首页 \ 研究员 \ 张忠华
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    研究员

  • 简介

    男,1979年8月出生,博士,研究员。
    中国农业科学院蔬菜花卉研究所蔬菜功能基因组学创新团队首席,生物技术研究室副主任。
    在Nature、Science、Nature Genetics等期刊共发表SCI论文31篇,累计影响因子超过360,共被引用1700余次,其中(并列)第一或通讯作者在Nature Genetics(2篇)、PNAS和Plant Cell等杂志发表11篇,编写了美国Science Publishers出版专著的两个章节。2013年获国家自然科学基金委“优秀青年”科学基金称号,主持国家自然科学基金面上项目2项,主持国家973和863计划子课题。
    教育背景
    1997.09 - 2001.07:青岛农业大学(原莱阳农学院),园艺专业,学士
    2001.09 - 2006.07:浙江大学,生命科学院生物信息学专业,博士
    工作经历
    2006.07 - 至今:中国农业科学院蔬菜花卉研究所,博士后/助研/副研/研究员
    2013.04 - 2013.10:比利时根特大学,访问学者
    主要研究内容
    蔬菜基因组学和遗传育种
    在“大数据时代”背景下,以基因组学为基础,借助生物信息学手段为蔬菜作物构建遗传、序列和变异等各种图谱,并通过比较基因组、进化、表达、关联等综合分析进行数据挖掘,快速鉴定重要功能候选基因,加速蔬菜作物遗传育种基础研究,为全基因组分子育种提供支持。
    主要科研项目
    (1) 国家自然科学委“优秀青年科学”基金项目,经费100万元,2014年1月至2016年12月。
    (2) 国家自然科学基金面上项目“黄瓜永久群体的基因组作图及其在果实性状中的研究”,经费85万,2013年1月至2016年12月。
    (3) 国家自然科学基金面上项目“”,经费32万,2010年1月至2012年12月。
    (4) 973计划项目“主要蔬菜重要品质性状形成的遗传机理与分子改良”子课题任务,经费100万元,2012年1月至2016年12月。
    (5) 863计划项目“基于全基因组的大规模功能基因标记开发”子课题任务,70万,2013年1月至2016年12月。
    主要论著
    论文
    1. Zhang Z., Mao L., Chen H., Bu F., Li G., Sun J., Li S., Sun H., Jiao C., Blakely R., Pan J., Cai R., Luo R., Peer Y., Jacobsen E., Fei Z., Huang S.,Genome-wide Mapping of Structural Variations Reveals a Copy Number Variant that Determines Reproductive Morphology in Cucumber.Plant Cell, 2015.DOI:10.1105/tpc.114.135848. (影响因子9.7)
    2. Qi, J., Liu, X., Shen, D., Miao, H., Xie, B., Li, X., Zeng, P., Wang, S., Shang, Y., Gu, X., Du, Y., Li, Y., Lin, T., Yuan, J., Yang, X., Chen, J., Chen, H., Xiong, X., Huang, K., Fei, Z., Mao, L., Tian, L., Stadler, T., Renner, S.S., Kamoun, S., Lucas, W.J., Zhang, Z., and Huang, S., A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet, 2013. 45(12): p. 1510-5. (并列通讯作者,影响因子35.2)
    3. The Potato Genome Sequencing Consortium, Genome sequence and analysis of the tuber crop potato. Nature, 2011. 475(7355): p. 189-95. (参与单位第二作者,第一作者是通讯作者,影响因子38.6)
    4. Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W.J., Wang, X., Xie, B., Ni, P., Ren, Y., Zhu, H., Li, J., Lin, K., Jin, W., Fei, Z., Li, G., Staub, J., Kilian, A., van der Vossen, E.A.G., Wu, Y., Guo, J., He, J., Jia, Z., Ren, Y., Tian, G., Lu, Y., Ruan, J., Qian, W., Wang, M., Huang, Q., Li, B., Xuan, Z., Cao, J., Asan, Wu, Z., Zhang, J., Cai, Q., Bai, Y., Zhao, B., Han, Y., Li, Y., Li, X., Wang, S., Shi, Q., Liu, S., Cho, W.K., Kim, J.-Y., Xu, Y., Heller-Uszynska, K., Miao, H., Cheng, Z., Zhang, S., Wu, J., Yang, Y., Kang, H., Li, M., Liang, H., Ren, X., Shi, Z., Wen, M., Jian, M., Yang, H., Zhang, G., Yang, Z., Chen, R., Liu, S., Li, J., Ma, L., Liu, H., Zhou, Y., Zhao, J., Fang, X., Li, G., Fang, L., Li, Y., Liu, D., Zheng, H., Zhang, Y., Qin, N., Li, Z., Yang, G., Yang, S., Bolund, L., Kristiansen, K., Zheng, H., Li, S., Zhang, X., Yang, H., Wang, J., Sun, R., Zhang, B., Jiang, S., Wang, J., Du, Y., and Li, S., The genome of the cucumber, Cucumis sativus L. Nat Genet, 2009. 41(12): p. 1275-1281. (并列第一作者,影响因子35.2)
