Login Register Cart 0
Generic placeholder image

Current Bioinformatics

Editor-in-Chief

ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
General Research Article

Bioinformatics Analysis Reveals Functions of MicroRNAs in Rice Under the Drought Stress

Author(s): Yan Peng, Yuewu Liu* and Xinbo Chen*

Volume 15, Issue 8, 2020

Page: [927 - 936] Pages: 10

DOI: 10.2174/1574893615666200207092410

Price: $65

Abstract

Background: Drought is one of the most damaging and widespread abiotic stresses that can severely limit the rice production. MicroRNAs (miRNAs) act as a promising tool for improving the drought tolerance of rice and have become a hot spot in recent years.

Objective: In order to further extend the understanding of miRNAs, the functions of miRNAs in rice under drought stress are analyzed by bioinformatics.

Methods: In this study, we integrated miRNAs and genes transcriptome data of rice under the drought stress. Some bioinformatics methods were used to reveal the functions of miRNAs in rice under drought stress. These methods included target genes identification, differentially expressed miRNAs screening, enrichment analysis of DEGs, network constructions for miRNA-target and target-target proteins interaction.

Results: (1) A total of 229 miRNAs with differential expression in rice under the drought stress, corresponding to 73 rice miRNAs families, were identified. (2) 1035 differentially expressed genes (DEGs) were identified, which included 357 up-regulated genes, 542 down-regulated genes and 136 up/down-regulated genes. (3) The network of regulatory relationships between 73 rice miRNAs families and 1035 DEGs was constructed. (4) 25 UP_KEYWORDS terms of DEGs, 125 GO terms and 7 pathways were obtained. (5) The protein-protein interaction network of 1035 DEGs was constructed.

Conclusion: (1) MiRNA-regulated targets in rice might be mainly involved in a series of basic biological processes and pathways under drought conditions. (2) MiRNAs in rice might play critical roles in Lignin degradation and ABA biosynthesis. (3) MiRNAs in rice might play an important role in drought signal perceiving and transduction.

Keywords: MircoRNA-target, drought stress, protein kinase, ABA, Oryza sativa, rice.

