Comprehensive genome-wide identification and analysis of MYB transcription factors related to abiotic and biotic stress regulation in rice

comprehensive-genome-wide-identification-and-analysis-of-myb-transcription-factors-related-to-abiotic-and-biotic-stress-regulation-in-rice
Comprehensive genome-wide identification and analysis of MYB transcription factors related to abiotic and biotic stress regulation in rice

References

  1. Buti, M. et al. A Meta-Analysis of comparative transcriptomic data reveals a set of key genes involved in the tolerance to abiotic stresses in rice. Int. J. Mol. Sci. 20, 256 (2019).

  2. Jiao, W. et al. Transcriptional regulatory network reveals key transcription factors for regulating agronomic traits in soybean. Genome Biol. 25, 313. https://doi.org/10.1186/s13059-024-03454-w (2024).

    Google Scholar 

  3. Mishra, M., Shukla, N., Fatima, M. & Singh, N. K. Insights into genes and pathways regulating abiotic stress in Oryza sativa L.: a comprehensive transcriptome analysis. South. Afr. J. Bot. 179, 261–279. https://doi.org/10.1016/j.sajb.2025.02.028 (2025).

    Google Scholar 

  4. Mas-ud, M. A., Islam, M. S., Juthee, S. A., Matin, M. N. & Hosenuzzaman, M. Mechanisms and approaches for enhancing high-temperature stress tolerance in rice (Oryza sativa L). J. Agron. Crop. Sci. 211, e70093. https://doi.org/10.1111/jac.70093 (2025).

    Google Scholar 

  5. Wu, X. et al. MYB transcription factors in plants: a comprehensive review of their discovery, structure, classification, functional diversity and regulatory mechanism. Int. J. Biol. Macromol. 2024, 136652 (2024).

  6. Hou, M., Zhang, Y., Xu, X. & Ai, H. Advances in auxin synthesis, transport, and signaling in rice: implications for stress resilience and crop improvement. Front. Plant Sci. 15, 1516884 (2025).

    Google Scholar 

  7. Caliskan, I. T. et al. Unraveling the functional diversity of MYB transcription factors in plants: a systematic review of recent advances. Phyton 94, 2229 (2025).

    Google Scholar 

  8. Jian, L., Kang, K., Choi, Y., Suh, M. C. & Paek, N. C. Mutation of OsMYB60 reduces rice resilience to drought stress by attenuating cuticular wax biosynthesis. Plant J. 112, 339–351 (2022).

    Google Scholar 

  9. Zhang, H. C. et al. Genome-wide identification of R2R3-MYB transcription factor subfamily genes involved in salt stress in rice (Oryza sativa L). BMC Genom. 25, 797 (2024).

    Google Scholar 

  10. Fu, C. et al. LcMYB5, an R2R3-MYB family gene from lonicera caerulea L., enhances drought and salt tolerance in transgenic tobacco and blue honeysuckle. J. Plant Physiol. 304, 154409 (2025).

    Google Scholar 

  11. Peng, Y., Tang, N., Zou, J., Ran, J. & Chen, X. Rice MYB transcription factor OsMYB1R1 negatively regulates drought resistance. Plant. Growth Regul. 99, 515–525 (2023).

    Google Scholar 

  12. Yang, A., Dai, X. & Zhang, W. H. A R2R3-type MYB gene, OsMYB2, is involved in salt, cold, and dehydration tolerance in rice. J. Exp. Bot. 63, 2541–2556. https://doi.org/10.1093/jxb/err431 (2012).

    Google Scholar 

  13. Xiong, H. et al. Overexpression of OsMYB48-1, a novel MYB-Related transcription factor, enhances drought and salinity tolerance in rice. PLOS ONE. 9, e92913. https://doi.org/10.1371/journal.pone.0092913 (2014).

    Google Scholar 

  14. Bhatt, P. A., Gurav, T. P., Kondhare, K. R. & Giri, A. P. MYB proteins: versatile regulators of plant development, stress responses, and secondary metabolite biosynthetic pathways. Int. J. Biol. Macromol. 2024, 138588 (2024).

