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Vol. 12, Issue 5, 817-823, May 2002

LETTER
A Fine Physical Map of the Rice Chromosome 4

Qiang Zhao,1,8 Yu Zhang,1,8 Zhukuan Cheng,2,8 Mingsheng Chen,3,8 Shengyue Wang,4,8 Qi Feng,1 Yucheng Huang,1 Ying Li,1 Yesheng Tang,1 Bo Zhou,1 Zhehua Chen,1 Shuliang Yu,1 Jingjie Zhu,1 Xin Hu,1 Jie Mu,1 Kai Ying,1 Pei Hao,1 Lei Zhang,1 Yiqi Lu,1 Lei S. Zhang,1 Yilei Liu,1 Zhen Yu,1 Danlin Fan,1 Qijun Weng,1 Ling Chen,1 Tingting Lu,1 Xiaohui Liu,1 Peixin Jia,1 Tongguo Sun,1 Yongrui Wu,1 Yujun Zhang,1 Ying Lu,1 Can Li,1 Rong Wang,1 Haiyan Lei,1 Tao Li,1 Hao Hu,1 Mei Wu,1 Runquan Zhang,1 Jianping Guan,1 Jia Zhu,1 Gang Fu,4 Minghong Gu,5 Guofan Hong,1 Yongbiao Xue,6 Rod Wing,3 Jiming Jiang,2 and Bin Han1,7

1 National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; 2 Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; 3 Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; 4 Chinese Human Genome Center at Shanghai, Shanghai 201203, China; 5 Yangzhou University, Yangzhou, Jiangsu 225009, China; 6 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China.

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.

[The following individuals and institutions kindly provided reagents, samples, or unpublished information as indicated in the paper: S. McCouch, T. Sasaki, and Monsanto.]

7 Corresponding author.

8 These authors contributed equally to this work.

12:817-823 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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