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RESEARCH INTERESTS
1）Mechanism of the Development of Inflorescence and Spikelet in Rice
Rice (Oryza sativa), the model grass plant, has specialized morphology of inflorescence and spikelet, which determines the ultimate yield of rice. We are using various approaches such as forward and reverse genetics, biochemistry, cell biology etc to investigate the molecular mechanisms such as MADS box genes and the regulatory network involved in the morphogenesis and development of inflorescence and spikelet in rice.
2）Molecular Aspects of Rice Male Reproduction
The life cycle of flowering plants alternates between diploid sporophyte and haploid gametophyte generations. Male gametophytes develop in the anther compartment of the stamen within the flower and require cooperative functional interactions between gametophytic and sporophytic tissues.During the male reproductive development, there are numerous biological events including cell division, differentiation and degeneration of somatic tissues consisting of four concentric cell layers surrounding and supporting reproductive cells as they form mature pollen grains through meiosis and mitosis. To understand the mechanism of plant male reproduction, we are combining systematic biology (genomics, transcriptomics, proteomics, metabonomics) with other approaches such as genetics, cell biology, biochemistry, and structure biology to elucidate the molecular mechanism underlying each biological process of male reproduction, such as cell-to-cell communications, programmed cell death, and fatty acids metabolism.
3）Molecular Characterization of Transgenic Organisms
As more and more transgenic crops such as transgenic maize and soybean have been approved and consumed as foods and feeds, concerns about the safety of transgenic organisms among consumers and public increase Molecular characterization of transgenic organisms is the base for the safety assessment of transgenic organisms. We are developing detection methods to identify the changes occurred at genomic, transcriptomic, proteomic and metabolic levels, and to compare those changes between transgenic line and non-transgenic control line and between transgenic line and conventional cultivated lines, laying a foundation for safety assessment.
LAB MEMBERS:
RESEARCH STAFFS
Professors: Dr. Dabing Zhang and Dr. Wanqi Liang;
Associate Professors: Dr. Sheng Quan, Dr. Zheng Yuan, Dr. Litao Yang, Dr. Jianxin Shi and Dr. Canhua Wang;
Assistant professors: Dr. Jie Xu, Dr. Jing Yu, and Mr Changsong Yin;
Rice breeding experts: Mr. Zhijing Luo and Ms Yunjiao Chen;
Technicians: Ms Lu Zhu, Dr. Guorun Qu, Mr Peng Liu, Mr Zhibo Chen, Mr Changjian Zhang, Ms Hui Yang and Ms Yue Shen;
Administrative Staffs: Ms. Guihua Chen, Ms. Yiping Jiang, Ms Suzhen Yang, Mr. Hongbin Zong.
PROJECTES AND OUTPUTS
Our laboratory undertook research projects from both national and Shanghai local government, established the platform for plant developmental biology, National Center of Molecular Characterization for Genetically Modified Organism (GMO), and Shanghai Scientific Education Bases for Genetically Modified Organisms.
Within the past ten years, we have identified and characterized over 10 genes associated with the development of inflorescence and spikelet, and the formation of pollen as well in rice, and elucidated the mechanisms underlying the determination of inflorescence and floral meristem, tapetal programmed cell death, communication between vegetative and reproductive cells. We also developed various methods and techniques for the molecular characterization of genetically modified organisms.
In recent years, our lab has published more than 90 research papers in journals, such as Developmental Cell, PNAS, Nature Communications, Plant Cell, Plant Physiology, Nuclear Acid Research, Cell Research and Analytical Chemistry. Meanwhile, we applied 14 patents for the useful genes/mutants. In addition, we have developed more than 20 national standard methods and 4 ISO standard methods for GMO analysis, and won the First Class Prize of The Advance in Science and Technology in Shanghai twice (2004 and 2012) . Professor Zhang was awarded The Excellent Prize of MingZhi Dairy Life Science by Shanghai Municipality in 2006; Peony Award of Shanghai Natural Science in 2012, and Shanghai Rising-Star Program. Dr. Litao Yang was also awarded Shanghai Rising-Star Program. Most important, many alumni of the laboratory won Shanghai Outstanding Doctoral Thesis (Hui Li, 2012) and National or Shanghai Award for Distinguished Doctorates or Master.
