OpenLB
Open Library of Bioscience
Advanced Search
BMC genomics
Aug 23, 2024;25 (1): 797.

Genome-wide identification of R2R3-MYB transcription factor subfamily genes involved in salt stress in rice (Oryza sativa L.).

Hao-Cheng Zhang, Yuan-Hang Gong, Tao Tao, Shuai Lu, Wen-Yu Zhou, Han Xia, Xin-Yi Zhang, Qing-Qing Yang, Ming-Qiu Zhang, Lian-Min Hong, Qian-Qian Guo, Xin-Zhe Ren, Zhi-Di Yang, Xiu-Ling Cai, De-Yong Ren, Ji-Ping Gao, Su-Kui Jin, Yu-Jia Leng
Author Information
  1. Hao-Cheng Zhang: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  2. Yuan-Hang Gong: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  3. Tao Tao: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  4. Shuai Lu: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  5. Wen-Yu Zhou: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  6. Han Xia: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  7. Xin-Yi Zhang: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  8. Qing-Qing Yang: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  9. Ming-Qiu Zhang: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  10. Lian-Min Hong: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  11. Qian-Qian Guo: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  12. Xin-Zhe Ren: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  13. Zhi-Di Yang: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  14. Xiu-Ling Cai: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
  15. De-Yong Ren: State Key Laboratory of Rice Biology and Breeding, National Rice Research Institute, Hangzhou, 310006, China.
  16. Ji-Ping Gao: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China. jpgao@yzu.edu.cn.
  17. Su-Kui Jin: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China. skjin@yzu.edu.cn.
  18. Yu-Jia Leng: Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, China. yujialeng@yzu.edu.cn.
PMID: 39179980 DOI: 10.1186/s12864-024-10693-5

Abstract

BACKGROUND: R2R3-MYB transcription factors belong to one of the largest gene subfamilies in plants, and they are involved in diverse biological processes. However, the role of R2R3-MYB transcription factor subfamily genes in the response of rice (Oryza sativa L.) to salt stress has been rarely reported.
RESULTS: In this study, we performed a genome-wide characterization and expression identification of rice R2R3-MYB transcription factor subfamily genes. We identified a total of 117 R2R3-MYB genes in rice and characterized their gene structure, chromosomal location, and cis-regulatory elements. According to the phylogenetic relationships and amino acid sequence homologies, the R2R3-MYB genes were divided into four groups. qRT-PCR of the R2R3-MYB genes showed that the expression levels of 10 genes significantly increased after 3 days of 0.8% NaCl treatment. We selected a high expression gene OsMYB2-115 for further analysis. OsMYB2-115 was highly expressed in the roots, stem, leaf, and leaf sheath. OsMYB2-115 was found to be localized in the nucleus, and the yeast hybrid assay showed that OsMYB2-115 has transcriptional activation activity.
CONCLUSION: This result provides important information for the functional analyses of rice R2R3-MYB transcription factor subfamily genes related to the salt stress response and reveals that OsMYB2-115 may be an important gene associated with salt tolerance in rice.

