Reference "Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana"

Reference ID

16724

Title

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana

Source

Science, 2007, vol. 317, pp. 338-342

Authors (18)

Clark-R-M	Schweikert-G	Toomajian-C	Ossowski-S	Zeller-G
Shinn-P	Warthmann-N	Hu-T-T	Fu-G	Hinds-D-A
Chen-H	Frazer-K-A	Huson-D-H	Scholkopf-B	Nordborg-M
Ratsch-G	Ecker-J-R	Weigel-D

Abstract

The genomes of individuals from the same species vary in sequence as a result of
different evolutionary processes. To examine the patterns of, and the forces
shaping, sequence variation in Arabidopsis thaliana, we performed high-density
array resequencing of 20 diverse strains (accessions). More than 1 million
nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate
false discovery rates (FDRs), and approximately 4% of the genome was identified
as being highly dissimilar or deleted relative to the reference genome sequence.
Patterns of polymorphism are highly nonrandom among gene families, with genes
mediating interaction with the biotic environment having exceptional
polymorphism levels. At the chromosomal scale, regional variation in
polymorphism was readily apparent. A scan for recent selective sweeps revealed
several candidate regions, including a notable example in which almost all
variation was removed in a 500-kilobase window. Analyzing the polymorphisms we
describe in larger sets of accessions will enable a detailed understanding of
forces shaping population-wide sequence variation in A. thaliana.