About

Pseudogenomes for 1135 Arabidopsis thaliana strains were generated by combining reference and variant calls including deletions, with uncalled sites represented as Ns.

Credits

• Pseudogenomes (download FASTA files from the 1001 Genomes Data Center) were generated by Alexander Platzer.
• GWAS analysis was performed by Francesco Pezzini with the software GEMMA . Every climate factor was used as a phenotype and for every climate factor, one analysis run was carried out. In a data preprocessing step ecotypes related to missing values were filtered out from the phenotype vector. Minor allele frequency (MAF) and linkage disequilibrium (LD) thresholds in GEMMA were set to 1% and 0.8 respectively. This means only SNPs with a MAF of 1% or high were analysed. The obtained P-values were corrected for multiple comparisons using the Benjamini-Yekutieli method. The climate factor data was taken from the paper by Ferrero-Serrano and Assmann.
• The analysis of the SNP data was performed by Lasse Feldhahn .
• This tool was built on the basis of the 1001 Genomes Tool Pseudogenomes ( Github page) developed by Joffrey Fitz.
• The additional web app and database development was done by Benjamin Schmidt. The webapp uses bootstrap, selectize, jquery, popper the calipho-sib feature-viewer and sequence-viewer and the webix datatable .

References

• 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana 1001 Genomes Consortium Cell (2016), 166(2) 481-91.
• Angel Ferrero-Serrano, Sarah Mary Assmann: Phenotypic and genome-wide association with the local environment of Arabidopsis: Source of the climate factors used for the gwas analysis.