Keywords

Gene expression R2R3-MYB Rice (Oryza sativa L.) Salt stress Transcription factor

References

  1. Plant Sci. 2015 Jul;236:146-56 [PMID: 26025528]
  2. Sci Rep. 2015 Jun 05;5:11037 [PMID: 26047035]
  3. Front Plant Sci. 2019 Feb 18;10:168 [PMID: 30833955]
  4. Biology (Basel). 2020 Mar 24;9(3): [PMID: 32213912]
  5. Plant J. 1999 Sep;19(6):679-89 [PMID: 10571853]
  6. Plant J. 2008 Jan;53(1):53-64 [PMID: 17971045]
  7. Front Plant Sci. 2022 Jun 27;13:934877 [PMID: 35832230]
  8. BMB Rep. 2010 Jan;43(1):34-9 [PMID: 20132733]
  9. Plant Physiol. 2009 Sep;151(1):275-89 [PMID: 19625633]
  10. Mol Biol Evol. 2018 Jun 1;35(6):1547-1549 [PMID: 29722887]
  11. Curr Opin Plant Biol. 2001 Oct;4(5):447-56 [PMID: 11597504]
  12. Plants (Basel). 2022 Jun 02;11(11): [PMID: 35684271]
  13. Int J Biol Macromol. 2021 Nov 30;191:359-376 [PMID: 34534587]
  14. Nucleic Acids Res. 2020 Jan 8;48(D1):D1104-D1113 [PMID: 31701126]
  15. Plant Signal Behav. 2016;11(1):e1117723 [PMID: 26636625]
  16. Plant Biotechnol J. 2023 Jun;21(6):1140-1158 [PMID: 36752420]
  17. Front Plant Sci. 2015 Dec 24;6:1157 [PMID: 26734052]
  18. PLoS One. 2015 Jun 02;10(6):e0127831 [PMID: 26035591]
  19. Plant Physiol Biochem. 2023 Oct;203:108041 [PMID: 37722281]
  20. Bioinformatics. 2015 Apr 15;31(8):1296-7 [PMID: 25504850]
  21. Nucleic Acids Res. 2007 Jan;35(Database issue):D883-7 [PMID: 17145706]
  22. Plant Cell Environ. 2020 Aug;43(8):1925-1943 [PMID: 32406163]
  23. J Exp Bot. 2015 Sep;66(19):5997-6008 [PMID: 26139822]
  24. Proc Natl Acad Sci U S A. 1992 Jul 15;89(14):6428-32 [PMID: 1631139]
  25. Trends Plant Sci. 2010 Oct;15(10):573-81 [PMID: 20674465]
  26. Mol Cells. 2011 May;31(5):447-54 [PMID: 21399993]
  27. Nat Struct Biol. 1996 Feb;3(2):178-87 [PMID: 8564545]
  28. Hortic Res. 2023 Apr 21;10(6):uhad080 [PMID: 37323234]
  29. J Genet Genomics. 2009 Jan;36(1):17-29 [PMID: 19161942]
  30. Plant Mol Biol. 1999 Nov;41(5):577-85 [PMID: 10645718]
  31. Mol Plant. 2020 Aug 3;13(8):1194-1202 [PMID: 32585190]
  32. PLoS Genet. 2009 Mar;5(3):e1000440 [PMID: 19325888]
  33. J Exp Bot. 2012 Apr;63(7):2541-56 [PMID: 22301384]
  34. Plant Cell. 2007 Jul;19(7):2264-77 [PMID: 17644729]
  35. Plant Cell Physiol. 2013 Feb;54(2):e6 [PMID: 23299411]
  36. Front Plant Sci. 2022 Jan 03;12:782220 [PMID: 35046974]
  37. Plant Cell Physiol. 2006 Jan;47(1):141-53 [PMID: 16284406]
  38. EMBO J. 1994 Nov 15;13(22):5383-92 [PMID: 7957104]
  39. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W475-8 [PMID: 21470960]
  40. Annu Rev Plant Biol. 2008;59:651-81 [PMID: 18444910]
  41. PLoS One. 2014 Mar 25;9(3):e92913 [PMID: 24667379]
  42. Plants (Basel). 2022 Jul 25;11(15): [PMID: 35893632]
  43. Front Plant Sci. 2022 Oct 24;13:1022076 [PMID: 36352865]
  44. New Phytol. 2020 Jul;227(2):455-472 [PMID: 32167578]
  45. Trends Plant Sci. 2019 Oct;24(10):934-946 [PMID: 31358471]
  46. Plant J. 2013 Oct;76(2):258-73 [PMID: 23855375]
  47. Int J Mol Sci. 2021 Feb 24;22(5): [PMID: 33668247]
  48. Plant Cell. 2005 Mar;17(3):705-21 [PMID: 15722475]
  49. Hortic Res. 2023 Jul 05;10(8):uhad135 [PMID: 37694228]
  50. Methods Mol Biol. 2007;406:179-212 [PMID: 18287693]
  51. Nucleic Acids Res. 2021 Jan 8;49(D1):D412-D419 [PMID: 33125078]
  52. Methods. 2001 Dec;25(4):402-8 [PMID: 11846609]
  53. Int J Mol Sci. 2015 Jul 13;16(7):15811-51 [PMID: 26184177]
  54. Nucleic Acids Res. 1999 Jan 1;27(1):295-6 [PMID: 9847207]
  55. J Mol Evol. 1998 Jan;46(1):74-83 [PMID: 9419227]
  56. Plant Cell Physiol. 2016 Aug;57(8):1657-77 [PMID: 27279646]
  57. Plant Sci. 2021 Jul;308:110924 [PMID: 34034872]
  58. PLoS One. 2010 Jun 28;5(6):e11335 [PMID: 20596258]
  59. Plant J. 2015 Jun;82(6):962-977 [PMID: 25912720]
  60. Int J Mol Sci. 2021 Jun 07;22(11): [PMID: 34200125]
  61. Plant J. 2007 Nov;52(3):528-38 [PMID: 17727613]
  62. BMC Genomics. 2012 Oct 10;13:544 [PMID: 23050870]
  63. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8 [PMID: 19458158]
  64. Int J Mol Sci. 2020 Nov 04;21(21): [PMID: 33158201]
  65. EMBO J. 1987 Dec 1;6(12):3553-8 [PMID: 3428265]

Grants

  1. PL202403/Open funds of the Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding
  2. BE2022336 and JBGS[2021]001/Jiangsu Province Government
  3. BM2022008-02/Project of Zhongshan Biological Breeding Laboratory
  4. B21HJ0220/Hainan Yazhou Bay Seed Lab
  5. 22KJA210003/Natural Science Foundation of the Jiangsu Higher Education Institutions of China

MeSH Term

Oryza
Transcription Factors
Salt Stress
Phylogeny
Plant Proteins
Gene Expression Regulation, Plant
Genome, Plant
Multigene Family
Gene Expression Profiling
Chromosomes, Plant

Chemicals

Transcription Factors
Plant Proteins
Journal Article

Word Cloud

Created with Highcharts 10.0.0R2R3-MYBgenesricetranscriptionfactorOsMYB2-115genesubfamilysaltstressexpressionOryzasativaLinvolvedresponseidentificationshowedleafimportantBACKGROUND:factorsbelongonelargestsubfamiliesplantsdiversebiologicalprocessesHoweverrolerarelyreportedRESULTS:studyperformedgenome-widecharacterizationidentifiedtotal117characterizedstructurechromosomallocationcis-regulatoryelementsAccordingphylogeneticrelationshipsaminoacidsequencehomologiesdividedfourgroupsqRT-PCRlevels10significantlyincreased3days08%NaCltreatmentselectedhighanalysishighlyexpressedrootsstemsheathfoundlocalizednucleusyeasthybridassaytranscriptionalactivationactivityCONCLUSION:resultprovidesinformationfunctionalanalysesrelatedrevealsmayassociatedtoleranceGenome-wideGeneRiceSaltTranscription

Similar Articles

Cited By