水稻对白叶枯病菌侵染和低氮胁迫反应的共调控因子鉴定
|
摘要
在生产实践中，长期过量的氮肥施用会加重由水稻黄单胞菌（Xanthomonas oryzae pv.oryzae，简称Xoo）引起白叶枯病害的发生和为害，表明在水稻病害的发生与氮素使用之间存在着关联性。然而，这种关联性的分子机理尚不清楚。
本研究测定了水稻在不同氮素条件下的生长以及对白叶枯病菌侵染的抗性反应，发现与正常氮素(3mM KNO3)条件相比，在低氮(0.3mM KNO3)生长条件下，虽然水稻生物量显著下降，但水稻白叶枯病症状明显减轻，病斑长度缩短，病叶组织中病菌种群量降低。这些结果意味着水稻在抵抗低氮胁迫的同时，也表达出抗病性的增强。鉴此，我们假设在水稻对病菌侵染和低氮胁迫的抗性反应中，可能存在着共同的调控途径及其调控因子。
因此，本研究重点从转录和转录后水平层面分析了水稻对Xoo侵染和低氮胁迫的反应，试图揭示水稻这种抗生物和非生物胁迫的反应模式，鉴定出共调控途径及其因子。研究结果如下：
1.水稻在Xoo侵染和低氮胁迫反应中的共调控miRNA及其靶基因的鉴定。通过高通量测序，检测了水稻在Xoo侵染和低氮胁迫下miRNA的表达水平。在Xoo侵染胁迫反应中，有61个差异表达的水稻miRNA；在低氮胁迫反应中，有80个差异表达的水稻miRNA；在两种组合胁迫反应中，有72个差异表达的水稻miRNA，其中有28个通过了荧光定量PCR分析验证。在两种胁迫反应共调控miRNA中，miR5076、miR5072、miR156和miR1320均上调表达，而miR812、miR169、miR396和miR2869均下调表达。miR398和miR399在Xoo侵染反应中上调表达、在低氮胁迫反应中下调表达；而miR5540则在Xoo侵染反应中下调表达、在低氮胁迫侵染反应中上调表达。对这些miRNA上游启动子区域进行分析，发现它们存在与抗病和抗逆相关的顺式作用元件，如富含TC重复结构和W-box等。对miRNA的靶基因进行了预测和验证。
2.水稻对Xoo侵染和低氮胁迫的转录组反应的分析及其共调控因子的鉴定。通过数字表达谱（DGE）测序，比较分析了在Xoo侵染、或低氮胁迫、或两种胁迫组合处理的水稻转录组的反应，鉴定了248个在两种胁迫条件下共表达的差异基因（DEGs）。这些共调控基因参与了植物免疫反应、氮素代谢、氧化还原反应、蛋白质修饰以及信号传导途径等。对40个随机选择的DEGs表达进行荧光定量PCR测定，发现所有这些基因的表达模式和DGE测序结果一致。对6个DEGs在Xoo侵染和低氮胁迫条件下、不同时间的表达模式进行分析，发现在两种胁迫组合处理中，低氮胁迫是水稻基因表达发生变化的主要因素。
总之，本研究通过高通量测序和荧光定量PCR分析，鉴定了一些在Xoo侵染和低氮胁迫条件中起调控作用的水稻miRNA和基因，这些共调控因子可能在水稻多种不同的生物学过程中发挥功能。本研究结果为水稻对生物和非生物胁迫的共调控机制的解析提供了科学依据。需要进一步通过过量表达和基因沉默的转基因途径，对这些水稻共调控因子进行功能验证，阐明它们在水稻抗病反应和氮素高效利用中的作用。
Bacterial leaf blight of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is more severe atexcessive nitrogen use in the field. This observation suggested that crosstalk between disease resistanceand nitrogen (N) utilization pathways might exist in rice. However, the overlapping transcriptionalresponses in rice to pathogen and N stresses and co-regulatory components involved in this crosstalkhave not yet been elucidated.
In this study, we analyzed the biomass and defense response to Xoo in rice (Oryza sativa L. cv.Nipponbare) at different N conditions. Compared with normal N supply of3mM KNO3, N deficiencysupply of0.3mM KNO3significantly reduced the total biomass. When inoculated with Xoo, rice plantsgrown in N deficiency condition displayed weaker disease symptoms and much shorter lesion lengthsthan those in normal N supply condition. Bacterial numbers in the rice leaves grown in N deficiencycondition also decreased. These results indicated that disease resistance to Xoo was enhanced in rice atN deficiency condition. Therefore, we speculated that there might be co-regulatory components inresponding to Xoo infection and N deficiency condition in rice.
Thus, experiments were designed and carried out to reveal the regulatory mechanisms and co-regulatorycomponents at transcriptional and post-transcriptional levels in this crosstalk. The results are listedbelow.
We searched for differentially-expressed miRNAs in rice at Xoo infection and nitrogen deficiencycondition by high-throughput sequencing, and found61miRNAs only responded to Xoo stress,80miRNAs only responded to low nirtogten stress. Interestingly,72miRNAs responded to both stresses,28out of which were chosen for confirmation by qRT-PCR experiments. Expression of miR5076,miR5072, miR156and miR1320were induced, whereas miR812, miR169, miR396, and miR2869wererepressed at both stresses. Comparatively, expression of miR398and miR399were induced at Xoostress, but repressed at low nitrogen stress, and the expression of miR5540was repressed at Xoo stressbut induced at low nitrogen stress. By analyzing the promoter sequence of these miRNAs, severalknown stress-responsive elements were identified, such as defense and stress-responsive element(TC-rich repeats), defense and wounding-responsive element (W box), and so on. We also identifiedsome target genes of the co-regulated miRNA. The roles of the miRNAs and their target genes will befurther studied.
Digital gene expression analysis (DGE) based on Solexa/Illumina sequencing was used to investigatetranscriptomic responses to Xoo inoculation, low N treatment, or a combination of both stresses.248differentially-expressed genes (DEGs) of rice in overlapping responses to both stresses were identified,which were involved in innate immunity, nitrogen metabolism, oxidation-reduction, proteinphosphorylation and signaling. Expressions of40randomly-selected DEGs were validated byquantitative real-time PCR (qRT-PCR) assays. Temporal expression of six genes selected from different functional categories assayed by qRT-PCR suggested that N condition was the dominant factor whenboth stresses were present.
In conclusion, some miRNAs and DEGs were identified by high-throughput sequencing and qRT-PCR,which were very likely to be involved in the molecular crosstalk between Xoo stress and low nitrogenstress in rice. The findings will help us to understand the co-regulatory mechanisms of rice responses tomultiple biotic and abiotic stresses. Putative co-regulatory components identified here will be furtherfunctionally characterized for bacterial blight disease resistance and nitrogen use efficiency (NUE) inrice.
本研究测定了水稻在不同氮素条件下的生长以及对白叶枯病菌侵染的抗性反应，发现与正常氮素(3mM KNO3)条件相比，在低氮(0.3mM KNO3)生长条件下，虽然水稻生物量显著下降，但水稻白叶枯病症状明显减轻，病斑长度缩短，病叶组织中病菌种群量降低。这些结果意味着水稻在抵抗低氮胁迫的同时，也表达出抗病性的增强。鉴此，我们假设在水稻对病菌侵染和低氮胁迫的抗性反应中，可能存在着共同的调控途径及其调控因子。
因此，本研究重点从转录和转录后水平层面分析了水稻对Xoo侵染和低氮胁迫的反应，试图揭示水稻这种抗生物和非生物胁迫的反应模式，鉴定出共调控途径及其因子。研究结果如下：
1.水稻在Xoo侵染和低氮胁迫反应中的共调控miRNA及其靶基因的鉴定。通过高通量测序，检测了水稻在Xoo侵染和低氮胁迫下miRNA的表达水平。在Xoo侵染胁迫反应中，有61个差异表达的水稻miRNA；在低氮胁迫反应中，有80个差异表达的水稻miRNA；在两种组合胁迫反应中，有72个差异表达的水稻miRNA，其中有28个通过了荧光定量PCR分析验证。在两种胁迫反应共调控miRNA中，miR5076、miR5072、miR156和miR1320均上调表达，而miR812、miR169、miR396和miR2869均下调表达。miR398和miR399在Xoo侵染反应中上调表达、在低氮胁迫反应中下调表达；而miR5540则在Xoo侵染反应中下调表达、在低氮胁迫侵染反应中上调表达。对这些miRNA上游启动子区域进行分析，发现它们存在与抗病和抗逆相关的顺式作用元件，如富含TC重复结构和W-box等。对miRNA的靶基因进行了预测和验证。
2.水稻对Xoo侵染和低氮胁迫的转录组反应的分析及其共调控因子的鉴定。通过数字表达谱（DGE）测序，比较分析了在Xoo侵染、或低氮胁迫、或两种胁迫组合处理的水稻转录组的反应，鉴定了248个在两种胁迫条件下共表达的差异基因（DEGs）。这些共调控基因参与了植物免疫反应、氮素代谢、氧化还原反应、蛋白质修饰以及信号传导途径等。对40个随机选择的DEGs表达进行荧光定量PCR测定，发现所有这些基因的表达模式和DGE测序结果一致。对6个DEGs在Xoo侵染和低氮胁迫条件下、不同时间的表达模式进行分析，发现在两种胁迫组合处理中，低氮胁迫是水稻基因表达发生变化的主要因素。
总之，本研究通过高通量测序和荧光定量PCR分析，鉴定了一些在Xoo侵染和低氮胁迫条件中起调控作用的水稻miRNA和基因，这些共调控因子可能在水稻多种不同的生物学过程中发挥功能。本研究结果为水稻对生物和非生物胁迫的共调控机制的解析提供了科学依据。需要进一步通过过量表达和基因沉默的转基因途径，对这些水稻共调控因子进行功能验证，阐明它们在水稻抗病反应和氮素高效利用中的作用。
Bacterial leaf blight of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is more severe atexcessive nitrogen use in the field. This observation suggested that crosstalk between disease resistanceand nitrogen (N) utilization pathways might exist in rice. However, the overlapping transcriptionalresponses in rice to pathogen and N stresses and co-regulatory components involved in this crosstalkhave not yet been elucidated.
In this study, we analyzed the biomass and defense response to Xoo in rice (Oryza sativa L. cv.Nipponbare) at different N conditions. Compared with normal N supply of3mM KNO3, N deficiencysupply of0.3mM KNO3significantly reduced the total biomass. When inoculated with Xoo, rice plantsgrown in N deficiency condition displayed weaker disease symptoms and much shorter lesion lengthsthan those in normal N supply condition. Bacterial numbers in the rice leaves grown in N deficiencycondition also decreased. These results indicated that disease resistance to Xoo was enhanced in rice atN deficiency condition. Therefore, we speculated that there might be co-regulatory components inresponding to Xoo infection and N deficiency condition in rice.
Thus, experiments were designed and carried out to reveal the regulatory mechanisms and co-regulatorycomponents at transcriptional and post-transcriptional levels in this crosstalk. The results are listedbelow.
We searched for differentially-expressed miRNAs in rice at Xoo infection and nitrogen deficiencycondition by high-throughput sequencing, and found61miRNAs only responded to Xoo stress,80miRNAs only responded to low nirtogten stress. Interestingly,72miRNAs responded to both stresses,28out of which were chosen for confirmation by qRT-PCR experiments. Expression of miR5076,miR5072, miR156and miR1320were induced, whereas miR812, miR169, miR396, and miR2869wererepressed at both stresses. Comparatively, expression of miR398and miR399were induced at Xoostress, but repressed at low nitrogen stress, and the expression of miR5540was repressed at Xoo stressbut induced at low nitrogen stress. By analyzing the promoter sequence of these miRNAs, severalknown stress-responsive elements were identified, such as defense and stress-responsive element(TC-rich repeats), defense and wounding-responsive element (W box), and so on. We also identifiedsome target genes of the co-regulated miRNA. The roles of the miRNAs and their target genes will befurther studied.
Digital gene expression analysis (DGE) based on Solexa/Illumina sequencing was used to investigatetranscriptomic responses to Xoo inoculation, low N treatment, or a combination of both stresses.248differentially-expressed genes (DEGs) of rice in overlapping responses to both stresses were identified,which were involved in innate immunity, nitrogen metabolism, oxidation-reduction, proteinphosphorylation and signaling. Expressions of40randomly-selected DEGs were validated byquantitative real-time PCR (qRT-PCR) assays. Temporal expression of six genes selected from different functional categories assayed by qRT-PCR suggested that N condition was the dominant factor whenboth stresses were present.
In conclusion, some miRNAs and DEGs were identified by high-throughput sequencing and qRT-PCR,which were very likely to be involved in the molecular crosstalk between Xoo stress and low nitrogenstress in rice. The findings will help us to understand the co-regulatory mechanisms of rice responses tomultiple biotic and abiotic stresses. Putative co-regulatory components identified here will be furtherfunctionally characterized for bacterial blight disease resistance and nitrogen use efficiency (NUE) inrice.
引文
1.陈丽珍，叶剑秋，王荣香，水稻盐胁迫的研究进展.热带农业科学，2011,31（3）：87-93.
2.戴玉池，邓霞玲，姜孝成，陈良碧，不同水稻品种幼苗期耐寒生理鉴定及其利用.湖南师范大学自然科学学报，2004，27（3）：86-89.
3.方中达，刘经芬，水稻抗病性的研究I.水稻在不同施肥和土壤条件下对白叶枯病抗病性的变化.植物保护学报，1962,1（3）：231-236.
4.高必达，郭海明，黎用朝，陈贸，施氮对水稻抗白叶枯病反应的影响.湖南农学院学报，1992,18（2）：293-298.
5.郭培国，李荣华，夜间高温胁迫对水稻叶片光合机构的影响.植物学报，2000,47（2）：673-678.
6.候夫云，张立明，王庆美，李爱贤，张海燕，董顺旭，植物耐非生物胁迫的分子机制.分子植物育种，2007,5（6）：80-84.
7.曲雪萍，贺道耀，余叔文，水稻中p5cs基因的存在及其在高脯氨酸变异系中的作用.植物病理学报，1998,24（1）：49-54.
