A fine physical map of the rice chromosome 4.
As part of an international effort to completely sequence the rice genome, we have produced a fine bacterial artificial chromosome (BAC)-based physical map of the Oryza sativa japonica Nipponbare chromosome 4 through an integration of 114 sequenced BAC clones from a taxonomically related subspecies O. sativa indica Guangluai 4 and 182 RFLP and 407 expressed sequence tag (EST) markers with the fingerprinted data of the Nipponbare genome. The map consists of 11 contigs with a total length of 34.5 Mb covering 94% of the estimated chromosome size (36.8 Mb). BAC clones corresponding to telomeres, as well as to the centromere position, were determined by BAC-pachytene chromosome fluorescence in situ hybridization (FISH). This gave rise to an estimated length ratio of 5.13 for the long arm and 2.9 for the short arm (on the basis of the physical map), which indicates that the short arm is a highly condensed one. The FISH analysis and physical mapping also showed that the short arm and the pericentromeric region of the long arm are rich in heterochromatin, which occupied 45% of the chromosome, indicating that this chromosome is likely very difficult to sequence. To our knowledge, this map provides the first example of a rapid and reliable physical mapping on the basis of the integration of the data from two taxonomically related subspecies.
Zhao
Qiang
Q
National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
Zhang
Yu
Y
Cheng
Zhukuan
Z
Chen
Mingsheng
M
Wang
Shengyue
S
Feng
Qi
Q
Huang
Yucheng
Y
Li
Ying
Y
Tang
Yesheng
Y
Zhou
Bo
B
Chen
Zhehua
Z
Yu
Shuliang
S
Zhu
Jingjie
J
Hu
Xin
X
Mu
Jie
J
Ying
Kai
K
Hao
Pei
P
Zhang
Lei
L
Lu
Yiqi
Y
Zhang
Lei S
LS
Liu
Yilei
Y
Yu
Zhen
Z
Fan
Danlin
D
Weng
Qijun
Q
Chen
Ling
L
Lu
Tingting
T
Liu
Xiaohui
X
Jia
Peixin
P
Sun
Tongguo
T
Wu
Yongrui
Y
Zhang
Yujun
Y
Lu
Ying
Y
Li
Can
C
Wang
Rong
R
Lei
Haiyan
H
Li
Tao
T
Hu
Hao
H
Wu
Mei
M
Zhang
Runquan
R
Guan
Jianping
J
Zhu
Jia
J
Fu
Gang
G
Gu
Minghong
M
Hong
Guofan
G
Xue
Yongbiao
Y
Wing
Rod
R
Jiang
Jiming
J
Han
Bin
B
D002875:Chromosomes / Q000737:chemistry / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial; D020451:Contig Mapping; D020732:Cytogenetic Analysis / Q000379:methods; D018744:DNA, Plant / Q000235:genetics; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D012275:Oryza / Q000737:chemistry / Q000235:genetics*; D020161:Physical Chromosome Mapping / Q000379:methods*; D011995:Recombination, Genetic / Q000235:genetics; D012639:Seeds / Q000235:genetics
D018744:DNA, Plant