Abstract
Melatonin is an important phytohormone in plant development and stress responses. However, the functions of melatonin in rice salt tolerance during seed germination is largely undetermined. In this study, we investigated its potential molecular mechanism during rice seed germination under salinity through comprehensive transcriptome sequencing, metabolome profiling, and physiological assays. Transcriptome analysis revealed 4794 differentially expressed genes (DEGs) after melatonin pretreatment under salinity, including 2843 upregulated and 1951 downregulated genes. Functional annotation showed that many DEGs were associated with antioxidative activity and phytohormone biosynthesis and signal transduction. Consistent with the transcriptome results, physiological analysis revealed enhanced activity of antioxidant capacity, increased indole-3-acetic acid (IAA) level, and reduced abscisic acid (ABA) level under melatonin pretreatment. The enhanced antioxidative activity was also supported by metabolome assay that melatonin pretreatment increased the levels of non-enzymatic antioxidant organic acids and amino acids. The results demonstrated that exogenous melatonin can enhance rice seed tolerance to salinity during germination via activating antioxidants and modulating phytohormones.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
RNA-seq data has been uploaded to the National Center for Biotechnology Information Gene Expression Omnibus with accession number GSE143922 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143922).
Abbreviations
- ABA:
-
Abscisic acid
- APX:
-
Ascorbic acid peroxidase
- BA:
-
Benzyl aminopurine
- bHLH:
-
Basic helix-loop-helix
- bZIP:
-
Basic domain/Leu zipper
- CAT:
-
Catalase
- DEGs:
-
Differential expressed genes
- ET:
-
Ethylene
- GO:
-
Gene ontology
- GA:
-
Gibberellin
- GA2:
-
Gibberellin 2-oxidase
- HPLC:
-
High-performance liquid chromatography
- H2O2 :
-
Hydrogen peroxide
- IAA:
-
Indole-3-acetic acid
- JA:
-
Jasmonic acid
- OPP:
-
6-Phosphogluconate dehydrogenase
- POD:
-
Peroxidase
- PRX:
-
Peroxiredoxin
- RCI3:
-
Rare cold inducible genes
- ROS/RNS:
-
Reactive oxygen/nitrogen species
- RT-PCR:
-
Real-time polymerase chain reaction
- SOD:
-
Superoxide dismutase
- T-AOC:
-
Total antioxidant capacity
- T-SH:
-
Total sulfhydryl group
- ZFP:
-
Cys2/His2-type zinc-finger protein
- ZT:
-
Zeatin
References
Ahmad P, Jaleel CA, Salem MA, Nabi G, Sharma S (2010) Roles of enzymatic and nonenzymatic antioxidants in plants during abiotic stress. Crit Rev Biotechnol 30(3):161–175. https://doi.org/10.3109/07388550903524243
Arnao MB, Hernandez-Ruiz J (2013) Growth conditions determine different melatonin levels in Lupinus albus L. J Pineal Res 55(2):149–155. https://doi.org/10.1111/jpi.12055
Arnao MB, Hernandez-Ruiz J (2014) Melatonin: plant growth regulator and/or biostimulator during stress? Trends Plant Sci 19(12):789–797. https://doi.org/10.1016/j.tplants.2014.07.006
Arnao MB, Hernandez-Ruiz J (2018) Melatonin and its relationship to plant hormones. Ann Bot 121(2):195–207. https://doi.org/10.1093/aob/mcx114
Arora D, Bhatla SC (2017) Melatonin and nitric oxide regulate sunflower seedling growth under salt stress accompanying differential expression of Cu/Zn SOD and Mn SOD. Free Radic Biol Med 106:315–328. https://doi.org/10.1016/j.freeradbiomed.2017.02.042
Bai Y, Guo J, Reiter RJ, Wei Y, Shi H (2020) Melatonin synthesis enzymes interact with ascorbate peroxidase to protect against oxidative stress in cassava. J Exp Bot 71(18):5645–5655. https://doi.org/10.1093/jxb/eraa267
Bakshi M, Oelmuller R (2014) WRKY transcription factors: jack of many trades in plants. Plant Signal Behav 9(2):e27700. https://doi.org/10.4161/psb.27700
Burkhardt S, Tan DX, Manchester LC, Hardeland R, Reiter RJ (2001) Detection and quantification of the antioxidant melatonin in Montmorency and Balaton tart cherries (Prunus cerasus). J Agric Food Chem 49(10):4898–4902. https://doi.org/10.1021/jf010321+
