Plant Biotechnology Reports

, Volume 13, Issue 6, pp 567–578 | Cite as

Transcriptome analysis of rice-seedling roots under soil–salt stress using RNA-Seq method

  • Anil Kumar Nalini Chandran
  • Jeong-Won Kim
  • Yo-Han Yoo
  • Hye Lin Park
  • Yeon-Ju Kim
  • Man-Ho Cho
  • Ki-Hong JungEmail author
Original Article


Soil salinity is a major production constrain for agricultural crops, especially in Oryza sativa (rice). Analyzing physiological effect and molecular mechanism under salt stress is key for developing stress-tolerant plants. Roots system has a major role in coping with the osmotic change impacted by salinity and few salt-stress-related transcriptome studies in rice have been previously reported. However, transcriptome data sets using rice roots grown in soil condition are more relevant for further applications, but have not yet been available. The present work analyzed rice root and shoot physiological characteristics in response to salt stress using 250 mM NaCl for different timepoints. Subsequently, we identified that 5 day treatment is critical timepoint for stress response in the specific experimental design. We then generated RNA-Seq-based transcriptome data set with rice roots treated with 250 mM NaCl for 5 days along with untreated controls in soil condition using rice japonica cultivar Chilbo. We identified 447 upregulated genes under salt stress with more than fourfold changes (p value < 0.05, FDR < 0.05) and used qRT-PCR for six genes to confirm their salt-dependent induction patterns. GO-enrichment analysis indicated that carbohydrate and amino-acid metabolic process are significantly affected by the salt stress. MapMan overview analysis indicated that secondary metabolite-related genes are induced under salt stress. Metabolites profiling analysis confirmed that phenolics and flavonoids accumulate in root under salt stress. We further constructed a functional network consisting of regulatory genes based on predicted protein–protein interactions, suggesting useful regulatory molecular network for future applications.


Gene ontology MapMan Rice Root RNA-Seq Salt stress 



We thank Dr. Gynheung An for providing valuable comments and sharing research facilities. This work was supported by Grants from the Next-Generation BioGreen 21 Program (PJ01366401 and PJ01369001 to KHJ), the Rural Development Administration, Republic of Korea, and by the Collaborative Genome Program of the Korea Institute of Marine Science and Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries (MOF) (no. 2018043004 to KHJ).

Author contributions

KHJ, YJK, and MHC conceived and designed the research plans; AKNC and JWK performed most of the experiments; YHY carried out the network analysis; HLP estimated the secondary metabolites, AKNC and KHJ analyzed the data, AKNC, JWK, and KHJ wrote this paper.

Compliance with ethical standards

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Supplementary material

11816_2019_550_MOESM1_ESM.jpg (1.5 mb)
Venn diagram showing genes that are commonly identified among four transcriptome studies under salt stress condition. (JPEG 1498 kb)
11816_2019_550_MOESM2_ESM.docx (120 kb)
Supplementary material 2 (DOCX 120 kb)


