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凌宏清


凌宏清,博士,研究员,博士生导师

 

  1977年3月至1982年1月,就读于四川农学院(现四川农业大学)农学系,1982年2月毕业,获农学学士;1985年10月至1988年7月,在德国Kiel市Christian-Albrechts大学农学院攻读硕士学位,获得农学硕士。1989年1月至1993年1月在德国Kiel市Christian-Albrechts大学理学院攻读博士学位,获得理学博士;1993年2月至1998年4月,在德国植物遗传与栽培作物研究所(IPK-Gadtersleben)从事博士后研究;1998年5月-2001年6月就职于瑞士苏黎世大学植物生物学研究所。2000年入选中国科学院国外引进杰出人才“百人计划”;2001年7月回国,就职于中国科学院遗传与发育生物学研究所,任研究员。2002年获"国家杰出青年基金"资助。2004年入选国家7部委(人事部、科学技术部、教育部、财政部、国家发展和改革委员会、国家自然科学基金委员会、中国科学技术协会)"新世纪百千万人才工程"国家级人选。2006年获政府特殊津贴。2006年10月至2017年6月,任植物细胞与染色体工程国家重点实验室主任。2011年被科技部聘任为国家重点基础研究发展计划(973计划)“作物养分高效利用的信号转导和分子调控网络”项目首席科学家。任“International Symposium on Iron Nutrition and Interaction in Plants”会议的国际组委会委员,《Theoretical Applied Genetics》、《Frontier in Plant Nutrition》、《Functional & Integrative Genomics》等杂志编委。



        研究方向:小麦分子遗传学和植物营养分子生物学。用模式植物拟南芥和番茄为研究体系,克隆了参与磷、铁吸收代谢关键基因20余个,系统地研究了植物吸收铁的分子调控网络,揭示了植物高效吸收铁的分子机理。组织完成了小麦A基因组草图绘制,研究成果于2013年发表在“Nature”杂志,并入选为“2013年度中国科学十大进展”。在Nature、PNAS、Plant Cell等学术刊物发表相关论文90余篇。
 
        实验室的主要研究内容简介如下:
 
        1.植物营养分子生物学 
        植物营养分子生物学是近年来在植物营养学基础上发展起来的一门新型学科,拟在分子水平上揭示植物吸收、转运、同化与代谢各种营养元素的分子机制。为培育养分高效型农作物新品种提供理论依据和基因资源,对减少农业生产中的化肥投入,降低农产品成本,保护自然资源和减少环境污染具有重要理论和社会意义。课题组主要开展植物磷、铁营养分子生物学研究;分离与磷、铁吸收代谢相关的基因,揭示其在控制磷铁吸收、转运与代谢中的生物学功能以及它们之间的网络调控关系。
 
        植物高效吸收利用铁的分子调控机制:由于铁离子具有活跃的三价与二价的价态变化,是细胞内氧化还原反应所必需的组分,在细胞呼吸、光合作用和金属蛋白的催化反应过程中发挥重要作用,是重要的电子传递体。因此,铁在原核和真核生物的生命活动中具有不可替代的功能。尽管铁在地壳中的含量丰富,但主要以氧化态的Fe3+形式存在,在中性和碱性土壤中的溶解度极低,不能被吸收利用,从而引起许多生物的生存受到铁匮乏胁迫。植物缺铁会导致叶绿素合成减少,光合速率降低,严重缺铁时叶绿素合成停止,新叶变黄,生物量大幅度下降。农作物缺铁不仅影响产量和品质,造成经济损失,而且也影响人类对铁的获取,导致缺铁性疾病的发生,如Wilson、Pakinson、Menken、贫血病(anemia)等。课题组利用模式植物拟南芥和番茄为材料,研究“机理 I“型植物(所有双子叶植物和非禾本科单子叶植物)的铁高效吸收利用分子调控机制。从番茄和拟南芥中鉴定和分离了控制铁吸收的调控基因(FERFITAtbHLH38AtbHLH39AtbHLH100、AtbHLH101、SlbHLH68MED16SKB1)、参与铁吸收的基因(LeFRO1AtFROs)及铁利用基因(CHLNLeTHICClpC1)等。证明了番茄FER以及它在拟南芥中的同源基因FIT是控制“机理I”植物铁高效吸收的关键调控基因,它们编码蛋白在细胞核内与AtbHLH38、AtbHLH39、AtbHLH100或AtbHLH101互作形成异源二聚体,在MED16的参与下直接调控铁吸收基因IRT1FRO2的转录,控制铁的吸收;而SKB1编码一个蛋白精氨酸甲基转移酶,可根据细胞内铁离子含量的多少,动态结合到AtbHLH38AtbHLH39AtbHLH100AtbHLH101基因的启动子区,对组蛋白进行对称性双甲基化(H4R3sme2)修饰,从而负向调控这四个转录因子的表达强度,调控铁离子的吸收,避免过多铁吸入对细胞的伤害。目前正在对这些已分离调控基因的调控网络关系进行深入分析,同时利用正向和反向遗传学方法鉴定和分离更多参与铁吸收、转运和利用新基因,揭示其“机理I“植物高效吸收利用铁的分子机理及调控网络。
 