    5. Zhou, Q., MiaoH., LiS., ZhangS., WangY., WengY., ZhangZ., Huang S. and Gu X., A sequencing-based linkage map of cucumber. Mol Plant, 2015. DOI:10.1016/j.molp.2015.03.008.(并列通讯作者,影响因子6.6)
    6. Zhou, Q., Wang S., Hu B., Chen H., Zhang Z. and Huang S., An ACCUMULATION AND REPLICATION OF CHLOROPLASTS 5 gene mutation confers light green peel in cucumber. J Integr Plant Biol, 2015. DOI:10.1111/jipb.12355.(并列通讯作者,影响因子3.5)
    7. Han, Y., Zhang, Z., Liu, C., Liu, J., Huang, S., Jiang, J., and Jin, W., Centromere repositioning in cucurbit species: Implication of the genomic impact from centromere activation and inactivation. P NATL ACAD SCI USA, 2009. 106(35): p. 14937-14941. (并列第一作者,影响因子9.7)
    8. Ren, Y., Zhang, Z., Liu, J., Staub, J.E., Han, Y., Cheng, Z., Li, X., Lu, J., Miao, H., Kang, H., Xie, B., Gu, X., Wang, X., Du, Y., Jin, W., and Huang, S., An Integrated Genetic and Cytogenetic Map of the Cucumber Genome. PLoS ONE, 2009. 4(6): p. e5795. (并列第一作者,影响因子4.1)
    9. Sun, J., Zhang, Z., Zong, X., Huang, S., Li, Z., and Han, Y., A high-resolution cucumber cytogenetic map integrated with the genome assembly. BMC Genomics, 2013. 14: p. 461. (并列第一作者,影响因子4.4)
    10. Li, Z., Zhang, Z., Yan, P., Huang, S., Fei, Z., and Lin, K., RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics, 2011. 12(1): p. 540. (并列第一作者,影响因子4.4)
    11. Zhang, Z., Deng, Y., Tan, J., Hu, S., Yu, J., and Xue, Q., A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Res, 2007. 14(1): p. 37-45. (并列第一作者,影响因子4.4)
    12. Shang, Y., Ma, Y., Zhou, Y., Zhang, H., Duan, L., Chen, H., Zeng, J., Zhou, Q., Wang, S., Gu, W., Liu, M., Ren, J., Gu, X., Zhang, S., Wang, Y., Yasukawa, K., Bouwmeester, H.J., Qi, X., Zhang, Z., Lucas, W.J., and Huang, S., Plant science. Biosynthesis, regulation, and domestication of bitterness in cucumber. Science, 2014. 346(6213): p. 1084-8.
    13. Lin, T., Zhu, G., Zhang, J., Xu, X., Yu, Q., Zheng, Z., Zhang, Z., Lun, Y., Li, S., Wang, X., Huang, Z., Li, J., Zhang, C., Wang, T., Zhang, Y., Wang, A., Zhang, Y., Lin, K., Li, C., Xiong, G., Xue, Y., Mazzucato, A., Causse, M., Fei, Z., Giovannoni, J.J., Chetelat, R.T., Zamir, D., Stadler, T., Li, J., Ye, Z., Du, Y., and Huang, S., Genomic analyses provide insights into the history of tomato breeding. Nat Genet, 2014. 46(11): p. 1220-6.
    14. Lu, H., Lin, T., Klein, J., Wang, S., Qi, J., Zhou, Q., Sun, J., Zhang, Z., Weng, Y., and Huang, S., QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber. Theor Appl Genet, 2014. 127: 1491-1499.
