potential of these tools in investigating genetic variation in C. elegans. Our RILs and ILs are combinations of two of the most divergent genomes of C. elegans strains these are Bristol N2 and CB4856 (Hawaii). The translation of this knowledge to research in human disease is of great interest since many complex diseases are regulated by small effect genes that occur during stress or aging. This thesis expounds how C. elegans has gained a prominent position as a model organism for studying the genetic of complex disease pathways. Here I have presented different studies and concluded that environmental stress perturbation experiments in C. elegans represents a crucial implement in the way to increase our understanding of the genetics of human diseases such as Huntington’s disease, Parkinson’s disease, Alzheimer’s disease or cancer. We performed an exhaustive analysis of the current experiments and new insights that used C. elegans as a model organism for complex human diseases. This thesis contains a detailed study where we analyze the past, discuss about the present and suggest new possibilities for the future of C. elegans as a model organism (chapter 2). The experimental sections of the thesis consist of quantitative genetic analyses of genomic regions associated with phenotypic variations observed under a certain perturbation. We use genotypic and phenotypic data measured in our RILs and ILs together with QTL mapping techniques to estimate the position of candidate loci, which are associated with a phenotypic variation. In C. elegans, β-catenin genebar-1plays an important role in vulva development whereas in humans it plays an important role in cancer progression.In our study in bar-1 mutant RILs, we constructed different combinations of two genomes in C. elegans strains. The lack of β-catenin was included to the combination of the two genomes. These mutant RILs point us to the presence of polymorphic modifiers of vulva development in C. elegans and pave the way towards the development of a new tool to uncover cryptic variation in two genetic variants (chapter 3). To gain insight into the subtle effects of natural variants and more concretely into the genetics of heat-shock recovery, we exposed RILs to heat-stress. We investigated here the hormesis effects on life span and offspring, and described associated loci in C. elegans (chapter 4). Our observations showed that there is natural variation in hormesis effects on life span for heat-shock. As a combination of environmental and genetic perturbation, we studied the effects of heat stress in C. elegans combined with ILs (chapter 5). We demonstrate the importance of the chromosome IV and a concrete locus in heat stress response. In order to identify the role of a locus distal to chromosomeIV, we selected a set of ILs containing a fragment of CB4856 (Hawaii) genome introgressed in a N2 (Bristol) background around this candidate locus previously described in other studies. We studied gene expression in normal and heat stress conditions by quantitative RT-PCR. Through this study we are able to confirm the role of the locus distal to chromosome IV in heat stress response. In the general discussion (chapter 6) I discuss the final results of the thesis and put them into the perspective of the current progresses in genetics studies of C. elegans and how stress response is associated with variations in pathways and thus in cellular and molecular process in health and/or disease.   Overall this thesis demonstrates at least a part of the incredible potential of C. elegans as a complex genetic model using quantitative genetic analyses, which complement more established forward genetic screens.

AB - The genetic architecture of an organism could be considered ‘the most amazing piece of engineering’ existing in nature. Looking from a certain distance, the genetic complexity of an organism could be described as an immense jigsaw puzzle. As in a real jigsaw, the connection between two pieces will suggest or bring us to the third one and so on. The genetic responses to perturbation reveal interactions between many alleles of which effects are not that noticeable under optimal conditions. In the general introduction of this thesis (chapter 1), the reader can find a brief overview of the model organismCaenorhabditis elegans and how this nematode has increasingly taken a crucial position in relevant biological studies over the last few decades. Moreover, the outline of this thesis is extensively described in this section. My thesis brings together examples of perturbation in C. elegans at three different levels: phenotypic perturbation, as a result of genetic variation in Recombinant Inbred Lines (RILs), genetic perturbation, performed by genome combinations (RILs), introgressed fragments of exogenous genome in introgression lines (ILs) and induced mutations, and environmental perturbation (i.e. heat stress conditions). We have combined these perturbations in order to increase the potential of these tools in investigating genetic variation in C. elegans. Our RILs and ILs are combinations of two of the most divergent genomes of C. elegans strains these are Bristol N2 and CB4856 (Hawaii). The translation of this knowledge to research in human disease is of great interest since many complex diseases are regulated by small effect genes that occur during stress or aging. This thesis expounds how C. elegans has gained a prominent position as a model organism for studying the genetic of complex disease pathways. Here I have presented different studies and concluded that environmental stress perturbation experiments in C. elegans represents a crucial implement in the way to increase our understanding of the genetics of human diseases such as Huntington’s disease, Parkinson’s disease, Alzheimer’s disease or cancer. We performed an exhaustive analysis of the current experiments and new insights that used C. elegans as a model organism for complex human diseases. This thesis contains a detailed study where we analyze the past, discuss about the present and suggest new possibilities for the future of C. elegans as a model organism (chapter 2). The experimental sections of the thesis consist of quantitative genetic analyses of genomic regions associated with phenotypic variations observed under a certain perturbation. We use genotypic and phenotypic data measured in our RILs and ILs together with QTL mapping techniques to estimate the position of candidate loci, which are associated with a phenotypic variation. In C. elegans, β-catenin genebar-1plays an important role in vulva development whereas in humans it plays an important role in cancer progression.In our study in bar-1 mutant RILs, we constructed different combinations of two genomes in C. elegans strains. The lack of β-catenin was included to the combination of the two genomes. These mutant RILs point us to the presence of polymorphic modifiers of vulva development in C. elegans and pave the way towards the development of a new tool to uncover cryptic variation in two genetic variants (chapter 3). To gain insight into the subtle effects of natural variants and more concretely into the genetics of heat-shock recovery, we exposed RILs to heat-stress. We investigated here the hormesis effects on life span and offspring, and described associated loci in C. elegans (chapter 4). Our observations showed that there is natural variation in hormesis effects on life span for heat-shock. As a combination of environmental and genetic perturbation, we studied the effects of heat stress in C. elegans combined with ILs (chapter 5). We demonstrate the importance of the chromosome IV and a concrete locus in heat stress response. In order to identify the role of a locus distal to chromosomeIV, we selected a set of ILs containing a fragment of CB4856 (Hawaii) genome introgressed in a N2 (Bristol) background around this candidate locus previously described in other studies. We studied gene expression in normal and heat stress conditions by quantitative RT-PCR. Through this study we are able to confirm the role of the locus distal to chromosome IV in heat stress response. In the general discussion (chapter 6) I discuss the final results of the thesis and put them into the perspective of the current progresses in genetics studies of C. elegans and how stress response is associated with variations in pathways and thus in cellular and molecular process in health and/or disease.   Overall this thesis demonstrates at least a part of the incredible potential of C. elegans as a complex genetic model using quantitative genetic analyses, which complement more established forward genetic screens.

KW - caenorhabditis elegans

KW - genetica

KW - diermodellen

KW - stress

KW - warmtestress

KW - stressreactie

KW - genetische variatie

KW - caenorhabditis elegans

KW - genetics

KW - animal models

KW - stress

KW - heat stress

KW - stress response

KW - genetic variation

M3 - internal PhD, WU

SN - 9789461738516

PB - Wageningen University

CY - Wageningen

ER -

Rodriguez Sanchez M. Worms under stress: unravelling genetic complex traits through perturbation. Wageningen: Wageningen University, 2014. 124 p.