        植物磷高效的分子机制研究:磷是作物生长发育的一种大量营养元素,磷肥的利用效率非常低,当季磷肥利用率仅在10%-20%左右。磷肥的低效利用,使农业面源污染成为水系富营养化、土壤酸化与重金属污染最重要的因素,严重威胁我国生态安全与可持续发展。另外,磷矿是不可再生资源,磷矿在世界范围内濒临枯竭。在自然界中不同植物以及同种作物的不同品种对磷的吸收、利用存在明显差异。本实验室目前正在利用正向和反向遗传学方法鉴定和分离磷吸收代谢关键基因及QTLs,研究其生物学功能,拟揭示磷吸收代谢的分子机制,为培养磷高效农作物新品种提供理论依据和新的基因资源。

        2.
小麦分子遗传学
        小麦是全球最重要的粮食作物,养活了世界上40%的人口。生产上广泛种植的普通小麦是一个异源六倍体,含有A、B和D三个基因组。它是由祖先野生的一粒小麦(Triticum urartu,含AA基因组)与拟斯卑尔托山羊草(Aegilops speltoides,含BB基因组)杂交形成四倍体小麦(Triticum turgidum,含有AABB基因组)。大约在8000年前,四倍体小麦与粗山羊草(Aegilops tauschii, 含DD基因组)再一次自然杂交,经自然和人类的选择形成如今广泛栽培的普通小麦(Triticum aestivum, 含AABBDD基因组)。普通小麦基因组约为17 Gb(是水稻基因组的40倍),其中85%以上序列为重复序列,基因组测序研究具有极大的挑战性,也成了限制小麦基础和应用研究的一个瓶颈。含有A基因组的乌拉尔图小麦是小麦A基因组的原始二倍体供体种,也是小麦进化的基础性基因组,在小麦进化过程中起着核心作用。最近,组织植物细胞与染色体工程国家重点实验室的相关人员与深圳华大基因研究院和美国加州戴维斯大学合作完成了乌拉尔图小麦基因组(A基因组)草图的绘制,为科研工作者研究小麦驯化史提供一个全新的视角,并为多倍体小麦基因组的测序分析提供了二倍体基因组参照序列。在此基础上,最近又完成了乌拉尔图小麦基因组的精细图谱绘制。
  此外,课题组在前期的研究中,从基因组和转录组学入手,系统地分析了普通小麦低分子量麦谷蛋白基因的组成及表达规律。构建了一个含有约一百万个克隆的六倍体小麦小偃54的基因组 BAC文库,并利用该BAC文库,克隆了小麦叶锈病抗病基因LR1。目前,课题组的研究兴趣主要集中在小麦比较基因组学及进化、磷高效利用和籽粒灌浆分子机制等方面。
Key publications
 