Chen L, Liu L, Lu B, Ma T, Jiang D, Li J et al (2020) Exogenous melatonin promotes seed germination and osmotic regulation under salt stress in cotton (Gossypium hirsutum L.). PLoS ONE 15(1):e0228241. https://doi.org/10.1371/journal.pone.0228241
Chen R, Cheng Y, Han S, Van Handel B, Dong L, Li X et al (2017) Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar: sea rice 86. BMC Genom 18(1):655. https://doi.org/10.1186/s12864-017-4037-3
Chen SY, Chien CT, Baskin JM, Baskin CC (2010) Storage behavior and changes in concentrations of abscisic acid and gibberellins during dormancy break and germination in seeds of Phellodendron amurense var. wilsonii (Rutaceae). Tree Physiol 30(2):275–284. https://doi.org/10.1093/treephys/tpp111
Erland LA, Murch SJ, Reiter RJ, Saxena PK (2015) A new balancing act: the many roles of melatonin and serotonin in plant growth and development. Plant Signal Behav 10(11):e1096469. https://doi.org/10.1080/15592324.2015.1096469
Erland LAE, Shukla MR, Singh AS, Murch SJ, Saxena PK (2018) Melatonin and serotonin: mediators in the symphony of plant morphogenesis. J Pineal Res 64(2):e12452. https://doi.org/10.1111/jpi.12452
Hu H, Dai M, Yao J, Xiao B, Li X, Zhang Q et al (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci U S A 103(35):12987–12992. https://doi.org/10.1073/pnas.0604882103
Igamberdiev AU, Bykova NV (2018) Role of organic acids in the integration of cellular redox metabolism and mediation of redox signalling in photosynthetic tissues of higher plants. Free Radic Biol Med 122:74–85. https://doi.org/10.1016/j.freeradbiomed.2018.01.016
Ilangumaran G, Smith DL (2017) Plant Growth promoting rhizobacteria in amelioration of salinity stress: a systems biology perspective. Front Plant Sci 8:1768. https://doi.org/10.3389/fpls.2017.01768
Jain M, Kaur N, Garg R, Thakur JK, Tyagi AK, Khurana JP (2006) Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa). Funct Integr Genom 6(1):47–59. https://doi.org/10.1007/s10142-005-0005-0
Jensen MK, Kjaersgaard T, Petersen K, Skriver K (2010) NAC genes: time-specific regulators of hormonal signaling in Arabidopsis. Plant Signal Behav 5(7):907–910. https://doi.org/10.4161/psb.5.7.12099
Jin J, Tian F, Yang DC, Meng YQ, Kong L, Luo J et al (2017) PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res 45(D1):D1040–D1045. https://doi.org/10.1093/nar/gkw982
Kang DJ, Seo YJ, Lee JD, Ishii R, Kim KU, Shin DH et al (2005) Jasmonic acid differentially affects growth, ion uptake and abscisic acid concentration in salt-tolerant and salt-sensitive rice cultivars. J Agron Crop Sci 191(4):273–282. https://doi.org/10.1111/j.1439-037X.2005.00153.x
Kang K, Kim YS, Park S, Back K (2009) Senescence-induced serotonin biosynthesis and its role in delaying senescence in rice leaves. Plant Physiol 150(3):1380–1393. https://doi.org/10.1104/pp.109.138552
Kudo T, Makita N, Kojima M, Tokunaga H, Sakakibara H (2012) Cytokinin activity of cis-zeatin and phenotypic alterations induced by overexpression of putative cis-Zeatin-O-glucosyltransferase in rice. Plant Physiol 160(1):319–331. https://doi.org/10.1104/pp.112.196733
Kumar PP (2013) Regulation of biotic and abiotic stress responses by plant hormones. Plant Cell Rep 32(7):943. https://doi.org/10.1007/s00299-013-1460-z
Lee HY, Back K (2016) Mitogen-activated protein kinase pathways are required for melatonin-mediated defense responses in plants. J Pineal Res 60(3):327–335. https://doi.org/10.1111/jpi.12314
Lei P, Xu ZQ, Liang JF, Luo XH, Zhang YX, Feng XH et al (2016) Poly(gamma-glutamic acid) enhanced tolerance to salt stress by promoting proline accumulation in Brassica napus L. Plant Growth Regul 78(2):233–241. https://doi.org/10.1007/s10725-015-0088-0
Li C, Wang P, Wei Z, Liang D, Liu C, Yin L et al (2012) The mitigation effects of exogenous melatonin on salinity-induced stress in Malus hupehensis. J Pineal Res 53(3):298–306. https://doi.org/10.1111/j.1600-079X.2012.00999.x
Li P, Cao W, Fang H, Xu S, Yin S, Zhang Y et al (2017a) Transcriptomic profiling of the maize (Zea mays L.) leaf response to abiotic stresses at the seedling stage. Front Plant Sci 8:290. https://doi.org/10.3389/fpls.2017.00290