8.郑少玲，严小龙，盐胁迫下不同水稻基因型根内Na+和Cl-分布情况比较.华南农业大学学报，1996,17（4）：24-28.
9.宗会，徐照丽，刘娥娥，低温胁迫下氯丙嗪和氯化镧对水稻幼苗脯氨酸积累的影响.热带亚热带植物学报，2003,11（3）：241-244.
10. Abdel-Lateif, K., Vaissayre, V., Gherbi, H., Verries, C., Meudec, E., Perrine-Walker, F., Cheynier,V., Svistoonoff, S., Franche, C., Bogusz, D., and Hocher, V.(2013). Silencing of the chalconesynthase gene in Casuarina glauca highlights the important role of flavonoids during nodulation.The New phytologist199,1012-1021.
11. Abrahante, J.E., Daul, A.L., Li, M., Volk, M.L., Tennessen, J.M., Miller, E.A., and Rougvie, A.E.(2003). The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1controls developmental timeand is regulated by microRNAs. Developmental cell4,625-637.
12. Achard, P., Herr, A., Baulcombe, D.C., and Harberd, N.P.(2004). Modulation of floraldevelopment by a gibberellin-regulated microRNA. Development131,3357-3365.
13. Aida, M., Ishida, T., Fukaki, H., Fujisawa, H., and Tasaka, M.(1997). Genes involved in organseparation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. The Plant cell9,841-857.
14. Anders, S., and Huber, W.(2010). Differential expression analysis for sequence count data.Genome biology11, R106.
15. Antony, G., Zhou, J., Huang, S., Li, T., Liu, B., White, F., and Yang, B.(2010). Rice xa13recessiveresistance to bacterial blight is defeated by induction of the disease susceptibility gene Os-11N3.The Plant cell22,3864-3876.
16. Aravind, L., and Koonin, E.V.(1999). G-patch: a new conserved domain in eukaryoticRNA-processing proteins and type D retroviral polyproteins. Trends in biochemical sciences24,342-344.
17. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski,K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S.,Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., and Sherlock, G.(2000). Geneontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics25,25-29.
18. Aukerman, M.J., and Sakai, H.(2003). Regulation of flowering time and floral organ identity by aMicroRNA and its APETALA2-like target genes. The Plant cell15,2730-2741.
19. Baker, C.C., Sieber, P., Wellmer, F., and Meyerowitz, E.M.(2005). The early extra petals1mutantuncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Currentbiology: CB15,303-315.
20. Bartel, D.P.(2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell116,281-297.
21. Bernoux, M., Ellis, J.G., and Dodds, P.N.(2011). New insights in plant immunity signalingactivation. Current opinion in plant biology14,512-518.
22. Bi, Y.M., Wang, R.L., Zhu, T., and Rothstein, S.J.(2007). Global transcription profiling revealsdifferential responses to chronic nitrogen stress and putative nitrogen regulatory components inArabidopsis. BMC genomics8,281.
23. Blair, M.W., Garris, A.J., Iyer, A.S., Chapman, B., Kresovich, S., and McCouch, S.R.(2003). Highresolution genetic mapping and candidate gene identification at the xa5locus for bacterial blightresistance in rice (Oryza sativa L.). TAG. Theoretical and applied genetics. Theoretische undangewandte Genetik107,62-73.
24. Boller, T., and Felix, G.(2009). A renaissance of elicitors: perception of microbe-associatedmolecular patterns and danger signals by pattern-recognition receptors. Annual review of plantbiology60,379-406.
25. Brauer, E.K., Rochon, A., Bi, Y.M., Bozzo, G.G., Rothstein, S.J., and Shelp, B.J.(2011).Reappraisal of nitrogen use efficiency in rice overexpressing glutamine synthetase1. Physiologiaplantarum141,361-372.
26. Cai, H., Zhou, Y., Xiao, J., Li, X., Zhang, Q., and Lian, X.(2009). Overexpressed glutaminesynthetase gene modifies nitrogen metabolism and abiotic stress responses in rice. Plant cellreports28,527-537.
27. Cappellazzo, G., Lanfranco, L., and Bonfante, P.(2007). A limiting source of organic nitrogeninduces specific transcriptional responses in the extraradical structures of the endomycorrhizalfungus Glomus intraradices. Current genetics51,59-70.
28. Carballo, S.J., Blankenship, S.M., and Sanders, D.C.(1994). Drip fertigation with nitrogen andpotassium and postharvest susceptibility to bacterial soft rot of bell peppers. J. Plant Nutr.17,1175-1191.
29. Cercos, M., Gomez-Cadenas, A., and Ho, T.H.(1999). Hormonal regulation of a cysteineproteinase gene, EPB-1, in barley aleurone layers: cis-and trans-acting elements involved in theco-ordinated gene expression regulated by gibberellins and abscisic acid. The Plant journal: forcell and molecular biology19,107-118.
30. Chakravarthy, S., Velasquez, A.C., and Martin, G.B.(2009). Assay for pathogen-associatedmolecular pattern (PAMP)-triggered immunity (PTI) in plants. Journal of visualized experiments:JoVE.
31. Chellappan, P., Vanitharani, R., and Fauquet, C.M.(2005). MicroRNA-binding viral proteininterferes with Arabidopsis development. Proceedings of the National Academy of Sciences of theUnited States of America102,10381-10386.
32. Chen, C., Ridzon, D.A., Broomer, A.J., Zhou, Z., Lee, D.H., Nguyen, J.T., Barbisin, M., Xu, N.L.,Mahuvakar, V.R., Andersen, M.R., Lao, K.Q., Livak, K.J., and Guegler, K.J.(2005). Real-timequantification of microRNAs by stem-loop RT-PCR. Nucleic acids research33, e179.
33. Chen, L., Wang, T., Zhao, M., and Zhang, W.(2012). Ethylene-responsive miRNAs in roots ofMedicago truncatula identified by high-throughput sequencing at whole genome level. Plantscience: an international journal of experimental plant biology184,14-19.
34. Chen, X.(2004). A microRNA as a translational repressor of APETALA2in Arabidopsis flowerdevelopment. Science303,2022-2025.
35. Chen, X.(2005). MicroRNA biogenesis and function in plants. FEBS letters579,5923-5931.
36. Chen, X., Chern, M., Canlas, P.E., Ruan, D., Jiang, C., and Ronald, P.C.(2010). An ATPasepromotes autophosphorylation of the pattern recognition receptor XA21and inhibitsXA21-mediated immunity. Proceedings of the National Academy of Sciences of the United Statesof America107,8029-8034.
37. Chiou, T.J.(2007). The role of microRNAs in sensing nutrient stress. Plant, cell&environment30,323-332.
38. Chisholm, S.T., Coaker, G., Day, B., and Staskawicz, B.J.(2006). Host-microbe interactions:shaping the evolution of the plant immune response. Cell124,803-814.
39. Chu, Z., Fu, B., Yang, H., Xu, C., Li, Z., Sanchez, A., Park, Y.J., Bennetzen, J.L., Zhang, Q., andWang, S.(2006). Targeting xa13, a recessive gene for bacterial blight resistance in rice. TAG.Theoretical and applied genetics. Theoretische und angewandte Genetik112,455-461.
40. Chujo, T., Miyamoto, K., Shimogawa, T., Shimizu, T., Otake, Y., Yokotani, N., Nishizawa, Y.,Shibuya, N., Nojiri, H., Yamane, H., Minami, E., and Okada, K.(2013). OsWRKY28, aPAMP-responsive transrepressor, negatively regulates innate immune responses in rice against riceblast fungus. Plant molecular biology82,23-37.
41. Crawford, N.M., and Forde, B.G.(2002). Molecular and developmental biology of inorganicnitrogen nutrition. The Arabidopsis book/American Society of Plant Biologists1, e0011.
42. Cui, F., Liu, L., Zhao, Q., Zhang, Z., Li, Q., Lin, B., Wu, Y., Tang, S., and Xie, Q.(2012).Arabidopsis ubiquitin conjugase UBC32is an ERAD component that functions inbrassinosteroid-mediated salt stress tolerance. The Plant cell24,233-244.
43. De Vleesschauwer, D., Gheysen, G., and Hofte, M.(2013). Hormone defense networking in rice:tales from a different world. Trends in plant science18,555-565.
44. Denance, N., Sanchez-Vallet, A., Goffner, D., and Molina, A.(2013). Disease resistance or growth:the role of plant hormones in balancing immune responses and fitness costs. Frontiers in plantscience4,155.
45. Dharmasiri, N., Dharmasiri, S., and Estelle, M.(2005). The F-box protein TIR1is an auxinreceptor. Nature435,441-445.
46. Dietrich, R., Ploss, K., and Heil, M.(2004). Constitutive and induced resistance to pathogens inArabidopsis thaliana depends on nitrogen supply. Plant Cell and Environment27,896-906.
47. Dietrich, R., Ploss, K., and Heil, M.(2005). Growth responses and fitness costs after induction ofpathogen resistance depend on environmental conditions. Plant Cell and Environment28,211-222.
48. Doench, J.G., Petersen, C.P., and Sharp, P.A.(2003). siRNAs can function as miRNAs. Genes&development17,438-442.
49. Elbashir, S.M., Lendeckel, W., and Tuschl, T.(2001). RNA interference is mediated by21-and22-nucleotide RNAs. Genes&development15,188-200.
50. Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C., and Marks, D.S.(2003). MicroRNA targetsin Drosophila. Genome biology5, R1.
51. Fitzgerald, H.A., Canlas, P.E., Chern, M.S., and Ronald, P.C.(2005). Alteration of TGA factoractivity in rice results in enhanced tolerance to Xanthomonas oryzae pv. oryzae. The Plant journal:for cell and molecular biology43,335-347.
52. Furihata, T., Maruyama, K., Fujita, Y., Umezawa, T., Yoshida, R., Shinozaki, K., andYamaguchi-Shinozaki, K.(2006). Abscisic acid-dependent multisite phosphorylation regulates theactivity of a transcription activator AREB1. Proceedings of the National Academy of Sciences ofthe United States of America103,1988-1993.
53. Gaffney, T., Friedrich, L., Vernooij, B., Negrotto, D., Nye, G., Uknes, S., Ward, E., Kessmann, H.,and Ryals, J.(1993). Requirement of salicylic Acid for the induction of systemic acquiredresistance. Science261,754-756.
54. Gifford, M.L., Dean, A., Gutierrez, R.A., Coruzzi, G.M., and Birnbaum, K.D.(2008). Cell-specificnitrogen responses mediate developmental plasticity. Proceedings of the National Academy ofSciences of the United States of America105,803-808.
55. Glazinska, P., Zienkiewicz, A., Wojciechowski, W., and Kopcewicz, J.(2009). The putativemiR172target gene InAPETALA2-like is involved in the photoperiodic flower induction ofIpomoea nil. Journal of plant physiology166,1801-1813.
56. Gray, W.M.(2004). Hormonal regulation of plant growth and development. PLoS biology2, E311.
57. Griffiths-Jones, S., Saini, H.K., van Dongen, S., and Enright, A.J.(2008). miRBase: tools formicroRNA genomics. Nucleic acids research36, D154-158.
58. Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A., and Enright, A.J.(2006). miRBase:microRNA sequences, targets and gene nomenclature. Nucleic acids research34, D140-144.
59. Gu, K., Tian, D., Yang, F., Wu, L., Sreekala, C., Wang, D., Wang, G.L., and Yin, Z.(2004).High-resolution genetic mapping of Xa27(t), a new bacterial blight resistance gene in rice, Oryzasativa L. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik108,800-807.
60. Gu, K., Yang, B., Tian, D., Wu, L., Wang, D., Sreekala, C., Yang, F., Chu, Z., Wang, G.L., White,F.F., and Yin, Z.(2005). R gene expression induced by a type-III effector triggers disease resistancein rice. Nature435,1122-1125.
61. Gubler, F., Kalla, R., Roberts, J.K., and Jacobsen, J.V.(1995). Gibberellin-regulated expression ofa myb gene in barley aleurone cells: evidence for Myb transactivation of a high-pI alpha-amylasegene promoter. The Plant cell7,1879-1891.
62. Gubler, F., Raventos, D., Keys, M., Watts, R., Mundy, J., and Jacobsen, J.V.(1999). Target genesand regulatory domains of the GAMYB transcriptional activator in cereal aleurone. The Plantjournal: for cell and molecular biology17,1-9.
63. Guo, H.S., Xie, Q., Fei, J.F., and Chua, N.H.(2005). MicroRNA directs mRNA cleavage of thetranscription factor NAC1to downregulate auxin signals for Arabidopsis lateral root development.The Plant cell17,1376-1386.
64. Guo, J.H., Liu, X.J., Zhang, Y., Shen, J.L., Han, W.X., Zhang, W.F., Christie, P., Goulding, K.W.,Vitousek, P.M., and Zhang, F.S.(2010). Significant acidification in major Chinese croplands.Science327,1008-1010.
65. Gutierrez, R.A., Lejay, L.V., Dean, A., Chiaromonte, F., Shasha, D.E., and Coruzzi, G.M.(2007).Qualitative network models and genome-wide expression data define carbon/nitrogen-responsivemolecular machines in Arabidopsis. Genome biology8, R7.
66. Hoffland, E., Van Beusichem, M.L., and Jeger, M.G.(1999). Nitrogen availability andsusceptibility of tomato leaves to Botrytis cinerea. Plant and Soil210,263-272.
67. Hoffland, E., Jeger, M.G., and Van Beusichem, M.L.(2000). Effect of nitrogen supply rate ondisease resistance in tomato depends on the pathogen. Plant and Soil218,239-247.
68. Hu, H., You, J., Fang, Y., Zhu, X., Qi, Z., and Xiong, L.(2008). Characterization of transcriptionfactor gene SNAC2conferring cold and salt tolerance in rice. Plant molecular biology67,169-181.
69. Hu, H., Dai, M., Yao, J., Xiao, B., Li, X., Zhang, Q., and Xiong, L.(2006). Overexpressing a NAM,ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice.Proceedings of the National Academy of Sciences of the United States of America103,12987-12992.
70. Hua, C., Linling, L., Feng, X., Yan, W., Honghui, Y., Conghua, W., Shaobing, W., Zhiqin, L., Juan,H., Yuping, W., Shuiyuan, C., and Fuliang, C.(2013). Expression patterns of an isoflavonereductase-like gene and its possible roles in secondary metabolism in Ginkgo biloba. Plant cellreports32,637-650.
