Generation and analysis of end sequence database for T-DNA tagging lines in rice.
We analyzed 6749 lines tagged by the gene trap vector pGA2707. This resulted in the isolation of 3793 genomic sequences flanking the T-DNA. Among the insertions, 1846 T-DNAs were integrated into genic regions, and 1864 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 1846 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.
An
Suyoung
S
National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea.
Park
Sunhee
S
Jeong
Dong-Hoon
DH
Lee
Dong-Yeon
DY
Kang
Hong-Gyu
HG
Yu
Jung-Hwa
JH
Hur
Junghe
J
Kim
Sung-Ryul
SR
Kim
Young-Hea
YH
Lee
Miok
M
Han
Soonki
S
Kim
Soo-Jin
SJ
Yang
Jungwon
J
Kim
Eunjoo
E
Wi
Soo Jin
SJ
Chung
Hoo Sun
HS
Hong
Jong-Pil
JP
Choe
Vitnary
V
Lee
Hak-Kyung
HK
Choi
Jung-Hee
JH
Nam
Jongmin
J
Kim
Seong-Ryong
SR
Park
Phun-Bum
PB
Park
Ky Young
KY
Kim
Woo Taek
WT
Choe
Sunghwa
S
Lee
Chin-Bum
CB
An
Gynheung
G
D001483:Base Sequence; D017931:DNA Primers; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D004277:DNA, Single-Stranded / Q000235:genetics*; D005091:Exons; D005822:Genetic Vectors; D007438:Introns; D016254:Mutagenesis, Insertional; D012275:Oryza / Q000235:genetics*; D030821:Plants, Genetically Modified / Q000235:genetics; D016133:Polymerase Chain Reaction; D016324:Sequence Tagged Sites
D017931:DNA Primers; D004269:DNA, Bacterial; D004277:DNA, Single-Stranded; C036483:T-DNA