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AtMap1: a DNA microarray for genomic deletion mapping in Arabidopsis thaliana.

Authors :
Nagano, Atsushi J.
Fukazawa, Mitsue
Hayashi, Makoto
Ikeuchi, Momoko
Tsukaya, Hirokazu
Nishimura, Mikio
Hara-Nishimura, Ikuko
Source :
Plant Journal. Dec2008, Vol. 56 Issue 6, p1058-1065. 8p. 7 Charts, 4 Graphs.
Publication Year :
2008

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 L er 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. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
09607412
Volume :
56
Issue :
6
Database :
Academic Search Index
Journal :
Plant Journal
Publication Type :
Academic Journal
Accession number :
35604402
Full Text :
https://doi.org/10.1111/j.1365-313X.2008.03656.x