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Effects of inbreeding on gene expression in Arabidopsis

Menzel, Mandy (2013) MOBT19 20121
Degree Projects in Molecular Biology
Abstract
Abstract
Inbreeding (selfing) was investigated already by Charles Darwin, who wanted to understand why
outcrossing (non-selfing) is the predominant mating choice in the kingdom of plants. He found that
inbreeding often results in less viable and fertile plants compared to outcrossing, what is known as
inbreeding depression, and can be explained with increased homozygosity in the inbred, making them
more exposed to the effects of deleterious recessive mutations. Arabidopsis lyrata is a self-incompatible
perennial plant and close relative to the natural selfer and well-known model species Arabidopsis thaliana.
Previous studies have documented that inbreeding depresses viability and fertility in both these species,
but little is known... (More)
Abstract
Inbreeding (selfing) was investigated already by Charles Darwin, who wanted to understand why
outcrossing (non-selfing) is the predominant mating choice in the kingdom of plants. He found that
inbreeding often results in less viable and fertile plants compared to outcrossing, what is known as
inbreeding depression, and can be explained with increased homozygosity in the inbred, making them
more exposed to the effects of deleterious recessive mutations. Arabidopsis lyrata is a self-incompatible
perennial plant and close relative to the natural selfer and well-known model species Arabidopsis thaliana.
Previous studies have documented that inbreeding depresses viability and fertility in both these species,
but little is known about the effects of inbreeding on gene expression. Here, we introduce transcriptome
studies of two self-incompatible A. lyrata populations, which were experimentally selfed to compare their
gene expression level to their non-selfed counterparts. We found an up-regulation of stress-related genes in
the selfed of both populations compared with the non-selfed and gene expression changes in the selfed for
photosynthesis-related genes which were up-regulated in one population but down-regulated in the other.
A comparison of gene expression levels of genes differentially expressed between selfed and non-selfed A.
lyrata to A. thaliana showed that those genes did not have a significant different expression profile in A.
thaliana compared to genes not affected by selfing. This study shows strong and pathway-specific shortterm
effects of inbreeding in A. lyrata and is in agreement with findings in other organisms, like Drosophila.

Popular science summary:

Effects of inbreeding on gene expression in Arabidopsis

Two mating systems dominate the kingdom of plants, outcrossing (reproduction using
foreign pollen) and inbreeding (reproduction using the plants’ own pollen). Whereas
outcrossing is the more prevalent reproductive choice, selfing (inbreeding) is
predominantly seen in an environment lacking suitable mates and pollinators.
However, inbred offspring often shows less growth and seed production compared
with their outcrossing counterparts, a phenomenon known as inbreeding depression.
Inbreeding as well as inbreeding depression is well studied, but less focus has been
put on the effects they have on plant metabolism and gene expression. Recent
developments in next generation sequencing technologies allow studying the gene
expression of an entire organism (RNA-sequencing) and thus can aid unraveling
molecular pathways affected by inbreeding.
In this project we used the advantages of RNA-sequencing to study inbreeding in two
Scandinavian populations of Arabidopsis lyrata, a close relative to the model species
Arabidopsis thaliana. A. lyrata is a natural outcrossing species but was inbred for one
generation to enable a comparison between outcrossed and selfed individuals. The
main focus of this project was to find genes with a different expression pattern in the
selfed compared to the non-selfed of both populations. We found 507 differentially
expressed genes for the population Norway and 195 differentially expressed genes for
the population Sweden. To find genes, which to a large extent are affected by
inbreeding, the next step was to look for genes commonly differentially expressed in
both populations, which resulted in 62 candidate genes. These candidate genes were
annotated for their function and mapped into pathways. Genes mapped to two major
pathways, stress response and photosynthesis. We found the genes associated with
stress response were predominantly up-regulated in the selfed of both populations,
whereas genes associated with photosynthesis were down-regulated in population
Norway but up-regulated in population Sweden.
Since our samples were only inbred for one generation, our research is limited to
investigating short-term effects of inbreeding. To see how gene expression due to
inbreeding develops over longer time periods we compared our results to the natural
selfer A. thaliana. Here, we saw that in A. thaliana genes differentially expressed in
A. lyrata did not significantly differ in their expression from genes not differentially
expressed, suggesting that A. thaliana is able to retain a basal expression of genes
which has been seen affected by inbreeding in A. lyrata.
This project documents short-term effects of inbreeding on gene expression, which
are in agreement with other studies.