71. Hutvagner, G., and Zamore, P.D.(2002). A microRNA in a multiple-turnover RNAi enzymecomplex. Science297,2056-2060.
72. Iyer, A.S., and McCouch, S.R.(2004). The rice bacterial blight resistance gene xa5encodes a novelform of disease resistance. Molecular plant-microbe interactions: MPMI17,1348-1354.
73. Jagadeeswaran, G., Saini, A., and Sunkar, R.(2009). Biotic and abiotic stress down-regulatemiR398expression in Arabidopsis. Planta229,1009-1014.
74. Jiang, G.H., Xia, Z.H., Zhou, Y.L., Wan, J., Li, D.Y., Chen, R.S., Zhai, W.X., and Zhu, L.H.(2006).Testifying the rice bacterial blight resistance gene xa5by genetic complementation and furtheranalyzing xa5(Xa5) in comparison with its homolog TFIIAgamma1. Molecular genetics andgenomics: MGG275,354-366.
75. Jones, J.D., and Dangl, J.L.(2006). The plant immune system. Nature444,323-329.
76. Ju, X.T., Xing, G.X., Chen, X.P., Zhang, S.L., Zhang, L.J., Liu, X.J., Cui, Z.L., Yin, B., Christie, P.,Zhu, Z.L., and Zhang, F.S.(2009). Reducing environmental risk by improving N management inintensive Chinese agricultural systems. Proceedings of the National Academy of Sciences of theUnited States of America106,3041-3046.
77. Juarez, M.T., Kui, J.S., Thomas, J., Heller, B.A., and Timmermans, M.C.(2004).microRNA-mediated repression of rolled leaf1specifies maize leaf polarity. Nature428,84-88.
78. Kalamaki, M.S., Alexandrou, D., Lazari, D., Merkouropoulos, G., Fotopoulos, V., Pateraki, I.,Aggelis, A., Carrillo-Lopez, A., Rubio-Cabetas, M.J., and Kanellis, A.K.(2009). Over-expressionof a tomato N-acetyl-L-glutamate synthase gene (SlNAGS1) in Arabidopsis thaliana results inhigh ornithine levels and increased tolerance in salt and drought stresses. Journal of experimentalbotany60,1859-1871.
79. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima,S., Okuda, S., Tokimatsu, T., and Yamanishi, Y.(2008). KEGG for linking genomes to life and theenvironment. Nucleic acids research36, D480-484.
80. Kang, S., Kim, H.B., Lee, H., Choi, J.Y., Heu, S., Oh, C.J., Kwon, S.I., and An, C.S.(2006).Overexpression in Arabidopsis of a plasma membrane-targeting glutamate receptor from smallradish increases glutamate-mediated Ca2+influx and delays fungal infection. Molecules and cells21,418-427.
81. Kasschau, K.D., Xie, Z., Allen, E., Llave, C., Chapman, E.J., Krizan, K.A., and Carrington, J.C.(2003). P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis developmentand miRNA unction. Developmental cell4,205-217.
82. Katiyar-Agarwal, S., and Jin, H.(2010). Role of small RNAs in host-microbe interactions. Annualreview of phytopathology48,225-246.
83. Katsantonis, D., Koutroubas, S.D., Ntanos, D.A., and Lupotto, E.(2008). Effect of blast disease onnitrogen accumulation and remobilization to rice grain. J Plant Pathol90,263-272.
84. Kemmerling, B., Halter, T., Mazzotta, S., Mosher, S., and Nurnberger, T.(2011). A genome-widesurvey for Arabidopsis leucine-rich repeat receptor kinases implicated in plant immunity. Frontiersin plant science2,88.
85. Khraiwesh, B., Zhu, J.K., and Zhu, J.(2012). Role of miRNAs and siRNAs in biotic and abioticstress responses of plants. Biochimica et biophysica acta1819,137-148.
86. Kim, S.T., Cho, K.S., Kim, S.G., Kang, S.Y., and Kang, K.Y.(2003). A rice isoflavonereductase-like gene, OsIRL, is induced by rice blast fungal elicitor. Molecules and cells16,224-231.
87. Komatsu, S., and Konishi, H.(2005). Proteome analysis of rice root proteins regulated bygibberellin. Genomics, proteomics&bioinformatics/Beijing Genomics Institute3,132-142.
88. Kozomara, A., and Griffiths-Jones, S.(2011). miRBase: integrating microRNA annotation anddeep-sequencing data. Nucleic acids research39, D152-157.
89. Lai, Y., Dang, F., Lin, J., Yu, L., Shi, Y., Xiao, Y., Huang, M., Chen, C., Qi, A., Liu, Z., Guan, D.,Mou, S., Qiu, A., and He, S.(2013). Overexpression of a Chinese cabbage BrERF11transcriptionfactor enhances disease resistance to Ralstonia solanacearum in tobacco. Plant physiology andbiochemistry: PPB/Societe francaise de physiologie vegetale62,70-78.
90. Lan, A., Huang, J., Zhao, W., Peng, Y., Chen, Z., and Kang, D.(2013). A salicylic acid-induced rice(Oryza sativa L.) transcription factor OsWRKY77is involved in disease resistance of Arabidopsisthaliana. Plant Biol (Stuttg)15,452-461.
91. Laufs, P., Peaucelle, A., Morin, H., and Traas, J.(2004). MicroRNA regulation of the CUC genes isrequired for boundary size control in Arabidopsis meristems. Development131,4311-4322.
92. Lee, R.C., Feinbaum, R.L., and Ambros, V.(1993). The C. elegans heterochronic gene lin-4encodes small RNAs with antisense complementarity to lin-14. Cell75,843-854.
93. Leung, J., and Giraudat, J.(1998). Abscisic Acid Signal Transduction. Annual review of plantphysiology and plant molecular biology49,199-222.
94. Lewis, B.P., Burge, C.B., and Bartel, D.P.(2005). Conserved seed pairing, often flanked byadenosines, indicates that thousands of human genes are microRNA targets. Cell120,15-20.
95. Li, W.X., Oono, Y., Zhu, J., He, X.J., Wu, J.M., Iida, K., Lu, X.Y., Cui, X., Jin, H., and Zhu, J.K.(2008). The Arabidopsis NFYA5transcription factor is regulated transcriptionally andposttranscriptionally to promote drought resistance. The Plant cell20,2238-2251.
96. Li, X., Lin, H., Zhang, W., Zou, Y., Zhang, J., Tang, X., and Zhou, J.M.(2005). Flagellin inducesinnate immunity in nonhost interactions that is suppressed by Pseudomonas syringae effectors.Proceedings of the National Academy of Sciences of the United States of America102,12990-12995.
97. Li, Y., Zhang, Q., Zhang, J., Wu, L., Qi, Y., and Zhou, J.M.(2010a). Identification of microRNAsinvolved in pathogen-associated molecular pattern-triggered plant innate immunity. Plantphysiology152,2222-2231.
98. Li, Y.F., Zheng, Y., Addo-Quaye, C., Zhang, L., Saini, A., Jagadeeswaran, G., Axtell, M.J., Zhang,W., and Sunkar, R.(2010b). Transcriptome-wide identification of microRNA targets in rice. ThePlant journal: for cell and molecular biology62,742-759.
99. Liang, G., He, H., and Yu, D.(2012). Identification of nitrogen starvation-responsive microRNAsin Arabidopsis thaliana. PloS one7, e48951.
100. Liu, B., Xue, X., Cui, S., Zhang, X., Han, Q., Zhu, L., Liang, X., Wang, X., Huang, L., Chen, X.,and Kang, Z.(2010). Cloning and characterization of a wheat beta-1,3-glucanase gene induced bythe stripe rust pathogen Puccinia striiformis f. sp. tritici. Molecular biology reports37,1045-1052.
101. Liu, H.H., Tian, X., Li, Y.J., Wu, C.A., and Zheng, C.C.(2008). Microarray-based analysis ofstress-regulated microRNAs in Arabidopsis thaliana. RNA14,836-843.
102. Liu, J.X., and Howell, S.H.(2010). bZIP28and NF-Y transcription factors are activated by ERstress and assemble into a transcriptional complex to regulate stress response genes in Arabidopsis.The Plant cell22,782-796.
103. Liu, Q., Yuan, M., Zhou, Y., Li, X., Xiao, J., and Wang, S.(2011). A paralog of the MtN3/salivafamily recessively confers race-specific resistance to Xanthomonas oryzae in rice. Plant, cell&environment34,1958-1969.
104. Liu, Q., Zhang, Y.C., Wang, C.Y., Luo, Y.C., Huang, Q.J., Chen, S.Y., Zhou, H., Qu, L.H., andChen, Y.Q.(2009). Expression analysis of phytohormone-regulated microRNAs in rice, implyingtheir regulation roles in plant hormone signaling. FEBS letters583,723-728.
105. Liu, X., Bai, X., Wang, X., and Chu, C.(2007). OsWRKY71, a rice transcription factor, is involvedin rice defense response. Journal of plant physiology164,969-979.
106. Llave, C., Xie, Z., Kasschau, K.D., and Carrington, J.C.(2002). Cleavage of Scarecrow-likemRNA targets directed by a class of Arabidopsis miRNA. Science297,2053-2056.
107. Llave, C.(2004). MicroRNAs: more than a role in plant development? Molecular plant pathology5,361-366.
108. Long, D.H., Lee, F.N., and Tebeest, D.O.(2000). Effect of nitrogen fertilization on diseaseprogress of rice blast on susceptible and resistant cultivars. Plant disease84,403-409.
109. Lu, C., and Fedoroff, N.(2000). A mutation in the Arabidopsis HYL1gene encoding a dsRNAbinding protein affects responses to abscisic acid, auxin, and cytokinin. The Plant cell12,2351-2366.
110. Lu, Y., Luo, F., Yang, M., Li, X., and Lian, X.(2011). Suppression of glutamate synthase genessignificantly affects carbon and nitrogen metabolism in rice (Oryza sativa L.). Science China. Lifesciences54,651-663.
111. Mackowiak, S.D.(2011). Identification of novel and known miRNAs in deep-sequencing data withmiRDeep2. Current protocols in bioinformatics/editoral board, Andreas D. Baxevanis...[et al.]Chapter12, Unit1210.
112. Mallory, A.C., and Vaucheret, H.(2006). Functions of microRNAs and related small RNAs inplants. Nature genetics38Suppl, S31-36.
113. Mallory, A.C., Bartel, D.P., and Bartel, B.(2005). MicroRNA-directed regulation of ArabidopsisAUXIN RESPONSE FACTOR17is essential for proper development and modulates expression ofearly auxin response genes. The Plant cell17,1360-1375.
114. Mallory, A.C., Dugas, D.V., Bartel, D.P., and Bartel, B.(2004). MicroRNA regulation ofNAC-domain targets is required for proper formation and separation of adjacent embryonic,vegetative, and floral organs. Current biology: CB14,1035-1046.
115. Megraw, M., Baev, V., Rusinov, V., Jensen, S.T., Kalantidis, K., and Hatzigeorgiou, A.G.(2006).MicroRNA promoter element discovery in Arabidopsis. RNA12,1612-1619.
116. Millar, A.A., and Gubler, F.(2005). The Arabidopsis GAMYB-like genes, MYB33and MYB65,are microRNA-regulated genes that redundantly facilitate anther development. The Plant cell17,705-721.
117. Millar, A.A., and Waterhouse, P.M.(2005). Plant and animal microRNAs: similarities anddifferences. Functional&integrative genomics5,129-135.
118. Miller, A.J., Fan, X., Orsel, M., Smith, S.J., and Wells, D.M.(2007). Nitrate transport andsignalling. Journal of experimental botany58,2297-2306.
119. Moscou, M.J., and Bogdanove, A.J.(2009). A simple cipher governs DNA recognition by TALeffectors. Science326,1501.
120. Mugford, S.T., Qi, X., Bakht, S., Hill, L., Wegel, E., Hughes, R.K., Papadopoulou, K., Melton, R.,Philo, M., Sainsbury, F., Lomonossoff, G.P., Roy, A.D., Goss, R.J., and Osbourn, A.(2009). Aserine carboxypeptidase-like acyltransferase is required for synthesis of antimicrobial compoundsand disease resistance in oats. The Plant cell21,2473-2484.
121. Mukherjee, A.K., Mohapatra, N.K., Rao, A.V.S., and Nayak, P.(2005). Effect of nitrogenfertilization on the expression of slow-blasting resistance in rice. J Agr Sci143,385-393.
122. Mukhopadhyay, A., Vij, S., and Tyagi, A.K.(2004). Overexpression of a zinc-finger protein genefrom rice confers tolerance to cold, dehydration, and salt stress in transgenic tobacco. Proceedingsof the National Academy of Sciences of the United States of America101,6309-6314.
123. Nakai, Y., Nakahira, Y., Sumida, H., Takebayashi, K., Nagasawa, Y., Yamasaki, K., Akiyama, M.,Ohme-Takagi, M., Fujiwara, S., Shiina, T., Mitsuda, N., Fukusaki, E., Kubo, Y., and Sato, M.H.(2013). Vascular plant one-zinc-finger protein1/2transcription factors regulate abiotic and bioticstress responses in Arabidopsis. The Plant journal: for cell and molecular biology73,761-775.
124. Nambara, E., and Marion-Poll, A.(2005). Abscisic acid biosynthesis and catabolism. Annualreview of plant biology56,165-185.
125. Narsai, R., Wang, C., Chen, J., Wu, J., Shou, H., and Whelan, J.(2013). Antagonistic, overlappingand distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress.BMC genomics14,93.
126. Nath, U., Crawford, B.C., Carpenter, R., and Coen, E.(2003). Genetic control of surface curvature.Science299,1404-1407.
127. Navarro, L., Dunoyer, P., Jay, F., Arnold, B., Dharmasiri, N., Estelle, M., Voinnet, O., and Jones,J.D.(2006). A plant miRNA contributes to antibacterial resistance by repressing auxin signaling.Science312,436-439.