  15. Dai, X. et al. Overexpression of an R1R2R3 MYB gene, OsMYB3R-2, increases tolerance to freezing, drought, and salt stress in transgenic arabidopsis. Plant Physiol. 143, 1739–1751. https://doi.org/10.1104/pp.106.094532 (2007).

    Google Scholar 

  16. Zhang, L., Zhao, G., Jia, J., Liu, X. & Kong, X. Molecular characterization of 60 isolated wheat MYB genes and analysis of their expression during abiotic stress. J. Exp. Bot. 63, 203–214 (2012).

    Google Scholar 

  17. Wang, Z. et al. Unveiling the power of MYB transcription factors: master regulators of multi-stress responses and development in cotton. Int. J. Biol. Macromol. 2024, 133885 (2024).

  18. Ma, Q. et al. Enhanced tolerance to chilling stress in OsMYB3R-2 Transgenic rice is mediated by alteration in cell cycle and ectopic expression of stress genes. Plant Physiol. 150, 244–256. https://doi.org/10.1104/pp.108.133454 (2009).

    Google Scholar 

  19. Vannini, C. et al. Overexpression of the rice Osmyb4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants. Plant J. 37, 115–127 (2004).

    Google Scholar 

  20. Su, C. F. et al. A novel MYBS3-Dependent pathway confers cold tolerance in rice. Plant Physiol. 153, 145–158. https://doi.org/10.1104/pp.110.153015 (2010).

    Google Scholar 

  21. Lv, Y. et al. The OsMYB30 transcription factor suppresses cold tolerance by interacting with a JAZ protein and suppressing β-Amylase expression. Plant Physiol. 173, 1475–1491. https://doi.org/10.1104/pp.16.01725 (2017).

    Google Scholar 

  22. El-kereamy, A. et al. The rice R2R3-MYB transcription factor OsMYB55 is involved in the tolerance to high temperature and modulates amino acid metabolism. PLOS ONE. 7, e52030. https://doi.org/10.1371/journal.pone.0052030 (2012).

    Google Scholar 

  23. Zhang, B. et al. Genome-wide identification of the MYB gene family and FfMYB13 regulation analysis in cell wall synthesis underlying tissue toughening process of yellow flammulina filiformis stipes. Int. J. Biol. Macromol. 288, 138660 (2025).

    Google Scholar 

  24. Yu, Y. et al. The BpMYB4 transcription factor from betula platyphylla contributes toward abiotic stress resistance and secondary cell wall biosynthesis. Front. Plant Sci. 11, 606062 (2021).

    Google Scholar 

  25. Li, W. et al. Sclerenchyma cell thickening through enhanced lignification induced by OsMYB30 prevents fungal penetration of rice leaves. New Phytol. 226, 1850–1863 (2020).

    Google Scholar 

  26. Cao, W. L. et al. OsJAMyb, a R2R3-type MYB transcription factor, enhanced blast resistance in Transgenic rice. Physiol. Mol. Plant Pathol. 92, 154–160 (2015).

    Google Scholar 

  27. Zaynab, M. et al. Genome-wide and expression analysis to understand the DUF789 gene family during development of Arabidopsis thaliana. J. King Saud Univ. Sci. 36, 103478. https://doi.org/10.1016/j.jksus.2024.103478 (2024).

    Google Scholar 

  28. Makvandi, N., Ghorbani, A., Rostami, M., Rostami, A. & Ghasemi-Soloklui, A. A. Identification of key genes involved in heat stress response in Brassica napus L.: reconstruction of gene networks, hub genes, and promoter analysis. Iran. J. Genet. Plant. Breed. (IJGPB) 2022, 11 (2022).

  29. Ghorbani, A., Rostami, M. & Izadpanah, K. Gene network modeling and pathway analysis of maize transcriptomes in response to maize Iranian mosaic virus. Genomics 115, 110618. https://doi.org/10.1016/j.ygeno.2023.110618 (2023).

