A. 以主要完成单位发表论文：

1.　Wang, Y., and Li, J. (2008). Rice, rising. Nature Genetics 40: 1273-1275.25.556

2.　Wang, Y., and Li, J. (2008). Molecular basis of plant architecture. Annu. Rev. Plant. Biol. 59: 253-279.1

3.　Ammiraju, J. S., Lu, F., Sanyal, A., Yu, Y., Song, X., Jiang, N., Pontaroli, A. C., Ramboo, T., Currie, J., Kollura, K., Talag, J., Fan, C., Goicoechea, J. L., Zuccolo, A., Bennetzen, J. L., Chen, M., Jackson, S., and Wing R.A. (2008). Dynamic evolution of Oryza genomes revealed by comparative genome analysis of a genus-wide vertical dataset. Plant Cell 10.1105/tpc.108.063727.

4.　Yu, Y., Tang, T., Qian, Q., Wang, Y., Yan, M., Zeng, D., Han, Bin., Wu, C-I., Shi, S., and Li, J. (2008). Independent losses of function in a Polyphenol Oxidase in rice - differentiation in grain discoloration between subspecies and the role of positive selection. Plant Cell Accepted.

5.　Zhai, J., Liu, J., Liu, B., Li, P., Meyers, B., Chen, X., and Cao, X. (2008). Small RNA-directed Epigenetic Natural Variation in Arabidopsis thaliana. PLoS Genetics4(4): e1000056.

6.　Zheng, Q., and Wang, X. (2008). GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res.10.1093/nar/gkn276.

7.　Fang, J., Chai, C., Qian, Q., Li, C., Tang, J., Sun, L., Huang, Z., Guo, X., Sun, C., Liu, M., Zhang, Y., Lu, Q., Wang, Y., Lu, C, Han, B., Chen, F., Cheng, Z., and Chu, C. (2008).Mutations of genes in synthesis of the carotenoid precursors of ABA lead to preharvest sprouting and photo-oxidation in rice. Plant Journal 54: 177-189

8.　Wu, Y., Zhu, Z., Ma, L., and Chen, M. (2008). The preferential retention of starch synthesis genes reveals the impact of whole-genome duplication on grass evolution. Mol. Biol. Evol. 25: 1003-1006.

9.　Mu, J., Tan, H., Zheng, Q., Fu, F., Liang, Y., Zhang, J., Yang, X., Wang, T., Chong, K., Wang, X., and Zuo, J. (2008). LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis thaliana. Plant Physiology 148:1042-1054

10. Qi, J., Qian, Q., Bu, Q., Li, S., Chen, Q., Sun, J., Liang, W., Zhou, Y., Chu, C., Li, X., Ren F., Palme. K., Zhao, B., Chen, J., Chen, M., and Li, C. (2008). Mutation of the Rice NARROW LEAF1 Gene, Which Encodes a Novel Protein, Affects Vein Patterning and Polar Auxin Transport. Plant Physiology 147: 1947–1959.11. Teng, C., Dong, H., Shi, L., Deng, Y., Mu, J., Zhang, J., Yang, X., and Zuo, J. (2008). Serine palmitoyltransferase, a key enzyme for de novo synthesis of sphingolipids, is essential for male gametophyte development in Arabidopsis. Plant Physiology 146:1322-1332.

12. Niu, L., Zhang, Y., Pei, Y., Liu, C., and Cao, X. (2008). Redundant Requirement for a Pair of Protein Arginine Methyltransferase 4 Homologs for the Proper Regulation of Arabidopsis Flowering Time. Plant Physiology10.1104/pp.108.124727.

13. Duan C., Wang, C., Fang, R., and Guo H. (2008). Artificial microRNAs highly accessible to targets confer efficient virus resistance in plants. Journal of Virology 82: 11084-11095.

14. Wang, F., Zhong, N., Gao, P., Wang, G., Wang, H., and Xia, G.(2008). SsTypA1, a chloroplast-specific TypA/BipA-type GTPase from the halophytic plant Suaeda salsa, plays a role in oxidative stress tolerance. Plant Cell and Environment31(7), 982-994.

15. Qian, W., Han, Z., and He, C. (2008). Two-Component Signal Transduction Systems of Xanthomonas spp.: A Lesson from Genomics. Molecular Plant-Microbe Interactions 21:151-161.

