Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes.
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 it is a highly selfing hermaphrodite. As a result, the species largely exists as a collection of naturally occurring inbred lines, or accessions, which can be genotyped once and phenotyped repeatedly. Furthermore, linkage disequilibrium in such a species will be much more extensive than in a comparable outcrossing species. We tested 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. In spite of an extremely high rate of false positives due to population structure, we were able to identify known major genes for all phenotypes tested, thus demonstrating the potential of genome-wide association mapping in A. thaliana and other species with similar patterns of variation. The rate of false positives differed strongly between traits, with more clinal traits showing the highest rate. However, the false positive rates were always substantial regardless of the trait, highlighting the necessity of an appropriate genomic control in association studies.
Aranzana
María José
MJ
Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America.
Kim
Sung
S
Zhao
Keyan
K
Bakker
Erica
E
Horton
Matthew
M
Jakob
Katrin
K
Lister
Clare
C
Molitor
John
J
Shindo
Chikako
C
Tang
Chunlao
C
Toomajian
Christopher
C
Traw
Brian
B
Zheng
Honggang
H
Bergelson
Joy
J
Dean
Caroline
C
Marjoram
Paul
P
Nordborg
Magnus
M
D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping; D005189:False Positive Reactions; D017343:Genes, Plant; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D007113:Immunity, Innate; D015810:Linkage Disequilibrium