TEACHINGS
The undergraduate courses: Cell biology (bilingual), Biochemistry D, Biochemistry F, Plant biotechnology (bilingual), Animal biotechnology, An introduction to biosafety (bilingual), An introduction to biology (bilingual).
Additional undergraduate courses (participating): Principles and methods of biochemical analysis, Genetics, Developmental and reproductive biology, Biochemistry experiments, Biotechnology comprehensive experiment, An introduction to biology experiment.
The graduate courses: Cell and developmental biology (bilingual), Biosafety (bilingual). Additional graduate courses (participating): Principles and applications of biochemical techniques (bilingual).
REPRESENTATIVE PAPERS
1.Niu NN, Liang WQ, Yang XJ, Jin WL, Wilson ZA, Hu JP, Zhang DB*. EAT1 promotes tapetal cell death by regulating aspartic proteases during male reproductive development in rice. Nature Communications. DOI: 10.1038/ncomms2396 (2013).[full text]
2.Zhang H, Xu C, He Y, Zong J, Yang XJ, Si HM, Sun ZX, Hu JP, Liang WQ, Zhang DB*. Mutation in CSA creates a new photoperiod-sensitive genic male sterile line applicable for hybrid rice seed production. PNAS. 110(1) (2013), 76-81[full text].
3.Tan HX, Liang WQ, Hu, JP Zhang DB*. MICROSPORE AND TAPETUM REGULATOR 1 encodes a secretory fasciclin glycoprotein required for male reproductive development in rice. Developmental Cell. 22(6) (2012), 1127-1137[full text].
4.Wang CM, Marshall A, Zhang DB, Wilson ZA*, ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. Plant Physiology. 158(4) (2012), 1523-1533[full text].
5.Li W, Cui X, Meng ZL, Huang X, Xie Q, Wu H, Jin HL, Zhang DB, Liang WQ*, Transcriptional regulation of Arabidopsis MIR168a and ARGONAUTE1 homeostasis in ABA and abiotic stress responses. Plant Physiology. 158(3) (2012), 1279-1292[full text].
6.Chen WW, Yu XH, Zhang K, Shi JX, Schreiber L, Shanklin J, Zhang DB*, Male Sterile 2 encodes a plastid-localized fatty acyl ACP reductase required for pollen exine development in Arabidopsis thaliana. Plant Physiology. 157(2) (2011), 842-853[full text].
7.Li HF, Liang WQ, Hu Y, Zhu L, Yin CS, Xu J, Dreni L, Kater MM, Zhang DB*, Rice MADS6 interacts with the floral homeotic genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in specifying floral organ identities and meristem fate. The Plant Cell. 23(7) (2011), 2536-2552[full text].
8.Shi J, Tan HX, Yu XH, Liu YY, Liang WQ, Ranathunge K, Franke RB, Schreiber L, Wang YJ, Kai GY, Shanklin J, Ma H, Zhang DB*, Defective Pollen Wall (DPW) is required for anther and microspore development in rice and encodes a fatty acyl ACP reductase. The Plant Cell. 23(6) (2011), 2225-2246[full text].
9.Li H, Yuan Z, Vizcay-Barrena G, Yang CY, Liang WQ, Zong J, Wilson Z, Zhang DB*. PERSISTENT TAPETAL CELL 1 (PTC1) encodes a PHD-finger protein that is required for tapetal cell death and pollen development in rice. Plant Physioloy. 156(2) (2011), 615-630[full text].
10.Li HF, Liang WQ, Yin CS, Zhu L, and Zhang DB*. Genetic interaction of OsMADS3, DROOPING LEAF and OsMADS13 in specifying rice floral organs identities and meristem determinacy. Plant Physioloy. 156(1) (2011), 263-247[full text].