1. Li, Y., H. Wu, T. Zhao, H.-Q. Ling. Characterization of the AtSXP3 promoter elucidates its complex regulation in response to phosphorus deficiency. Plant & Cell Physiology 57: 1767-1778 (2016)
 
2. Yang, K., Z. Tian, C. Chen, L. Luo, B. Zhao, Z. Wang, L. Yu, Y. Li, Y. Sun, W. Li, Y. Chen, Y. Li, Y. Zhang, D. Ai, J. Zhao, C. Shang, Y. Ma, B. Wu, M. Wang, L. Gao, D. Sun, P. Zhang, F. Guo, W. Wang, Y. Li, J. Wang, R.K. Varshney, J. Wang, H.-Q. Ling, P. Wan. Genome sequencing of adzuki bean (Vigna angularis) provides insight into high starch and low fat accumulation and domestication. Proc. Natl. Acad. Sci. USA 112: 13213-13218 (2015)
 
3. Zamioudis, C., J. Korteland, J. Van Pelt, M. Van Hamersveld, N. Dombrowski, Y. Bai, J. Hanson, M. Van Verk, H.-Q. Ling, P. Schulze-Lefert, C. Pieterse. Rhizobacterial volatiles and photosynthesis-related signals coordinate MYB72 in Arabidopsis roots during onset of induced systemic resistance and iron deficiency responses. The Plant Journal 84: 309-322 (2015)
 
4. Du, J., Z. Huang, B. Wang, H. Sun, C. Chen, H.-Q. Ling and H. Wu. SlbHLH068 interacts with FER to regulate the iron-deficiency response in tomato. Annals of Botany 116: 23-34 (2015).
 
5. Sun, H., F.-J. Fan, H.-Q. Ling. Genome-wide identification and characterization of the bHLH gene family in tomato. BMC Genomics 16:9 (2015)
 
6. Zhang, Y., H.L. Wu, N. Wang, J. Fan, C.L. Chen, Y. Cui, H.F. Liu, H.-Q. Ling. Mediator subunit 16 functions in the regulation of iron uptake gene expression in Arabidopsis. New Phytologist 203: 770-783 (2014).
 
7. Fan, H.J., Z.L. Zhang, N. Wang, Y. Cui, H. Sun, Y. Liu, H.L. Wu, S.S. Zheng, S.L. Bao, H.-Q. Ling. SKB1/PRMT5-mediated histone H4R3 dimethylation of Ib subgroup bHLH genes negatively regulates iron homeostasis in Arabidopsis thaliana. The Plant Journal 77: 209-221 (2014)
 
8. Long, W.B., Y. Li, W.J. Zhou, H.-Q. Ling, S.S. Zheng. Sequence-based SSR marker development and their application in defining the introgressions of LA0716 (Solanum pennellii) in the background of cv. M82 (Solanum lycopersicum). PLoS ONE 8(12): e81091 (2013)
 
9. Kong, D.Y., C.L. Chen, H.L. Wu, Y. Li, J.M. Li, H.-Q. Ling. Sequence diversity and enzyme activity of ferric-chelate reductase LeFRO1 in tomato. Journal of Genetics and Genomics 40: 565-573 (2013)
 
10. Ling H.-Q., S. Zhao, D. Liu, J. Wang, H. Sun, C. Zhang, H. Fan, D. Li, L. Dong, Y. Tao, C. Gao, H. Wu., Y. Li, Y. Cui, X. Guo, S. Zheng, B. Wang, K. Yu, Q. Liang, W. Yang, X. Lou, J. Chen, M. Feng, J. Jian, X. Zhang, G. Luo, Y. Jiang, J. Liu, Z. Wang, Y. Sha, B. Zhang, H. Wu, D. Tang, Q. Shen, P. Xue, S. Zou, X. Wang, X. Liu, F. Wang, Y. Yang, X. An, Z. Dong, K. Zhang, X. Zhang, M.-C. Luo, J. Dvorak, Y. Tong, Ji. Wang, H. Yang, Z. Li, D. Wang, A. Zhang, Ju. Wang. Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496: 87-90 (2013).
 