« Previous Next »
Graphical Abstract

[1]
Burkhardt PK, Beyer P, Wünn J, et al. Transgenic rice (Oryza sativa) endosperm expressing daffodil (Narcissus pseudonarcissus) phytoene synthase accumulates phytoene, a key intermediate of provitamin A biosynthesis. Plant J 1997; 11(5): 1071-8.
[http://dx.doi.org/10.1046/j.1365-313X.1997.11051071.x] [PMID: 9193076]
[2]
Zhang F, Luo X, Zhou Y, Xie J. Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.). Biotechnol Lett 2016; 38(4): 711-21.
[http://dx.doi.org/10.1007/s10529-015-2012-0] [PMID: 26667133]
[3]
Luo LJ. Breeding for water-saving and drought-resistance rice (WDR) in China. J Exp Bot 2010; 61(13): 3509-17.
[http://dx.doi.org/10.1093/jxb/erq185] [PMID: 20603281]
[4]
Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116(2): 281-97.
[http://dx.doi.org/10.1016/S0092-8674(04)00045-5] [PMID: 14744438]
[5]
Nataraja KN, Parvathi MS. Drought Stress Tolerance in Plants. In: Hossain MA, Wani SH, Bhattacharjee S, Burritt DJ, Tran L.-S.P., Eds. Springer International Publishing 2016; pp. 71-90.
[6]
Jeong DH, Park S, Zhai J, et al. Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell 2011; 23(12): 4185-207.
[http://dx.doi.org/10.1105/tpc.111.089045] [PMID: 22158467]
[7]
Xia K, Wang R, Ou X, et al. OsTIR1 and OsAFB2 downregulation via OsmiR393 overexpression leads to more tillers, early flowering and less tolerance to salt and drought in rice. PLoS One 2012; 7(1)e30039
[http://dx.doi.org/10.1371/journal.pone.0030039] [PMID: 22253868]
[8]
Zhou M, Li D, Li Z, et al. Constitutive expression of a miR319 gene alters plant development and enhances salt and drought tolerance in transgenic creeping bentgrass. Plant Physiol 2013; 161(3): 1375-91.
[http://dx.doi.org/10.1104/pp.112.208702] [PMID: 23292790]
[9]
Shi BJ. Drought Stress Tolerance in Plants. 217-36.
[10]
Chen JJ, Li LZ. Multiple regression analysis reveals MicroRNA regulatory networks in Oryza sativa under drought stress. Int J Gen 2018; 20189395261
[http://dx.doi.org/10.1155/2018/9395261]
[11]
Barrera-Figueroa BE, Gao L, Wu Z, et al. High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice. BMC Plant Biol 2012; 12(1): 132.
[http://dx.doi.org/10.1186/1471-2229-12-132] [PMID: 22862743]
[12]
Zhou L, Liu Y, Liu Z, Kong D, Duan M, Luo L. Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. J Exp Bot 2010; 61(15): 4157-68.
[http://dx.doi.org/10.1093/jxb/erq237] [PMID: 20729483]
[13]
Zhao B, Liang R, Ge L, et al. Identification of drought-induced microRNAs in rice. Biochem Biophys Res Commun 2007; 354(2): 585-90.
[http://dx.doi.org/10.1016/j.bbrc.2007.01.022] [PMID: 17254555]
[14]
Chung PJ, Jung H, Jeong DH, Ha SH, Choi YD, Kim JK. Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice. BMC Genomics 2016; 17(1): 563.
[http://dx.doi.org/10.1186/s12864-016-2997-3] [PMID: 27501838]
[15]
Ahn H, Jung I, Shin SJ, et al. Transcriptional network analysis reveals drought resistance mechanisms of AP2/ERF transgenic rice. Front Plant Sci 2017; 8: 1044.
[http://dx.doi.org/10.3389/fpls.2017.01044] [PMID: 28663756]
[16]
Wei H, Chen C, Ma X, et al. Comparative analysis of expression profiles of panicle development among tolerant and sensitive rice in response to drought stress. Front Plant Sci 2017; 8: 437.
[http://dx.doi.org/10.3389/fpls.2017.00437] [PMID: 28405199]
[17]
Krishnan A, Gupta C, Ambavaram MMR, Pereira A. RECoN: Rice Environment Coexpression Network for systems level analysis of abiotic-stress response. Front Plant Sci 2017; 8: 1640.
[http://dx.doi.org/10.3389/fpls.2017.01640] [PMID: 28979289]
[18]
Park SH, Chung PJ, Juntawong P, et al. Posttranscriptional control of photosynthetic mRNA decay under stress conditions requires 3′ and 5′ untranslated regions and correlates with differential polysome association in rice. Plant Physiol 2012; 159(3): 1111-24.
[http://dx.doi.org/10.1104/pp.112.194928] [PMID: 22566494]
[19]
Dai X, Zhuang Z, Zhao PX. psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res 2018; 46(W1)W49-54
[http://dx.doi.org/10.1093/nar/gky316] [PMID: 29718424]
[20]
Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4(1): 44-57.
[http://dx.doi.org/10.1038/nprot.2008.211] [PMID: 19131956]
[21]
Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 2015; 43(Database issue): D447-52.
[http://dx.doi.org/10.1093/nar/gku1003] [PMID: 25352553]
[22]
