1. A fine physical map of the rice chromosome 5
- Author
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Mei-Chu Chung, Shu-Jen Lin, Shin-Hsin Hsiao, Hong-Pang Wu, Shi-Kuang Chen, Takuji Sasaki, Takashi Matsumoto, Hong-Hwa Chen, J. F. Shaw, Yue-Ie C. Hsing, Ching-San Chen, Jianzhong Wu, I-Chieh Tseng, Chia Hsiung Cheng, Fang-Yi Kao, Shu-Mei Liu, and Teh-Yuan Chow
- Subjects
Chromosomes, Artificial, Bacterial ,DNA, Plant ,Positional cloning ,Centromere ,Biology ,Genes, Plant ,Genome ,Sequence-tagged site ,Contig Mapping ,Genetics ,Molecular Biology ,In Situ Hybridization, Fluorescence ,Gene Library ,Bacterial artificial chromosome ,Expressed sequence tag ,Contig ,Chromosome Mapping ,food and beverages ,Chromosome ,Oryza ,General Medicine ,Physical Chromosome Mapping ,Genetic Techniques ,Genome, Plant - Abstract
A fine physical map of the rice (Oryza sativa spp. Japonica var. Nipponbare) chromosome 5 with bacterial artificial chromosome (BAC) and PI-derived artificial chromosome (PAC) clones was constructed through integration of 280 sequenced BAC/PAC clones and 232 sequence tagged site/expressed sequence tag markers with the use of fingerprinted contig data of the Nipponbare genome. This map consists of five contigs covering 99% of the estimated chromosome size (30.08 Mb). The four physical gaps were estimated at 30 and 20 kb for gaps 1-3 and gap 4, respectively. We have submitted 42.2-Mb sequences with 29.8 Mb of nonoverlapping sequences to public databases. BAC clones corresponding to telomere and centromere regions were confirmed by BAC-fluorescence in situ hybridization (FISH) on a pachytene chromosome. The genetically centromeric region at 54.6 cM was covered by a minimum tiling path spanning 2.1 Mb with no physical gaps. The precise position of the centromere was revealed by using three overlapping BAC/PACs for approximately 150 kb. In addition, FISH results revealed uneven chromatin condensation around the centromeric region at the pachytene stage. This map is of use for positional cloning and further characterization of the rice functional genomics.
- Published
- 2005