    Google Scholar 

  30. Mas-ud, M. A. et al. Small heat shock proteins: key genes for regulating heat stress responses in rice. Discover Plants. 2, 267. https://doi.org/10.1007/s44372-025-00353-7 (2025).

    Google Scholar 

  31. Bano, N., Fakhrah, S., Mohanty, C. S. & Bag, S. K. Transcriptome Meta-Analysis associated targeting hub genes and pathways of drought and salt stress responses in cotton (Gossypium hirsutum): a network biology approach. Front. Plant. Sci. 13, 2022 (2022).

  32. Szklarczyk, D. et al. The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 51, D638–D646. https://doi.org/10.1093/nar/gkac1000 (2023).

    Google Scholar 

  33. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504. https://doi.org/10.1101/gr.1239303 (2003).

    Google Scholar 

  34. Reza, M. S. et al. Metadata analysis to explore hub of the hub-genes highlighting their functions, pathways and regulators for cervical cancer diagnosis and therapies. Discover Oncol. 13, 79. https://doi.org/10.1007/s12672-022-00546-6 (2022).

    Google Scholar 

  35. Basar, M. A. et al. Identification of drug and protein-protein interaction network among stress and depression: a bioinformatics approach. Inf. Med. Unlocked. 37, 101174 (2023).

    Google Scholar 

  36. Olszewski, K., Tulyakov, S., Woodford, O., Li, H. & Luo, L. Transformable bottleneck networks. In Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV) 7648–7657 (2019).

  37. Evans, T. S. & Chen, B. Linking the network centrality measures closeness and degree. Commun. Phys. 5, 172 (2022).

    Google Scholar 

  38. Chin, C. H. et al. CytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst. Biol. 8, 1–7 (2014).

    Google Scholar 

  39. Artimo, P. et al. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 40, W597–W603 (2012).

    Google Scholar 

  40. Zhou, T. et al. itol. Toolkit accelerates working with iTOL (Interactive tree of Life) by an automated generation of annotation files. Bioinformatics 39, btad339 (2023).

    Google Scholar 

  41. Sigrist, C. J. A. et al. New and continuing developments at PROSITE. Nucleic Acids Res. 41, D344–D347 (2012).

    Google Scholar 

  42. Chen, C. et al. TBtools-II: a one for all, all for one bioinformatics platform for biological big-data mining. Mol. Plant. 16, 1733–1742 (2023).

    Google Scholar 

  43. Hu, B. et al. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31, 1296–1297 (2015).

    Google Scholar 

  44. Lescot, M. et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in Silico analysis of promoter sequences. Nucleic Acids Res. 30, 325–327 (2002).

    Google Scholar 

  45. Darzentas, N. Circoletto: visualizing sequence similarity with circos. Bioinformatics 26, 253 (2010).

  46. Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303. https://doi.org/10.1093/nar/gky427 (2018).

    Google Scholar 

  47. Laskowski, R. A., MacArthur, M. W. & Thornton, J. M. PROCHECK: validation of protein structure coordinates. In Crystallography of Biological Macromolecules (Rossmann, M. G. & Arnold, E. D.) 722–725 (Kluwer Academic, 2001).

  48. Buitrago, S., Yang, X., Wang, L., Pan, R. & Zhang, W. Evolutionary analysis of anthocyanin biosynthetic genes: insights into abiotic stress adaptation. Plant Mol. Biol. 115, 6. https://doi.org/10.1007/s11103-024-01540-y (2024).

    Google Scholar 

  49. Liu, L. et al. Salinity inhibits rice seed germination by reducing α-Amylase activity via decreased bioactive Gibberellin content. Front. Plant. Sci. 9, 2018 (2018).

  50. Zou, X. et al. Salt-induced Inhibition of rice seminal root growth is mediated by ethylene-jasmonate interaction. J. Exp. Bot. 72, 5656–5672 (2021).

