title: AtMap1: a DNA microarray for genomic deletion mapping in Arabidopsis thaliana.
abstract: We have designed a novel tiling array, AtMap1, for genomic deletion mapping. AtMap1 is a 60-mer oligonucleotide microarray consisting of 42 497 data probes designed from the genomic sequence of Arabidopsis thaliana Col-0. The average probe interval is 2.8 kb. The performance of the AtMap1 array was assessed using the deletion mutants mag2-2, rot3-1 and zig-2. Eight of the probes showed threefold lower signals in mag2-2 than Col-0. Seven of these probes were located in one region on chromosome 3. We considered these adjacent probes to represent one deletion. This deletion was consistent with a reported deleted region. The other probe was located near the end of chromosome 4. A newly identified deletion around the probe was confirmed by PCR. We also detected the responsible deletions for rot3-1 and zig-2. Thus we concluded that the AtMap1 array was sufficiently sensitive to identify a deletion without any a priori knowledge of the deletion. An analysis of the result of hybridization of Ler and previously reported polymorphism data revealed that the signal decrease tended to depend on the overlap size of sequence polymorphisms. Mutation mapping is time-consuming, laborious and costly. The AtMap1 array removes these limitations.
authors.affiliation: Division of Biological Science, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
authors.forename: Atsushi J
authors.initials: AJ
authors.lastname: Nagano
authors.forename: Mitsue
authors.initials: M
authors.lastname: Fukazawa
authors.forename: Makoto
authors.initials: M
authors.lastname: Hayashi
authors.forename: Momoko
authors.initials: M
authors.lastname: Ikeuchi
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Tsukaya
authors.forename: Mikio
authors.initials: M
authors.lastname: Nishimura
authors.forename: Ikuko
authors.initials: I
authors.lastname: Hara-Nishimura
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping; D015342:DNA Probes; D018744:DNA, Plant / Q000235:genetics; D017353:Gene Deletion; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
chemical_list: D015342:DNA Probes; D018744:DNA, Plant