A Fine Physical Map of the Rice Chromosome 4
- Qiang Zhao1,8,
- Yu Zhang1,8,
- Zhukuan Cheng2,8,
- Mingsheng Chen3,8,
- Shengyue Wang4,8,
- Qi Feng1,
- Yucheng Huang1,
- Ying Li1,
- Yesheng Tang1,
- Bo Zhou1,
- Zhehua Chen1,
- Shuliang Yu1,
- Jingjie Zhu1,
- Xin Hu1,
- Jie Mu1,
- Kai Ying1,
- Pei Hao1,
- Lei Zhang1,
- Yiqi Lu1,
- Lei S. Zhang1,
- Yilei Liu1,
- Zhen Yu1,
- Danlin Fan1,
- Qijun Weng1,
- Ling Chen1,
- Tingting Lu1,
- Xiaohui Liu1,
- Peixin Jia1,
- Tongguo Sun1,
- Yongrui Wu1,
- Yujun Zhang1,
- Ying Lu1,
- Can Li1,
- Rong Wang1,
- Haiyan Lei1,
- Tao Li1,
- Hao Hu1,
- Mei Wu1,
- Runquan Zhang1,
- Jianping Guan1,
- Jia Zhu1,
- Gang Fu4,
- Minghong Gu5,
- Guofan Hong1,
- Yongbiao Xue6,
- Rod Wing3,
- Jiming Jiang2, and
- Bin Han1,7
- 1National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; 2Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA; 3Clemson University Genomics Institute, Clemson, South Carolina 29634, USA; 4Chinese Human Genome Center at Shanghai, Shanghai 201203, China; 5Yangzhou University, Yangzhou, Jiangsu 225009, China; 6Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Zhongguancun, Beijing 100080, China.
Abstract
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 japonicaNipponbare 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.]
