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Abstract

The MAGIC genetic reference panel of recombinant inbred lines (Kover et al 2009, PLoS Genet) is descended from 19 founder accessions. We have sequenced the genomes of 18, (the 19th being the reference Col-0) using Illumina short reads and assembled them using a novel algorithm IMR/DENOM that integrates iterative alignment with denovo assembly. The resulting assemblies have an error rate of about 1 SNP per 10kb,in the 80% non-repetitive fraction of the genome. The genome of each MAGIC line is a mosaic of the founders, so in order to impute the MAGIC genomes from the 19 founders,we re-sequenced over 500 MAGIC lines at very low coverage, in barcoded pools of 96 samples, giving about 300,000 usable randomly positioned SNPs per line, from which we could determine the mosaic breakpoints with an accuracy of about 1kb. Using the resulting imputed genomes, it is possible to test genotype-phenotype association between any phenotype measured on the MAGIC lines and the actual causal variants. We have also generated RNAseq data for some of these lines and show that it is possible to deduce the mosaic structure from these as well. We present the genome assembly pipeline we used to assemble the MAGIC progenitor sequences and to generate the imputedgenomes, and present initial results on the association of phenotypes to variants.