Li XJ, Yu BJ, Cui YQ, Yin YF (2017b) Melatonin application confers enhanced salt tolerance by regulating Na+ and Cl- accumulation in rice. Plant Growth Regul 83(3):441–454. https://doi.org/10.1007/s10725-017-0310-3
Liu G, Ji Y, Bhuiyan NH, Pilot G, Selvaraj G, Zou J et al (2010) Amino acid homeostasis modulates salicylic acid-associated redox status and defense responses in Arabidopsis. Plant Cell 22(11):3845–3863. https://doi.org/10.1105/tpc.110.079392
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25(4):402–408. https://doi.org/10.1006/meth.2001.1262
Marta B, Szafranska K, Posmyk MM (2016) Exogenous melatonin improves antioxidant defense in cucumber seeds (Cucumis sativus L.) germinated under chilling stress. Front Plant Sci 7:575. https://doi.org/10.3389/fpls.2016.00575
Nawaz MA, Huang Y, Bie Z, Ahmed W, Reiter RJ, Niu M et al (2015) Melatonin: current status and future perspectives in plant science. Front Plant Sci 6:1230. https://doi.org/10.3389/fpls.2015.01230
Negrao S, Schmockel SM, Tester M (2017) Evaluating physiological responses of plants to salinity stress. Ann Bot 119(1):1–11. https://doi.org/10.1093/aob/mcw191
Petrov V, Hille J, Mueller-Roeber B, Gechev TS (2015) ROS-mediated abiotic stress-induced programmed cell death in plants. Front Plant Sci 6:69. https://doi.org/10.3389/fpls.2015.00069
Rajjou L, Duval M, Gallardo K, Catusse J, Bally J, Job C et al (2012) Seed germination and vigor. Annu Rev Plant Biol 63:507–533. https://doi.org/10.1146/annurev-arplant-042811-105550
Ryu H, Cho YG (2015) Plant hormones in salt stress tolerance. J Plant Biol 58(3):147–155. https://doi.org/10.1007/s12374-015-0103-z
Salehi B, Sharopov F, Fokou PVT, Kobylinska A, Jonge L, Tadio K et al (2019) Melatonin in medicinal and food plants: occurrence, bioavailability, and health potential for humans. Cells 8(7):681. https://doi.org/10.3390/cells8070681
Sanchez Mde L, Gurusinghe SH, Bradford KJ, Vazquez-Ramos JM (2005) Differential response of PCNA and Cdk-A proteins and associated kinase activities to benzyladenine and abscisic acid during maize seed germination. J Exp Bot 56(412):515–523. https://doi.org/10.1093/jxb/eri029
Schippers KJ, Nichols SA (2014) Deep, dark secrets of melatonin in animal evolution. Cell 159(1):9–10. https://doi.org/10.1016/j.cell.2014.09.004
Shi H, Jiang C, Ye T, Tan DX, Reiter RJ, Zhang H et al (2015) Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L.) Pers.] by exogenous melatonin. J Exp Bot 66(3):681–694. https://doi.org/10.1093/jxb/eru373
Smith CA, Want EJ, O’Maille G, Abagyan R, Siuzdak G (2006) XCMS: Processing mass spectrometry data for metabolite profiling using Nonlinear peak alignment, matching, and identification. Anal Chem 78(3):779–787. https://doi.org/10.1021/ac051437y
Sueishi Y, Masamoto H, Kotake Y (2019) Heat treatments of ginger root modify but not diminish its antioxidant activity as measured with multiple free radical scavenging (MULTIS) method. J Clin Biochem Nutr 64(2):143–147. https://doi.org/10.3164/jcbn.18-41
Tal O, Haim A, Harel O, Gerchman Y (2011) Melatonin as an antioxidant and its semi-lunar rhythm in green macroalga Ulva sp. J Exp Bot 62(6):1903–1910. https://doi.org/10.1093/jxb/erq378
Van Tassel DL, Roberts N, Lewy A, O’Neill SD (2001) Melatonin in plant organs. J Pineal Res 31(1):8–15. https://doi.org/10.1034/j.1600-079x.2001.310102.x
Wang L, Feng C, Zheng X, Guo Y, Zhou F, Shan D et al (2017) Plant mitochondria synthesize melatonin and enhance the tolerance of plants to drought stress. J Pineal Res 63(3):e12429. https://doi.org/10.1111/jpi.12429
Wang WS, Zhao XQ, Li M, Huang LY, Xu JL, Zhang F et al (2016) Complex molecular mechanisms underlying seedling salt tolerance in rice revealed by comparative transcriptome and metabolomic profiling. J Exp Bot 67(1):405–419. https://doi.org/10.1093/jxb/erv476
Wing RA, Purugganan MD, Zhang Q (2018) The rice genome revolution: from an ancient grain to Green Super Rice. Nat Rev Genet 19(8):505–517. https://doi.org/10.1038/s41576-018-0024-z
