Zhao Qiang, Zhang Yu, Cheng Zhukuan, Chen Mingsheng, Wang Shengyue, Feng Qi, Huang Yucheng, Li Ying, Tang Yesheng, Zhou Bo, Chen Zhehua, Yu Shuliang, Zhu Jingjie, Hu Xin, Mu Jie, Ying Kai, Hao Pei, Zhang Lei, Lu Yiqi, Zhang Lei S, Liu Yilei, Yu Zhen, Fan Danlin, Weng Qijun, Chen Ling, Lu Tingting, Liu Xiaohui, Jia Peixin, Sun Tongguo, Wu Yongrui, Zhang Yujun, Lu Ying, Li Can, Wang Rong, Lei Haiyan, Li Tao, Hu Hao, Wu Mei, Zhang Runquan, Guan Jianping, Zhu Jia, Fu Gang, Gu Minghong, Hong Guofan, Xue Yongbiao, Wing Rod, Jiang Jiming, Han Bin
National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
Genome Res. 2002 May;12(5):817-23. doi: 10.1101/gr.48902.
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.
作为水稻基因组全序列测定国际合作项目的一部分，我们通过整合来自分类学上相关亚种——水稻籼稻广陆矮4号的114个已测序细菌人工染色体（BAC）克隆、182个限制性片段长度多态性（RFLP）标记和407个表达序列标签（EST）标记以及日本晴基因组的指纹数据，构建了一张基于BAC的高质量日本晴4号染色体物理图谱。该图谱由11个重叠群组成，总长34.5兆碱基对（Mb），覆盖了估计染色体大小（36.8 Mb）的94%。通过BAC-粗线期染色体荧光原位杂交（FISH）确定了与端粒以及着丝粒位置相对应的BAC克隆。由此得出长臂与短臂的估计长度比分别为5.13和2.9（基于物理图谱），这表明短臂是高度浓缩的。FISH分析和物理图谱绘制还表明，短臂以及长臂的着丝粒周围区域富含异染色质，占染色体的45%，这表明该染色体可能极难进行测序。据我们所知，该图谱提供了首个基于两个分类学相关亚种数据整合的快速可靠物理图谱构建的实例。
