Evolutionary conservation of salinity responsive miRNAs from Indian wheat (Triticum aestivum) landrace, Kharchia Local

MAHENDRA  C; KUMAR NUPUR  HRISHIKESHAN; AHMED MOHAMMED  ISMAIL; PRADEEP KUMAR  JAIN; KISHOR  GAIKWAD; KANIKA  KUMAR

doi:10.56093/ijas.v94i12.147730

Authors

MAHENDRA C ICAR-Indian Agricultural Research Institute, New Delhi
KUMAR NUPUR HRISHIKESHAN ICAR-Indian Agricultural Research Institute, New Delhi
AHMED MOHAMMED ISMAIL ICAR-Indian Agricultural Research Institute, New Delhi
PRADEEP KUMAR JAIN ICAR-National Institute for Plant Biotechnology, New Delhi
KISHOR GAIKWAD ICAR-National Institute for Plant Biotechnology, New Delhi
KANIKA KUMAR ICAR-National Institute for Plant Biotechnology, New Delhi

https://doi.org/10.56093/ijas.v94i12.147730

Keywords:

Abiotic stress, MicroRNA, mRNA target, Phylogenetic analysis, Seed sequence

Abstract

Being temporal, majority of abiotic stresses induces responses in plants that needs to be regulated in energy efficient manner. These regulations are carried out by many regulatory molecules including microRNAs and transcription factors. Like protein coding genes, miRNAs are also conserved across the plant species to exhibit their conserved function during growth, development and response to biotic or abiotic stresses. The present study was carried out during 2020 and 2021 at National phytotron facility, ICAR-Indian Agricultural Research Institute, New Delhi. Control and salinity treated plants of Kharchia Local, a highly salt tolerant landrace of wheat (Triticum aestivum L.) from India, were grown in hydroponics and after sequencing and analysis of small RNA data, salinity responsive mature miRNA sequences from Kharchia Local were analyzed for their evolutionary relationship with sequences from the public databases. The phylogenetic study, sequence similarity (identity scores) and multiple sequence comparison was used for evolutionary conservation analysis. The study revealed that, miRNA sequences from Kharchia Local are diverse and did not group with the salinity responsive miRNAs from the database except miR1551. Interestingly, a total of 25 known or conserved miRNA families were identified as salinity responsive across the plant species. The miRNAs from Kharchia Local appears to play regulatory role in novel mechanisms of salinity tolerance.

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References

Barik S, Kumar A, Sarkar Das S, Yadav S, Gautam V, Singh A, Singh S and Sarkar A K. 2015. Coevolution pattern and functional conservation or divergence of miR167s and their targets across diverse plant species. Scientific Reports 5(1): 14611. DOI: https://doi.org/10.1038/srep14611

Chen X, Chen Z, Fiorentino A, Kuess M, Tharayil N, Kumar R, Leonard E, Noorai R, Hu Q and Luo H. 2024. MicroRNA169 integrates multiple factors to modulate plant growth and abiotic stress responses. Plant Biotechnology Journal 22(9): 2541–57. DOI: https://doi.org/10.1111/pbi.14367

Dai X, Zhuang Z and Zhao P X. 2018. psRNATarget: A plant small RNA target analysis server (2017 release). Nucleic Acids Research 46(W1): 49–54. DOI: https://doi.org/10.1093/nar/gky316

Feng H, Wang B, Zhang Q, Fu Y, Huang L, Wang X and Kang Z. 2015. Exploration of microRNAs and their targets engaging in the resistance interaction between wheat and stripe rust. Frontiers in Plant Science 30(6): 469. DOI: https://doi.org/10.3389/fpls.2015.00469

Ferdous J, Sanchez-Ferrero J C, Langridge P, Milne L, Chowdhury J, Brien C and Tricker P J. 2017. Differential expression of microRNAs and potential targets under drought stress in barley. Plant, Cell and Environment 40(1): 11–24. DOI: https://doi.org/10.1111/pce.12764