128. Nelson, D.E., Repetti, P.P., Adams, T.R., Creelman, R.A., Wu, J., Warner, D.C., Anstrom, D.C.,Bensen, R.J., Castiglioni, P.P., Donnarummo, M.G., Hinchey, B.S., Kumimoto, R.W., Maszle, D.R.,Canales, R.D., Krolikowski, K.A., Dotson, S.B., Gutterson, N., Ratcliffe, O.J., and Heard, J.E.(2007). Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improvedcorn yields on water-limited acres. Proceedings of the National Academy of Sciences of the UnitedStates of America104,16450-16455.
129. Ohtake, Y., Takahashi, T., and Komeda, Y.(2000). Salicylic acid induces the expression of anumber of receptor-like kinase genes in Arabidopsis thaliana. Plant&cell physiology41,1038-1044.
130. Oka, M., Shimoda, Y., Sato, N., Inoue, J., Yamazaki, T., Shimomura, N., and Fujiyama, H.(2012).Abscisic acid substantially inhibits senescence of cucumber plants (Cucumis sativus) grown underlow nitrogen conditions. Journal of plant physiology169,789-796.
131. Pageau, K., Reisdorf-Cren, M., Morot-Gaudry, J.F., and Masclaux-Daubresse, C.(2006). The twosenescence-related markers, GS1(cytosolic glutamine synthetase) and GDH (glutamatedehydrogenase), involved in nitrogen mobilization, are differentially regulated during pathogenattack and by stress hormones and reactive oxygen species in Nicotiana tabacum L. leaves. Journalof experimental botany57,547-557.
132. Palatnik, J.F., Allen, E., Wu, X., Schommer, C., Schwab, R., Carrington, J.C., and Weigel, D.(2003). Control of leaf morphogenesis by microRNAs. Nature425,257-263.
133. Palenchar, P.M., Kouranov, A., Lejay, L.V., and Coruzzi, G.M.(2004). Genome-wide patterns ofcarbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen(CN)-signaling hypothesis in plants. Genome biology5, R91.
134. Pan, Y., Seymour, G.B., Lu, C., Hu, Z., Chen, X., and Chen, G.(2012). An ethylene response factor(ERF5) promoting adaptation to drought and salt tolerance in tomato. Plant cell reports31,349-360.
135. Pant, B.D., Musialak-Lange, M., Nuc, P., May, P., Buhtz, A., Kehr, J., Walther, D., and Scheible,W.R.(2009). Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs bycomprehensive real-time polymerase chain reaction profiling and small RNA sequencing. Plantphysiology150,1541-1555.
136. Park, C.J., Han, S.W., Chen, X., and Ronald, P.C.(2010). Elucidation of XA21-mediated innateimmunity. Cellular microbiology12,1017-1025.
137. Park, C.J., Peng, Y., Chen, X., Dardick, C., Ruan, D., Bart, R., Canlas, P.E., and Ronald, P.C.(2008). Rice XB15, a protein phosphatase2C, negatively regulates cell death and XA21-mediatedinnate immunity. PLoS biology6, e231.
138. Peng, Y., Bartley, L.E., Chen, X., Dardick, C., Chern, M., Ruan, R., Canlas, P.E., and Ronald, P.C.(2008). OsWRKY62is a negative regulator of basal and Xa21-mediated defense againstXanthomonas oryzae pv. oryzae in rice. Molecular plant1,446-458.
139. Price, M.B., Jelesko, J., and Okumoto, S.(2012). Glutamate receptor homologs in plants: functionsand evolutionary origins. Frontiers in plant science3,235.
140. Qiu, D., Xiao, J., Xie, W., Liu, H., Li, X., Xiong, L., and Wang, S.(2008). Rice gene networkinferred from expression profiling of plants overexpressing OsWRKY13, a positive regulator ofdisease resistance. Molecular plant1,538-551.
141. Razem, F.A., El-Kereamy, A., Abrams, S.R., and Hill, R.D.(2006). The RNA-binding protein FCAis an abscisic acid receptor. Nature439,290-294.
142. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., and Bartel, D.P.(2002). MicroRNAs inplants. Genes&development16,1616-1626.
143. Reyes, J.L., and Chua, N.H.(2007). ABA induction of miR159controls transcript levels of twoMYB factors during Arabidopsis seed germination. The Plant journal: for cell and molecularbiology49,592-606.
144. Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B., and Bartel, D.P.(2002).Prediction of plant microRNA targets. Cell110,513-520.
145. Robert, C., Bancal, M.O., and Lannou, C.(2004). Wheat leaf rust uredospore production on adultplants: Influence of leaf nitrogen content and Septoria tritici blotch. Phytopathology94,712-721.
146. Roberts, A., Pimentel, H., Trapnell, C., and Pachter, L.(2011). Identification of novel transcripts inannotated genomes using RNA-Seq. Bioinformatics27,2325-2329.
147. Roy Choudhury, S., Roy, S., Singh, S.K., and Sengupta, D.N.(2010). Molecular characterizationand differential expression of beta-1,3-glucanase during ripening in banana fruit in response toethylene, auxin, ABA, wounding, cold and light-dark cycles. Plant cell reports29,813-828.
148. Sadumpati, V., Kalambur, M., Vudem, D.R., Kirti, P.B., and Khareedu, V.R.(2013). Transgenicindica rice lines, expressing Brassica juncea Nonexpressor of pathogenesis-related genes1(BjNPR1), exhibit enhanced resistance to major pathogens. Journal of biotechnology166,114-121.
149. Sanabria, N.M., van Heerden, H., and Dubery, I.A.(2012). Molecular characterisation andregulation of a Nicotiana tabacum S-domain receptor-like kinase gene induced during an earlyrapid response to lipopolysaccharides. Gene501,39-48.
150. Schluter, U., Mascher, M., Colmsee, C., Scholz, U., Brautigam, A., Fahnenstich, H., andSonnewald, U.(2012). Maize source leaf adaptation to nitrogen deficiency affects not onlynitrogen and carbon metabolism but also control of phosphate homeostasis. Plant physiology160,1384-1406.
151. Schmittgen, T.D., and Livak, K.J.(2008). Analyzing real-time PCR data by the comparative C(T)method. Nature protocols3,1101-1108.
152. Schommer, C., Palatnik, J.F., Aggarwal, P., Chetelat, A., Cubas, P., Farmer, E.E., Nath, U., andWeigel, D.(2008). Control of jasmonate biosynthesis and senescence by miR319targets. PLoSbiology6, e230.
153. Sels, J., Mathys, J., De Coninck, B.M., Cammue, B.P., and De Bolle, M.F.(2008). Plantpathogenesis-related (PR) proteins: a focus on PR peptides. Plant physiology and biochemistry:PPB/Societe francaise de physiologie vegetale46,941-950.
154. Shirasu, K., Nakajima, H., Rajasekhar, V.K., Dixon, R.A., and Lamb, C.(1997). Salicylic acidpotentiates an agonist-dependent gain control that amplifies pathogen signals in the activation ofdefense mechanisms. The Plant cell9,261-270.
155. Shukla, L.I., Chinnusamy, V., and Sunkar, R.(2008). The role of microRNAs and otherendogenous small RNAs in plant stress responses. Biochimica et biophysica acta1779,743-748.
156. Snoeijers, S.S., Vossen, P., Goosen, T., Van den Broek, H.W., and De Wit, P.J.(1999). Transcriptionof the avirulence gene Avr9of the fungal tomato pathogen Cladosporium fulvum is regulated by aGATA-type transcription factor in Aspergillus nidulans. Molecular&general genetics: MGG261,653-659.
157. Snoeijers, S.S., Perez-Garcia, A., Joosten, M.H.A.J., and De Wit, P.J.G.M.(2000). The effect ofnitrogen on disease development and gene expression in bacterial and fungal plant pathogens. EurJ Plant Pathol106,493-506.
158. Son, G.H., Wan, J., Kim, H.J., Nguyen, X.C., Chung, W.S., Hong, J.C., and Stacey, G.(2012).Ethylene-responsive element-binding factor5, ERF5, is involved in chitin-induced innateimmunity response. Molecular plant-microbe interactions: MPMI25,48-60.
159. Song, W.Y., Wang, G.L., Chen, L.L., Kim, H.S., Pi, L.Y., Holsten, T., Gardner, J., Wang, B., Zhai,W.X., Zhu, L.H., Fauquet, C., and Ronald, P.(1995). A receptor kinase-like protein encoded by therice disease resistance gene, Xa21. Science270,1804-1806.
160. Stone, J.M., Liang, X., Nekl, E.R., and Stiers, J.J.(2005). Arabidopsis AtSPL14, a plant-specificSBP-domain transcription factor, participates in plant development and sensitivity to fumonisin B1.The Plant journal: for cell and molecular biology41,744-754.
161. Stutz, H.E., Ouixley, K.W.M., McMaster, L.D., and Reid, S.J.(2007). Co-regulation of thenitrogen-assimilatory gene cluster in Clostridium saccharobutylicum. Microbiol-Sgm153,3081-3090.
162. Sun, P., Tian, Q.Y., Zhao, M.G., Dai, X.Y., Huang, J.H., Li, L.H., and Zhang, W.H.(2007).Aluminum-induced ethylene production is associated with inhibition of root elongation in Lotusjaponicus L. Plant&cell physiology48,1229-1235.
163. Sun, X., Cao, Y., Yang, Z., Xu, C., Li, X., Wang, S., and Zhang, Q.(2004). Xa26, a gene conferringresistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein.The Plant journal: for cell and molecular biology37,517-527.
164. Sunkar, R., and Zhu, J.K.(2004). Novel and stress-regulated microRNAs and other small RNAsfrom Arabidopsis. The Plant cell16,2001-2019.
165. Sunkar, R., Li, Y.F., and Jagadeeswaran, G.(2012). Functions of microRNAs in plant stressresponses. Trends in plant science17,196-203.
166. Sunkar, R., Kapoor, A., and Zhu, J.K.(2006). Posttranscriptional induction of two Cu/Znsuperoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398andimportant for oxidative stress tolerance.(vol18, pg2051,2006). The Plant cell18,2415-2415.
167. Swain, S.M., and Singh, D.P.(2005). Tall tales from sly dwarves: novel functions of gibberellins inplant development. Trends in plant science10,123-129.
168. Swarup, R., Perry, P., Hagenbeek, D., Van Der Straeten, D., Beemster, G.T., Sandberg, G., Bhalerao,R., Ljung, K., and Bennett, M.J.(2007). Ethylene upregulates auxin biosynthesis in Arabidopsisseedlings to enhance inhibition of root cell elongation. The Plant cell19,2186-2196.
169. Takahara, K., Akashi, K., and Yokota, A.(2005). Purification and characterization of glutamateN-acetyltransferase involved in citrulline accumulation in wild watermelon. The FEBS journal272,5353-5364.
170. Tao, Y., Xie, Z., Chen, W., Glazebrook, J., Chang, H.S., Han, B., Zhu, T., Zou, G., and Katagiri, F.(2003). Quantitative nature of Arabidopsis responses during compatible and incompatibleinteractions with the bacterial pathogen Pseudomonas syringae. The Plant cell15,317-330.
171. Thimm, O., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Muller, L.A., Rhee,S.Y., and Stitt, M.(2004). MAPMAN: a user-driven tool to display genomics data sets ontodiagrams of metabolic pathways and other biological processes. The Plant journal: for cell andmolecular biology37,914-939.
172. Tilman, D., Cassman, K.G., Matson, P.A., Naylor, R., and Polasky, S.(2002). Agriculturalsustainability and intensive production practices. Nature418,671-677.
173. Trapnell, C., Pachter, L., and Salzberg, S.L.(2009). TopHat: discovering splice junctions withRNA-Seq. Bioinformatics25,1105-1111.
174. Tsay, Y.F., Chiu, C.C., Tsai, C.B., Ho, C.H., and Hsu, P.K.(2007). Nitrate transporters and peptidetransporters. FEBS letters581,2290-2300.
175. Tsuda, K., Sato, M., Glazebrook, J., Cohen, J.D., and Katagiri, F.(2008). Interplay betweenMAMP-triggered and SA-mediated defense responses. The Plant journal: for cell and molecularbiology53,763-775.
176. Ueguchi-Tanaka, M., Ashikari, M., Nakajima, M., Itoh, H., Katoh, E., Kobayashi, M., Chow, T.Y.,Hsing, Y.I., Kitano, H., Yamaguchi, I., and Matsuoka, M.(2005). GIBBERELLIN INSENSITIVEDWARF1encodes a soluble receptor for gibberellin. Nature437,693-698.
177. Van den Ackerveken, G.F., Dunn, R.M., Cozijnsen, A.J., Vossen, J.P., Van den Broek, H.W., and DeWit, P.J.(1994). Nitrogen limitation induces expression of the avirulence gene avr9in the tomatopathogen Cladosporium fulvum. Molecular&general genetics: MGG243,277-285.
178. Vidal, E.A., Araus, V., Lu, C., Parry, G., Green, P.J., Coruzzi, G.M., and Gutierrez, R.A.(2010).Nitrate-responsive miR393/AFB3regulatory module controls root system architecture inArabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States ofAmerica107,4477-4482.
179. Vijayan, P., Shockey, J., Levesque, C.A., Cook, R.J., and Browse, J.(1998). A role for jasmonate inpathogen defense of Arabidopsis. Proceedings of the National Academy of Sciences of the UnitedStates of America95,7209-7214.
180. Voinnet, O.(2003). RNA silencing bridging the gaps in wheat extracts. Trends in plant science8,307-309.
181. Vriezen, W.H., Hulzink, R., Mariani, C., and Voesenek, L.A.(1999).1-aminocyclopropane-1-carboxylate oxidase activity limits ethylene biosynthesis in Rumexpalustris during submergence. Plant physiology121,189-196.
182. Wang, K.L., Li, H., and Ecker, J.R.(2002). Ethylene biosynthesis and signaling networks. ThePlant cell14Suppl, S131-151.
183. Wang, R., Okamoto, M., Xing, X., and Crawford, N.M.(2003). Microarray analysis of the nitrateresponse in Arabidopsis roots and shoots reveals over1,000rapidly responding genes and newlinkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism. Plant physiology132,556-567.
