Sequence evolution in a chromosomal region of Arabidopsis thaliana
(2002)- Abstract
- Recently there has been a lot of interest in the use of liknage disequilibrium (LD) in genome wide scans for new genes, so called association mapping. Of crucial importance to a genome wide scan for associations between genetic markers and the trait of interest is the extent of LD, as it determines both how closely a trait can be mapped and also how many markers is needed to map it. Most outbreeding organisms such as Drosophila melanogaster and maize have too little LD to be useful for association mapping. As LD breaks down much more slowly in predominantly self-fertilising organisms, they can, however, be expected to have much higher levels of LD.
It is shown here that the self-fertilising model plant Arabidopsis... (More) - Recently there has been a lot of interest in the use of liknage disequilibrium (LD) in genome wide scans for new genes, so called association mapping. Of crucial importance to a genome wide scan for associations between genetic markers and the trait of interest is the extent of LD, as it determines both how closely a trait can be mapped and also how many markers is needed to map it. Most outbreeding organisms such as Drosophila melanogaster and maize have too little LD to be useful for association mapping. As LD breaks down much more slowly in predominantly self-fertilising organisms, they can, however, be expected to have much higher levels of LD.
It is shown here that the self-fertilising model plant Arabidopsis thaliana holds a lot of promise of being a suitable organism for LD-mapping. Around the flowering time locus FRI, the levels of LD were suitable for LD-mapping. Some of the problems with LD-mapping is also addressed as allelic heterogeneity had a major impact on LD in the region studied. Also some of the basic population genetic parameters for the region are discussed as is geographical subdivision among Arabidopsis thaliana and possible history of the different FRI alleles. (Less) - Abstract (Swedish)
- Popular Abstract in Swedish
Den genetiska variation som finns i en population är inte slumpmässigt fördelad mellan olika delar av genomet. I stället beror den på populationens historia och faktorer som selektion och populationsstruktur. Det har visat sig hos människa att samband som finns mellan sjukdomsalleler och andra genetiska markörer kan användas för att hitta gener.
I många organismer finns dessa samband, kallade kopplingsojämvikter, endast över korta bitar av genomet och kan därför inte användas i karteringssyfte. I delvis självbefruktande organismer kan man dock förvänta sig kopplingsojämvikt över större områden eftersom självbefruktare till största delen är homozygoter, något som bevarar... (More) - Popular Abstract in Swedish
Den genetiska variation som finns i en population är inte slumpmässigt fördelad mellan olika delar av genomet. I stället beror den på populationens historia och faktorer som selektion och populationsstruktur. Det har visat sig hos människa att samband som finns mellan sjukdomsalleler och andra genetiska markörer kan användas för att hitta gener.
I många organismer finns dessa samband, kallade kopplingsojämvikter, endast över korta bitar av genomet och kan därför inte användas i karteringssyfte. I delvis självbefruktande organismer kan man dock förvänta sig kopplingsojämvikt över större områden eftersom självbefruktare till största delen är homozygoter, något som bevarar kopplingsojämvikt.
Jag har studerat den i huvudsak självbefruktande växten Arabidopsis thaliana och visat att mängden kopplingsojämvikt i området kring blomningstidsgenen FRI är lämplig för s.k. kopplingsojämviktskartering. Jag visar också på de problem som kan uppstå när en egenskap påverkas av flera alleler med likartad effekt i samma gen, samt diskuterar hur geografi och historia har påverkat området kring FRI. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/464803
- author
- Hagenblad, Jenny LU
- supervisor
- opponent
-
- Prof. Savolainen, Outi
- organization
- publishing date
- 2002
- type
- Thesis
- publication status
- published
- subject
- keywords
- Växtgenetik, Plant genetics, flowering time, mapping, polymorphism, Linkage disequilibrium, Arabidopsis thaliana
- pages
- 76 pages
- publisher
- Jenny Hagenblad, Genetics, Sölvegatan 29, 22362 Lund, Sweden,
- defense location
- Genetics building, Sölveg. 29, Lund
- defense date
- 2002-09-21 10:00:00
- ISBN
- 91-628-5356-2
- language
- English
- LU publication?
- yes
- additional info
- Article: Nordborg M, Borevitz JO, et al. The extent of Linkage Disequilibrium in Arabidopsis thaliana. Nature Genetics 30:190-193, 2002Hagenblad J, Nordborg M. Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana. Genetics 161:289-298, 2002Hagenblad J, Nordborg M. Molecular genetics of the allotetraploid Arabidopsis suecica and its parental species. Manuscript, 2002Hagenblad J, Nordborg M. Haplotype evolution around the locus FRI in Arabidopsis thaliana. Manuscript, 2002 The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Genetics (Closed 2011) (011005100)
- id
- 0cffdf94-80d1-4d2c-8e1b-b3fe07a54a9c (old id 464803)
- date added to LUP
- 2016-04-04 11:18:18
- date last changed
- 2018-11-21 21:03:57
@phdthesis{0cffdf94-80d1-4d2c-8e1b-b3fe07a54a9c,
abstract = {{Recently there has been a lot of interest in the use of liknage disequilibrium (LD) in genome wide scans for new genes, so called association mapping. Of crucial importance to a genome wide scan for associations between genetic markers and the trait of interest is the extent of LD, as it determines both how closely a trait can be mapped and also how many markers is needed to map it. Most outbreeding organisms such as Drosophila melanogaster and maize have too little LD to be useful for association mapping. As LD breaks down much more slowly in predominantly self-fertilising organisms, they can, however, be expected to have much higher levels of LD.<br/><br>
<br/><br>
It is shown here that the self-fertilising model plant Arabidopsis thaliana holds a lot of promise of being a suitable organism for LD-mapping. Around the flowering time locus FRI, the levels of LD were suitable for LD-mapping. Some of the problems with LD-mapping is also addressed as allelic heterogeneity had a major impact on LD in the region studied. Also some of the basic population genetic parameters for the region are discussed as is geographical subdivision among Arabidopsis thaliana and possible history of the different FRI alleles.}},
author = {{Hagenblad, Jenny}},
isbn = {{91-628-5356-2}},
keywords = {{Växtgenetik; Plant genetics; flowering time; mapping; polymorphism; Linkage disequilibrium; Arabidopsis thaliana}},
language = {{eng}},
publisher = {{Jenny Hagenblad, Genetics, Sölvegatan 29, 22362 Lund, Sweden,}},
school = {{Lund University}},
title = {{Sequence evolution in a chromosomal region of Arabidopsis thaliana}},
year = {{2002}},
}