A. thaliana genetic resources

> 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 (Atwell et al., 2010), 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 (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).

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.

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 (Toomajian et al., 2006), the composite likelihood ratio test (Nielsen et al., 2005), and a global FST scan (Lewontin et al., 1973). 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 (Hancock et al., 2011). 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. 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.

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 (Anastasio et al., 2011). 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 accessions. The lists of accessions included in each set are available below.
Members of the 196
Justins 360 lines
Members of the 1307-RegMap
Swedish_accessions (accessions used in the study of local adaptation described here)

References

Atwell, Susanna, Yu S Huang, Bjarni J Vilhjálmsson, Glenda Willems, Matthew Horton, Yan Li, Dazhe Meng, et al. 2010. “Genome-Wide Association Study of 107 Phenotypes in Arabidopsis Thaliana Inbred Lines.” Nature 465 (7298): 627–31. doi:10.1038/nature08800. Cite
Horton, Matthew W., Angela M. Hancock, Yu S. Huang, Christopher Toomajian, Susanna Atwell, Adam Auton, N. Wayan Muliyati, et al. 2012. “Genome-Wide Patterns of Genetic Variation in Worldwide Arabidopsis Thaliana Accessions from the RegMap Panel.” Nature Genetics 44 (2): 212–16. doi:10.1038/ng.1042. Cite
Platt, Alexander, Matthew Horton, Yu S Huang, Yan Li, Alison E Anastasio, Ni Wayan Mulyati, Jon Agren, et al. 2010. “The Scale of Population Structure in Arabidopsis Thaliana.” PLoS Genetics 6 (2): e1000843. doi:10.1371/journal.pgen.1000843. Cite
Anastasio, Alison E., Alexander Platt, Matthew Horton, Erich Grotewold, Randy Scholl, Justin O. Borevitz, Magnus Nordborg, and Joy Bergelson. 2011. “Source Verification of Mis-Identified Arabidopsis Thaliana Accessions.” The Plant Journal 67 (3): 554–66. doi:10.1111/j.1365-313X.2011.04606.x. Cite
Toomajian, Christopher, Tina T Hu, Maria José Aranzana, Clare Lister, Chunlao Tang, Honggang Zheng, Keyan Zhao, Peter Calabrese, Caroline Dean, and Magnus Nordborg. 2006. “A Nonparametric Test Reveals Selection for Rapid Flowering in the Arabidopsis Genome.” PLoS Biol 4 (5): e137. doi:10.1371/journal.pbio.0040137. Cite
Nielsen, Rasmus, Scott Williamson, Yuseob Kim, Melissa J. Hubisz, Andrew G. Clark, and Carlos Bustamante. 2005. “Genomic Scans for Selective Sweeps Using SNP Data.” Genome Research 15 (11): 1566–75. doi:10.1101/gr.4252305. Cite
Lewontin, R. C., and J. Krakauer. 1973. “Distribution of Gene Frequency as a Test of the Theory of the Selective Neutrality of Polymorphisms.” Genetics 74 (1): 175–95. Cite
Hancock, Angela M., Benjamin Brachi, Nathalie Faure, Matthew W. Horton, Lucien B. Jarymowycz, F. Gianluca Sperone, Chris Toomajian, Fabrice Roux, and Joy Bergelson. 2011. “Adaptation to Climate Across the Arabidopsis Thaliana Genome.” Science 334 (6052): 83–86. doi:10.1126/science.1209244. Cite

University of Chicago, Dept. of Ecology & Evolution