16. Qian, W., Han, Z., Tao, J. and He, C. (2008) Genome-Scale Mutagenesis and Phenotypic Characterization of Two-Component Signal Transduction Systems in Xanthomonas campestris pv. campestris ATCC 33913. Molecular Plant-Microbe Interactions 21:1128-1138

17. Wang, L., Rong, W., and He, C. (2008). Two Xanthomonas extracellular polygalacturonases, PghAxc and PghBxc, are regulated by Type III secretion regulators HrpX and HrpG and are required for virulence. Molecular Plant-Microbe Interactions 21:555-563.

18. Bu, Q., Jiang, H., Li, C.-B., Zhai, Q., Zhang, J., Wu, X., Sun, J., Xie, Q., and Li, C. (2008). Role of the Arabidopsis thaliana NAC transcription factors ANAC019 and ANAC055 in regulating jasmonic acid-signaled defense responses. Cell Research 18: 756-767.

19. Liao, Y., Zou, H., Wang, H., Zhang, W., Ma, B., Zhang, J., and Chen, S. (2008). Soybean GmMYB76, GmMYB92 and GmMYB177 genes confer stress tolerance in transgenic Arabidopsis plants. Cell Research 1-14.

20. Xu, W., Huang, J., Li, B., Li, J., and Wang, Y. (2008). Is kinase activity essential for biological functions of BRI1? Cell Research 18: 472-478.

21. Wang, Q., Guan, Y., Wu, Y., Chen, H., Chen, F., and Chu, C. (2008). Overexpression of a rice OsDREB1F gene increases salt, drought, and low temperature tolerance in both Arabidopsis and rice. Plant Molecular Biology 67: 589-602.

22. Yin, L. Lan, Y., and Zhu, L. (2008). Analysis of the protein expression profiling during rice callus differentiation under different plant hormone conditions. Plant Molecular Biology 68:597–617.

23. Zhang, D., Yang, Q. Ding, Y., Cao, X., Xue, Y., and Cheng, Z. (2008). Cytological characterization of the tandem repetitive sequences and their methylation status in the Antirrhinum majus genome. Genomics 92: 107–114.

24. Zhou, Q., Tian, A., Zou, H., Xie, Z., Lei, G., Huang, Jian., Wang, C., Wang, H., Zhang, J., and Chen S. (2008). Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants. Plant Biotechnology Journal doi: 10.1111/j.1467-7652.2008.00336.x.

25. Li, D., Yang, C., Li, X., Ji, G., and Zhu, L. (2008). Sense and Antisense OsDof12 Transcripts in Rice. BMC Molecular Biology doi:10.1186/1471-2199-9-80.

26. He, X., Fang, Y., Feng L., and Guo, H. (2008).Characterization of conserved and novel microRNAs and their targets, including a TuMV-induced TIR-NBS-LRR class R gene-derived novel miRNA in Brassica. FEBS letter 582: 2445-2452.

27. Wang, Y., Xiao, Y., Chai, C., Wei, G., Wei, X., Xu, H., Zhang, Y., Ouwerkerk, P.B.F., Wang, M., and Zhu, Z. (2008). Molecular cloning, functional characterization and expression analysis of a novel monosaccharide transporter gene OsMST6 from rice (Oryza sativa L.). Planta 228(4):525-35.

28. Yu, D., Ranathunge, K., Huang, H., Pei, Z., Franke, R., Schreiber, L., and He, C. (2008). Wax Crystal-Sparse Leaf1 encodes a β–ketoacyl CoA synthase involved in biosynthesis of cuticular waxes on rice leaf. Planta228: 675–685.

29. Liao,,Y., Tian, A., Zou, H., Zhang, J., and Chen, S. (2008). Soybean GmbZIP44, GmbZIP62 and GmbZIP78 genes function as negative regulator of ABA signaling and confer salt and freezing tolerance in transgenic plants. Planta DOI 10.1007/s00425-008-0731-3.

30. Fang, J., and Chu, C.(2008). Abscisic acid and the pre-harvest sprouting in cereals. Plant Signaling & Behavior 3 (12):1-3.

31. Bai, X., Wang, Q., and Chu, C. (2008). Excision of a selective marker in transgenic rice using a novel Cre/loxP system controlled by a floral specific promoter. Transgenic Research 17: 1035-1043.

32. Huang, Q., Wang, H., Gao, P., Wang, G., and Xia, G.(2008). Cloning and characterization of a calcium dependent protein kinase gene associated with cotton fiber development. Plant Cell Rep. 27(12): 1869-75.