  1. AbdElgawad H, Zinta G, Hegab MM, Pandey R, Asard H, Abuelsoud W (2016) High salinity induces different oxidative stress and antioxidant responses in maize seedlings organs. Front Plant Sci 7:276. CrossRefPubMedPubMedCentralGoogle Scholar
  2. Cao P, Jung KH, Choi D, Hwang D, Zhu J, Ronald PC (2012) The rice oligonucleotide array database: an atlas of rice gene expression. Rice 5:17. CrossRefPubMedPubMedCentralGoogle Scholar
  3. Chandran AKN, Priatama RA, Kumar V, Xuan Y, Je BI, Kim CM, Jung KH, Han CD (2016) Genome-wide transcriptome analysis of expression in rice seedling roots in response to supplemental nitrogen. J Plant Physiol 200:62–75. CrossRefPubMedGoogle Scholar
  4. Chen X, Wang Y, Lv B, Li J, Luo L, Lu S, Zhang X, Ma H, Ming F (2014) The NAC family transcription factor OsNAP confers abiotic stress response through the ABA pathway. Plant Cell Physiol 55:604–619. CrossRefPubMedGoogle Scholar
  5. Chi Y, Yang Y, Zhou Y, Zhou J, Fan B, Yu JQ, Chen Z (2013) Protein–protein interactions in the regulation of WRKY transcription factors. Mol Plant 6:287–300. CrossRefPubMedGoogle Scholar
  6. Dewanto V, Wu X, Adom KK, Liu RH (2002) Thermal processing enhances the nutritional value of tomatoes by increasing total antioxidant activity. J Agric Food Chem 50:3010–3014. CrossRefPubMedGoogle Scholar
  7. Diédhiou CJ, Popova OV, Dietz K-J, Golldack D (2008) The SNF1-type serine–threonine protein kinase SAPK4 regulates stress-responsive gene expression in rice. BMC Plant Biol 8:49CrossRefGoogle Scholar
  8. Du H, Wang N, Cui F, Li X, Xiao J, Xiong L (2010) Characterization of the β-carotene hydroxylase gene DSM2 conferring drought and oxidative stress resistance by increasing xanthophylls and abscisic acid synthesis in rice. Plant Physiol 154:1304–1318CrossRefGoogle Scholar
  9. Egamberdieva D, Davranov K, Wirth S, Hashem A, Fathi E, Allah A (2017) Impact of soil salinity on the plant-growth—promoting and biological control abilities of root associated bacteria. Saudi J Biol Sci 24:1601–1608. CrossRefPubMedPubMedCentralGoogle Scholar
  10. Fini A, Brunetti C, Di Ferdinando M, Ferrini F, Tattini M (2011) Stress-induced flavonoid biosynthesis and the antioxidant machinery of plants. Plant Signal Behav 6:709–711. CrossRefPubMedPubMedCentralGoogle Scholar
  11. Formentin E, Sudiro C, Perin G, Riccadonna S, Barizza E, Baldoni E, Lavezzo E, Stevanato P, Sacchi GA, Fontana P, Toppo S, Morosinotto T, Zottini M, Lo Schiavo F (2018) Transcriptome and cell physiological analyses in different rice cultivars provide new insights into adaptive and salinity stress responses. Front Plant Sci 9:204CrossRefGoogle Scholar
  12. Ghosh D, Xu J (2014) Abiotic stress responses in plant roots: a proteomics perspective. Front Plant Sci 5:6. CrossRefPubMedPubMedCentralGoogle Scholar
  13. Ho CL, Wu Y, Shen H, Provart NJ, Geisler M (2012) A predicted protein interactome for rice. Rice (N Y) 5:15CrossRefGoogle Scholar
  14. Hoang TML, Moghaddam L, Williams B, Khanna H (2015) Development of salinity tolerance in rice by constitutive-overexpression of genes involved in the regulation of programmed cell death. Front Plant Sci 6:175. CrossRefPubMedPubMedCentralGoogle Scholar
  15. Hong Y, Zhang H, Huang L, Li D, Song F (2016) Overexpression of a stress-responsive NAC transcription factor gene ONAC022 improves drought and salt tolerance in rice. Front Plant Sci 7:4. CrossRefPubMedPubMedCentralGoogle Scholar
  16. Hong WJ, Yoo YH, Park SA, Moon S, Kim SR, An G, Jung KH (2017) Genome-wide identification and extensive analysis of rice-endosperm preferred genes using reference expression database. J Plant Biol 60:249–258. CrossRefGoogle Scholar
  17. Hossain MR, Bassel GW, Pritchard J, Sharma GP (2016) Trait specific expression profiling of salt stress responsive genes in diverse rice genotypes as determined by modified significance analysis of microarrays. Front Plant Sci 7:567. CrossRefPubMedPubMedCentralGoogle Scholar
