The pattern of polymorphism in Arabidopsis thaliana.
We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.
Nordborg
Magnus
M
Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA. magnus@usc.edu
Hu
Tina T
TT
Ishino
Yoko
Y
Jhaveri
Jinal
J
Toomajian
Christopher
C
Zheng
Honggang
H
Bakker
Erica
E
Calabrese
Peter
P
Gladstone
Jean
J
Goyal
Rana
R
Jakobsson
Mattias
M
Kim
Sung
S
Morozov
Yuri
Y
Padhukasahasram
Badri
B
Plagnol
Vincent
V
Rosenberg
Noah A
NA
Shah
Chitiksha
C
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Jeffrey D
JD
Wang
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Zhao
Keyan
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Kalbfleisch
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Kreitman
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Bergelson
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D017360:Arabidopsis / Q000235:genetics*; D005787:Gene Frequency; D005828:Genetics, Population; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide