Blocking miR396 increases rice yield by shaping inflorescence architecture

Nature Plants

Volumn 1, Issue , 2015, Pages

  Gao, Feng ^a   Wang, Kun ^a   Liu, Ying ^a   Chen, Yunping ^a   Chen, Pian ^a   Shi, Zhenying ^b   Luo, Jie ^c   Jiang, Daqing ^a   Fan, Fengfeng ^a   Zhu, Yingguo ^a   Li, Shaoqing ^a  

^a WUHAN UNIVERSITY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c Huazhong Agricultural University   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PHYTOHORMONE; PLANT PROTEIN;

GENE EXPRESSION REGULATION; GENETICS; INFLORESCENCE; METABOLISM; ORYZA; PHYSIOLOGY; PLANT SEED; TRANSGENIC PLANT;

GENE EXPRESSION REGULATION, PLANT; INFLORESCENCE; MICRORNAS; ORYZA; PLANT GROWTH REGULATORS; PLANT PROTEINS; PLANTS, GENETICALLY MODIFIED; SEEDS;

EID: 84952020811     PISSN: None     EISSN: 20550278     Source Type: Journal    
DOI: 10.1038/nplants.2015.196     Document Type: Article

References (45)

1. McClung, C. R. Making hunger yield. Science 344, 699-700 (2014).
2. Xing, Y. & Zhang, Q. Genetic and molecular bases of rice yield. Annu. Rev. Plant Biol. 61, 421-442 (2010).
3. Sreenivasulu, N. & Schnurbusch, T. A genetic playground for enhancing grain number in cereals. Trends Plant Sci. 17, 91-101 (2012).
4. Jones-Rhoades, M.W., Bartel, D. P. & Bartel, B. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 57, 19-53 (2006).
5. He, L. & Hannon, G. J. MicroRNAs: small RNAs with a big role in gene regulation. Nature Rev. Genet. 5, 522-531 (2004).
6. Chen, X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303, 2022-2025 (2004).
7. Mallory, A. C. & Vaucheret, H. Functions of microRNAs and related small RNAs in plants. Nature Genet. 38, S31-S36 (2006).
8. Navarro, L. et al. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312, 436-439 (2006).
9. Jiao, Y. et al. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nature Genet. 42, 541-544 (2010).
10. Lu, Z. et al. Genome-wide binding analysis of the transcription activator IDEAL PLANT ARCHITECTURE1 reveals a complex network regulating rice plant architecture. Plant Cell 25, 3743-3759 (2013).
11. Miura, K. et al. OsSPL14 promotes panicle branching and higher grain productivity in rice. Nature Genet. 42, 545-549 (2010).
12. Zhang, Y.-C. et al. Overexpression of microRNA OsmiR397 improves rice yield by increasing grain size and promoting panicle branching. Nature Biotech. 31, 848-852 (2013).
13. Yoshida, A. et al. TAWAWA1, a regulator of rice inflorescence architecture, functions through the suppression of meristem phase transition. Proc. Natl Acad. Sci. USA 110, 767-772 (2012).
14. Yoshida, A., Ohmori, Y., Kitano, H., Taguchi-Shiobara, F. & Hirano, H.-Y. Aberrant spikelet and panicle1, encoding a TOPLESS-related transcriptional corepressor, is involved in the regulation of meristem fate in rice. Plant J. 70, 327-339 (2012).
15. Ikeda, K., Ito, M., Nagasawa, N., Kyozuka, J. & Nagato, Y. Rice ABERRANT PANICLE ORGANIZATION 1, encoding an F-box protein, regulates meristem fate. Plant J. 51, 1030-1040 (2007).
16. Oikawa, T. & Kyozuka, J. Two-step regulation of LAX PANICLE1 protein accumulation in axillary meristem formation in rice. Plant Cell 21, 1095-1108 (2009).
17. Bazin, J. et al. MiR396 affects mycorrhization and root meristem activity in the legume Medicago truncatula. Plant J. 74, 920-934 (2013).
18. Rodriguez, R. E. et al. Control of cell proliferation in Arabidopsis thaliana by microRNA miR396. Development 137, 103-112 (2010).
19. Liu, H. et al. OsmiR396d-regulated OsGRFs function in floral organogenesis in rice through binding to their targets OsJMJ706 and OsCR4. Plant Physiol. 165, 160-174 (2014).
