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 In 1992, the National Center for Gene Research (NCGR) was established jointly by the Ministry of Science and Technology, the Chinese Academy of Sciences (CAS), and the Shanghai city government to provide a major focus in China for mapping and sequencing the rice genome, and genomes of other organisms. The director of NCGR is Doctor Bin Han.
Since 1998 NCGR has been a member of the International Rice Genome Sequencing Project (IRGSP) to completely sequence the entire rice japonica genome. NCGR has been working on the chromosome 4 sequencing in close collaboration with the IRGSP members, the Chinese National Human Genome Center at Shanghai, and Institute of Genetics and Developmental Biology of CAS.
NCGR has a staff size of 43, consists of three research groups: Sequencing Department, Large Scale Platform and Bioinformatics Department. And over 50 million base pairs of rice genomic DNA sequences are now in the public database.
NCGR has a high-performance DNA sequencing facility with 16 DNA sequencers. There are many other types of equipment such as SGI-3800 server, lots of SUN workstations, PCR amplifiers, real-time PCR, DNA synthesizers, automatic workstation, fluorescent microscope, ultra centrifuge, incubators, and ultra-low temperature freezers.
NCGR has also various rice clone resources, including two rice japonica BAC/PAC clone libraries, three rice indica BAC/PAC clone libraries, rice indica full-length cDNA library, and some other BAC and cDNA libraries.
Website: http://www.ncgr.ac.cn
Director: Dr. Bin Han, Professor. Email: bhan@ncgr.ac.cn
Department Heads: Dr. Xiao-Hui Liu, Research Associate; Qi Feng, Research Assistant; Dr. Ting-Ting Lu, Research Assistant; Tao Huang, Research Intern
Staff: Jiang-Hong Luo, Research Associate; Qiang Zhao, Research Assistant; Lei Zhang, Research Assistant; Jian-Ping Guan, Research Assistant; Qi-Jun Weng, Research Assistant; Jing-Jie Zhu, Research Assistant; Yi-Qi Lu, Research Assistant; Dan-Lin Fan, Technician; Chuan-Rang Zhu, Assistant Engineer; Yun-Li Guo, Research Intern; Liu-Wei Deng, Research Intern; Wen-Jun Li, Research Intern; Yi-Wen Yan, Research Intern; Ying-Ying Shangguan, Research Intern; Can-Yang Li, Research Intern; Zhang Lin, Research Intern
Graduate Students: Wen-Huo Hu; Chen-Xi Gao; Bo Chen; Xing-Nan Zheng; Xi-Lin Liu; Lu Wang; Hui Liu; A-Hong Wang; Guo-Jun Lv; Guo-Cheng Hu; Yan Zhou; Dan-Feng Lv; Wei Li; Bo-Feng Zhu; Xue-Hui Huang; Guo Zong; Tao-Ying Zhou; Ben-Guo Gu; Jun-Ping Shi
Graduated Students: Zhen-Yu Gao, 2004 (PhD); Tong-Guo Sun, 2000 (MS); Ting-Ting Lu (PhD)
Researches
We focused on two major projects, one is the comparative genomics and functional genomics analysis of rice, and another is to construct high-throughput technical platform of plant functional genomics analysis based on the next-generation sequencer.
By comparative genomics analysis, we identified the variations distribution and frequency between rice indica and japonica subspecies. Also, with the completion of rice fine genome sequencing, we constructed corresponding greenhouse and experimental field for rice trans-gene and over-expression technology. At the same time, we collected 10,096 indica Guangluai-4 full-length cDNAs and constructed the rice indica cDNAs database. (http://202.127.18.228/ricd/) We expect that some rice genes with important agronomic traits could be systematically identified.
Basing on previous research achievements and with the next-generation sequencing technology, our laboratory developed whole genome-wide high-throughput genotype identification platform of various rice subspecies and corresponding systemic comparative transcriptome analysis. The next-generation sequencing technology permits fast, accurate and cost-effective genotyping for genetic analysis. We developed a method for determining genotypes and recombination breakpoints based on single nucleotide polymorphisms (SNPs) identified from sequences generated by the Illumina Genome Analyzer.
Major Publications:
Han B, Zhang QF. (2008) Rice genome research: current status and future perspectives. The Plant Genome 1: 71-76. Lu TT, Huang XH, Zhu CR, Huang T, Zhao Q, Xie KB, Xiong LZ, Zhang QF, Han B. (2008) RICD: A rice indica cDNA database resource for rice functional genomics. BMC Plant Biology 8: 118. Zhang QF, Li JY, Xue YB, Han B, Deng XW. (2008) Rice 2020: A call for an international coordinated effort in rice functional genomics. Molecular Plant 1: 715-719. Lu TT, Yu SL, Fan DL, Mu J, Shangguan YY, Wang ZX, Minobe Y, Lin ZX, Han B. (2008) Collection and comparative analysis of 1888 full-length cDNAs from wild rice Oryza rufipogon Griff. W1943. DNA Res. 15: 285-295. Huang XH, Lu GJ, Zhao Q, Liu XH, Han B. (2008) Genome-wide analysis of transposon insertion polymorphisms reveals intra-specific variation in cultivated rice. Plant Physiol. 148: 25-40.
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