    15. Lin, K., Limpens, E., Zhang, Z., Ivanov, S., Saunders, D.G.O., Mu, D., Pang, E., Cao, H., Cha, H., Lin, T., Zhou, Q., Shang, Y., Li, Y., Sharma, T., van Velzen, R., de Ruijter, N., Aanen, D.K., Win, J., Kamoun, S., Bisseling, T., Geurts, R., and Huang, S., Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus. PLoS Genet, 2014. 10(1): p. e1004078.
    16. Sharma, S.K., Bolser, D., de Boer, J., Sonderkaer, M., Amoros, W., Carboni, M.F., D'Ambrosio, J.M., de la Cruz, G., Di Genova, A., Douches, D.S., Eguiluz, M., Guo, X., Guzman, F., Hackett, C.A., Hamilton, J.P., Li, G., Li, Y., Lozano, R., Maass, A., Marshall, D., Martinez, D., McLean, K., Mejia, N., Milne, L., Munive, S., Nagy, I., Ponce, O., Ramirez, M., Simon, R., Thomson, S.J., Torres, Y., Waugh, R., Zhang, Z., Huang, S., Visser, R.G., Bachem, C.W., Sagredo, B., Feingold, S.E., Orjeda, G., Veilleux, R.E., Bonierbale, M., Jacobs, J.M., Milbourne, D., Martin, D.M., and Bryan, G.J., Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps. G3 (Bethesda), 2013. 3(11): p. 2031-47.
    17. Lou, Q., He, Y., Cheng, C., Zhang, Z., Li, J., Huang, S., and Chen, J., Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber. PLoS One, 2013. 8(5): p. e62676.
    18. Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W.J., Zhang, H., Zheng, Y., Mao, L., Ren, Y., Wang, Z., Min, J., Guo, X., Murat, F., Ham, B.K., Zhang, Z., Gao, S., Huang, M., Xu, Y., Zhong, S., Bombarely, A., Mueller, L.A., Zhao, H., He, H., Zhang, Y., Zhang, Z., Huang, S., Tan, T., Pang, E., Lin, K., Hu, Q., Kuang, H., Ni, P., Wang, B., Liu, J., Kou, Q., Hou, W., Zou, X., Jiang, J., Gong, G., Klee, K., Schoof, H., Huang, Y., Hu, X., Dong, S., Liang, D., Wang, J., Wu, K., Xia, Y., Zhao, X., Zheng, Z., Xing, M., Liang, X., Huang, B., Lv, T., Wang, J., Yin, Y., Yi, H., Li, R., Wu, M., Levi, A., Zhang, X., Giovannoni, J.J., Wang, J., Li, Y., Fei, Z., and Xu, Y., The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet, 2013. 45(1): p. 51-8.
    19. Tomato Genome Consortium, The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 2012. 485(7400): p. 635-41.
    20. Lv, J., Qi, J., Shi, Q., Shen, D., Zhang, S., Shao, G., Li, H., Sun, Z., Weng, Y., Shang, Y., Gu, X., Li, X., Zhu, X., Zhang, J., van Treuren, R., van Dooijeweert, W., Zhang, Z., and Huang, S., Genetic Diversity and Population Structure of Cucumber (Cucumis sativus L.). PLoS One, 2012. 7(10): p. e46919.
    21. Zhao, X., Lu, J., Zhang, Z., Hu, J., Huang, S., and Jin, W., Comparison of the distribution of the repetitive DNA sequences in three variants of Cucumis sativus reveals their phylogenetic relationships. J Genet Genomics, 2011. 38(1): p. 39-45.
