Emerging Genome Technologies
Zhang, Xu , Byrnes, Jake , Borevitz, Justin .
Survey of splicing variation and allele specific expression in natural accessions of Arabidopsis thaliana using SNP-tiling array.
Natural variation in gene expression underlies phenotypic diversity. We have performed a global gene expression survey focused on variation in known and unknown transcript abundance, alternative splicing, and allele specific expression using a new Arabidopsis SNP tiling array (AtSNPtile1). This tool is a unique platform allowing simultaneous studies of different aspects of gene expression. This new array contains 1.7 million 25mer tiling probes covering the non-repetitive part of the genome at ~35bp resolution. Our analysis of expression/splicing variation currently involves both an annotation based linear regression model testing additive dominance and maternal effects as well as an unbiased Hidden Markov model identifying alternative transcription fragments. Since both SNP alleles are present, the transcript levels AND the genotype of the message can be jointly assayed, which allows direct test of allele specific expression. As ~56,000 of the 250,000 non-singleton SNPs on AtSNPtile1 are annotated as transcribed, many genes can be assayed redundantly for allele specific expression in heterozygotes. We present methods and give examples between Columbia and Vancouver, two wild Arabidopsis thaliana accessions.
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1 - The University of Chicago, Ecology and Evolution, 1101 E. 57th Street, Chicago, IL, 60637, USA
2 - The University of Chicago, Ecology and Evolution
allele specific expression.
Presentation Type: ASPB Minisymposium
Location: Continental A/Hilton
Date: Sunday, July 8th, 2007
Time: 3:15 PM