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ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA
by
Keyan Zhao
A Dissertation Presented to the
FACULTY OF THE GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(COMPUTATIONAL BIOLOGY)
August 2007
Copyright 2007 Keyan Zhao
Object Description
| Title | Association mapping in Arabidopsis thaliana |
| Author | Zhao, Keyan |
| Author email | kyzhao@gmail.com |
| Degree | Doctor of Philosophy |
| Document type | Thesis |
| Degree program | Biology |
| School | College of Letters, Arts and Sciences |
| Date defended/completed | 2007-06-21 |
| Date submitted | 2007 |
| Restricted until | Restricted until 25 July 2009. |
| Date published | 2009-07-25 |
| Advisor (committee chair) | Nordborg, Magnus |
| Advisor (committee member) |
Sun, Fengzhu Z. Conti, David V. |
| Abstract | There is currently tremendous interest in the possibility of using genome-wide association mapping to identify genes responsible for natural variation, particularly for human disease susceptibility. The model plant Arabidopsis thaliana is in many ways an ideal candidate for such studies, because of its highly selfing nature. We test the feasibility of genome-wide association mapping in A. thaliana by searching for associations with flowering time and pathogen resistance in a sample of 95 accessions for which genome-wide polymorphism data were available. A strong population structure confounding effect is found there.; Various methods to reduce the false positives due to population structure are evaluated. By combining the association results with results from linkage mapping in F2 crosses, we identify one previously known true positive and several promising new associations, but also demonstrate the existence of both false positives and false negatives. Our results illustrate the potential of genome-wide association scans as a tool for dissecting the genetics of natural variation, while at the same time highlighting the pitfalls. While statistical methods can be used to ameliorate the confounding effect of population structure, they cannot always be effective and are certainly not a substitute for independent evidence, such as that obtained via crosses or transgenic experiments.; We also explore the permutation method for correcting population structure. Our results show promise for the future. Various factors affecting the power and false positive rates due to population structure confounding are examined through extensive simulation study. We find the informativeness of causal SNPs is the strongest factor affecting false positive rates, while allele frequency is the stronger factor affecting power in complex genetic architectures. |
| Keyword | association mapping |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Type | texts |
| Legacy record ID | usctheses-m669 |
| Contributing entity | University of Southern California |
| Rights | Zhao, Keyan |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | cisadmin@dots.usc.edu |
| Filename | etd-Zhao-20070725 |
| Archival file | uscthesesreloadpub_Volume51/etd-Zhao-20070725.pdf |
Description
| Title | Page 1 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@dots.usc.edu |
| Full text | ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA by Keyan Zhao A Dissertation Presented to the FACULTY OF THE GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (COMPUTATIONAL BIOLOGY) August 2007 Copyright 2007 Keyan Zhao |
