First published online November 20, 2003; 10.1104/pp.103.030478
Plant Physiology 133:2040-2047 (2003)
© 2003 American Society of Plant Biologists
GENETICS, GENOMICS, AND MOLECULAR EVOLUTION
Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice1
Suyoung An2,
Sunhee Park2,
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 Choi,
Jongmin Nam,
Seong-Ryong Kim,
Phun-Bum Park,
Ky Young Park,
Woo Taek Kim,
Sunghwa Choe,
Chin-Bum Lee and
Gynheung An*
National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea (S.A., S.P., D.-H.J., D.-Y.L., H.-G.K., J.-H.Y., J.H., S.-R.K., Y.-H.K., M.L., G.A.); Department of Life Science, Sogang University, Seoul 121-742, Korea (S.H., S.-J.K., S.-R.K.); Department of Genetic Engineering, Suwon University, Suwon 445-743, Korea (J.Y., E.K., P.-B.P.); Department of Biology, Sunchon National University, Sunchon 540-742, Korea (S.J.W., K.Y.P.); Department of Biology, Yonsei University, Seoul 120-749, Korea (H.S.C., J-.P.H., W.T.K.); Department of Biology, Seoul National University, Seoul 151-747, Korea (V.C., S.C.); Department of Biology, Dong-eui University, Pusan 614-714, Korea. (H.-K.L., J.-H.C., C.-B.L.); and Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 208 Mueller Laboratory, University Park, Pennsylvania 16802 (J.N.)
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.
1 This work was supported in part by the Biogreen 21 Program, Rural Development Administration (grant).
2 These authors contributed equally to the paper.
Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.103.030478.
* Corresponding author; e-mail genean{at}postech.ac.kr; fax 82-54-279-2199.
Received July 18, 2003;
returned for revision September 2, 2003;
accepted September 12, 2003.
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