184. Wang, R., Tischner, R., Gutierrez, R.A., Hoffman, M., Xing, X., Chen, M., Coruzzi, G., andCrawford, N.M.(2004a). Genomic analysis of the nitrate response using a nitrate reductase-nullmutant of Arabidopsis. Plant physiology136,2512-2522.
185. Wang, W.C., Lin, F.M., Chang, W.C., Lin, K.Y., Huang, H.D., and Lin, N.S.(2009). miRExpress:analyzing high-throughput sequencing data for profiling microRNA expression. BMCbioinformatics10,328.
186. Wang, X.J., Reyes, J.L., Chua, N.H., and Gaasterland, T.(2004b). Prediction and identification ofArabidopsis thaliana microRNAs and their mRNA targets. Genome biology5, R65.
187. Wei, L.Y., Zhang, D.F., Xiang, F., and Zhang, Z.X.(2009). Differentially expressed miRNAspotentially involved in the regulation of defense mechanism to drought stress in maize seedings.International journal of plant sciences170,979-989.
188. Wu, X., Shiroto, Y., Kishitani, S., Ito, Y., and Toriyama, K.(2009). Enhanced heat and droughttolerance in transgenic rice seedlings overexpressing OsWRKY11under the control of HSP101promoter. Plant cell reports28,21-30.
189. Xie, D.X., Feys, B.F., James, S., Nieto-Rostro, M., and Turner, J.G.(1998). COI1: an Arabidopsisgene required for jasmonate-regulated defense and fertility. Science280,1091-1094.
190. Xu, J., Duan, X., Yang, J., Beeching, J.R., and Zhang, P.(2013). Enhanced reactive oxygen speciesscavenging by overproduction of superoxide dismutase and catalase delays postharvestphysiological deterioration of cassava storage roots. Plant physiology161,1517-1528.
191. Xu, X., Zhou, Y., Wei, S., Ren, D., Yang, M., Bu, H., Kang, M., Wang, J., and Feng, J.(2009).Molecular cloning and expression of a Cu/Zn-Containing superoxide dismutase from Thellungiellahalophila. Molecules and cells27,423-428.
192. Xu, Z., Zhong, S., Li, X., Li, W., Rothstein, S.J., Zhang, S., Bi, Y., and Xie, C.(2011).Genome-wide identification of microRNAs in response to low nitrate availability in maize leavesand roots. PloS one6, e28009.
193. Yang, B., Sugio, A., and White, F.F.(2006). Os8N3is a host disease-susceptibility gene forbacterial blight of rice. Proceedings of the National Academy of Sciences of the United States ofAmerica103,10503-10508.
194. Yoshimura, S., Umehara, Y., Kurata, N., Nagamura, Y., Sasaki, T., Minobe, Y., and Iwata, N.(1996). Identification of a YAC clone carrying the Xa-1allele, a bacterial blight resistance gene inrice. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik93,117-122.
195. Yoshimura, S., Yamanouchi, U., Katayose, Y., Toki, S., Wang, Z.X., Kono, I., Kurata, N., Yano, M.,Iwata, N., and Sasaki, T.(1998). Expression of Xa1, a bacterial blight-resistance gene in rice, isinduced by bacterial inoculation. Proceedings of the National Academy of Sciences of the UnitedStates of America95,1663-1668.
196. Yu, S., Ligang, C., Liping, Z., and Diqiu, Y.(2010). Overexpression of OsWRKY72geneinterferes in the abscisic acid signal and auxin transport pathway of Arabidopsis. Journal ofbiosciences35,459-471.
197. Zeng, Y., Yi, R., and Cullen, B.R.(2003). MicroRNAs and small interfering RNAs can inhibitmRNA expression by similar mechanisms. Proceedings of the National Academy of Sciences ofthe United States of America100,9779-9784.
198. Zhai, Y., Wang, Y., Li, Y., Lei, T., Yan, F., Su, L., Li, X., Zhao, Y., Sun, X., Li, J., and Wang, Q.(2013). Isolation and molecular characterization of GmERF7, a soybean ethylene-response factorthat increases salt stress tolerance in tobacco. Gene513,174-183.
199. Zhang, B., Xie, D., and Jin, Z.(2012a). Global analysis of non-coding small RNAs in Arabidopsisin response to jasmonate treatment by deep sequencing technology. Journal of integrative plantbiology54,73-86.
200. Zhang, H., Ni, L., Liu, Y., Wang, Y., Zhang, A., Tan, M., and Jiang, M.(2012b). The C2H2-typezinc finger protein ZFP182is involved in abscisic acid-induced antioxidant defense in rice. Journalof integrative plant biology54,500-510.
201. Zhang, J., and Zhou, J.M.(2010). Plant immunity triggered by microbial molecular signatures.Molecular plant3,783-793.
202. Zhang, J.F., Yuan, L.J., Shao, Y., Du, W., Yan, D.W., and Lu, Y.T.(2008). The disturbance of smallRNA pathways enhanced abscisic acid response and multiple stress responses in Arabidopsis. Plant,cell&environment31,562-574.
203. Zhang, Y., Cheng, Y.T., Bi, D., Palma, K., and Li, X.(2005). MOS2, a protein containing G-patchand KOW motifs, is essential for innate immunity in Arabidopsis thaliana. Current biology: CB15,1936-1942.
204. Zhao, B., Liang, R., Ge, L., Li, W., Xiao, H., Lin, H., Ruan, K., and Jin, Y.(2007). Identification ofdrought-induced microRNAs in rice. Biochemical and biophysical research communications354,585-590.
205. Zhao, J., Davis, L.C., and Verpoorte, R.(2005). Elicitor signal transduction leading to productionof plant secondary metabolites. Biotechnology advances23,283-333.
206. Zhou, G.A., Chang, R.Z., and Qiu, L.J.(2010a). Overexpression of soybean ubiquitin-conjugatingenzyme gene GmUBC2confers enhanced drought and salt tolerance through modulating abioticstress-responsive gene expression in Arabidopsis. Plant molecular biology72,357-367.
207. Zhou, L., Liu, Y., Liu, Z., Kong, D., Duan, M., and Luo, L.(2010b). Genome-wide identificationand analysis of drought-responsive microRNAs in Oryza sativa. Journal of experimental botany61,4157-4168.
208. Zhou, X., Wang, G., and Zhang, W.(2007). UV-B responsive microRNA genes in Arabidopsisthaliana. Molecular systems biology3,103.
209. Zuo, J., Zhu, B., Fu, D., Zhu, Y., Ma, Y., Chi, L., Ju, Z., Wang, Y., Zhai, B., and Luo, Y.(2012).Sculpting the maturation, softening and ethylene pathway: the influences of microRNAs on tomatofruits. BMC genomics13,7.
2.戴玉池，邓霞玲，姜孝成，陈良碧，不同水稻品种幼苗期耐寒生理鉴定及其利用.湖南师范大学自然科学学报，2004，27（3）：86-89.
3.方中达，刘经芬，水稻抗病性的研究I.水稻在不同施肥和土壤条件下对白叶枯病抗病性的变化.植物保护学报，1962,1（3）：231-236.
4.高必达，郭海明，黎用朝，陈贸，施氮对水稻抗白叶枯病反应的影响.湖南农学院学报，1992,18（2）：293-298.
5.郭培国，李荣华，夜间高温胁迫对水稻叶片光合机构的影响.植物学报，2000,47（2）：673-678.
6.候夫云，张立明，王庆美，李爱贤，张海燕，董顺旭，植物耐非生物胁迫的分子机制.分子植物育种，2007,5（6）：80-84.
7.曲雪萍，贺道耀，余叔文，水稻中p5cs基因的存在及其在高脯氨酸变异系中的作用.植物病理学报，1998,24（1）：49-54.
8.郑少玲，严小龙，盐胁迫下不同水稻基因型根内Na+和Cl-分布情况比较.华南农业大学学报，1996,17（4）：24-28.
9.宗会，徐照丽，刘娥娥，低温胁迫下氯丙嗪和氯化镧对水稻幼苗脯氨酸积累的影响.热带亚热带植物学报，2003,11（3）：241-244.
10. Abdel-Lateif, K., Vaissayre, V., Gherbi, H., Verries, C., Meudec, E., Perrine-Walker, F., Cheynier,V., Svistoonoff, S., Franche, C., Bogusz, D., and Hocher, V.(2013). Silencing of the chalconesynthase gene in Casuarina glauca highlights the important role of flavonoids during nodulation.The New phytologist199,1012-1021.
11. Abrahante, J.E., Daul, A.L., Li, M., Volk, M.L., Tennessen, J.M., Miller, E.A., and Rougvie, A.E.(2003). The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1controls developmental timeand is regulated by microRNAs. Developmental cell4,625-637.
12. Achard, P., Herr, A., Baulcombe, D.C., and Harberd, N.P.(2004). Modulation of floraldevelopment by a gibberellin-regulated microRNA. Development131,3357-3365.
13. Aida, M., Ishida, T., Fukaki, H., Fujisawa, H., and Tasaka, M.(1997). Genes involved in organseparation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. The Plant cell9,841-857.
14. Anders, S., and Huber, W.(2010). Differential expression analysis for sequence count data.Genome biology11, R106.
15. Antony, G., Zhou, J., Huang, S., Li, T., Liu, B., White, F., and Yang, B.(2010). Rice xa13recessiveresistance to bacterial blight is defeated by induction of the disease susceptibility gene Os-11N3.The Plant cell22,3864-3876.
16. Aravind, L., and Koonin, E.V.(1999). G-patch: a new conserved domain in eukaryoticRNA-processing proteins and type D retroviral polyproteins. Trends in biochemical sciences24,342-344.
17. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski,K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S.,Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., and Sherlock, G.(2000). Geneontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics25,25-29.
18. Aukerman, M.J., and Sakai, H.(2003). Regulation of flowering time and floral organ identity by aMicroRNA and its APETALA2-like target genes. The Plant cell15,2730-2741.
19. Baker, C.C., Sieber, P., Wellmer, F., and Meyerowitz, E.M.(2005). The early extra petals1mutantuncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Currentbiology: CB15,303-315.
20. Bartel, D.P.(2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell116,281-297.
21. Bernoux, M., Ellis, J.G., and Dodds, P.N.(2011). New insights in plant immunity signalingactivation. Current opinion in plant biology14,512-518.
22. Bi, Y.M., Wang, R.L., Zhu, T., and Rothstein, S.J.(2007). Global transcription profiling revealsdifferential responses to chronic nitrogen stress and putative nitrogen regulatory components inArabidopsis. BMC genomics8,281.
23. Blair, M.W., Garris, A.J., Iyer, A.S., Chapman, B., Kresovich, S., and McCouch, S.R.(2003). Highresolution genetic mapping and candidate gene identification at the xa5locus for bacterial blightresistance in rice (Oryza sativa L.). TAG. Theoretical and applied genetics. Theoretische undangewandte Genetik107,62-73.
24. Boller, T., and Felix, G.(2009). A renaissance of elicitors: perception of microbe-associatedmolecular patterns and danger signals by pattern-recognition receptors. Annual review of plantbiology60,379-406.
25. Brauer, E.K., Rochon, A., Bi, Y.M., Bozzo, G.G., Rothstein, S.J., and Shelp, B.J.(2011).Reappraisal of nitrogen use efficiency in rice overexpressing glutamine synthetase1. Physiologiaplantarum141,361-372.
26. Cai, H., Zhou, Y., Xiao, J., Li, X., Zhang, Q., and Lian, X.(2009). Overexpressed glutaminesynthetase gene modifies nitrogen metabolism and abiotic stress responses in rice. Plant cellreports28,527-537.
27. Cappellazzo, G., Lanfranco, L., and Bonfante, P.(2007). A limiting source of organic nitrogeninduces specific transcriptional responses in the extraradical structures of the endomycorrhizalfungus Glomus intraradices. Current genetics51,59-70.
28. Carballo, S.J., Blankenship, S.M., and Sanders, D.C.(1994). Drip fertigation with nitrogen andpotassium and postharvest susceptibility to bacterial soft rot of bell peppers. J. Plant Nutr.17,1175-1191.
29. Cercos, M., Gomez-Cadenas, A., and Ho, T.H.(1999). Hormonal regulation of a cysteineproteinase gene, EPB-1, in barley aleurone layers: cis-and trans-acting elements involved in theco-ordinated gene expression regulated by gibberellins and abscisic acid. The Plant journal: forcell and molecular biology19,107-118.
30. Chakravarthy, S., Velasquez, A.C., and Martin, G.B.(2009). Assay for pathogen-associatedmolecular pattern (PAMP)-triggered immunity (PTI) in plants. Journal of visualized experiments:JoVE.
31. Chellappan, P., Vanitharani, R., and Fauquet, C.M.(2005). MicroRNA-binding viral proteininterferes with Arabidopsis development. Proceedings of the National Academy of Sciences of theUnited States of America102,10381-10386.
32. Chen, C., Ridzon, D.A., Broomer, A.J., Zhou, Z., Lee, D.H., Nguyen, J.T., Barbisin, M., Xu, N.L.,Mahuvakar, V.R., Andersen, M.R., Lao, K.Q., Livak, K.J., and Guegler, K.J.(2005). Real-timequantification of microRNAs by stem-loop RT-PCR. Nucleic acids research33, e179.
33. Chen, L., Wang, T., Zhao, M., and Zhang, W.(2012). Ethylene-responsive miRNAs in roots ofMedicago truncatula identified by high-throughput sequencing at whole genome level. Plantscience: an international journal of experimental plant biology184,14-19.
34. Chen, X.(2004). A microRNA as a translational repressor of APETALA2in Arabidopsis flowerdevelopment. Science303,2022-2025.
35. Chen, X.(2005). MicroRNA biogenesis and function in plants. FEBS letters579,5923-5931.
36. Chen, X., Chern, M., Canlas, P.E., Ruan, D., Jiang, C., and Ronald, P.C.(2010). An ATPasepromotes autophosphorylation of the pattern recognition receptor XA21and inhibitsXA21-mediated immunity. Proceedings of the National Academy of Sciences of the United Statesof America107,8029-8034.
37. Chiou, T.J.(2007). The role of microRNAs in sensing nutrient stress. Plant, cell&environment30,323-332.
38. Chisholm, S.T., Coaker, G., Day, B., and Staskawicz, B.J.(2006). Host-microbe interactions:shaping the evolution of the plant immune response. Cell124,803-814.
