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          Institute: MPI für Pflanzenzüchtungsforschung     Collection: Dept. Plant Developmental Biology (George Coupland)     Display Documents



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ID: 28776.0, MPI für Pflanzenzüchtungsforschung / Dept. Plant Developmental Biology (George Coupland)
Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome
Authors:Szabados, L.; Kovacs, I.; Oberschall, A.; Abraham, E.; Kerekes, I.; Zsigmond, L.; Nagy, R.; Alvarado, M. C.; Krasovskaja, I.; Gal, M.; Berente, A.; Redei, G. P.; Ben Haim, A.; Koncz, C.
Language:English
Date of Publication (YYYY-MM-DD):2002-10
Title of Journal:Plant Journal
Journal Abbrev.:Plant J.
Volume:32
Issue / Number:2
Start Page:233
End Page:242
Review Status:Peer-review
Audience:Experts Only
Abstract / Description: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 .
Free Keywords:T-DNA; insertion mutagenesis; Arabidopsis; sequenced tags; functional genomics
Comment of the Author/Creator:Date: 2002, OCT
External Publication Status:published
Document Type:Article
Communicated by:N.N.
Affiliations:MPI für Pflanzenzüchtungsforschung
External Affiliations:Max Planck Inst Zuchtungsforsch, Carl Von Linne Weg 10, D-50829; Cologne, Germany; Max Planck Inst Zuchtungsforsch, D-50829 Cologne, Germany; Hungarian Acad Sci, Biol Res Ctr, Inst Plant Biol, H-6701 Szeged, Hungary; Vital Biotechnol Ltd, IL-39101 Haifa, Israel
Identifiers:ISI:000178605000009 [ID No:1]
ISSN:0960-7412 [ID No:2]
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