Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice

Suyoung An, Sunhee Park, Dong Hoon Jeong, Dong Yeon Lee, Hong Gyu Kang, Jung Hwa Yu, Junghe Hur, Sung Ryul Kim, Young Hea Kim, Miok Lee, Soonki Han, Soo Jin Kim, Jungwon Yang, Eunjoo Kim, Soo Jin Wi, Hoo Sun Chung, Jong Pil Hong, Vitnary Choe, Hak Kyung Lee, Jung Hee ChoiJongmin Nam, Seong Ryong Kim, Phun Bum Park, Ky Young Park, Woo Taek Kim, Sunghwa Choe, Chin Bum Lee, Gynheung An

Research output: Contribution to journalArticle

191 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)2040-2047
Number of pages8
JournalPlant physiology
Volume133
Issue number4
DOIs
Publication statusPublished - 2003 Dec

All Science Journal Classification (ASJC) codes

  • Physiology
  • Genetics
  • Plant Science

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    An, S., Park, S., Jeong, D. H., Lee, D. Y., Kang, H. G., Yu, J. H., Hur, J., Kim, S. R., Kim, Y. H., Lee, M., Han, S., Kim, S. J., Yang, J., Kim, E., Wi, S. J., Chung, H. S., Hong, J. P., Choe, V., Lee, H. K., ... An, G. (2003). Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice. Plant physiology, 133(4), 2040-2047. https://doi.org/10.1104/pp.103.030478