Wu MJ, Wu JY, Gan YB (2020) The new insight of auxin functions: transition from seed dormancy to germination and floral opening in plants. Plant Growth Regul 91(2):169–174. https://doi.org/10.1007/s10725-020-00608-1
Xie Z, Wang J, Wang W, Wang Y, Xu J, Li Z et al (2020) Integrated analysis of the transcriptome and metabolome revealed the molecular mechanisms underlying the enhanced salt tolerance of rice due to the application of exogenous melatonin. Front Plant Sci 11:618680. https://doi.org/10.3389/fpls.2020.618680
Yan FY, Wei HM, Ding YF, Li WW, Chen L, Ding CQ et al (2021) Melatonin enhances Na+/K+ homeostasis in rice seedlings under salt stress through increasing the root H+-pump activity and Na+/K+ transporters sensitivity to ROS/RNS. Environ Exp Bot. https://doi.org/10.1016/j.envexpbot.2020.104328
Zhan H, Nie X, Zhang T, Li S, Wang X, Du X et al (2019) Melatonin: a small molecule but important for salt stress tolerance in plants. Int J Mol Sci. https://doi.org/10.3390/ijms20030709
Zhang HM, Zhang Y (2014) Melatonin: a well-documented antioxidant with conditional pro-oxidant actions. J Pineal Res 57(2):131–146. https://doi.org/10.1111/jpi.12162
Zhang M, Smith JA, Harberd NP, Jiang C (2016) The regulatory roles of ethylene and reactive oxygen species (ROS) in plant salt stress responses. Plant Mol Biol 91(6):651–659. https://doi.org/10.1007/s11103-016-0488-1
Zhang N, Zhang HJ, Sun QQ, Cao YY, Li X, Zhao B et al (2017) Proteomic analysis reveals a role of melatonin in promoting cucumber seed germination under high salinity by regulating energy production. Sci Rep 7(1):503. https://doi.org/10.1038/s41598-017-00566-1
Zhang Z, Liu H, Sun C, Ma Q, Bu H, Chong K et al (2018) A C2H2 zinc-finger protein OsZFP213 interacts with OsMAPK3 to enhance salt tolerance in rice. J Plant Physiol 229:100–110. https://doi.org/10.1016/j.jplph.2018.07.003
Zhou DY, Zhang XL, Xu Q, Xue XY, Zhang FF, Liang XM (2009) UPLC/Q-TOFMS/MS as a powerful technique for rapid identification of polymethoxylated flavones in Fructus aurantii. J Pharm Biomed 50(1):2–8. https://doi.org/10.1016/j.jpba.2009.03.010
Zhu G, Ye N, Zhang J (2009) Glucose-induced delay of seed germination in rice is mediated by the suppression of ABA catabolism rather than an enhancement of ABA biosynthesis. Plant Cell Physiol 50(3):644–651. https://doi.org/10.1093/pcp/pcp022
Zhu JK (2016) Abiotic stress signaling and responses in plants. Cell 167(2):313–324. https://doi.org/10.1016/j.cell.2016.08.029
Zong W, Tang N, Yang J, Peng L, Ma S, Xu Y et al (2016) Feedback regulation of ABA signaling and biosynthesis by a bZIP transcription factor targets drought-resistance-related genes. Plant Physiol 171(4):2810–2825. https://doi.org/10.1104/pp.16.00469
Funding
This study was supported by grants from the National Natural Science Foundations (32070558, 91535103, 31571608 and 31601810), the National Key Technology Research and Development Program of MOST (2016YFD0100300), A project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), the Key Technology Research and Development Program of Jiangsu (BE2018325), and the Innovative Research Team of Ministry of Agriculture.
Author information
Authors and Affiliations
Contributions
ZY, YZ and CX conceived and designed the research. LH, ZZ, HF, PL, YX and RC conducted the experiments. LH, YL, EZ and SY performed the metabolomic and transcriptomic analyses. LH, YL, CX and ZY wrote the manuscript. YY and YZ edited the manuscript. All authors read and approved the manuscript for publication.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interests.
Additional information
Communicated by Vijay Pratap Singh.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Huangfu, L., Zhang, Z., Zhou, Y. et al. Integrated physiological, metabolomic and transcriptomic analyses provide insights into the roles of exogenous melatonin in promoting rice seed germination under salt stress. Plant Growth Regul 95, 19–31 (2021). https://doi.org/10.1007/s10725-021-00721-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10725-021-00721-9