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

Research output: Contribution to journalArticle

13 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)337-345
Number of pages9
JournalMolecular Genetics and Genomics
Volume274
Issue number4
DOIs
Publication statusPublished - Nov 2005
Externally publishedYes

Fingerprint

Bacterial Artificial Chromosomes
Chromosomes, Human, Pair 5
Artificial Chromosomes
Clone Cells
Centromere
Fluorescence In Situ Hybridization
Chromosomes
Pachytene Stage
Sequence Tagged Sites
Expressed Sequence Tags
Telomere
Genomics
Chromatin
Organism Cloning
Oryza
Genome
Databases

Keywords

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

ASJC Scopus subject areas

  • Genetics

Cite this

Cheng, C. H., Chung, M. C., Liu, S. M., Chen, S. K., Kao, F. Y., Lin, S. J., ... Chow, T. Y. (2005). A fine physical map of the rice chromosome 5. Molecular Genetics and Genomics, 274(4), 337-345. https://doi.org/10.1007/s00438-005-0039-y

A fine physical map of the rice chromosome 5. / Cheng, Chia Hsiung; Chung, Mei Chu; Liu, Shu Mei; Chen, Shi Kuang; Kao, Fang Yi; Lin, Shu Jen; Hsiao, Shin Hsin; Tseng, I. Chieh; Hsing, Yue Ie C; Wu, Hong Pang; Chen, Ching San; Shaw, Jei Fu; Wu, Jianzhong; Matsumoto, Takashi; Sasaki, Takuji; Chen, Hong Hwa; Chow, Teh Yuan.

In: Molecular Genetics and Genomics, Vol. 274, No. 4, 11.2005, p. 337-345.

Research output: Contribution to journalArticle

Cheng, CH, Chung, MC, Liu, SM, Chen, SK, Kao, FY, Lin, SJ, Hsiao, SH, Tseng, IC, Hsing, YIC, Wu, HP, Chen, CS, Shaw, JF, Wu, J, Matsumoto, T, Sasaki, T, Chen, HH & Chow, TY 2005, 'A fine physical map of the rice chromosome 5', Molecular Genetics and Genomics, vol. 274, no. 4, pp. 337-345. https://doi.org/10.1007/s00438-005-0039-y
Cheng, Chia Hsiung ; Chung, Mei Chu ; Liu, Shu Mei ; Chen, Shi Kuang ; Kao, Fang Yi ; Lin, Shu Jen ; Hsiao, Shin Hsin ; Tseng, I. Chieh ; Hsing, Yue Ie C ; Wu, Hong Pang ; Chen, Ching San ; Shaw, Jei Fu ; Wu, Jianzhong ; Matsumoto, Takashi ; Sasaki, Takuji ; Chen, Hong Hwa ; Chow, Teh Yuan. / A fine physical map of the rice chromosome 5. In: Molecular Genetics and Genomics. 2005 ; Vol. 274, No. 4. pp. 337-345.
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AU - Hsiao, Shin Hsin

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AU - Chen, Ching San

AU - Shaw, Jei Fu

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AU - Sasaki, Takuji

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