11.Wang CM and Zhang DB*. A novel compression tool for efficient storage of genome resequencing data. Nucleic Acids Research. 39(7) (2011), e45[full text].
12.Hu LF, Liang WQ, Yin CS, Cui X, Zong J, Wang X, Hu JP and Zhang DB*. Rice MADS3 regulates ROS homeostasis during late anther development. The Plant Cell. 23(2) (2011), 515-533[full text].
13.Zhang Z, Zhang Y, Tan HX,Wang Y, Li G, Liang WQ, Yuan Z, Hu JP, Ren HY, and Zhang DB*. RICE MORPHOLOGY DETERMINANT encodes the type II formin FH5 and regulates rice morphogenesis. The Plant Cell. 23(2) (2011), 681-700[full text].
14.Xu J, Yang CY, Yuan Z, Zhang DS, Gondwe MY, Ding ZW, Liang WQ, Zhang DB*, and Wilson ZA. Regulatory network of ABORTED MICROSPORES (AMS) required for postmeiotic male reproductive development in Arabidopsis thaliana. The Plant Cell. 22(1) (2010), 91-107[full text].
15.Wang CM, Xu J, Zhang DS, Wilson ZA, and Zhang DB*. An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data. BMC Bioinformatics. 11 (2010), 81[full text].
16.Li H, Pinot F, Sauveplane V, Werck-Reichhart D, Diehl P, Schreiber L, Franke R, Zhang P, Chen L, Gao YW, Liang WQ, and Zhang DB*. CYP704B2 catalyzing the ω-hydroxylation of fatty acids is required for anther cutin biosynthesis and pollen exine formation in rice. The Plant Cell. 22(1) (2010), 173-190[full text].
17.Li HF, Liang WQ, Jia RD, Yin CS, Zong J, Kong HZ, and Zhang DB*. The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice. Cell Research. 20(3) (2010), 299-313[full text].
18.Zhang H, Liang WQ, Yang XJ, Luo X, Jiang N, Ma H, and Zhang DB*. Carbon Starved Anther (CSA) encoding a MYB domain protein regulates sugar partitioning required for rice pollen development. The Plant Cell. 22(3) (2010), 672-689[full text].
19.Zhang DS, Liang WQ, Yin C, Zong J, Gu F, and Zhang DB*. OsC6, encoding a lipid transfer protein (LTP), is required for postmeiotic anther development in rice. Plant Physiology. 154(1) (2010), 149-162[full text].
20.Gao XC, Liang WQ, Yin CS, Ji SM, Wang HM, Su X, Guo CC, Kong HZ, Xue HW, Zhang DB*. The SEPALLATA-like geneOsMADS34 is required for rice inflorescence and spikelet. Plant Physiology. 153(2) (2010), 728-740[full text].
21.Liu DE, Shen J, Yang LT, Zhang DB*. Evaluation of the impacts of different nuclear DNA content in the hull, endosperm, and embryo of rice seeds on GM rice quantification. Journal of Agriculture Food Chemistry. 58(8) (2010), 4582-4587[full text].
22.Wang C, Jiang LX, Rao J, Liu YN, Yang LT, Zhang DB*. Evaluation of four genes in rice for their suitability as endogenous reference standards in quantitative PCR. Journal of Agriculture Food Chemistry. 58(22) (2010), 11543-11547[full text].
23.Yuan Z, Gao S, Xue DW, Luo D, Li LT, Ding SY, Yao X, Wilson ZA, Qian Q, and Zhang DB*. RETARDED PALEA1 (REP1) controls palea development and floral zygomorphy in rice. Plant Physiology. 149(1) (2009), 235-244[full text].
24.Zhang DB*, and Wilson ZA. Stamen specification and anther development in rice. Chinese Science Bulletin. 54(14) (2009), 2342-2353[full text].
