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Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome

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Oberschall,  A.
Dept. of Genetic Principles of Plant Breeding (Jozef Schell), MPI for Plant Breeding Research, Max Planck Society;

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Koncz,  C.
Dept. of Plant Developmental Biology (George Coupland), MPI for Plant Breeding Research, Max Planck Society;

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Citation

Szabados, L., Kovacs, I., Oberschall, A., Abraham, E., Kerekes, I., Zsigmond, L., et al. (2002). Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome. Plant Journal, 32(2), 233-242.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0012-3D67-F
Abstract
Induction of knockout mutations by T-DNA insertion mutagenesis is widely used in studies of plant gene functions. To assess the efficiency of this genetic approach, we have sequenced PCR amplified junctions of 1000 T-DNA insertions and analysed their distribution in the Arabidopsis genome. Map positions of 973 tags could be determined unequivocally, indicating that the majority of T-DNA insertions landed in chromosomal domains of high gene density. Only 4.7% of insertions were found in interspersed, centromeric, telomeric and rDNA repeats, whereas 0.6% of sequenced tags identified chromosomally integrated segments of organellar DNAs. 35.4% of T-DNAs were localized in intervals flanked by ATG and stop codons of predicted genes, showing a distribution of 62.2% in exons and 37.8% in introns. The frequency of T-DNA tags in coding and intergenic regions showed a good correlation with the predicted size distribution of these sequences in the genome. However, the frequency of T- DNA insertions in 3'- and 5'-regulatory regions of genes, corresponding to 300 bp intervals 3' downstream of stop and 5' upstream of ATG codons, was 1.7-2.3-fold higher than in any similar interval elsewhere in the genome. The additive frequency of insertions in 5'-regulatory regions and coding domains provided an estimate for the mutation rate, suggesting that 47.8% of mapped T-DNA tags induced knockout mutations in Arabidopsis .