1. Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice
- Author
-
Woo Taek Kim, Seong-Ryong Kim, Dong-Yeon Lee, Junghe Hur, Gynheung An, Soo Jin Wi, Hak Kyung Lee, Sunghwa Choe, Jungwon Yang, Jung Hwa Yu, Sunhee Park, Jongmin Nam, Dong-Hoon Jeong, Chin Bum Lee, Soon-Ki Han, Soo-Jin Kim, Vitnary Choe, Jong Pil Hong, Hoo Sun Chung, Phun Bum Park, Ky Young Park, Miok Lee, Young Hea Kim, Jung Hee Choi, Suyoung An, Hong Gyu Kang, Eunjoo Kim, and Sung-Ryul Kim
- Subjects
DNA, Bacterial ,Physiology ,Genetic Vectors ,DNA, Single-Stranded ,Plant Science ,Biology ,Polymerase Chain Reaction ,Genome ,Sequence-tagged site ,Intergenic region ,Genetics, Genomics, and Molecular Evolution ,Genetics ,Coding region ,Insertion ,Gene ,DNA Primers ,Sequence Tagged Sites ,Base Sequence ,Nucleic acid sequence ,food and beverages ,Oryza ,Exons ,Plants, Genetically Modified ,Introns ,Mutagenesis, Insertional ,GC-content - Abstract
We analyzed 6,749 lines tagged by the gene trap vector pGA2707. This resulted in the isolation of 3,793 genomic sequences flanking the T-DNA. Among the insertions, 1,846 T-DNAs were integrated into genic regions, and 1,864 were located in intergenic regions. Frequencies were also higher at the beginning and end of the coding regions and upstream near the ATG start codon. The overall GC content at the insertion sites was close to that measured from the entire rice (Oryza sativa) genome. Functional classification of these 1,846 tagged genes showed a distribution similar to that observed for all the genes in the rice chromosomes. This indicates that T-DNA insertion is not biased toward a particular class of genes. There were 764, 327, and 346 T-DNA insertions in chromosomes 1, 4 and 10, respectively. Insertions were not evenly distributed; frequencies were higher at the ends of the chromosomes and lower near the centromere. At certain sites, the frequency was higher than in the surrounding regions. This sequence database will be valuable in identifying knockout mutants for elucidating gene function in rice. This resource is available to the scientific community at http://www.postech.ac.kr/life/pfg/risd.
- Published
- 2003
- Full Text
- View/download PDF