Filipowicz W, Bhattacharyya S N and Sonenberg N. 2008. Mechanisms of post-transcriptional regulation by microRNAs: Are the answers in sight? Nature Review Genetics 9: 102–14. Gupta A, Ghosh D, Rao S and Mathur S. 2024. Deciphering the role of MIR169d: NF-YA2 module under individual as well as combined drought and heat stress in Arabidopsis. Plant Physiology Reports 29(1): 153–64. DOI: https://doi.org/10.1007/s40502-023-00775-z

Hashimoto Y, Akiyama Y and Yuasa Y. 2013. Multiple-to-multiple relationships between microRNAs and target genes in gastric cancer. PloSONE 8(5): 62589. DOI: https://doi.org/10.1371/journal.pone.0062589

He C, Li Y X, Zhang G, Gu Z, Yang R, Li J, Lu Z J, Zhou Z H, Zhang C and Wang J. 2012. MiRmat: Mature microRNA sequence prediction. PLoS ONE 7(12): 51673. DOI: https://doi.org/10.1371/journal.pone.0051673

Hyoung S, Cho S H, Chung J H, So W M, Cui M H and Shin J S. 2020. Cytokinin oxidase PpCKX1 plays regulatory roles in development and enhances dehydration and salt tolerance in Physcomitrella patens. Plant Cell Reports 39: 419–30. DOI: https://doi.org/10.1007/s00299-019-02500-3

Jatan R, Chauhan P S and Lata C. 2020. High-throughput sequencing and expression analysis suggest the involvement of Pseudomonas putida RA-responsive microRNAs in growth and development of Arabidopsis. International Journal of Molecular Sciences 21(15): 5468. DOI: https://doi.org/10.3390/ijms21155468

Kozomara A, Birgaoanu M and Griffiths-Jones S. 2019. miRBase: From microRNA sequences to function. Nucleic Acids Research 47(D1): 155–62. DOI: https://doi.org/10.1093/nar/gky1141

Kumar S, Stecher G, Li M, Knyaz C and Tamura K. 2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35: 1547–49. DOI: https://doi.org/10.1093/molbev/msy096

Kumar V, Khare T, Shriram V and Wani S H. 2018. Plant small RNAs: The essential epigenetic regulators of gene expression for salt-stress responses and tolerance. Plant Cell Reports 37: 61–75. DOI: https://doi.org/10.1007/s00299-017-2210-4

Liu B and Sun G. 2017. microRNAs contribute to enhanced salt adaptation of the autopolyploid Hordeum bulbosum compared with its diploid ancestor. The Plant Journal 91(1): 57–69. DOI: https://doi.org/10.1111/tpj.13546

Lotfi A, Pervaiz T, Jiu S, Faghihi F, Jahanbakhshian Z, Khorzoghi E G, Fang J and Seyedi S M. 2017. Role of microRNAs and their target genes in salinity response in plants. Plant Growth Regulation 82: 377–90. DOI: https://doi.org/10.1007/s10725-017-0277-0

Martin-Rodriguez J A, Ariani A, Leija A, Elizondo A, Fuentes S I, Ramirez M, Gepts P, Hernandez G and Formey D. 2021. Phaseolus vulgaris MIR1511 genotypic variations differentially regulate plant tolerance to aluminium toxicity. The Plant Journal 105(6): 1521–33. DOI: https://doi.org/10.1111/tpj.15129

Muhire B M, Varsani A and Martin D P. 2014. SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE 9(9): 108277. DOI: https://doi.org/10.1371/journal.pone.0108277

Pradhan U K, Meher P K, Naha S, Rao A R, Kumar U, Pal S and Gupta A. 2023. ASmiR: A machine learning framework for prediction of abiotic stress-specific miRNAs in plants. Functional and Integrative Genomics 23: 92. DOI: https://doi.org/10.1007/s10142-023-01014-2

