Distribution and characterization of over 1000 T‐DNA tags in rice genome
Open Access
- 28 August 2003
- journal article
- research article
- Published by Wiley in The Plant Journal
- Vol. 36 (1), 105-113
- https://doi.org/10.1046/j.1365-313x.2003.01860.x
Abstract
We generated T-DNA insertions throughout the rice genome for saturation mutagenesis. More than 1000 flanking sequences were mapped on 12 rice chromosomes. Our results showed that T-DNA tags were not randomly spread on rice chromosomes and were preferentially inserted in gene-rich regions. Few insertions (2.4%) were found in repetitive regions. T-DNA insertions in genic (58.1%) and intergenic regions (41.9%) showed a good correlation with the predicted size distribution of these sequences in the rice genome. Whereas, obvious biases were found for the insertions in the 5′- and 3′-regulatory regions outside the coding regions both at 500-bp size and in introns rather than in exons. Such distribution patterns and biases for T-DNA integration in rice are similar to that of the previous report in Arabidopsis, which may result from T-DNA integration mechanism itself. Rice will require approximately the same number of T-DNA insertions for saturation mutagenesis as will Arabidopsis. A database of the T-DNA insertion sites in rice is publicly available at our web site (http://www.genomics.zju.edu.cn/ricetdna).Keywords
This publication has 47 references indexed in Scilit:
- A New Resource of Locally Transposed DissociationElements for Screening Gene-Knockout Lines in Silico on the Arabidopsis GenomePlant Physiology, 2002
- Characterization of T-DNA Insertion Sites inArabidopsis thalianaand the Implications for Saturation MutagenesisOMICS: A Journal of Integrative Biology, 2002
- A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag SitesPlant Cell, 2002
- Tagged Transcriptome Display (TTD) in indica rice using Ac transpositionMolecular Genetics and Genomics, 2001
- T‐DNA insertional mutagenesis for functional genomics in riceThe Plant Journal, 2000
- Display and isolation of transposon-flanking sequences starting from genomic DNA or RNAThe Plant Journal, 2000
- Molecular analysis of rice plants harboring an Ac/Ds transposable element‐mediated gene trapping systemThe Plant Journal, 1999
- The structures of integration sites in transgenic riceThe Plant Journal, 1997
- Chromosomal mapping of T-DNA inserts in transgenicPetunia byin situ hybridizationTransgenic Research, 1995
- Tagging genomic sequences that direct transgene expression by activation of a promoter trap in plantsTransgenic Research, 1993