A fine physical map of the rice chromosome 4

Qiang Zhao, Yu Zhang, Zhukuan Cheng, Mingsheng Chen, Shengyue Wang, Qi Feng, Yucheng Huang, Ying Li, Yesheng Tang, Bo Zhou, Zhehua Chen, Shuliang Yu, Jingjie Zhu, Xin Hu, Jie Mu, Kai Ying, Pei Hao, Lei Zhang, Yiqi Lu, Lei S. ZhangYilei Liu, Zhen Yu, Danlin Fan, Qijun Weng, Ling Chen, Tingting Lu, Xiaohui Liu, Peixin Jia, Tongguo Sun, Yongrui Wu, Yujun Zhang, Ying Lu, Can Li, Rong Wang, Haiyan Lei, Tao Li, Hao Hu, Mei Wu, Runquan Zhang, Jianping Guan, Jia Zhu, Gang Fu, Minghong Gu, Guofan Hong, Yongbiao Xue, Rod A Wing, Jiming Jiang, Bin Han

Research output: Contribution to journalArticle

62 Citations (Scopus)

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 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 II 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.

Original languageEnglish (US)
Pages (from-to)817-823
Number of pages7
JournalGenome Research
Volume12
Issue number5
DOIs
StatePublished - 2002
Externally publishedYes

Fingerprint

Bacterial Artificial Chromosomes
Chromosomes, Human, Pair 4
Chromosomes
Fluorescence In Situ Hybridization
Clone Cells
Genome
Heterochromatin
Centromere
Expressed Sequence Tags
Telomere
Restriction Fragment Length Polymorphisms
Oryza

ASJC Scopus subject areas

  • Genetics

Cite this

Zhao, Q., Zhang, Y., Cheng, Z., Chen, M., Wang, S., Feng, Q., ... Han, B. (2002). A fine physical map of the rice chromosome 4. Genome Research, 12(5), 817-823. https://doi.org/10.1101/gr.48902

A fine physical map of the rice chromosome 4. / 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 A; Jiang, Jiming; Han, Bin.

In: Genome Research, Vol. 12, No. 5, 2002, p. 817-823.

Research output: Contribution to journalArticle

Zhao, Q, Zhang, Y, Cheng, Z, Chen, M, Wang, S, Feng, Q, Huang, Y, Li, Y, Tang, Y, Zhou, B, Chen, Z, Yu, S, Zhu, J, Hu, X, Mu, J, Ying, K, Hao, P, Zhang, L, Lu, Y, Zhang, LS, Liu, Y, Yu, Z, Fan, D, Weng, Q, Chen, L, Lu, T, Liu, X, Jia, P, Sun, T, Wu, Y, Zhang, Y, Lu, Y, Li, C, Wang, R, Lei, H, Li, T, Hu, H, Wu, M, Zhang, R, Guan, J, Zhu, J, Fu, G, Gu, M, Hong, G, Xue, Y, Wing, RA, Jiang, J & Han, B 2002, 'A fine physical map of the rice chromosome 4', Genome Research, vol. 12, no. 5, pp. 817-823. https://doi.org/10.1101/gr.48902
Zhao Q, Zhang Y, Cheng Z, Chen M, Wang S, Feng Q et al. A fine physical map of the rice chromosome 4. Genome Research. 2002;12(5):817-823. https://doi.org/10.1101/gr.48902
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 A ; Jiang, Jiming ; Han, Bin. / A fine physical map of the rice chromosome 4. In: Genome Research. 2002 ; Vol. 12, No. 5. pp. 817-823.
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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 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 II 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.",
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T1 - A fine physical map of the rice chromosome 4

AU - Zhao, Qiang

AU - Zhang, Yu

AU - Cheng, Zhukuan

AU - Chen, Mingsheng

AU - Wang, Shengyue

AU - Feng, Qi

AU - Huang, Yucheng

AU - Li, Ying

AU - Tang, Yesheng

AU - Zhou, Bo

AU - Chen, Zhehua

AU - Yu, Shuliang

AU - Zhu, Jingjie

AU - Hu, Xin

AU - Mu, Jie

AU - Ying, Kai

AU - Hao, Pei

AU - Zhang, Lei

AU - Lu, Yiqi

AU - Zhang, Lei S.

AU - Liu, Yilei

AU - Yu, Zhen

AU - Fan, Danlin

AU - Weng, Qijun

AU - Chen, Ling

AU - Lu, Tingting

AU - Liu, Xiaohui

AU - Jia, Peixin

AU - Sun, Tongguo

AU - Wu, Yongrui

AU - Zhang, Yujun

AU - Lu, Ying

AU - Li, Can

AU - Wang, Rong

AU - Lei, Haiyan

AU - Li, Tao

AU - Hu, Hao

AU - Wu, Mei

AU - Zhang, Runquan

AU - Guan, Jianping

AU - Zhu, Jia

AU - Fu, Gang

AU - Gu, Minghong

AU - Hong, Guofan

AU - Xue, Yongbiao

AU - Wing, Rod A

AU - Jiang, Jiming

AU - Han, Bin

PY - 2002

Y1 - 2002

N2 - 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 II 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.

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