33. Zheng, N., Jesús Pérez, J., Zhang, Z., Domínguez, E., Garcia, J., and Xie, Q. (2008). Specific and efficient cleavage of fusion proteins by recombinant plum pox virus NIa protease. Protein Expression and Purification 57(2): 153-162. 

34. Gao, P., Zhao, P., Wang, J., Wang, H., Du, X., Wang, G., and Xia, G. (2008). Co-expression and preferential interaction between two calcineurin B-Like proteins and a CBL-interacting protein kinase from cotton. Plant Physiology and Biochemistry 46(10): 935-940

35. Zhang, Y., Li, Y., Gao, T., Zhu, H., Wang, D., Zhang, H., Ning, Y., Liu, L., Wu, Y., Chu, C., Guo, H., and Xie, Q. (2008). Arabidopsis SDIR1 enhances drought tolerance in crop plants. Biosci Biotechnol Biochem. 72(8):2251-2254.

36. Ge, C., and He, C. (2008). Regulation of the Type II secretion structural gene xpsE in Xanthomonas campestris pathovar campestris by the global transcription regulator Clp. Current Microbiology 56:122-127.

37. Li, C.-B., Zhao, J., Jiang, H., Geng, Y., Dai, Y., Fan, H., Zhang, D., Chen, J., Lu, F., Shi, J., Sun, S., Chen, J., Yan, X., Lu, C., Chen, M., Cheng, Z., Ling, H., Wang, Y., Xue, Y., and Li, C. (2008). A snapshot of the Chinese SOL Project. Journal of Genomics and Genetics 35: 387-390.

38. Liu, J., Ha, D., Xie, Z., Wang, C., Zhang, W., Zhang, J., and Chen, S. (2008). Ectopic expression of soybean GmKNT1 in Arabidopsis results in altered leaf morphology and flower identity. Journal of Genetics and Genomics 35: 441-449.

39. Duan, C., Wang, C., and Guo, H. (2008). Delayed resistance to Cucumber Mosaic Virus mediated by 3’UTR derived hairpin RNA. Chinese Science Bulletin 53:3301-3310

40. Cao, Y., Li, Z., Chen, T., Zhang, Z., Zhang, J., and Chen, S. (2008). Overexpression of tobacco small G protein NtRop1 causes salt sensitivity and hydrogen peroxide production in transgenic plants. Science in China Series, C 51(5): 383-390.

41. Wang, C., Wang, H., Zhang, J., and Chen S. (2008). A seed-specific AP2-domain transcription factor from soybean pays a certain role in regulation of seed germination. Science in China, C 51(4):10-10.

42. Bhatti, K., Xu, C., Wu, J., and He, C. (2008) Overexpression of rice OsLOL2 gene confers disease resistance in tobacco to Pseudomonas syringae pv. tabaci. Progress in Natural Science18:807-812

43. Gao, P., Zhao, P., Wang, J., Wang, H., and Xia, G.(2008). Cloning and characterization of two putative seven-transmembrane receptor genes from cotton. Progress in Natural Science 18(10): 1225-1231.

44. Li, Z., Cao, Y., Zhang, J., and Chen S. (2008). Characterization of Arabidopsis calreticulin mutants in response to calcium and salinity stresses. Progress in Natural Science 18:1219-1224.

45. Wang, C., Wu, X., Jia F., Zhang J., and Chen, S. (2008). Genetic variations of glycinin subunit genes among cultivatied and wild type soybean species. Progress in Natural Science 18: 33-41.

46. Lu, F., Li, G., Cui, X., Liu, C., Wang, X., and Cao, X. (2008). Comparative Analysis of JmjC Domain-containing Proteins in Higher Plants and Human Reveals Potential Histone Demethylases in Arabidopsis and Rice. Journal of Integration Plant Biology50: 886-896.

47. Wang, Y., Wei, X., Xu, H., Chai, C., Meng, K., Zhai, H., Sun, A., Peng, Y., Wu, B., Xiao, G., and Zhu, Z. (2008). Cell-wall Invertases from Rice are Differentially Expressed in Caryopsis During the Grain Filling Stage Journal of Integrative Plant Biology 50 (4):466–474.

48. Xie, Q., and Gong, Z. (2008). Understanding abiotic stresses and the solution. J. Integr. Plant Biol. 50:1185-1186.

49. Sun, A., Xu, H., Gong, W., Zhai, H., Meng, K., Wang, Y., Wei, X., Xiao, G., and Zhu, Z. (2008). Cloning and Expression Analysis of Rice Sucrose Transporter Genes OsSUT2M and OsSUT5Z. Journal of Integrative Plant Biology. 50 (1): 62–75.