39. Chu, Z., Fu, B., Yang, H., Xu, C., Li, Z., Sanchez, A., Park, Y.J., Bennetzen, J.L., Zhang, Q., andWang, S.(2006). Targeting xa13, a recessive gene for bacterial blight resistance in rice. TAG.Theoretical and applied genetics. Theoretische und angewandte Genetik112,455-461.
40. Chujo, T., Miyamoto, K., Shimogawa, T., Shimizu, T., Otake, Y., Yokotani, N., Nishizawa, Y.,Shibuya, N., Nojiri, H., Yamane, H., Minami, E., and Okada, K.(2013). OsWRKY28, aPAMP-responsive transrepressor, negatively regulates innate immune responses in rice against riceblast fungus. Plant molecular biology82,23-37.
41. Crawford, N.M., and Forde, B.G.(2002). Molecular and developmental biology of inorganicnitrogen nutrition. The Arabidopsis book/American Society of Plant Biologists1, e0011.
42. Cui, F., Liu, L., Zhao, Q., Zhang, Z., Li, Q., Lin, B., Wu, Y., Tang, S., and Xie, Q.(2012).Arabidopsis ubiquitin conjugase UBC32is an ERAD component that functions inbrassinosteroid-mediated salt stress tolerance. The Plant cell24,233-244.
43. De Vleesschauwer, D., Gheysen, G., and Hofte, M.(2013). Hormone defense networking in rice:tales from a different world. Trends in plant science18,555-565.
44. Denance, N., Sanchez-Vallet, A., Goffner, D., and Molina, A.(2013). Disease resistance or growth:the role of plant hormones in balancing immune responses and fitness costs. Frontiers in plantscience4,155.
45. Dharmasiri, N., Dharmasiri, S., and Estelle, M.(2005). The F-box protein TIR1is an auxinreceptor. Nature435,441-445.
46. Dietrich, R., Ploss, K., and Heil, M.(2004). Constitutive and induced resistance to pathogens inArabidopsis thaliana depends on nitrogen supply. Plant Cell and Environment27,896-906.
47. Dietrich, R., Ploss, K., and Heil, M.(2005). Growth responses and fitness costs after induction ofpathogen resistance depend on environmental conditions. Plant Cell and Environment28,211-222.
48. Doench, J.G., Petersen, C.P., and Sharp, P.A.(2003). siRNAs can function as miRNAs. Genes&development17,438-442.
49. Elbashir, S.M., Lendeckel, W., and Tuschl, T.(2001). RNA interference is mediated by21-and22-nucleotide RNAs. Genes&development15,188-200.
50. Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C., and Marks, D.S.(2003). MicroRNA targetsin Drosophila. Genome biology5, R1.
51. Fitzgerald, H.A., Canlas, P.E., Chern, M.S., and Ronald, P.C.(2005). Alteration of TGA factoractivity in rice results in enhanced tolerance to Xanthomonas oryzae pv. oryzae. The Plant journal:for cell and molecular biology43,335-347.
52. Furihata, T., Maruyama, K., Fujita, Y., Umezawa, T., Yoshida, R., Shinozaki, K., andYamaguchi-Shinozaki, K.(2006). Abscisic acid-dependent multisite phosphorylation regulates theactivity of a transcription activator AREB1. Proceedings of the National Academy of Sciences ofthe United States of America103,1988-1993.
53. Gaffney, T., Friedrich, L., Vernooij, B., Negrotto, D., Nye, G., Uknes, S., Ward, E., Kessmann, H.,and Ryals, J.(1993). Requirement of salicylic Acid for the induction of systemic acquiredresistance. Science261,754-756.
54. Gifford, M.L., Dean, A., Gutierrez, R.A., Coruzzi, G.M., and Birnbaum, K.D.(2008). Cell-specificnitrogen responses mediate developmental plasticity. Proceedings of the National Academy ofSciences of the United States of America105,803-808.
55. Glazinska, P., Zienkiewicz, A., Wojciechowski, W., and Kopcewicz, J.(2009). The putativemiR172target gene InAPETALA2-like is involved in the photoperiodic flower induction ofIpomoea nil. Journal of plant physiology166,1801-1813.
56. Gray, W.M.(2004). Hormonal regulation of plant growth and development. PLoS biology2, E311.
57. Griffiths-Jones, S., Saini, H.K., van Dongen, S., and Enright, A.J.(2008). miRBase: tools formicroRNA genomics. Nucleic acids research36, D154-158.
58. Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A., and Enright, A.J.(2006). miRBase:microRNA sequences, targets and gene nomenclature. Nucleic acids research34, D140-144.
59. Gu, K., Tian, D., Yang, F., Wu, L., Sreekala, C., Wang, D., Wang, G.L., and Yin, Z.(2004).High-resolution genetic mapping of Xa27(t), a new bacterial blight resistance gene in rice, Oryzasativa L. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik108,800-807.
60. Gu, K., Yang, B., Tian, D., Wu, L., Wang, D., Sreekala, C., Yang, F., Chu, Z., Wang, G.L., White,F.F., and Yin, Z.(2005). R gene expression induced by a type-III effector triggers disease resistancein rice. Nature435,1122-1125.
61. Gubler, F., Kalla, R., Roberts, J.K., and Jacobsen, J.V.(1995). Gibberellin-regulated expression ofa myb gene in barley aleurone cells: evidence for Myb transactivation of a high-pI alpha-amylasegene promoter. The Plant cell7,1879-1891.
62. Gubler, F., Raventos, D., Keys, M., Watts, R., Mundy, J., and Jacobsen, J.V.(1999). Target genesand regulatory domains of the GAMYB transcriptional activator in cereal aleurone. The Plantjournal: for cell and molecular biology17,1-9.
63. Guo, H.S., Xie, Q., Fei, J.F., and Chua, N.H.(2005). MicroRNA directs mRNA cleavage of thetranscription factor NAC1to downregulate auxin signals for Arabidopsis lateral root development.The Plant cell17,1376-1386.
64. Guo, J.H., Liu, X.J., Zhang, Y., Shen, J.L., Han, W.X., Zhang, W.F., Christie, P., Goulding, K.W.,Vitousek, P.M., and Zhang, F.S.(2010). Significant acidification in major Chinese croplands.Science327,1008-1010.
65. Gutierrez, R.A., Lejay, L.V., Dean, A., Chiaromonte, F., Shasha, D.E., and Coruzzi, G.M.(2007).Qualitative network models and genome-wide expression data define carbon/nitrogen-responsivemolecular machines in Arabidopsis. Genome biology8, R7.
66. Hoffland, E., Van Beusichem, M.L., and Jeger, M.G.(1999). Nitrogen availability andsusceptibility of tomato leaves to Botrytis cinerea. Plant and Soil210,263-272.
67. Hoffland, E., Jeger, M.G., and Van Beusichem, M.L.(2000). Effect of nitrogen supply rate ondisease resistance in tomato depends on the pathogen. Plant and Soil218,239-247.
68. Hu, H., You, J., Fang, Y., Zhu, X., Qi, Z., and Xiong, L.(2008). Characterization of transcriptionfactor gene SNAC2conferring cold and salt tolerance in rice. Plant molecular biology67,169-181.
69. Hu, H., Dai, M., Yao, J., Xiao, B., Li, X., Zhang, Q., and Xiong, L.(2006). Overexpressing a NAM,ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice.Proceedings of the National Academy of Sciences of the United States of America103,12987-12992.
70. Hua, C., Linling, L., Feng, X., Yan, W., Honghui, Y., Conghua, W., Shaobing, W., Zhiqin, L., Juan,H., Yuping, W., Shuiyuan, C., and Fuliang, C.(2013). Expression patterns of an isoflavonereductase-like gene and its possible roles in secondary metabolism in Ginkgo biloba. Plant cellreports32,637-650.
71. Hutvagner, G., and Zamore, P.D.(2002). A microRNA in a multiple-turnover RNAi enzymecomplex. Science297,2056-2060.
72. Iyer, A.S., and McCouch, S.R.(2004). The rice bacterial blight resistance gene xa5encodes a novelform of disease resistance. Molecular plant-microbe interactions: MPMI17,1348-1354.
73. Jagadeeswaran, G., Saini, A., and Sunkar, R.(2009). Biotic and abiotic stress down-regulatemiR398expression in Arabidopsis. Planta229,1009-1014.
74. Jiang, G.H., Xia, Z.H., Zhou, Y.L., Wan, J., Li, D.Y., Chen, R.S., Zhai, W.X., and Zhu, L.H.(2006).Testifying the rice bacterial blight resistance gene xa5by genetic complementation and furtheranalyzing xa5(Xa5) in comparison with its homolog TFIIAgamma1. Molecular genetics andgenomics: MGG275,354-366.
75. Jones, J.D., and Dangl, J.L.(2006). The plant immune system. Nature444,323-329.
76. Ju, X.T., Xing, G.X., Chen, X.P., Zhang, S.L., Zhang, L.J., Liu, X.J., Cui, Z.L., Yin, B., Christie, P.,Zhu, Z.L., and Zhang, F.S.(2009). Reducing environmental risk by improving N management inintensive Chinese agricultural systems. Proceedings of the National Academy of Sciences of theUnited States of America106,3041-3046.
77. Juarez, M.T., Kui, J.S., Thomas, J., Heller, B.A., and Timmermans, M.C.(2004).microRNA-mediated repression of rolled leaf1specifies maize leaf polarity. Nature428,84-88.
78. Kalamaki, M.S., Alexandrou, D., Lazari, D., Merkouropoulos, G., Fotopoulos, V., Pateraki, I.,Aggelis, A., Carrillo-Lopez, A., Rubio-Cabetas, M.J., and Kanellis, A.K.(2009). Over-expressionof a tomato N-acetyl-L-glutamate synthase gene (SlNAGS1) in Arabidopsis thaliana results inhigh ornithine levels and increased tolerance in salt and drought stresses. Journal of experimentalbotany60,1859-1871.
79. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima,S., Okuda, S., Tokimatsu, T., and Yamanishi, Y.(2008). KEGG for linking genomes to life and theenvironment. Nucleic acids research36, D480-484.
80. Kang, S., Kim, H.B., Lee, H., Choi, J.Y., Heu, S., Oh, C.J., Kwon, S.I., and An, C.S.(2006).Overexpression in Arabidopsis of a plasma membrane-targeting glutamate receptor from smallradish increases glutamate-mediated Ca2+influx and delays fungal infection. Molecules and cells21,418-427.
81. Kasschau, K.D., Xie, Z., Allen, E., Llave, C., Chapman, E.J., Krizan, K.A., and Carrington, J.C.(2003). P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis developmentand miRNA unction. Developmental cell4,205-217.
82. Katiyar-Agarwal, S., and Jin, H.(2010). Role of small RNAs in host-microbe interactions. Annualreview of phytopathology48,225-246.
83. Katsantonis, D., Koutroubas, S.D., Ntanos, D.A., and Lupotto, E.(2008). Effect of blast disease onnitrogen accumulation and remobilization to rice grain. J Plant Pathol90,263-272.
84. Kemmerling, B., Halter, T., Mazzotta, S., Mosher, S., and Nurnberger, T.(2011). A genome-widesurvey for Arabidopsis leucine-rich repeat receptor kinases implicated in plant immunity. Frontiersin plant science2,88.
85. Khraiwesh, B., Zhu, J.K., and Zhu, J.(2012). Role of miRNAs and siRNAs in biotic and abioticstress responses of plants. Biochimica et biophysica acta1819,137-148.
86. Kim, S.T., Cho, K.S., Kim, S.G., Kang, S.Y., and Kang, K.Y.(2003). A rice isoflavonereductase-like gene, OsIRL, is induced by rice blast fungal elicitor. Molecules and cells16,224-231.
87. Komatsu, S., and Konishi, H.(2005). Proteome analysis of rice root proteins regulated bygibberellin. Genomics, proteomics&bioinformatics/Beijing Genomics Institute3,132-142.
88. Kozomara, A., and Griffiths-Jones, S.(2011). miRBase: integrating microRNA annotation anddeep-sequencing data. Nucleic acids research39, D152-157.
89. Lai, Y., Dang, F., Lin, J., Yu, L., Shi, Y., Xiao, Y., Huang, M., Chen, C., Qi, A., Liu, Z., Guan, D.,Mou, S., Qiu, A., and He, S.(2013). Overexpression of a Chinese cabbage BrERF11transcriptionfactor enhances disease resistance to Ralstonia solanacearum in tobacco. Plant physiology andbiochemistry: PPB/Societe francaise de physiologie vegetale62,70-78.
90. Lan, A., Huang, J., Zhao, W., Peng, Y., Chen, Z., and Kang, D.(2013). A salicylic acid-induced rice(Oryza sativa L.) transcription factor OsWRKY77is involved in disease resistance of Arabidopsisthaliana. Plant Biol (Stuttg)15,452-461.
91. Laufs, P., Peaucelle, A., Morin, H., and Traas, J.(2004). MicroRNA regulation of the CUC genes isrequired for boundary size control in Arabidopsis meristems. Development131,4311-4322.
92. Lee, R.C., Feinbaum, R.L., and Ambros, V.(1993). The C. elegans heterochronic gene lin-4encodes small RNAs with antisense complementarity to lin-14. Cell75,843-854.
93. Leung, J., and Giraudat, J.(1998). Abscisic Acid Signal Transduction. Annual review of plantphysiology and plant molecular biology49,199-222.
94. Lewis, B.P., Burge, C.B., and Bartel, D.P.(2005). Conserved seed pairing, often flanked byadenosines, indicates that thousands of human genes are microRNA targets. Cell120,15-20.
95. Li, W.X., Oono, Y., Zhu, J., He, X.J., Wu, J.M., Iida, K., Lu, X.Y., Cui, X., Jin, H., and Zhu, J.K.(2008). The Arabidopsis NFYA5transcription factor is regulated transcriptionally andposttranscriptionally to promote drought resistance. The Plant cell20,2238-2251.
