Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana     

Clark RM  Schweikert G  Toomajian C  Ossowski S  Zeller G  Shinn P  Warthmann N  Hu TT  Fu G  Hinds DA  Chen H  Frazer KA  Huson DH  Schölkopf B  Nordborg M  Rätsch G  Ecker JR  Weigel D 《Science (New York, N.Y.)》2007,317(5836):338-342

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.  相似文献   

Whole-genome patterns of common DNA variation in three human populations     

Hinds DA  Stuve LL  Nilsen GB  Halperin E  Eskin E  Ballinger DG  Frazer KA  Cox DR 《Science (New York, N.Y.)》2005,307(5712):1072-1079

Individual differences in DNA sequence are the genetic basis of human variability. We have characterized whole-genome patterns of common human DNA variation by genotyping 1,586,383 single-nucleotide polymorphisms (SNPs) in 71 Americans of European, African, and Asian ancestry. Our results indicate that these SNPs capture most common genetic variation as a result of linkage disequilibrium, the correlation among common SNP alleles. We observe a strong correlation between extended regions of linkage disequilibrium and functional genomic elements. Our data provide a tool for exploring many questions that remain regarding the causal role of common human DNA variation in complex human traits and for investigating the nature of genetic variation within and between human populations.  相似文献