  18. Hu H, Dai M, Yao J, Xiao B, Li X, Zhang Q, Xiong L (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci USA 103:12987–12992. CrossRefPubMedGoogle Scholar
  19. Jacoby R, Peukert M, Succurro A, Koprivova A (2017) The role of soil microorganisms in plant mineral nutrition—current knowledge and future directions. Front Plant Sci 8:1617. CrossRefPubMedPubMedCentralGoogle Scholar
  20. Jan A, Maruyama K, Todaka D, Kidokoro S, Abo M, Yoshimura E, Shinozaki K, Nakashima K, Yamaguchi-Shinozaki K (2013) OsTZF1, a CCCH-tandem zinc finger protein, confers delayed senescence and stress tolerance in rice by regulating stress-related genes. Plant Physiol 161:1202–1216CrossRefGoogle Scholar
  21. Kim JS (2016) Investigation of phenolic, flavonoid, and vitamin contents in different parts of Korean ginseng (Panax ginseng C.A. Meyer). Prev Nutr Food Sci 21:263–270. CrossRefPubMedPubMedCentralGoogle Scholar
  22. Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360CrossRefGoogle Scholar
  23. Krasensky J, Jonak C (2018) Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks. J Exp Bot 63:1593–1608. CrossRefGoogle Scholar
  24. Kumar K, Kumar M, Kim SR, Ryu H, Cho YG (2013) Insights into genomics of salt stress response in rice. Rice 6:27CrossRefGoogle Scholar
  25. Li Q, Yang A, Zhang W (2017) Comparative studies on tolerance of rice genotypes differing in their tolerance to moderate salt stress. BMC Plant Biol 17:1–13. CrossRefPubMedPubMedCentralGoogle Scholar
  26. Liao Y, Smyth GK, Shi W (2014) FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930. CrossRefPubMedPubMedCentralGoogle Scholar
  27. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:1–21. CrossRefGoogle Scholar
  28. Lowe R, Shirley N, Bleackley M, Dolan S, Shafee T (2017) Transcriptomics technologies. PLoS Comput Biol 13:e1005457CrossRefGoogle Scholar
  29. Mizuno H, Kawahara Y, Sakai H, Kanamori H, Wakimoto H, Yamagata H, Oono Y, Wu J, Ikawa H, Itoh T, Matsumoto T (2010) Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.). BMC Genom 11:683CrossRefGoogle Scholar
  30. Negr S, Schmo SM (2017) Evaluating physiological responses of plants to salinity stress. Ann Bot 119:1–11. CrossRefGoogle Scholar
  31. Okazaki Y, Saito K (2014) Roles of lipids as signaling molecules and mitigators during stress response in plants. Plant J 79:584–596. CrossRefPubMedGoogle Scholar
  32. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR (2007) The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 35(Database issue):D883–887. CrossRefPubMedGoogle Scholar
  33. Park HL, Lee SW, Jung KH, Hahn TR, Cho MH (2013) Transcriptomic analysis of UV-treated rice leaves reveals UV-induced phytoalexin biosynthetic pathways and their regulatory networks in rice. Phytochemistry 96:57–71. CrossRefPubMedGoogle Scholar
  34. Park HJ, Kim WY, Yun DJ (2016) A new insight of salt stress signaling in plant. Mol Cells 39:447–459CrossRefGoogle Scholar
  35. Qadir M, Quillérou E, Nangia V, Murtaza G, Singh M, Thomas RJ, Drechsel P, Noble AD (2014) Economics of salt-induced land degradation and restoration. Nat Resour Forum 38:282–295CrossRefGoogle Scholar
  36. Seo S, Mitsuhara I, Feng J, Iwai T, Hasegawa M, Ohashi Y (2011) Cyanide, a coproduct of plant hormone ethylene biosynthesis, contributes to the resistance of rice to blast fungus. Plant Physiol 155:502–514CrossRefGoogle Scholar
  37. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape : a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504. CrossRefPubMedPubMedCentralGoogle Scholar
  38. Shi H, Ye T, Chen F, Cheng Z, Wang Y, Yang P, Zhang Y, Chan Z (2013) Manipulation of arginase expression modulates abiotic stress tolerance in Arabidopsis: effect on arginine metabolism and ROS accumulation. J Exp Bot 64:1367–1379. CrossRefPubMedPubMedCentralGoogle Scholar
  39. Siahpoosh MR, Sanchez DH, Schlereth A, Scofield GN, Furbank RT, Van Dongen JT, Kopka J (2012) Modification of OsSUT1 gene expression modulates the salt response of rice Oryza sativa cv. Taipei 309. Plant Sci 182:101–111. CrossRefPubMedGoogle Scholar
