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The Regional Mapping Project

1,307  accessions of A.thaliana have been genotyped using the Affymetrix Arabidopsis 250k - SNP chip (Horton et al., 2012), after first selecting unique lines from a collection of ~6,000 accessions genotyped using 149 genome-wide SNPs (Platt et al., 2010). We have collected high quality geographic coordinates for 1,193 of these samples (Anastasio et al., 2011). 

collection_sites

New Zealand (NZ-1) not shown.


Due to the extensive size of this collection, these accessions enable mapping using either global or regional populations, and thus enable one to compare the genetic basis of ecologically important traits among distinct subsets (Horton et al., 2012). These genotyped lines were created in collaboration with the Borevitz and Nordborg laboratories, and will be made available through the Ohio State Arabidopsis Stock Center.

 

Genotypes 

Both imputed and unimputed SNPs are available; for samples with high-quality geographic data, please click here

The latitude and longitude for these accessions are available. The annotations of individual SNPs are here.


Selection Signals

The regional mapping panel was used to search for candidate targets of selection using the pairwise haplotype sharing statistic (Toomajian et al., 2006), the composite likelihood ratio test (Nielsen et al., 2005), and a global FST scan (Lewontin & Krakauer, 1973).

You can visualize these scores in a genomic context using the selection browser:

http://regmap.uchicago.edu/cgi-bin/gbrowse/arabidopsis/

 

For example, the top 20 candidate targets of selection (10-kb windows) are shown here:

 

The selection browser is based on an earlier idea by Pickrell and colleagues (Pickrell et al., 2009; the hgdp browser):

http://hgdp.uchicago.edu 

which has been useful for researchers conducting human-related GWAS.

Citations

  1. Horton, M. W. et al. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat Genet 44, 212-216.
    1. Supplementary materials are found here.
  2. Atwell, S. et al. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465, 627-631 (2010).
  3. Platt et al. (2010), The scale of population structure in Arabidopsis thaliana, PLoS Genet. 6:e1000843.
  4. Anastasio, A.E. et al. Source verification of misidentified Arabidopsis thaliana accessions. Plant J (2011).
  5. Nielsen, R. et al. Genomic scans for selective sweeps using SNP data. Genome Res 15, 1566-75 (2005).
  6. Toomajian, C. et al. A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome. PLoS Biol 4, e137 (2006).
  7. Lewontin, R.C. & Krakauer, J. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74, 175-95 (1973).
  8. Pickrell, J.K. et al. Signals of recent positive selection in a worldwide sample of human populations. Genome Res 19, 826-37 (2009).

 

 

 

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