11. Wang N., Cui Y., Liu Y., Fan H., Du J., Huang Z., Yuan Y., Wu H., Ling H.-Q. Requirement and functional redundancy of Ib subgroup bHLH proteins for iron deficiency responses and uptake in Arabidopsis thaliana. Molecular Plant 6: 503-513 (2013)
 
12. Du J., D. Zeng, B. Wang, Q. Qian, S. Zheng, H.-Q. Ling. Environmental effects on mineral accumulation in rice grains and identification of ecological specific QTLs. Environmental Geochemistry and Health 30: 161-170 (2013)
 
13. The Tomato Consortium. The tomato genome sequence provides insight into fleshy fruit evolution. Nature 485: 635-641 (2012)
 
14. Huang Z.-A., T. Zhao, H.-J. Fan, N. Wang, S.-S. Zheng, H.-Q. Ling. The upregulation of NtAN2 expression at low temperature is required for anthocyanin accumulation in juvenile leaves of Lc-transgenic tobacco (Nicotiana tabacum L.). Journal of Genetics and Genomics 39: 149-156 (2012)
 
15. Wu H., C. Chen, J. Du, H. Liu, Y. Cui, Y. Zhang, Y. He, Y. Wang, C. Chu, Z. Feng, J. Li, H.-Q. Ling. Co-overexpression FIT with AtbHLH38 or AtbHLH39 in Arabidopsis enhanced cadmium tolerance via increased cadmium sequestration in roots and improved iron homeostasis of shoots. Plant Physiology 158: 790-800 (2012)
 
16. Zhao, W., X. Cheng, Z. Huang, H. Fan, H. Wu, H.-Q. Ling: Tomato LeTHIC is a Fe-required HMP-P synthase involved in thiamine synthesis and regulated by multiple factors. Plant and Cell Physiology 52(6): 967-982 (2011)
 
17. Zhao, N., S. Zheng, H.-Q. Ling: An efficient regeneration system and Agrobacterium-mediated transformation of Chinese upland rice cultivar Handao297. Plant Cell Tissue and Organ Culture 106: 475-483 (2011)
 
18. Dong, L., X. Zhang, D. Liu, H. Fan, J. Sun, Z. Zhang, H. Qin, B. Li, S. Hao, Z. Li, D. Wang, A. Zhang, H.-Q. Ling: New insight into the organization, recombination, expression and functional mechanism of low molecular weight glutenin subunit genes in bread wheat. PLoS ONE 5(10): e13548. doi:10.1371/journal.pone.0013548 (2010)
 
19. Wu, H., Y. Ji, J. Du, D. Kong, H. Liang, H.-Q. Ling: ClpC1, an ATP-dependent Clp protease in plastids, is involved in iron homeostasis in Arabidopsis leaves. Annals of Botany 105: 823-833 (2010)
 
20. Ma, J.F., H.-Q. Ling: Iron for plants and humans. Plants and Soil 325: 1-3 (2009)
 
21. Cheng, X., D. Zhang, Z. Cheng, B. Keller, H.-Q. Ling: A new family of Ty1-copia-like retrotransposons originated in the tomato genome by a recent horizontal transfer event. Genetics 181: 1183-1193 (2009)
 
22. Ling, H.-Q., J. Du, N. Wang: Progress in understanding the molecular regulation of iron uptake in strategy I plants. In: Development and Uses of Biofortified Agricultural products, ed by Gary S.Banuelos and Zhi-Qing Lin. CRC press, Taylor & Francis Group. Pp 221-229.
 
23. Li, J., X.D. Wu, S.-T. Hao, X.J. Wang, H.-Q. Ling: Proteomic response to iron deficiency in tomato root. Proteomics 8, 2299-2311 (2008)
 
24. Kong, D., Y. Zhu, H. Wu, X. Cheng, H. Liang, H.-Q. Ling: AtTHIC, a gene involved in thiamine biosynthesis in Arabidopsis thaliana. Cell Research 18, 566-576 (2008).
 