96. Li, X., Lin, H., Zhang, W., Zou, Y., Zhang, J., Tang, X., and Zhou, J.M.(2005). Flagellin inducesinnate immunity in nonhost interactions that is suppressed by Pseudomonas syringae effectors.Proceedings of the National Academy of Sciences of the United States of America102,12990-12995.
97. Li, Y., Zhang, Q., Zhang, J., Wu, L., Qi, Y., and Zhou, J.M.(2010a). Identification of microRNAsinvolved in pathogen-associated molecular pattern-triggered plant innate immunity. Plantphysiology152,2222-2231.
98. Li, Y.F., Zheng, Y., Addo-Quaye, C., Zhang, L., Saini, A., Jagadeeswaran, G., Axtell, M.J., Zhang,W., and Sunkar, R.(2010b). Transcriptome-wide identification of microRNA targets in rice. ThePlant journal: for cell and molecular biology62,742-759.
99. Liang, G., He, H., and Yu, D.(2012). Identification of nitrogen starvation-responsive microRNAsin Arabidopsis thaliana. PloS one7, e48951.
100. Liu, B., Xue, X., Cui, S., Zhang, X., Han, Q., Zhu, L., Liang, X., Wang, X., Huang, L., Chen, X.,and Kang, Z.(2010). Cloning and characterization of a wheat beta-1,3-glucanase gene induced bythe stripe rust pathogen Puccinia striiformis f. sp. tritici. Molecular biology reports37,1045-1052.
101. Liu, H.H., Tian, X., Li, Y.J., Wu, C.A., and Zheng, C.C.(2008). Microarray-based analysis ofstress-regulated microRNAs in Arabidopsis thaliana. RNA14,836-843.
102. Liu, J.X., and Howell, S.H.(2010). bZIP28and NF-Y transcription factors are activated by ERstress and assemble into a transcriptional complex to regulate stress response genes in Arabidopsis.The Plant cell22,782-796.
103. Liu, Q., Yuan, M., Zhou, Y., Li, X., Xiao, J., and Wang, S.(2011). A paralog of the MtN3/salivafamily recessively confers race-specific resistance to Xanthomonas oryzae in rice. Plant, cell&environment34,1958-1969.
104. Liu, Q., Zhang, Y.C., Wang, C.Y., Luo, Y.C., Huang, Q.J., Chen, S.Y., Zhou, H., Qu, L.H., andChen, Y.Q.(2009). Expression analysis of phytohormone-regulated microRNAs in rice, implyingtheir regulation roles in plant hormone signaling. FEBS letters583,723-728.
105. Liu, X., Bai, X., Wang, X., and Chu, C.(2007). OsWRKY71, a rice transcription factor, is involvedin rice defense response. Journal of plant physiology164,969-979.
106. Llave, C., Xie, Z., Kasschau, K.D., and Carrington, J.C.(2002). Cleavage of Scarecrow-likemRNA targets directed by a class of Arabidopsis miRNA. Science297,2053-2056.
107. Llave, C.(2004). MicroRNAs: more than a role in plant development? Molecular plant pathology5,361-366.
108. Long, D.H., Lee, F.N., and Tebeest, D.O.(2000). Effect of nitrogen fertilization on diseaseprogress of rice blast on susceptible and resistant cultivars. Plant disease84,403-409.
109. Lu, C., and Fedoroff, N.(2000). A mutation in the Arabidopsis HYL1gene encoding a dsRNAbinding protein affects responses to abscisic acid, auxin, and cytokinin. The Plant cell12,2351-2366.
110. Lu, Y., Luo, F., Yang, M., Li, X., and Lian, X.(2011). Suppression of glutamate synthase genessignificantly affects carbon and nitrogen metabolism in rice (Oryza sativa L.). Science China. Lifesciences54,651-663.
111. Mackowiak, S.D.(2011). Identification of novel and known miRNAs in deep-sequencing data withmiRDeep2. Current protocols in bioinformatics/editoral board, Andreas D. Baxevanis...[et al.]Chapter12, Unit1210.
112. Mallory, A.C., and Vaucheret, H.(2006). Functions of microRNAs and related small RNAs inplants. Nature genetics38Suppl, S31-36.
113. Mallory, A.C., Bartel, D.P., and Bartel, B.(2005). MicroRNA-directed regulation of ArabidopsisAUXIN RESPONSE FACTOR17is essential for proper development and modulates expression ofearly auxin response genes. The Plant cell17,1360-1375.
114. Mallory, A.C., Dugas, D.V., Bartel, D.P., and Bartel, B.(2004). MicroRNA regulation ofNAC-domain targets is required for proper formation and separation of adjacent embryonic,vegetative, and floral organs. Current biology: CB14,1035-1046.
115. Megraw, M., Baev, V., Rusinov, V., Jensen, S.T., Kalantidis, K., and Hatzigeorgiou, A.G.(2006).MicroRNA promoter element discovery in Arabidopsis. RNA12,1612-1619.
116. Millar, A.A., and Gubler, F.(2005). The Arabidopsis GAMYB-like genes, MYB33and MYB65,are microRNA-regulated genes that redundantly facilitate anther development. The Plant cell17,705-721.
117. Millar, A.A., and Waterhouse, P.M.(2005). Plant and animal microRNAs: similarities anddifferences. Functional&integrative genomics5,129-135.
118. Miller, A.J., Fan, X., Orsel, M., Smith, S.J., and Wells, D.M.(2007). Nitrate transport andsignalling. Journal of experimental botany58,2297-2306.
119. Moscou, M.J., and Bogdanove, A.J.(2009). A simple cipher governs DNA recognition by TALeffectors. Science326,1501.
120. Mugford, S.T., Qi, X., Bakht, S., Hill, L., Wegel, E., Hughes, R.K., Papadopoulou, K., Melton, R.,Philo, M., Sainsbury, F., Lomonossoff, G.P., Roy, A.D., Goss, R.J., and Osbourn, A.(2009). Aserine carboxypeptidase-like acyltransferase is required for synthesis of antimicrobial compoundsand disease resistance in oats. The Plant cell21,2473-2484.
121. Mukherjee, A.K., Mohapatra, N.K., Rao, A.V.S., and Nayak, P.(2005). Effect of nitrogenfertilization on the expression of slow-blasting resistance in rice. J Agr Sci143,385-393.
122. Mukhopadhyay, A., Vij, S., and Tyagi, A.K.(2004). Overexpression of a zinc-finger protein genefrom rice confers tolerance to cold, dehydration, and salt stress in transgenic tobacco. Proceedingsof the National Academy of Sciences of the United States of America101,6309-6314.
123. Nakai, Y., Nakahira, Y., Sumida, H., Takebayashi, K., Nagasawa, Y., Yamasaki, K., Akiyama, M.,Ohme-Takagi, M., Fujiwara, S., Shiina, T., Mitsuda, N., Fukusaki, E., Kubo, Y., and Sato, M.H.(2013). Vascular plant one-zinc-finger protein1/2transcription factors regulate abiotic and bioticstress responses in Arabidopsis. The Plant journal: for cell and molecular biology73,761-775.
124. Nambara, E., and Marion-Poll, A.(2005). Abscisic acid biosynthesis and catabolism. Annualreview of plant biology56,165-185.
125. Narsai, R., Wang, C., Chen, J., Wu, J., Shou, H., and Whelan, J.(2013). Antagonistic, overlappingand distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress.BMC genomics14,93.
126. Nath, U., Crawford, B.C., Carpenter, R., and Coen, E.(2003). Genetic control of surface curvature.Science299,1404-1407.
127. Navarro, L., Dunoyer, P., Jay, F., Arnold, B., Dharmasiri, N., Estelle, M., Voinnet, O., and Jones,J.D.(2006). A plant miRNA contributes to antibacterial resistance by repressing auxin signaling.Science312,436-439.
128. Nelson, D.E., Repetti, P.P., Adams, T.R., Creelman, R.A., Wu, J., Warner, D.C., Anstrom, D.C.,Bensen, R.J., Castiglioni, P.P., Donnarummo, M.G., Hinchey, B.S., Kumimoto, R.W., Maszle, D.R.,Canales, R.D., Krolikowski, K.A., Dotson, S.B., Gutterson, N., Ratcliffe, O.J., and Heard, J.E.(2007). Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improvedcorn yields on water-limited acres. Proceedings of the National Academy of Sciences of the UnitedStates of America104,16450-16455.
129. Ohtake, Y., Takahashi, T., and Komeda, Y.(2000). Salicylic acid induces the expression of anumber of receptor-like kinase genes in Arabidopsis thaliana. Plant&cell physiology41,1038-1044.
130. Oka, M., Shimoda, Y., Sato, N., Inoue, J., Yamazaki, T., Shimomura, N., and Fujiyama, H.(2012).Abscisic acid substantially inhibits senescence of cucumber plants (Cucumis sativus) grown underlow nitrogen conditions. Journal of plant physiology169,789-796.
131. Pageau, K., Reisdorf-Cren, M., Morot-Gaudry, J.F., and Masclaux-Daubresse, C.(2006). The twosenescence-related markers, GS1(cytosolic glutamine synthetase) and GDH (glutamatedehydrogenase), involved in nitrogen mobilization, are differentially regulated during pathogenattack and by stress hormones and reactive oxygen species in Nicotiana tabacum L. leaves. Journalof experimental botany57,547-557.
132. Palatnik, J.F., Allen, E., Wu, X., Schommer, C., Schwab, R., Carrington, J.C., and Weigel, D.(2003). Control of leaf morphogenesis by microRNAs. Nature425,257-263.
133. Palenchar, P.M., Kouranov, A., Lejay, L.V., and Coruzzi, G.M.(2004). Genome-wide patterns ofcarbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen(CN)-signaling hypothesis in plants. Genome biology5, R91.
134. Pan, Y., Seymour, G.B., Lu, C., Hu, Z., Chen, X., and Chen, G.(2012). An ethylene response factor(ERF5) promoting adaptation to drought and salt tolerance in tomato. Plant cell reports31,349-360.
135. Pant, B.D., Musialak-Lange, M., Nuc, P., May, P., Buhtz, A., Kehr, J., Walther, D., and Scheible,W.R.(2009). Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs bycomprehensive real-time polymerase chain reaction profiling and small RNA sequencing. Plantphysiology150,1541-1555.
136. Park, C.J., Han, S.W., Chen, X., and Ronald, P.C.(2010). Elucidation of XA21-mediated innateimmunity. Cellular microbiology12,1017-1025.
137. Park, C.J., Peng, Y., Chen, X., Dardick, C., Ruan, D., Bart, R., Canlas, P.E., and Ronald, P.C.(2008). Rice XB15, a protein phosphatase2C, negatively regulates cell death and XA21-mediatedinnate immunity. PLoS biology6, e231.
138. Peng, Y., Bartley, L.E., Chen, X., Dardick, C., Chern, M., Ruan, R., Canlas, P.E., and Ronald, P.C.(2008). OsWRKY62is a negative regulator of basal and Xa21-mediated defense againstXanthomonas oryzae pv. oryzae in rice. Molecular plant1,446-458.
139. Price, M.B., Jelesko, J., and Okumoto, S.(2012). Glutamate receptor homologs in plants: functionsand evolutionary origins. Frontiers in plant science3,235.
140. Qiu, D., Xiao, J., Xie, W., Liu, H., Li, X., Xiong, L., and Wang, S.(2008). Rice gene networkinferred from expression profiling of plants overexpressing OsWRKY13, a positive regulator ofdisease resistance. Molecular plant1,538-551.
141. Razem, F.A., El-Kereamy, A., Abrams, S.R., and Hill, R.D.(2006). The RNA-binding protein FCAis an abscisic acid receptor. Nature439,290-294.
142. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., and Bartel, D.P.(2002). MicroRNAs inplants. Genes&development16,1616-1626.
143. Reyes, J.L., and Chua, N.H.(2007). ABA induction of miR159controls transcript levels of twoMYB factors during Arabidopsis seed germination. The Plant journal: for cell and molecularbiology49,592-606.
144. Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B., and Bartel, D.P.(2002).Prediction of plant microRNA targets. Cell110,513-520.
145. Robert, C., Bancal, M.O., and Lannou, C.(2004). Wheat leaf rust uredospore production on adultplants: Influence of leaf nitrogen content and Septoria tritici blotch. Phytopathology94,712-721.
146. Roberts, A., Pimentel, H., Trapnell, C., and Pachter, L.(2011). Identification of novel transcripts inannotated genomes using RNA-Seq. Bioinformatics27,2325-2329.
147. Roy Choudhury, S., Roy, S., Singh, S.K., and Sengupta, D.N.(2010). Molecular characterizationand differential expression of beta-1,3-glucanase during ripening in banana fruit in response toethylene, auxin, ABA, wounding, cold and light-dark cycles. Plant cell reports29,813-828.
148. Sadumpati, V., Kalambur, M., Vudem, D.R., Kirti, P.B., and Khareedu, V.R.(2013). Transgenicindica rice lines, expressing Brassica juncea Nonexpressor of pathogenesis-related genes1(BjNPR1), exhibit enhanced resistance to major pathogens. Journal of biotechnology166,114-121.
149. Sanabria, N.M., van Heerden, H., and Dubery, I.A.(2012). Molecular characterisation andregulation of a Nicotiana tabacum S-domain receptor-like kinase gene induced during an earlyrapid response to lipopolysaccharides. Gene501,39-48.
150. Schluter, U., Mascher, M., Colmsee, C., Scholz, U., Brautigam, A., Fahnenstich, H., andSonnewald, U.(2012). Maize source leaf adaptation to nitrogen deficiency affects not onlynitrogen and carbon metabolism but also control of phosphate homeostasis. Plant physiology160,1384-1406.
151. Schmittgen, T.D., and Livak, K.J.(2008). Analyzing real-time PCR data by the comparative C(T)method. Nature protocols3,1101-1108.
152. Schommer, C., Palatnik, J.F., Aggarwal, P., Chetelat, A., Cubas, P., Farmer, E.E., Nath, U., andWeigel, D.(2008). Control of jasmonate biosynthesis and senescence by miR319targets. PLoSbiology6, e230.
153. Sels, J., Mathys, J., De Coninck, B.M., Cammue, B.P., and De Bolle, M.F.(2008). Plantpathogenesis-related (PR) proteins: a focus on PR peptides. Plant physiology and biochemistry:PPB/Societe francaise de physiologie vegetale46,941-950.