50. W, Y., Wei, X., Xu, H., Chai, C., Meng, K., Zhai, H., Sun, A., Peng, Y., Wu, B., Xiao, G., and Zhu, Z. (2008). Cloning and Expression Analysis of Rice Sucrose Transporter Genes OsSUT2M and OsSUT5Z. Journal of Integrative Plant Biology 50 (4):466–474.

51. Zhang, R., Wang, B., Ouyang, J., Li, J., and Wang, Y. (2008). Arabidopsis Indole Synthase (INS), a Homolog of Tryptophan Synthase Alpha (TSA1), is an enzyme involved in the Trp-independent metabolite biosynthesis pathway. J Integrative Plant Biology 50: 1070-1077.

52. Zhang, Y., Lai, J., Sun, S., Li, Y., Liu, Y., Liang, L., Chen, M., and Xie, Q. (2008). Comparison analysis of transcripts from the halophyte Thellungiella halophila. J. Integr. Plant. Biol. 50:1327-1335.

53. 徐鸿林，翟红利，王锋，朴建华，杨晓光，朱祯 (2008) 豇豆胰蛋白酶抑制剂基因（cpti）及其在抗虫转基因作物中的应用. 中国农业科技导报 10(1): 36-45.

54. 陈红霖，王义琴，储成才，李平植物非寄主抗性研究进展. 遗传 30(8): 977-982.

55. 杨鹍, 傅亚萍, 张玉满, 颜永胜, 赵志强, 方荣祥, 孙宗修, 陈晓英 (2008). 水稻OsPLD3和OsPLD4基因及其启动子. 生物工程学报24: 368-375.

56. 赵志强, 傅亚萍, 杨鹍, 张玉满, 颜永胜, 方荣祥, 孙宗修, 陈晓英 (2008). 水稻小G蛋白OsPra2基因的克隆及功能分析. 生物工程学报24: 2027-2033.

　 B. 共同通讯作者或共同第一作者

57. Xiang, T., Zong, N., Zou, Y., Wu, Y., Zhang, J., Xing, W., Li, Y., Tang, X,. Zhu, L., Chai, J., and Zhou, J. (2008). Pseudomonas syringae effector AvrPto blocks innate immunity by targeting receptor kinases. Current Biology 18: 74-80.

58. Xu, Y., Ye, J., Liu, H., Cheng, E., Yang, Y., Wang, W., Zhao, M., Zhou, D., Liu, D., and Fang, R. (2008). DNA-templated CMV viral capsid proteins assemble into nanotubes. Chemical Communications1: 49-51.

59. Li, Y., Zhang, Z., Jia, Y., Shen, Y., He, H., Fang, R., Chen, X., and Hao, X. (2008). 3-acetonyl-3-hydroxyoxindole: a new inducer of systemic acquired resistance in plants. Plant Biotechnology Journal 6: 301-308.

60. Yuan, X., Li, X., Pan, J., Wang, G., Jiang, S., Li, X., Deng, S., He, H., Si, M., Lai, L., Wu, A., Zhu, L., and Cai, R. (2008). Genetic linkage map construction and location of QTLs for fruit-related traits in cucumber. Plant Breeding 127: 180-188.

61. Yuan, X., Pan, J., Cai, R., Guan, Y., Liu, L., Zhang, W., Li, Z., He, H., Zhang, C., Si, L., and Zhu, L. Genetic mapping and QTL analysis of fruit and flower related traits in cucumber (Cucumis sativus L.) using recombinant inbred lines. Euphytica 164: 473–491.

　 C. 合作完成论文：

62. Tada, Y., Spoel, S.H., Pajerowska-Mukhtar, K., Mou, Z., Song, J., Wang, C., Zuo, J., and Dong, X. (2008). Plant immunity requires conformational charges of NPR1 via S-nitrosylation and thioredoxins. Science 321: 952-956.

63. Yu, J., Rubio, V., Lee, N., Bai, S., Lee, S., Kim, S., Liu, L., Zhang, Y., Irigoyen, M., Sullivan, J., Zhang, Y., Lee, I., Xie, Q., Paek, N., and Deng, X. (2008). COP1 and ELF3 control circadian function and photoperiodic flowering by regulating GI stability. Molecular Cell 32: 617-630.