25.Wilson ZA*, and Zhang DB. From Arabidopsis to rice, pathways in pollen development. Journal of Experimental Botany. 60(5) (2009), 1479-1492[full text].
26.Jiang LX, Yang LT, Zhang HB, Guo JC, Marco M, Van den EG, and Zhang DB*. International collaborative study of the endogenous reference gene, Sucrose Phosphate Synthase (SPS), used for qualitative and quantitative analysis of genetically modified rice. Journal of Agriculture Food Chemistry. 57(9) (2009),3525-3532[full text].
27.Yang LT, Zhang HB, Guo JC, Pan LW, and Zhang DB*. International collaborative study for the endogenous reference gene, LAT52, used for qualitative and quantitative analysis of genetically modified tomato. Journal of Agriculture Food Chemistry. 56(10) (2008), 3438-3443[full text].
28.Dong W, Yang LT, Shen KL, Kim BH, Kleter GA, Marvin HJP, Guo R, Liang WQ, and Zhang DB*. GMDD, a database of GMO detection methods. BMC Bioinformatics. 9 (2008), 260[full text].
29.Zhang DS, Liang WQ, Yuan Z, Lia N, Shi J, Wang J , Liu YM, Yu WJ, and Zhang DB*. Tapetum Degeneration Retardation is critical for aliphatic metabolism and gene regulation during rice pollen development. Molecular Plant. 1(4) (2008), 599-610[full text].
30.Li N, Zhang DS, Liu HS, Yin CS, Li XX, Liang WQ, Yuan Z, Xu B, Chu HW, Wang J, Wen TQ, Huang H, Luo D, Ma H, and Zhang DB*. The rice Tapetum Degeneration Retardation gene is required for tapetum degradation and anther development. The Plant Cell. 18(11) (2006), 2999-3014[full text].
31.Chu HW, Qian Q, Liang WQ, Yin CS, Tan HX, Yao X, Yuan Z, Yang J, Huang H, Luo D, Ma H, and Zhang DB*. The FLORAL ORGAN NUMBER4 gene encoding a putative ortholog of Arabidopsis CLAVATA3 regulates apical meristem size in rice. Plant Physiology. 142(3) (2006), 1039-1052[full text].
32.Li XX, Duan XP, Jiang HX, Sun YJ, Tang YP, Yuan Z, Guo JK, Liang WQ, Chen L, Wang J, Ma H, Yin JY, and Zhang DB*. Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiology. 141(4) (2006), 1167-1184[full text].
33.Jiang DH, Yin CS, Yu AP, Zhou XF, Liang WQ, Yuan Z, Xu Y, Yu QB, Wen TQ, and Zhang DB*. Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice. Cell Research. 16(5) (2006), 507-518[full text].
34.Yang LT, Pan AH, Jia JW, Ding JY, Chen JX, Huang C, Zhang CM, and Zhang DB*. Validation of a tomato specific gene, LAT52, used as an endogenous reference gene in qualitative and real-time quantitative PCR detection of transgenic tomatoes. Journal of Agriculture Food Chemistry. 53(2) (2005), 183-190[full text].
35.Ding JY, Jia JW, Yang LT, Wen HB, Zhang CM, Liu WX, and Zhang DB*. Validation of a rice specific gene, Sucrose Phosphate Synthase, used as the endogenous reference gene for qualitative and real-time quantitative PCR detection of transgenes. Journal of Agriculture Food Chemistry. 52(11) (2004), 3372-3377[full text].
36.Huang YH, Liang WQ, Pan AH, Zhou ZA,Cheng H, Chen JX, and Zhang DB*. Production of FaeG, the major subunit of K88 fimbriae, in transgenic tobacco plants and its immunogenicity in mice. Infection and Immunity. 71(9) (2003), 5436-5439[full text].
37.Zhang YL, Zhang DB*, Li WQ, Chen JQ, Peng YF, and Cao W. A novel real-time quantitative PCR method using attached universal template probe. Nucleic Acids Research. 31(20) (2003), e123[full text].
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