Advisor: Bengt Hansson
Master´s Degree Project 60 credits in Molecular Biology, Molecular Genetics 2012/13
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Menzel, Mandy
supervisor
organization
course
MOBT19 20121
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
3562405
date added to LUP
2013-03-07 14:35:10
date last changed
2013-03-26 13:59:02
@misc{3562405,
  abstract     = {Abstract
Inbreeding (selfing) was investigated already by Charles Darwin, who wanted to understand why
outcrossing (non-selfing) is the predominant mating choice in the kingdom of plants. He found that
inbreeding often results in less viable and fertile plants compared to outcrossing, what is known as
inbreeding depression, and can be explained with increased homozygosity in the inbred, making them
more exposed to the effects of deleterious recessive mutations. Arabidopsis lyrata is a self-incompatible
perennial plant and close relative to the natural selfer and well-known model species Arabidopsis thaliana.
Previous studies have documented that inbreeding depresses viability and fertility in both these species,
but little is known about the effects of inbreeding on gene expression. Here, we introduce transcriptome
studies of two self-incompatible A. lyrata populations, which were experimentally selfed to compare their
gene expression level to their non-selfed counterparts. We found an up-regulation of stress-related genes in
the selfed of both populations compared with the non-selfed and gene expression changes in the selfed for
photosynthesis-related genes which were up-regulated in one population but down-regulated in the other.
A comparison of gene expression levels of genes differentially expressed between selfed and non-selfed A.
lyrata to A. thaliana showed that those genes did not have a significant different expression profile in A.
thaliana compared to genes not affected by selfing. This study shows strong and pathway-specific shortterm
effects of inbreeding in A. lyrata and is in agreement with findings in other organisms, like Drosophila.

Popular science summary:

Effects of inbreeding on gene expression in Arabidopsis

Two mating systems dominate the kingdom of plants, outcrossing (reproduction using
foreign pollen) and inbreeding (reproduction using the plants’ own pollen). Whereas
outcrossing is the more prevalent reproductive choice, selfing (inbreeding) is
predominantly seen in an environment lacking suitable mates and pollinators.
However, inbred offspring often shows less growth and seed production compared
with their outcrossing counterparts, a phenomenon known as inbreeding depression.
Inbreeding as well as inbreeding depression is well studied, but less focus has been
put on the effects they have on plant metabolism and gene expression. Recent
developments in next generation sequencing technologies allow studying the gene
expression of an entire organism (RNA-sequencing) and thus can aid unraveling
molecular pathways affected by inbreeding.
In this project we used the advantages of RNA-sequencing to study inbreeding in two
Scandinavian populations of Arabidopsis lyrata, a close relative to the model species
Arabidopsis thaliana. A. lyrata is a natural outcrossing species but was inbred for one
generation to enable a comparison between outcrossed and selfed individuals. The
main focus of this project was to find genes with a different expression pattern in the
selfed compared to the non-selfed of both populations. We found 507 differentially
expressed genes for the population Norway and 195 differentially expressed genes for
the population Sweden. To find genes, which to a large extent are affected by
inbreeding, the next step was to look for genes commonly differentially expressed in
both populations, which resulted in 62 candidate genes. These candidate genes were
annotated for their function and mapped into pathways. Genes mapped to two major
pathways, stress response and photosynthesis. We found the genes associated with
stress response were predominantly up-regulated in the selfed of both populations,
whereas genes associated with photosynthesis were down-regulated in population
Norway but up-regulated in population Sweden.
Since our samples were only inbred for one generation, our research is limited to
investigating short-term effects of inbreeding. To see how gene expression due to
inbreeding develops over longer time periods we compared our results to the natural
selfer A. thaliana. Here, we saw that in A. thaliana genes differentially expressed in
A. lyrata did not significantly differ in their expression from genes not differentially
expressed, suggesting that A. thaliana is able to retain a basal expression of genes
which has been seen affected by inbreeding in A. lyrata.
This project documents short-term effects of inbreeding on gene expression, which
are in agreement with other studies.

Advisor: Bengt Hansson
Master´s Degree Project 60 credits in Molecular Biology, Molecular Genetics 2012/13
Department of Biology, Lund University},
  author       = {Menzel, Mandy},
  language     = {eng},
  note         = {Student Paper},
  title        = {Effects of inbreeding on gene expression in Arabidopsis},
  year         = {2013},
}