    22. Wang, X., Wang, H., Wang, J., Sun, R., Wu, J., Liu, S., Bai, Y., Mun, J.H., Bancroft, I., Cheng, F., Huang, S., Li, X., Hua, W., Freeling, M., Pires, J.C., Paterson, A.H., Chalhoub, B., Wang, B., Hayward, A., Sharpe, A.G., Park, B.S., Weisshaar, B., Liu, B., Li, B., Tong, C., Song, C., Duran, C., Peng, C., Geng, C., Koh, C., Lin, C., Edwards, D., Mu, D., Shen, D., Soumpourou, E., Li, F., Fraser, F., Conant, G., Lassalle, G., King, G.J., Bonnema, G., Tang, H., Belcram, H., Zhou, H., Hirakawa, H., Abe, H., Guo, H., Jin, H., Parkin, I.A., Batley, J., Kim, J.S., Just, J., Li, J., Xu, J., Deng, J., Kim, J.A., Yu, J., Meng, J., Min, J., Poulain, J., Hatakeyama, K., Wu, K., Wang, L., Fang, L., Trick, M., Links, M.G., Zhao, M., Jin, M., Ramchiary, N., Drou, N., Berkman, P.J., Cai, Q., Huang, Q., Li, R., Tabata, S., Cheng, S., Zhang, S., Sato, S., Sun, S., Kwon, S.J., Choi, S.R., Lee, T.H., Fan, W., Zhao, X., Tan, X., Xu, X., Wang, Y., Qiu, Y., Yin, Y., Li, Y., Du, Y., Liao, Y., Lim, Y., Narusaka, Y., Wang, Z., Li, Z., Xiong, Z., and Zhang, Z., The genome of the mesopolyploid crop species Brassica rapa. Nat Genet, 2011. 43(10): p. 1035-1039.
    23. Miao, H., Zhang, S., Wang, X., Zhang, Z., Li, M., Mu, S., Cheng, Z., Zhang, R., Huang, S., Xie, B., Fang, Z., Zhang, Z., Weng, Y., and Gu, X., A linkage map of cultivated cucumber (Cucumis sativus L.) with 248 microsatellite marker loci and seven genes for horticulturally important traits. Euphytica, 2011(2): p. 167-176.
    24. Han, Y., Zhang, Z., Huang, S., and Jin, W., An integrated molecular cytogenetic map of Cucumis sativus L. chromosome 2. BMC Genet, 2011. 12(1): p. 18.
    25. Liu, C., Liu, J., Li, H., Zhang, Z., Han, Y., Huang, S., and Jin, W., Karyotyping in melon (Cucumis melo L.) by cross-species fosmid fluorescence in situ hybridization. Cytogenetic and Genome Research, 2010. 129(1-3): p. 241-249.
    26. Kang, H., Weng, Y., Yang, Y., Zhang, Z., Zhang, S., Mao, Z., Cheng, G., Gu, X., Huang, S., and Xie, B., Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster. Theor Appl Genet, 2010. 122:p795-803.
    27. Guo, S., Zheng, Y., Joung, J.G., Liu, S., Zhang, Z., Crasta, O.R., Sobral, B.W., Xu, Y., Huang, S., and Fei, Z., Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics, 2010. 11: p. 384.
    28. Liu, Q., Wang, H., Zhang, Z., Wu, J., Feng, Y., and Zhu, Z., Divergence in function and expression of the NOD26-like intrinsic proteins in plants. BMC Genomics, 2009. 10(1): p. 313.
    29. Li, Z., Huang, S., Liu, S., Pan, J., Zhang, Z., Tao, Q., Shi, Q., Jia, Z., Zhang, W., Chen, H., Si, L., Zhu, L., and Cai, R., Molecular Isolation of the M Gene Suggests That a Conserved-Residue Conversion Induces the Formation of Bisexual Flowers in Cucumber Plants. Genetics, 2009. 182(4): p. 1381-1385.
    30. Han, Y.H., Zhang, Z.H., Liu, J.H., Lu, J.Y., Huang, S.W., and Jin, W.W., Distribution of the tandem repeat sequences and karyotyping in cucumber ( Cucumis sativus L.) by fluorescence in situ hybridization. Cytogenetic and Genome Research, 2008. 122(1): p. 80-88.
    编写著作
    1. Zhang, Z., He, J., and Huang, S., Chapter 11 Cucumber Genomics, in Genetics, Genomics and Breeding of Cucurbits, Wang, Y.-H., Behera, T.K., and Chittaranjan, K., Editors. 2011, Science Publishers. p. 335-352.
    2. Huang, S. and Zhang, Z., Chapter11 Comparative Genome Sequencing of Tomato and Potato: Methods and Analysis, in Genetics, Genomics, and Breeding of Tomato, Liedl, E.B., et al., Editors. 2013, Science Publishers. p. 361-380.