154. Shirasu, K., Nakajima, H., Rajasekhar, V.K., Dixon, R.A., and Lamb, C.(1997). Salicylic acidpotentiates an agonist-dependent gain control that amplifies pathogen signals in the activation ofdefense mechanisms. The Plant cell9,261-270.
155. Shukla, L.I., Chinnusamy, V., and Sunkar, R.(2008). The role of microRNAs and otherendogenous small RNAs in plant stress responses. Biochimica et biophysica acta1779,743-748.
156. Snoeijers, S.S., Vossen, P., Goosen, T., Van den Broek, H.W., and De Wit, P.J.(1999). Transcriptionof the avirulence gene Avr9of the fungal tomato pathogen Cladosporium fulvum is regulated by aGATA-type transcription factor in Aspergillus nidulans. Molecular&general genetics: MGG261,653-659.
157. Snoeijers, S.S., Perez-Garcia, A., Joosten, M.H.A.J., and De Wit, P.J.G.M.(2000). The effect ofnitrogen on disease development and gene expression in bacterial and fungal plant pathogens. EurJ Plant Pathol106,493-506.
158. Son, G.H., Wan, J., Kim, H.J., Nguyen, X.C., Chung, W.S., Hong, J.C., and Stacey, G.(2012).Ethylene-responsive element-binding factor5, ERF5, is involved in chitin-induced innateimmunity response. Molecular plant-microbe interactions: MPMI25,48-60.
159. Song, W.Y., Wang, G.L., Chen, L.L., Kim, H.S., Pi, L.Y., Holsten, T., Gardner, J., Wang, B., Zhai,W.X., Zhu, L.H., Fauquet, C., and Ronald, P.(1995). A receptor kinase-like protein encoded by therice disease resistance gene, Xa21. Science270,1804-1806.
160. Stone, J.M., Liang, X., Nekl, E.R., and Stiers, J.J.(2005). Arabidopsis AtSPL14, a plant-specificSBP-domain transcription factor, participates in plant development and sensitivity to fumonisin B1.The Plant journal: for cell and molecular biology41,744-754.
161. Stutz, H.E., Ouixley, K.W.M., McMaster, L.D., and Reid, S.J.(2007). Co-regulation of thenitrogen-assimilatory gene cluster in Clostridium saccharobutylicum. Microbiol-Sgm153,3081-3090.
162. Sun, P., Tian, Q.Y., Zhao, M.G., Dai, X.Y., Huang, J.H., Li, L.H., and Zhang, W.H.(2007).Aluminum-induced ethylene production is associated with inhibition of root elongation in Lotusjaponicus L. Plant&cell physiology48,1229-1235.
163. Sun, X., Cao, Y., Yang, Z., Xu, C., Li, X., Wang, S., and Zhang, Q.(2004). Xa26, a gene conferringresistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein.The Plant journal: for cell and molecular biology37,517-527.
164. Sunkar, R., and Zhu, J.K.(2004). Novel and stress-regulated microRNAs and other small RNAsfrom Arabidopsis. The Plant cell16,2001-2019.
165. Sunkar, R., Li, Y.F., and Jagadeeswaran, G.(2012). Functions of microRNAs in plant stressresponses. Trends in plant science17,196-203.
166. Sunkar, R., Kapoor, A., and Zhu, J.K.(2006). Posttranscriptional induction of two Cu/Znsuperoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398andimportant for oxidative stress tolerance.(vol18, pg2051,2006). The Plant cell18,2415-2415.
167. Swain, S.M., and Singh, D.P.(2005). Tall tales from sly dwarves: novel functions of gibberellins inplant development. Trends in plant science10,123-129.
168. Swarup, R., Perry, P., Hagenbeek, D., Van Der Straeten, D., Beemster, G.T., Sandberg, G., Bhalerao,R., Ljung, K., and Bennett, M.J.(2007). Ethylene upregulates auxin biosynthesis in Arabidopsisseedlings to enhance inhibition of root cell elongation. The Plant cell19,2186-2196.
169. Takahara, K., Akashi, K., and Yokota, A.(2005). Purification and characterization of glutamateN-acetyltransferase involved in citrulline accumulation in wild watermelon. The FEBS journal272,5353-5364.
170. Tao, Y., Xie, Z., Chen, W., Glazebrook, J., Chang, H.S., Han, B., Zhu, T., Zou, G., and Katagiri, F.(2003). Quantitative nature of Arabidopsis responses during compatible and incompatibleinteractions with the bacterial pathogen Pseudomonas syringae. The Plant cell15,317-330.
171. Thimm, O., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Muller, L.A., Rhee,S.Y., and Stitt, M.(2004). MAPMAN: a user-driven tool to display genomics data sets ontodiagrams of metabolic pathways and other biological processes. The Plant journal: for cell andmolecular biology37,914-939.
172. Tilman, D., Cassman, K.G., Matson, P.A., Naylor, R., and Polasky, S.(2002). Agriculturalsustainability and intensive production practices. Nature418,671-677.
173. Trapnell, C., Pachter, L., and Salzberg, S.L.(2009). TopHat: discovering splice junctions withRNA-Seq. Bioinformatics25,1105-1111.
174. Tsay, Y.F., Chiu, C.C., Tsai, C.B., Ho, C.H., and Hsu, P.K.(2007). Nitrate transporters and peptidetransporters. FEBS letters581,2290-2300.
175. Tsuda, K., Sato, M., Glazebrook, J., Cohen, J.D., and Katagiri, F.(2008). Interplay betweenMAMP-triggered and SA-mediated defense responses. The Plant journal: for cell and molecularbiology53,763-775.
176. Ueguchi-Tanaka, M., Ashikari, M., Nakajima, M., Itoh, H., Katoh, E., Kobayashi, M., Chow, T.Y.,Hsing, Y.I., Kitano, H., Yamaguchi, I., and Matsuoka, M.(2005). GIBBERELLIN INSENSITIVEDWARF1encodes a soluble receptor for gibberellin. Nature437,693-698.
177. Van den Ackerveken, G.F., Dunn, R.M., Cozijnsen, A.J., Vossen, J.P., Van den Broek, H.W., and DeWit, P.J.(1994). Nitrogen limitation induces expression of the avirulence gene avr9in the tomatopathogen Cladosporium fulvum. Molecular&general genetics: MGG243,277-285.
178. Vidal, E.A., Araus, V., Lu, C., Parry, G., Green, P.J., Coruzzi, G.M., and Gutierrez, R.A.(2010).Nitrate-responsive miR393/AFB3regulatory module controls root system architecture inArabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States ofAmerica107,4477-4482.
179. Vijayan, P., Shockey, J., Levesque, C.A., Cook, R.J., and Browse, J.(1998). A role for jasmonate inpathogen defense of Arabidopsis. Proceedings of the National Academy of Sciences of the UnitedStates of America95,7209-7214.
180. Voinnet, O.(2003). RNA silencing bridging the gaps in wheat extracts. Trends in plant science8,307-309.
181. Vriezen, W.H., Hulzink, R., Mariani, C., and Voesenek, L.A.(1999).1-aminocyclopropane-1-carboxylate oxidase activity limits ethylene biosynthesis in Rumexpalustris during submergence. Plant physiology121,189-196.
182. Wang, K.L., Li, H., and Ecker, J.R.(2002). Ethylene biosynthesis and signaling networks. ThePlant cell14Suppl, S131-151.
183. Wang, R., Okamoto, M., Xing, X., and Crawford, N.M.(2003). Microarray analysis of the nitrateresponse in Arabidopsis roots and shoots reveals over1,000rapidly responding genes and newlinkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism. Plant physiology132,556-567.
184. Wang, R., Tischner, R., Gutierrez, R.A., Hoffman, M., Xing, X., Chen, M., Coruzzi, G., andCrawford, N.M.(2004a). Genomic analysis of the nitrate response using a nitrate reductase-nullmutant of Arabidopsis. Plant physiology136,2512-2522.
185. Wang, W.C., Lin, F.M., Chang, W.C., Lin, K.Y., Huang, H.D., and Lin, N.S.(2009). miRExpress:analyzing high-throughput sequencing data for profiling microRNA expression. BMCbioinformatics10,328.
186. Wang, X.J., Reyes, J.L., Chua, N.H., and Gaasterland, T.(2004b). Prediction and identification ofArabidopsis thaliana microRNAs and their mRNA targets. Genome biology5, R65.
187. Wei, L.Y., Zhang, D.F., Xiang, F., and Zhang, Z.X.(2009). Differentially expressed miRNAspotentially involved in the regulation of defense mechanism to drought stress in maize seedings.International journal of plant sciences170,979-989.
188. Wu, X., Shiroto, Y., Kishitani, S., Ito, Y., and Toriyama, K.(2009). Enhanced heat and droughttolerance in transgenic rice seedlings overexpressing OsWRKY11under the control of HSP101promoter. Plant cell reports28,21-30.
189. Xie, D.X., Feys, B.F., James, S., Nieto-Rostro, M., and Turner, J.G.(1998). COI1: an Arabidopsisgene required for jasmonate-regulated defense and fertility. Science280,1091-1094.
190. Xu, J., Duan, X., Yang, J., Beeching, J.R., and Zhang, P.(2013). Enhanced reactive oxygen speciesscavenging by overproduction of superoxide dismutase and catalase delays postharvestphysiological deterioration of cassava storage roots. Plant physiology161,1517-1528.
191. Xu, X., Zhou, Y., Wei, S., Ren, D., Yang, M., Bu, H., Kang, M., Wang, J., and Feng, J.(2009).Molecular cloning and expression of a Cu/Zn-Containing superoxide dismutase from Thellungiellahalophila. Molecules and cells27,423-428.
192. Xu, Z., Zhong, S., Li, X., Li, W., Rothstein, S.J., Zhang, S., Bi, Y., and Xie, C.(2011).Genome-wide identification of microRNAs in response to low nitrate availability in maize leavesand roots. PloS one6, e28009.
193. Yang, B., Sugio, A., and White, F.F.(2006). Os8N3is a host disease-susceptibility gene forbacterial blight of rice. Proceedings of the National Academy of Sciences of the United States ofAmerica103,10503-10508.
194. Yoshimura, S., Umehara, Y., Kurata, N., Nagamura, Y., Sasaki, T., Minobe, Y., and Iwata, N.(1996). Identification of a YAC clone carrying the Xa-1allele, a bacterial blight resistance gene inrice. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik93,117-122.
195. Yoshimura, S., Yamanouchi, U., Katayose, Y., Toki, S., Wang, Z.X., Kono, I., Kurata, N., Yano, M.,Iwata, N., and Sasaki, T.(1998). Expression of Xa1, a bacterial blight-resistance gene in rice, isinduced by bacterial inoculation. Proceedings of the National Academy of Sciences of the UnitedStates of America95,1663-1668.
196. Yu, S., Ligang, C., Liping, Z., and Diqiu, Y.(2010). Overexpression of OsWRKY72geneinterferes in the abscisic acid signal and auxin transport pathway of Arabidopsis. Journal ofbiosciences35,459-471.
197. Zeng, Y., Yi, R., and Cullen, B.R.(2003). MicroRNAs and small interfering RNAs can inhibitmRNA expression by similar mechanisms. Proceedings of the National Academy of Sciences ofthe United States of America100,9779-9784.
198. Zhai, Y., Wang, Y., Li, Y., Lei, T., Yan, F., Su, L., Li, X., Zhao, Y., Sun, X., Li, J., and Wang, Q.(2013). Isolation and molecular characterization of GmERF7, a soybean ethylene-response factorthat increases salt stress tolerance in tobacco. Gene513,174-183.
199. Zhang, B., Xie, D., and Jin, Z.(2012a). Global analysis of non-coding small RNAs in Arabidopsisin response to jasmonate treatment by deep sequencing technology. Journal of integrative plantbiology54,73-86.
200. Zhang, H., Ni, L., Liu, Y., Wang, Y., Zhang, A., Tan, M., and Jiang, M.(2012b). The C2H2-typezinc finger protein ZFP182is involved in abscisic acid-induced antioxidant defense in rice. Journalof integrative plant biology54,500-510.
201. Zhang, J., and Zhou, J.M.(2010). Plant immunity triggered by microbial molecular signatures.Molecular plant3,783-793.
202. Zhang, J.F., Yuan, L.J., Shao, Y., Du, W., Yan, D.W., and Lu, Y.T.(2008). The disturbance of smallRNA pathways enhanced abscisic acid response and multiple stress responses in Arabidopsis. Plant,cell&environment31,562-574.
203. Zhang, Y., Cheng, Y.T., Bi, D., Palma, K., and Li, X.(2005). MOS2, a protein containing G-patchand KOW motifs, is essential for innate immunity in Arabidopsis thaliana. Current biology: CB15,1936-1942.
204. Zhao, B., Liang, R., Ge, L., Li, W., Xiao, H., Lin, H., Ruan, K., and Jin, Y.(2007). Identification ofdrought-induced microRNAs in rice. Biochemical and biophysical research communications354,585-590.
205. Zhao, J., Davis, L.C., and Verpoorte, R.(2005). Elicitor signal transduction leading to productionof plant secondary metabolites. Biotechnology advances23,283-333.
206. Zhou, G.A., Chang, R.Z., and Qiu, L.J.(2010a). Overexpression of soybean ubiquitin-conjugatingenzyme gene GmUBC2confers enhanced drought and salt tolerance through modulating abioticstress-responsive gene expression in Arabidopsis. Plant molecular biology72,357-367.
207. Zhou, L., Liu, Y., Liu, Z., Kong, D., Duan, M., and Luo, L.(2010b). Genome-wide identificationand analysis of drought-responsive microRNAs in Oryza sativa. Journal of experimental botany61,4157-4168.
208. Zhou, X., Wang, G., and Zhang, W.(2007). UV-B responsive microRNA genes in Arabidopsisthaliana. Molecular systems biology3,103.
209. Zuo, J., Zhu, B., Fu, D., Zhu, Y., Ma, Y., Chi, L., Ju, Z., Wang, Y., Zhai, B., and Luo, Y.(2012).Sculpting the maturation, softening and ethylene pathway: the influences of microRNAs on tomatofruits. BMC genomics13,7.