A. thaliana genetic resources

VARIABLES_INFO> Genomic polymorphism data in A. thaliana
> Regional Mapping (RegMap) lines
> Climate genome scans
> 1001 Genomes Project
> 149-SNP primers
> List of putative contaminants among stock center lines
> Various lists of accessions

Genomic polymorphism data in A. thaliana

We have devoted substantial effort over the last decade establishing the ability to perform Genome Wide Association mapping in A. thaliana. This began with early work to understand genetic variation in the species, followed by later work to characterize patterns of linkage disequilibrium and the ability to association map simple traits. The work has come to fruition in a collaborative effort between the Bergelson, Borevitz and Nordborg labs in which 107 phenotypes are mapped [zotpressInText item=”FN58M3SN” etal=”yes”], and the associated database can be found on the GMI website.

 Regional Mapping (RegMap) lines

1,307 accessions of A. thaliana have been genotyped using the Affymetrix Arabidopsis 250k – SNP chip [zotpressInText item=”HJCDD6N3″ etal=”yes”], after first selecting unique lines from a collection of ~6,000 accessions genotyped using 149 genome-wide SNPs [zotpressInText item=”2VNF75PM” etal=”yes”]. We have collected high quality geographic coordinates for 1,193 of these samples [zotpressInText item=”P2VBETB5″ etal=”yes”].

Due to the extensive size of this collection, these accessions enable mapping using either global or regional populations, and thus allow to compare the genetic basis of ecologically important traits among distinct subsets [zotpressInText item=”HJCDD6N3″ etal=”yes”]. These genotyped lines were created in collaboration with the Borevitz and Nordborg laboratories, and are available through the Ohio State Arabidopsis Stock Center.

SNPs genotypes are available here. The latitude and longitude for these accessions are included in the archive. The annotations of individual SNPs are here.

The regional mapping panel was used to search for candidate targets of selection using the pairwise haplotype sharing statistic [zotpressInText item=”M3GP6Z39″ etal=”yes”], the composite likelihood ratio test [zotpressInText item=”9BA3QMRR” etal=”yes”], and a global FST scan [zotpressInText item=”XBCZ53EE” etal=”yes”]. You can download these scores here. The map of recombination hot spots can be dowloaded here.

Climate genome scans

The Regmap lines were used to identify the genetics underlying climate adaptation in A. thaliana [zotpressInText items=”B3QJBJSV” etal=”yes”]. Association scores for each climate variable are available here. The archive includes a list of the top SNPs identified in this study. The climate data for 948 accessions is available here and explanation of the variables can be downloaded here. Please note that the genome browser allowing to view the results in their genomic context was taken offline.

1001 Genomes Project

Our group participates in the international collaboration that fully sequenced the genomes of 1001 A. thaliana accessions. More information can be found on the project website 1001genomes.org and the publication [zotpressInText item=”{EC9MH4PZ}” etal=”yes” format=”%a%, %d%”].

149-SNP primers and list of putative contaminants among stock center lines

A set of primers for 149 SNPs has been established to quickly and cheaply fingerprint accessions, which is especially important in confirming the identify of stock center lines. Primer sequences can be downloaded here. We identified a set of Arabidopsis thaliana accessions that have previously been misidentified [zotpressInText item=”P2VBETB5″ etal=”yes”]. The genetic fingerprint of 5965 accessions for the 149 SNPs and a list of putative contaminants among stock center lines can be downloaded here.

Various lists of accessions

Different studies used different sets of A. thaliana. Lists with genotypes included in each set are available below:

References

[zotpressInTextBib style=”chicago-author-date” sort=”ASC” download=”no” cite=”yes”]

University of Chicago, Dept. of Ecology & Evolution