    Google Scholar 

  51. Katiyar, A. et al. Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC Genom. 13, 544. https://doi.org/10.1186/1471-2164-13-544 (2012).

    Google Scholar 

  52. Xue, Y., Li, K., Feng, W., Lai, Z. & Liu, S. Identification of R2R3-MYB transcription factor family based on Amaranthus tricolor genome and AtrMYB72 promoting betalain biosynthesis by directly activating AtrCYP76AD1 expression. Plants 14, 236 (2025).

  53. Mas-ud, M. A. et al. Unravelling the current status of rice stripe Mosaic Virus: its geographical spread, biology, epidemiology, and management. Agronomy 14, 236 (2024).

  54. Tang, R. J. et al. The Woody plant Poplar has a functionally conserved salt overly sensitive pathway in response to salinity stress. Plant Mol. Biol. 74, 367–380. https://doi.org/10.1007/s11103-010-9680-x (2010).

    Google Scholar 

  55. Yan, H. et al. Developmental variations of the reproductive organs of Ganders from different Goose breeds and the underlying mechanisms. Poult. Sci. 103, 104233. https://doi.org/10.1016/j.psj.2024.104233 (2024).

    Google Scholar 

  56. Suresh, N. T., Ravindran, V. E. & Krishnakumar, U. A computational framework to identify cross association between complex disorders by Protein-protein interaction network analysis. Curr. Bioinform. 16, 433–445. https://doi.org/10.2174/1574893615999200724145434 (2021).

    Google Scholar 

  57. Mas-ud, M. A. et al. Current Understanding of heat shock protein-mediated responses to heat stress in rice. Environ. Exp. Bot. 237, 106192. https://doi.org/10.1016/j.envexpbot.2025.106192 (2025).

    Google Scholar 

  58. Sferra, G., Fantozzi, D., Scippa, G. S. & Trupiano, D. Key pathways and genes of Arabidopsis thaliana and Arabidopsis halleri roots under cadmium stress responses: differences and similarities. Plants 12, 2563 (2023).

  59. Peng, W., Zhang, Y., Xie, H., Yu, Y. & Zhu, M. Research progress on the synergistic regulation of MYB transcription factor-mediated developmental plasticity and stress responses in rice. Front. Plant. Sci. 16, 2025 (2025).

  60. Saha, J. et al. Phylogenetic, structural, functional characterisation and effect of exogenous spermidine on rice (Oryza sativa) HAK transporters under salt stress. Funct. Plant Biol. 50, 160–182 (2023).

    Google Scholar 

  61. Abiraami, T. V., Sanyal, R. P., Misra, H. S. & Saini, A. Genome-wide analysis of bromodomain gene family in Arabidopsis and rice. Front. Plant. Sci. 14, 963 (2023).

  62. Dong, J. et al. Genome-Wide identification of the NHX gene family in Punica granatum L. and their expressional patterns under salt stress. Agronomy 11, 586 (2021).

  63. Zhang, Z. et al. Genome-Wide characterization and expression analysis of the HD-ZIP gene family in response to salt stress in pepper. Int. J. Genomics. 2021, 8105124. https://doi.org/10.1155/2021/8105124 (2021).

  64. Solis, C. A. et al. Evolutionary significance of NHX family and NHX1 in salinity stress adaptation in the genus Oryza. Int. J. Mol. Sci. 23, 369 (2022).

  65. Chen, C. et al. Characterization of imprinted genes in rice reveals conservation of regulation and imprinting with other plant species. Plant Physiol. 177, 1754–1771. https://doi.org/10.1104/pp.17.01621 (2018).

    Google Scholar 

  66. Liu, H. et al. Genome-wide analysis of the actinidia chinensis NHX family and characterization of the roles of AcNHX3 and AcNHX7 in regulating salt tolerance in Arabidopsis. Environ. Exp. Bot. 214, 105477. https://doi.org/10.1016/j.envexpbot.2023.105477 (2023).

