Deletion mapping by the AtMap1 array

We designed a novel tiling array, AtMap1, for genomic deletion mapping. The AtMap1 is a 60-mer oligonucleotide microarray consisting of 42,497 data probes designed from the genomic sequence of Arabidopsis thaliana Col-0. The data probes are almost evenly distributed over the genome except around centromeres. The average probe interval is 2.8 kb. The performance of the AtMap1 array was assessed using the mag2-2 mutant, which is a well-studied deletion mutant. Eight of the probes showed 3-fold lower signals in mag2-2 than Col-0. Seven of these probes were located in one region on chromosome 3. We treated these adjacent probes as one deletion. This deletion included previously reported deleted region. The other probe was located near the end of chromosome 4. A deletion around the probe was confirmed by PCR. This deletion was newly identified in this study. Thus, we concluded that the AtMap1 array was sufficiently sensitive to identify a deletion without a priori knowledge. From an analysis using the result of hybridization of Ler and previously reported polymorphism data, we found a tendency that the signal decrease depended on the overlap size of sequence polymorphisms. Mutation mapping is time-consuming, laborious and costly. The AtMap1 array removes the difficulties. The AtMap1 array is useful especially for mutations for which linkage-based mapping is difficult, e.g., mutations whose phenotype is highly variable among ecotypes, mutations whose phenotype is difficult to measure and revertant mutations. Keywords: comparative genomic hybridization This series includes: Three self-comparison experiments to assess the reproducablity of the AtMap1 array. Comparison of Col-0 and mag2-2, which is a well-studied deletion mutant induced by T-DNA insertion. Comparison of Col-0 and rot3-1, which is a well-studied deletion mutant induced by fast-neutron irradiation. Comparison of Col-0 and zig-2, which is a well-studied deletion mutant induced by fast-neutron irradiation. Comparison of Col-0 and Ler, which is one of A. thaliana ecotypes. Comparison of different sets of restriction enzymes for genome digestion.