  40. Srivastava AK, Zhang C, Yates G, Bailey M, Brown A, Sadanandom A (2016) SUMO is a critical regulator of salt stress responses in rice. Plant Physiol 170:2378–2391. CrossRefPubMedPubMedCentralGoogle Scholar
  41. Tao J, Chen H, Ma B, Zhang W, Chen S, Zhang J (2015) The role of ethylene in plants under salinity stress. Front Plant Sci 6:1059. CrossRefPubMedPubMedCentralGoogle Scholar
  42. Toda Y, Tanaka M, Ogawa D, Kurata K, Kurotani K, Habu Y, Ando T, Sugimoto K, Mitsuda N, Katoh E, Abe K, Miyao A, Hirochika H, Hattori T, Takeda S (2013) RICE SALT SENSITIVE3 forms a ternary complex with JAZ and class-C bHLH factors and regulates jasmonate-induced gene expression and root cell elongation. Plant Cell 25:1709–1725CrossRefGoogle Scholar
  43. Ulrich D, Stephan AB, Tomoaki H, Wei L, Guohua X, Schroeder IJ (2014) Plant salt-tolerance mechanisms. Trends Plant Sci 19:371–379CrossRefGoogle Scholar
  44. Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell Environ 32:1211–1229. CrossRefPubMedGoogle Scholar
  45. Virdi AS, Singh S, Singh P (2015) Abiotic stress responses in plants: roles of calmodulin-regulated proteins. Front Plant Sci 6:809. CrossRefPubMedPubMedCentralGoogle Scholar
  46. Walia H, Wilson C, Ismail AM, Close TJ, Cui X (2009) Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress. BMC Genom 13:3–5. CrossRefGoogle Scholar
  47. Wang W, Zhao X, Li M, Huang L, Xu J, Zhang F, Cui Y, Fu B, Li Z (2016) Complex molecular mechanisms underlying seedling salt tolerance in rice revealed by comparative transcriptome and metabolomic profiling. J Exp Bot 67:405–419. CrossRefPubMedGoogle Scholar
  48. Xiang Y, Tang N, Du H, Ye H, Xiong L (2008) Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiol 148:1938–1952. CrossRefPubMedPubMedCentralGoogle Scholar
  49. Yamamoto E, Yonemaru J, Yamamoto T, Yano M (2012) OGRO: the overview of functionally characterized genes in rice online database. Rice 5:26. CrossRefPubMedPubMedCentralGoogle Scholar
  50. Yoo YH, Nalini Chandran AK, Park JC, Gho YS, Lee SW, An G, Jung KH (2017) OsPhyB-mediating novel regulatory pathway for drought tolerance in rice root identified by a global RNA-Seq transcriptome analysis of rice genes in response to water deficiencies. Front Plant Sci 8:580. CrossRefPubMedPubMedCentralGoogle Scholar
  51. Zhang Y, Zhu Y, Peng Y, Yan D, Li Q, Wang J, Wang L, He Z (2008) Gibberellin homeostasis and plant height control by EUI and a role for gibberellin in root gravity responses in rice. Cell Res 18:412–421. CrossRefPubMedGoogle Scholar
  52. Zhang Y, Gao P, Yuan JS (2010) Plant protein–protein interaction network and interactome. Curr Genom 11:40–46CrossRefGoogle Scholar
  53. Zhang J, Liu H, Sun J, Li B, Zhu Q, Chen S, Zhang H (2012) Arabidopsis fatty acid desaturase FAD2 is required for salt tolerance during seed germination and early seedling growth. PLoS One 7:e30355CrossRefGoogle Scholar
  54. Zhou Y, Yang P, Cui F, Zhang F, Luo X, Xie J (2016) Transcriptome analysis of salt stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.). PLoS One 11:e0146242. CrossRefPubMedPubMedCentralGoogle Scholar
  55. Zhou Y, Tang N, Huang L, Zhao Y, Tang X, Wang K (2018) Effects of salt stress on plant growth, antioxidant capacity, glandular trichome density, and volatile exudates of Schizonepeta tenuifolia briq. Int J Mol Sci 19:252. CrossRefPubMedCentralGoogle Scholar
  56. Zhu J (2003) Regulation of ion homeostasis under salt stress. Curr Opin Plant Biol 6:441–445. CrossRefPubMedGoogle Scholar

Copyright information

© Korean Society for Plant Biotechnology 2019

Authors and Affiliations

  1. 1.Graduate School of Biotechnology and Crop Biotech InstituteKyung Hee UniversityYonginRepublic of Korea
  2. 2.Graduate School of Biotechnology and College of Life ScienceKyung Hee UniversityYonginRepublic of Korea
  3. 3.Department of Oriental Medicinal Materials and ProcessingKyung Hee UniversityYonginRepublic of Korea

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