    Google Scholar 

  67. Pan, X., Zheng, Y., Lei, K., Tao, W. & Zhou, N. Systematic analysis of heat shock protein 70 (HSP70) gene family in radish and potential roles in stress tolerance. BMC Plant Biol. 24, 2. https://doi.org/10.1186/s12870-023-04653-6 (2024).

    Google Scholar 

  68. Li, N. et al. Plant Hormone-Mediated regulation of heat tolerance in response to global climate change. Front. Plant. Sci. 11, 236 (2021).

  69. Durmusoglu, S., Saglam, A. & Kadıoglu, A. In Improving Stress Resilience in Plants (eds. Mohammad, A. A. et al.) 277–295 (Academic Press, 2024).

  70. Chen, C. L. et al. Methyl jasmonate enhances rice tolerance to alkaline stress via the auxin pathway. Plant. Stress. 14, 100612. https://doi.org/10.1016/j.stress.2024.100612 (2024).

    Google Scholar 

  71. Wu, J. et al. Effects of jasmonic acid on stress response and quality formation in vegetable crops and their underlying molecular mechanisms. Plants 13, 253 (2024).

  72. Li, Y. et al. Reversing anther thermotolerance by manipulating the cis-elements in the promoter of a high-temperature upregulated gene casein kinase I in upland cotton. Sci. China Life Sci. https://doi.org/10.1007/s11427-024-2755-9 (2025).

    Google Scholar 

  73. Mas-ud, M. A. et al. Signaling, homeostasis, transport, and regulatory mechanisms of cytokinin in rice and Arabidopsis response to heat stress. J. Plant Growth Regul. 44, 3491–3509. https://doi.org/10.1007/s00344-025-11743-2 (2025). Biosynthesis.

  74. Zhu, N. et al. The R2R3-type MYB gene OsMYB91 has a function in coordinating plant growth and salt stress tolerance in rice. Plant Sci. 236, 146–156. https://doi.org/10.1016/j.plantsci.2015.03.023 (2015).

    Google Scholar 

  75. Saidi, A. & Hajibarat, Z. Characterization of cis-elements in hormonal stress-responsive genes in Oryza sativa. Asia Pac. J. Mol. Biol. Biotechnol. 27, 95–102 (2019).

    Google Scholar 

  76. Ghosh, P. & Roychoudhury, A. Molecular basis of Salicylic acid–phytohormone crosstalk in regulating stress tolerance in plants. Braz. J. Bot. 47, 735–750. https://doi.org/10.1007/s40415-024-00983-3 (2024).

    Google Scholar 

  77. Gul, R. M. S., Rauf, S., Ortiz, R., Waqas Khalid, M. & Kaya, Y. Understanding abscisic acid-mediated stress signaling to affect rice development under stress. Front. Sustain. Food Syst. 8, 253 (2024).

  78. Pasquali, G., Biricolti, S., Locatelli, F., Baldoni, E. & Mattana, M. Osmyb4 expression improves adaptive responses to drought and cold stress in Transgenic apples. Plant Cell Rep. 27, 1677–1686. https://doi.org/10.1007/s00299-008-0587-9 (2008).

    Google Scholar 

  79. Wang, F., Wan, C., Wu, W., Yang, S. & Chen, X. Exogenous melatonin (MT) enhances salt tolerance of Okra (Abelmoschus esculentus L.) plants by regulating proline, photosynthesis, ion homeostasis and ROS pathways. Vegetos 37, 224–238. https://doi.org/10.1007/s42535-023-00568-7 (2024).

    Google Scholar 

  80. Tiwari, P. et al. Auxin-salicylic acid cross-talk ameliorates OsMYB–R1 mediated defense towards heavy metal, drought and fungal stress. J. Hazard. Mater. 399, 122811. https://doi.org/10.1016/j.jhazmat.2020.122811 (2020).