25. Yuan, Y., H. Wu, N. Wang, J. Li, W. Zhao, J. Du, D. Wang, H.-Q. Ling: FIT interacts with AtbHLH38 and AtbHLH39 in regulating iron uptake gene expression for iron homeostasis in Arabidopsis. Cell Research 18, 385-397 (2008)
 
26. Bauer, P., H.-Q. Ling, M.L. Guerinot: FIT, the FER-LIKE IRON DEFICIENCY INDUCED TRANSCRIPTION FACOR in Arabidopsis. Plant Physiology and Biochemistry 45: 260-261 (2007)
 
27. Qiu J-W, Schuerch A, Yahiaoui N, Dong L, Fan H, Zhang Z, Keller B, Ling H-Q: Physical mapping and identification of a candidate for the leaf rust resistance gene Lr1 of wheat. Theoretical Applied Genetics 115: 159-168 (2007)
 
28. Zhao, T., H.-Q. Ling: Effects of pH and nitrogen forms on expression profiles of genes involved in iron homeostasis in tomato. Plant, Cell & Environment 30: 518-527 (2007)
 
29. Zhang, J., H.-F. Zhu, H. Liang, K.-F. Liu, A.-M., Zhang, H.-Q. Ling, D.-W. Wang: Further analysis of the function of AtbHLH29 in regulating the iron uptake process in Arabidopsis thaliana. Journal of Integrative Plant Biology 48(1): 75-84 (2006)
 
30. Wu, H., L. Li, J. Du, Y. Yuan, X. Cheng, H.-Q. Ling: Molecular and biochemical characterization of Fe(III)-chelate reductase gene family in Arabidopsis thaliana. Plant and Cell Physiology 46 (9): 1505-1514 (2005)
 
31. Yuan, Y.X, J. Zhang, D.W. Wang, H.-Q. Ling: AtbHLH29 of Arabidopsis thaliana is a functional ortholog of tomato FER involved in controlling iron acquisition in strategy I plants. Cell Research 15(8): 613-621 (2005)
 
32. Guyot, R., X. Cheng, Y. Su, Z. Cheng, E. Schlagenhauf, B. Keller, H.-Q. Ling: Complex organization and evolution of the tomato pericentromeric region at the FER gene locus. Plant Physiology 138: 1205-1215 (2005)
 
33. Li, L., X. Cheng, H.-Q. Ling: Isolation and characterization of Fe(III)-chelate reductase gene LeFRO1 in tomato. Plant Molecular Biology 54: 125-136 (2004)
 
34. Ling, H.-Q., J. Qiu, R.P. Singh, B. Keller: Identification and genetic characterization of an Aegilops tauschii ortholog of the wheat leaf rust disease resistance gene Lr1. Theoretical Applied Genetics 109: 1133-1138 (2004)
 
35. Ling, H.-Q., Y.X. Zhu and B. Keller: High-resolution mapping of the leaf rust disease resistance gene Lr1 in wheat and physical walking to the gene using a BAC library of Aegilops tauschii. Theoretical Applied Genetics 106: 875-882 (2003)
 
36. Ling, H.-Q., and B. Keller: Genetic transformation of Linum species. In: Plant Genetic Engineering Vol 4: Improvement of Commercial Plants-II. Ed by Pawan K Jaiwal and Rana P. Singh. Sci Tech Publishing LLC, U.S.A. pp235-260 (2003)
 
37. Ling, H.-Q., P. Bauer, B. Keller, M. Ganal: The fer gene encoding a bHLH transcriptional regulator controls development and physiology in response to iron in tomato. Proc. Natl. Acad. Sci. USA, vol. 99, 13938-13943 (2002)
 
38. Ling, H.-Q. and M. W. Ganal: Towards map-based cloning of two genes involved in iron uptake of tomato. Journal of Plant Nutrition 23: 1953-1967 (2000).
 
39. Ling, H.-Q., G. Koch, H. Baeumlein, M. W. Ganal: Map-based cloning of chloronerva – a gene involved in iron uptake of higher plants encoding nicotianamine synthase. Proc. Natl. Acad. Sci. USA, Vol. 96, 7098-7103 (1999)