20. Debernardi, J. M., Rodriguez, R. E., Mecchia, M. A. & Palatnik, J. F. Functional specialization of the plant miR396 regulatory network through distinct microRNA-target interactions. PLoS Genet. 8, e1002419 (2012).
21. Kyozuka, J., Tokunaga, H. & Yoshida, A. Control of grass inflorescence form by the fine-tuning of meristem phase change. Curr. Opin. Plant Biol. 17, 110-115 (2014).
22. Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 7, 1728-1740 (2012).
23. Gao, X. et al. The SEPALLATA-like gene OsMADS34 is required for rice inflorescence and spikelet development. Plant Physiol. 153, 728-740 (2010).
24. Huang da, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protoc. 4, 44-57 (2009).
25. Peer, W. A. From perception to attenuation: auxin signalling and responses. Curr. Opin. Plant Biol. 16, 561-568 (2013).
26. Gallavotti, A. et al. Sparse inflorescence1 encodes a monocot-specific YUCCA-like gene required for vegetative and reproductive development in maize. Proc. Natl Acad. Sci. 105, 15196-15201 (2008).
27. Tanaka, W., Pautler, M., Jackson, D. & Hirano, H.-Y. Grass meristems II: inflorescence architecture, flower development and meristem fate. Plant Cell Physiol. 54, 313-324 (2013).
28. Zhang, D. & Yuan, Z. Molecular control of grass inflorescence development. Annu. Rev. Plant Biol. 65, 553-578 (2014).
29. Barazesh, S. & McSteen, P. Hormonal control of grass inflorescence development. Trends Plant Sci. 13, 656-662 (2008).
30. Gallavotti, A. The role of auxin in shaping shoot architecture. J. Exp. Bot. 64, 2593-2608 (2013).
31. Yamamoto, Y., Kamiya, N., Morinaka, Y., Matsuoka, M. & Sazuka, T. Auxin biosynthesis by the YUCCA genes in rice. Plant Physiol. 143, 1362-1371 (2007).
32. Nelissen, H. et al. Dynamic changes in ANGUSTIFOLIA3 complex composition reveal a growth regulatory mechanism in the maize leaf. Plant Cell 27, 1605-1619 (2015).
33. Kim, J. H. & Tsukaya, H. Regulation of plant growth and development by the GROWTH-REGULATING FACTOR and GRF-INTERACTING FACTOR duo. J. Exp. Bot. 66, 6093-6107 (2015).
34. Karimi, M., Inzé, D. & Depicker, A. GATEWAY™ vectors for Agrobacteriummediated plant transformation. Trends Plant Sci. 7, 193-195 (2002).
35. Franco-Zorrilla, J. M. et al. Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genet. 39, 1033-1037 (2007).
36. Hiei, Y., Ohta, S., Komari, T. & Kumashiro, T. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J. 6, 271-282 (1994).
37. Javelle, M. & Timmermans, M. C. P. In situ localization of small RNAs in plants by using LNA probes. Nature Protoc. 7, 533-541 (2012).
38. Ouyang, S. et al. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res. 35, D883-D887 (2007).
39. Saleh, A., Alvarez-Venegas, R. & Avramova, Z. An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants. Nature Protoc. 3, 1018-1025 (2008).
40. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
41. Zhang, Y. et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
42. Bailey, T. L. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27, 1653-1659 (2011).
43. Wang, K. et al. Using FAM labeled DNA oligos to do RNA electrophoretic mobility shift assay. Mol. Biol. Rep. 37, 2871-2875 (2010).
44. Hellman, L. M. & Fried, M. G. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nature Protoc. 2, 1849-1861 (2007).
45. Chen, W. et al. A novel integrated method for large-scale detection, identification, and quantification of widely targeted metabolites: application in the study of rice metabolomics. Mol. Plant 6, 1769-1780 (2013).