64. Lu, C., Jeong, D-H., Kulkarni, K., Pillay, M., Nobuta, K., German, R., Thatcher, S., Maher, C., Zhang, L., Ware, D., Liu, B., Cao, X., Meyers, B., and Green, P. (2008). Genome-wide analysis for discovery of new rice miRNAs reveals natural antisense miRNAs (nat-miRNAs). Proc. Natl. Acad. Sci., USA 105: 4951-4956.

65. Meyers, B., Axtel, M., Bartel, B., Bartel, D., Baulcombe, D., Bowman, J., Cao, X., Carrington, J., Chen, X., Green, P., Griffiths-Jones, S., Jacobsen, S., Mallory, A., Martienssen, R., Poethig, R., Qi, Y., Vaucheret, H., Vazquez, F., Voinnet, O. Weigel, D., and Zhu, J. (2008). CRITERIA FOR ANNOTATION OF PLANT microRNAs. Plant CellDOI:10.1105/tpc.108.064311.

66. Liu, J., Zhang, Y., Qin, G., Tsuge, T., Sakaguchi, N., Luo, G., Sun, K., Shi, D., Aki, S., Zheng, N., Aoyama, T., Oka, A., Yang, W., Umeda, M., Xie, Q., Gu, H., and Qu L. (2008). Targeted Degradation of the Cyclin-Dependent Kinase Inhibitor ICK4/KRP6 by RING-Type E3 Ligases Is Essential for Mitotic Cell Cycle Progression during Arabidopsis Gametogenesis. Plant cell 20: 1538-1554.

67. Chen, S., Yang, Y., Shi, W., Ji, Q., He, F., Zhang, Z., Cheng, Z., Liu, X, and Xu, M. (2008). Badh2, Encoding Betaine Aldehyde Dehydrogenase, Inhibits the Biosynthesis of 2-Acetyl-1-Pyrroline, a Major Component in Rice Fragrance. Plant Cell 20: 1850-1861.

68. Nian, H., Zhang, W., Shi, H., Zhao, Q., Xie, Q., Liao, S., Zhang, Y., Zhang, Z., Wang, C., and Han, C. (2008). Mouse RING finger protein Rnf133 is a testis-specific endoplasmic reticulum-associated E3 ubiquitin ligase. Cell Research 18(7):800-802.

69. Wan, L., Li, D., Zhang, D., Liu, X., Fu, W.J., Zhu, L., Deng, M., Sun, F., and Qian, M. Conservation and implications of eukaryote transcriptional regulatory regions across multiple soecies. BMC Genomics 9: 623 doi:10.1186/1471-2164-9-623.

70. Hong, J., Yun, B., Kang, J., Raja, M., Kwon, E., Sorhagen, K., Chu, C., Wang, Y., and Loake, G. (2008).Nitric oxide function and signalling in plant disease resistance. Journal of Experimental Botany. 59(2):147-154.

71. Adamantia, A., Sigit, P., Elin, O., Henrik, J., Zhu, X., Amy, E., Rolf , J.K,, Peter, E., Inez, H.S., Zhu, Z., Wang, M., Xiong, L., Annemarie, H.M., and Pieter, B.F.O. (2008). A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members. Plant Mol. Biol. 66: 87-103.

72. Yan, S., Yan, C., Zeng, X., Yang, Y., Fang, Y., Tian, C., Sun, Y., Cheng, Z., and Gu, M. (2008). ROLLED LEAF 9, encoding a GARP protein, regulates the leaf abaxial cell fate in rice. PMB 68: 239–250.

73. Lacombe, S., Nagasaki, H.i,Santi, C.,Duval,D.,Piégu, B., Bangratz, M., Breitler, J-C., Guiderdoni, E., Brugidou, C., Cao. X., Brice, C., Panaud, O., Karlowski, W., Sato, Y., and Echeverria, M. (2008). Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice. BMC Plant Biology Accepted.

74. Geng, H., Shi, L., Li, W., Zhang, B., Chu, C., Li, H., and Zhang, G. (2008). Gene expression of jojoba (Simmondsia chinensis) leaves exposed to drying. Environmental and Experimental Botany 63: 137–146.

 75. Liu, L., Yuan, X., Cai, R., Pan, J., He, H., Yuan, L.., Guan, Y., and Zhu, L. (2008) Quantitative Trait Loci for Resistance to Powdery Mildew in Cucumber under Seedling Spray Inoculation and Leaf Disc Infection. J. Phytopathology 156: 691-697.

76. Bennetzen, J., and Chen, M. (2008) Grass genomic synteny illuminates plant genome function and evolution. Rice 1: 109-118.