AtMap1: a DNA microarray for genomic deletion mapping in Arabidopsis thaliana
AtMap1: a DNA microarray for genomic deletion mapping in Arabidopsis thaliana
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DOI：
10.1111/j.1365-313x.2008.03656.x
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发表时间：
2008-12-01
期刊：
影响因子：
7.2
通讯作者：
Hara-Nishimura, Ikuko
中科院分区：
文献类型：
--
作者：
Nagano, Atsushi J.;Fukazawa, Mitsue;Hara-Nishimura, Ikuko
我们设计了一种新的平铺阵列，AtMap1，用于基因组缺失定位。AtMap1是由拟南芥Col-0基因组序列设计的42 497个数据探针组成的60个寡核苷酸微阵列。平均探测间隔为2.8 kb。使用缺失突变体mag2-2、rot3-1和zig2来评估AtMap1阵列的性能。其中8个探测器的磁-2信号比Col-0低3倍。其中7个探针位于3号染色体的一个区域。我们认为这些相邻的探针代表一个缺失。此删除与报告的删除区域一致。另一个探针位于4号染色体末端附近。PCR证实了探针周围新发现的缺失。我们还检测到rot3-1和zig2的相关缺失。因此，我们得出结论，AtMap1阵列足够敏感，可以在没有任何先验知识的情况下识别缺失。对Ler杂交结果和先前报道的多态性数据的分析表明，信号的减少倾向于依赖于序列多态性的重叠大小。突变映射是费时、费力和昂贵的。AtMap1数组消除了这些限制。
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.