    Google Scholar 

  81. Zhang, L. et al. The wheat MYB-related transcription factor TaMYB72 promotes flowering in rice. J. Integr. Plant Biol. 58, 701–704. https://doi.org/10.1111/jipb.12461 (2016).

    Google Scholar 

  82. Mariyam, S. et al. Functional diversification and mechanistic insights of MYB transcription factors in mediating plant growth and development, secondary Metabolism, and stress responses. J. Plant Growth Regul. https://doi.org/10.1007/s00344-025-11622-w (2025).

    Google Scholar 

  83. Santhoshkumar, R. & Yusuf, A. In Silico structural modeling and analysis of physicochemical properties of Curcumin synthase (CURS1, CURS2, and CURS3) proteins of curcuma longa. J. Genetic Eng. Biotechnol. 18, 24. https://doi.org/10.1186/s43141-020-00041-x (2020).

  84. Kokwe, L., Nnolim, N. E., Ezeogu, L. I., Sithole, B. & Nwodo, U. U. Thermoactive metallo-keratinase from Bacillus sp. NFH5: Characterization, structural elucidation, and potential application as detergent additive. Heliyon 9, 236. https://doi.org/10.1016/j.heliyon.2023.e13635 (2023).

  85. Tan, Q. W. et al. Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nat. Commun. 14, 986. https://doi.org/10.1038/s41467-023-36517-w (2023).

    Google Scholar 

  86. Chen, G. et al. Variation in the abundance of OsHAK1 transcript underlies the differential salinity tolerance of an indica and a Japonica rice cultivar. Front. Plant. Sci. 8, 236 (2018).

  87. Hwang, J. U., Kim, S., Son, H. & Kwak, J. M. MYB transcription factors in plant developmental plasticity. J. Plant. Biol. https://doi.org/10.1007/s12374-025-09493-5 (2025).

    Google Scholar 

  88. Inukai, S., Kock, K. H. & Bulyk, M. L. Transcription factor–DNA binding: beyond binding site motifs. Curr. Opin. Genet. Dev. 43, 110–119. https://doi.org/10.1016/j.gde.2017.02.007 (2017).

    Google Scholar 

  89. Vishwakarma, H. et al. Heat stress transcripts, differential expression, and profiling of heat stress tolerant gene TaHsp90 in Indian wheat (Triticum aestivum L.) Cv C306. PLOS ONE. 13, e0198293. https://doi.org/10.1371/journal.pone.0198293 (2018).

    Google Scholar 

  90. Panzade, K. P., Kale, S. S., Kapale, V. & Chavan, N. R. Genome-Wide analysis of heat shock transcription factors in Ziziphus Jujuba identifies potential candidates for crop improvement under abiotic stress. Appl. Biochem. Biotechnol. 193, 1023–1041. https://doi.org/10.1007/s12010-020-03463-y (2021).

    Google Scholar 

  91. Yuan, C. et al. Genome-Wide identification and characterization of HSP90-RAR1-SGT1-Complex members from Arachis genomes and their responses to biotic and abiotic stresses. Front. Genet. 12, 236 (2021).

  92. Li, Q. et al. Hub gene identification and Heat-Stress-Related transcriptional regulation mechanism in cabbage (Brassica oleracea L). Horticulturae 2023, 9 (2023).

  93. He, Q. et al. Genome-wide characterization of RsHSP70 gene family reveals positive role of RsHSP70-20 gene in heat stress response in radish (Raphanus sativus L). Plant Physiol. Biochem. 199, 107710. https://doi.org/10.1016/j.plaphy.2023.107710 (2023).

    Google Scholar 

  94. Wang, H. et al. Genome-Wide analysis of heat shock protein family and identification of their functions in rice quality and yield. Int. J. Mol. Sci. 25, 253 (2024).

  95. Mas-ud, M. A., Juthee, S. A., Matin, M. N. & Hosenuzzaman, M. Brassinosteroids regulated target genes and their molecular evolution and interaction in rice (Oryza sativa L.) response to salt stress. Plant Sci. Today (2025).

Download references