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Complementary approaches to find functional molecular variation in the core cell cycle genes of Arabidopsis

Roel Sterken UGent (2008)
abstract
Unraveling the genetic networks underlying natural variation of quantitative traits is a challenging task. The initial research goal of this thesis was to identify quantitative trait loci (QTL) that underlie the natural variation of biomass production in Arabidopsis thaliana. One approach to analyze quantitative traits is by using genome-wide association or linkage disequilibrium (LD)-based mapping. At the time when this project was conceived, it was claimed that LD in A. thaliana extended up to 250 kb and that allelic diversity was limited (Nordborg et al. 2002). Under this assumption, it would be feasible to do successful association analysis in A. thaliana with ~2000 evenly spaced genome-wide markers in a sample of 96 accessions. Therefore, we wanted to adopt this association strategy to elucidate the genetic determinants underlying natural variation of biomass in A. thaliana. Subsequently, the aim of the first part of this thesis (Chapter 2-3) was to asses the feasibility of the genome-wide association strategy and to establish the tools and data sets eventually required. Chapter two describes the analysis of natural variation of biomass production in A. thaliana in a sample of ~90 accessions. Chapter three describes the analysis of LD extent in A. thaliana. We wanted to independently validate the findings of Nordborg et al. (2002) on a genome-wide scale using AFLP generated markers and publicly available SNP markers. Conclusions from both chapter 2 and 3 however showed that the preconceived assumptions were unfounded, making a genome-wide association strategy to map biomass production QTLs currently impracticable. Given the conclusions from the first part of this thesis, we chose to re-orient our research strategy towards candidate gene approaches to identify functional molecular variation. The mitotic cell cycle is a much studied biological system in A. thaliana and the cell cycle has a central role in the development, differentiation and proliferation of plant organs. Given that the genes controlling the cell cycle progression have been identified and that many cell cycle related traits show natural variation, we selected the core cell cycle (CCC) genes of A. thaliana as candidate genes in our further approaches. In addition, we focused the natural variation studies on endoreduplication and root cortical cell length, because these phenotypes are directly controlled by the cell cycle regulation and easier to measure than biomass variation. Introduction 33 Chapter four describes a population genetics approach to assess if particular CCC genes have been affected by selective constraint or by directional positive selection, either directly or through linkage, as opposed to neutral evolutionary forces. When the neutral evolution hypothesis can be rejected, it can be that the CCC genes, or the region they are located in, contain genetic variants that affect phenotypic variation of adaptive traits. In chapter five we used a candidate gene association approach to find associations between haplotypes of CCC genes and natural variation in two cell cycle related phenotypes: endoreduplication and root cortical cell length. Finally, in chapter six, we summarize and discuss the conclusions and future prospects of the work described in this thesis.
Please use this url to cite or link to this publication:
author
promoter
UGent and UGent
organization
year
type
dissertation (monograph)
subject
pages
167 pages
publisher
Ghent University. Faculty of Sciences
place of publication
Ghent, Belgium
defense location
Zwijnaarde : Technologiepark (FSVM building)
defense date
2008-11-28 16:00
language
English
UGent publication?
yes
classification
D1
additional info
dissertation consists of copyrighted material
copyright statement
I have transferred the copyright for this publication to the publisher
id
3007654
handle
http://hdl.handle.net/1854/LU-3007654
date created
2012-10-05 14:50:22
date last changed
2012-10-08 15:05:30
@phdthesis{3007654,
  abstract     = {Unraveling the genetic networks underlying natural variation of quantitative traits is a challenging task. The initial research goal of this thesis was to identify quantitative trait loci (QTL) that underlie the natural variation of biomass production in Arabidopsis thaliana. One approach to analyze quantitative traits is by using genome-wide association or linkage disequilibrium (LD)-based mapping. At the time when this project was conceived, it was claimed that LD in A. thaliana extended up to 250 kb and that allelic diversity was limited (Nordborg et al. 2002). Under this assumption, it would be feasible to do successful association analysis in A. thaliana with {\texttildelow}2000 evenly spaced genome-wide markers in a sample of 96 accessions. Therefore, we wanted to adopt this association strategy to elucidate the genetic determinants underlying natural variation of biomass in A. thaliana. Subsequently, the aim of the first part of this thesis (Chapter 2-3) was to asses the feasibility of the genome-wide association strategy and to establish the tools and data sets eventually required. Chapter two describes the analysis of natural variation of biomass production in A. thaliana in a sample of {\texttildelow}90 accessions. Chapter three describes the analysis of LD extent in A. thaliana. We wanted to independently validate the findings of Nordborg et al. (2002) on a genome-wide scale using AFLP generated markers and publicly available SNP markers. Conclusions from both chapter 2 and 3 however showed that the preconceived assumptions were unfounded, making a genome-wide association strategy to map biomass production QTLs currently impracticable. Given the conclusions from the first part of this thesis, we chose to re-orient our research strategy towards candidate gene approaches to identify functional molecular variation. The mitotic cell cycle is a much studied biological system in A. thaliana and the cell cycle has a central role in the development, differentiation and proliferation of plant organs. Given that the genes controlling the cell cycle progression have been identified and that many cell cycle related traits show natural variation, we selected the core cell cycle (CCC) genes of A. thaliana as candidate genes in our further approaches. In addition, we focused the natural variation studies on endoreduplication and root cortical cell length, because these phenotypes are directly controlled by the cell cycle regulation and easier to measure than biomass variation. Introduction 33 Chapter four describes a population genetics approach to assess if particular CCC genes have been affected by selective constraint or by directional positive selection, either directly or through linkage, as opposed to neutral evolutionary forces. When the neutral evolution hypothesis can be rejected, it can be that the CCC genes, or the region they are located in, contain genetic variants that affect phenotypic variation of adaptive traits. In chapter five we used a candidate gene association approach to find associations between haplotypes of CCC genes and natural variation in two cell cycle related phenotypes: endoreduplication and root cortical cell length. Finally, in chapter six, we summarize and discuss the conclusions and future prospects of the work described in this thesis.},
  author       = {Sterken, Roel},
  language     = {eng},
  pages        = {167},
  publisher    = {Ghent University. Faculty of Sciences},
  school       = {Ghent University},
  title        = {Complementary approaches to find functional molecular variation in the core cell cycle genes of Arabidopsis},
  year         = {2008},
}

Chicago
Sterken, Roel. 2008. “Complementary Approaches to Find Functional Molecular Variation in the Core Cell Cycle Genes of Arabidopsis”. Ghent, Belgium: Ghent University. Faculty of Sciences.
APA
Sterken, R. (2008). Complementary approaches to find functional molecular variation in the core cell cycle genes of Arabidopsis. Ghent University. Faculty of Sciences, Ghent, Belgium.
Vancouver
1.
Sterken R. Complementary approaches to find functional molecular variation in the core cell cycle genes of Arabidopsis. [Ghent, Belgium]: Ghent University. Faculty of Sciences; 2008.
MLA
Sterken, Roel. “Complementary Approaches to Find Functional Molecular Variation in the Core Cell Cycle Genes of Arabidopsis.” 2008 : n. pag. Print.