Swetha C, Basu D, Pachamuthu K, et al. Major domestication-related phenotypes in indica rice are due to loss of miRNA-mediated laccase silencing. Plant Cell 2018; 30(11): 2649-62.
[http://dx.doi.org/10.1105/tpc.18.00472] [PMID: 30341147]
[23]
Nambara E, Marion-Poll A. Abscisic acid biosynthesis and catabolism. Annu Rev Plant Biol 2005; 56: 165-85.
[http://dx.doi.org/10.1146/annurev.arplant.56.032604.144046] [PMID: 15862093]
[24]
Park HY, Seok HY, Park BK, et al. Overexpression of Arabidopsis ZEP enhances tolerance to osmotic stress. Biochem Biophys Res Commun 2008; 375(1): 80-5.
[http://dx.doi.org/10.1016/j.bbrc.2008.07.128] [PMID: 18680727]
[25]
Yan J, Zhao C, Zhou J, et al. The miR165/166 Mediated Regulatory Module Plays Critical Roles in ABA Homeostasis and Response in Arabidopsis thaliana. PLoS Genet 2016; 12(11)e1006416
[http://dx.doi.org/10.1371/journal.pgen.1006416] [PMID: 27812104]
[26]
Cheng Y, Qi Y, Zhu Q, et al. New changes in the plasma-membrane-associated proteome of rice roots under salt stress. Proteomics 2009; 9(11): 3100-14.
[http://dx.doi.org/10.1002/pmic.200800340] [PMID: 19526560]
[27]
Zou Y, Liu X, Wang Q, et al. OsRPK1, a Novel Leucine-Rich Repeat Receptor-like Kinase, Negatively Regulates Polar Auxin Transport and Root Development in Rice. BBA - General Subjects 2014; 1840(6): 1676-85.
[28]
Ouyang SQ, Liu YF, Liu P, et al. Receptor-like kinase OsSIK1 improves drought and salt stress tolerance in rice (Oryza sativa) plants. Plant J 2010; 62(2): 316-29.
[http://dx.doi.org/10.1111/j.1365-313X.2010.04146.x] [PMID: 20128882]
[29]
Chen LJ, Wuriyanghan H, Zhang YQ, et al. An S-domain receptor-like kinase, OsSIK2, confers abiotic stress tolerance and delays dark-induced leaf senescence in rice. Plant Physiol 2013; 163(4): 1752-65.
[http://dx.doi.org/10.1104/pp.113.224881] [PMID: 24143807]
[30]
Yamaguchi K, Yoshimura Y, Nakagawa S, Mezaki H, Yoshimura S, Kawasaki T. OsDRE2 contributes to chitin-triggered response through its interaction with OsRLCK185. Biosci Biotechnol Biochem 2019; 83(2): 281-90.
[http://dx.doi.org/10.1080/09168451.2018.1543012] [PMID: 30418086]
[31]
Yamaguchi K, Yamada K, Ishikawa K, et al. A receptor-like cytoplasmic kinase targeted by a plant pathogen effector is directly phosphorylated by the chitin receptor and mediates rice immunity. Cell Host Microbe 2013; 13(3): 347-57.
[http://dx.doi.org/10.1016/j.chom.2013.02.007] [PMID: 23498959]
[32]
Giri J, Vij S, Dansana PK, Tyagi AK. Rice A20/AN1 zinc-finger containing stress-associated proteins (SAP1/11) and a receptor-like cytoplasmic kinase (OsRLCK253) interact via A20 zinc-finger and confer abiotic stress tolerance in transgenic Arabidopsis plants. New Phytol 2011; 191(3): 721-32.
[http://dx.doi.org/10.1111/j.1469-8137.2011.03740.x] [PMID: 21534973]
[33]
Ramegowda V, Basu S, Krishnan A, Pereira A. Rice GROWTH UNDER DROUGHT KINASE is required for drought tolerance and grain yield under normal and drought stress conditions. Plant Physiol 2014; 166(3): 1634-45.
[http://dx.doi.org/10.1104/pp.114.248203] [PMID: 25209982]
[34]
Liu J, Ishitani M, Halfter U, Kim CS, Zhu JK. The Arabidopsis thaliana SOS2 gene encodes a protein kinase that is required for salt tolerance. Proc Natl Acad Sci USA 2000; 97(7): 3730-4.
[http://dx.doi.org/10.1073/pnas.97.7.3730] [PMID: 10725382]
[35]
Xiang Y, Huang Y, Xiong L. Characterization of stress-responsive CIPK genes in rice for stress tolerance improvement. Plant Physiol 2007; 144(3): 1416-28.
[http://dx.doi.org/10.1104/pp.107.101295] [PMID: 17535819]
[36]
Peng Y, Hou F, Bai Q, et al. Rice Calcineurin B-Like Protein-Interacting Protein Kinase 31 (OsCIPK31) Is Involved in the Development of Panicle Apical Spikelets. Front Plant Sci 2018; 9: 1661.
[http://dx.doi.org/10.3389/fpls.2018.01661] [PMID: 30524455]
[37]
Yang W, Kong Z, Omo-Ikerodah E, Xu W, Li Q, Xue Y. Calcineurin B-like interacting protein kinase OsCIPK23 functions in pollination and drought stress responses in rice (Oryza sativa L.). J Genet Genomics 2008; 35(9): 531-43.
[38]
Cao J, Jiang M, Li P, Chu Z. Genome-wide identification and evolutionary analyses of the PP2C gene family with their expression profiling in response to multiple stresses in Brachypodium distachyon. BMC Genomics 2016; 17(1): 175.
[http://dx.doi.org/10.1186/s12864-016-2526-4] [PMID: 26935448]

Rights & Permissions Print Cite
Article Metrics
18
© 2024 Bentham Science Publishers | Privacy Policy