Molecular Genetics and Genomics

, Volume 274, Issue 4, pp 337–345 | Cite as

A fine physical map of the rice chromosome 5

  • Chia-Hsiung Cheng
  • Mei-Chu Chung
  • Shu-Mei Liu
  • Shi-Kuang Chen
  • Fang-Yi Kao
  • Shu-Jen Lin
  • Shin-Hsin Hsiao
  • I-Chieh Tseng
  • Yue-Ie C. Hsing
  • Hong-Pang Wu
  • Ching-San Chen
  • Jei-Fu Shaw
  • Jianzhong Wu
  • Takashi Matsumoto
  • Takuji Sasaki
  • Hong-Hwa Chen
  • Teh-Yuan Chow
Original Paper

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 ~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.

Keywords

Centromere Contig Fluorescence in situ hybridization (FISH) Physical mapping Rice chromosome 5 

Notes

Acknowledgments

We thank Ming-Ru Liou for assisting the experiment of screening of fosmid library, and Yao-Cheng Lin for preparing the Figure S2 and the analysis of Cent O repeats. This work was supported by Academia Sinica, the National Science Council, and the Council of Agriculture, Taipei, Taiwan.

Supplementary material

438_2005_39_MOESM1_ESM.pdf (148 kb)
Supplementary material

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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Chia-Hsiung Cheng
    • 1
  • Mei-Chu Chung
    • 1
  • Shu-Mei Liu
    • 1
  • Shi-Kuang Chen
    • 1
  • Fang-Yi Kao
    • 1
  • Shu-Jen Lin
    • 1
  • Shin-Hsin Hsiao
    • 1
  • I-Chieh Tseng
    • 1
  • Yue-Ie C. Hsing
    • 1
  • Hong-Pang Wu
    • 1
  • Ching-San Chen
    • 1
  • Jei-Fu Shaw
    • 1
  • Jianzhong Wu
    • 2
  • Takashi Matsumoto
    • 2
  • Takuji Sasaki
    • 2
  • Hong-Hwa Chen
    • 1
    • 3
  • Teh-Yuan Chow
    • 1
    • 4
  1. 1.Institute of BotanyAcademia SinicaTaipei 115Taiwan
  2. 2.Rice Genome Research ProgramNational Institute of Agrobiological Sciences, and Institute of the Society for Techno-innovation of Agriculture, Forestry and FisheriesTsukuba, IbarakiJapan
  3. 3.Department of Life Sciences and Institute of BiotechnologyNational Cheng Kung UniversityTainan 701Taiwan
  4. 4.Institute of BiotechnologyCentral Taiwan University of Sciences and TechnologyTaichung 406Taiwan

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