Pritchard C C, Cheng H H and Tewari M. 2012. MicroRNA profiling: Approaches and considerations. Nature Review Genetics 13: 358–69. DOI: https://doi.org/10.1038/nrg3198

Ragupathy R, Ravichandran S, Mahdi M S R, Huang D, Reimer E, Domaratzki M and Cloutier S. 2016. Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV. Scientific Reports 6(1): 39373. DOI: https://doi.org/10.1038/srep39373

Ravichandran S, Ragupathy R, Edwards T, Domaratzki M and Cloutier S. 2019. MicroRNA-guided regulation of heat stress response in wheat. BMC Genomics 20(1): 1–16. DOI: https://doi.org/10.1186/s12864-019-5799-6

Sanz-Carbonell A, Marques M C, Bustamante A, Fares M A, Rodrigo G and Gomez G. 2019. Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon. BMC Plant Biology 19: 1–17. DOI: https://doi.org/10.1186/s12870-019-1679-0

Saroha M, Arya A, Singh G and Sharma P. 2024. Enome-wide expression analysis of novel heat-responsive microRNAs and their targets in contrasting wheat genotypes at reproductive stage under terminal heat stress. Frontiers in Plant Science 15: 1328114. DOI: https://doi.org/10.3389/fpls.2024.1328114

Seo J S, Kim S H, Shim J S, Um T, Oh N, Park T, Kim Y S, Oh S J and Kim J K. 2024. The rice NUCLEAR FACTOR-YA5

and MICRORNA169a module promotes nitrogen utilization during nitrogen deficiency. Plant Physiology 194(1): 491–510. DOI: https://doi.org/10.1093/plphys/kiad504

Shukla L I, Chinnusamy V and Sunkar R. 2008. The role of microRNAs and other endogenous small RNAs in plant stress responses. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1779(11): 743–48. DOI: https://doi.org/10.1016/j.bbagrm.2008.04.004

Song X, Li Y, Cao X and Qi Y. 2019. MicroRNAs and their regulatory roles in plant-environment interactions. Annual Review of Plant Biology 70: 489–525. DOI: https://doi.org/10.1146/annurev-arplant-050718-100334

Su Y, Zhang Y, Huang N, Liu F, Su W, Xu L, Ahmad W, Wu Q, Guo J and Que Y. 2017. Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection. BMC Genomics 18(1): 1–19. DOI: https://doi.org/10.1186/s12864-017-3716-4

Wu W, Wu Y, Hu D, Zhou Y, Hu Y, Chen Y and Chen M. 2020. PncStress: A manually curated database of experimentally validated stress-responsive non-coding RNAs in plants. Database 2020: 1–6. DOI: https://doi.org/10.1093/database/baaa001

Yang G, Pan W, Cao R, Guo Q, Cheng Y, Zhao Q, Cui L and Nie X. 2022. Multi-omics reveals the key and specific miRNA-mRNA modules underlying salt tolerance in wild emmer wheat (Triticum dicoccoides L.). BMC Genomics 23(1): 724. DOI: https://doi.org/10.1186/s12864-022-08945-3

Yuan H, Cheng M, Wang R, Wang Z, Fan F, Wang W, Si F, Gao F and Li S. 2024. miR396b/GRF6 module contributes to salt tolerance in rice. Plant Biotechnology Journal 22(8): 2079–92. DOI: https://doi.org/10.1111/pbi.14326

Zeeshan M, Qiu C W, Naz S, Cao F and Wu F. 2021. Genome- wide discovery of miRNAs with differential expression patterns in responses to salinity in the two contrasting wheat cultivars. International Journal of Molecular Sciences 22(22): 12556. DOI: https://doi.org/10.3390/ijms222212556

Zhao Y, Xu K, Liu G, Li S, Zhao S, Liu X, Yang X and Xiao K. 2020. Global identification and characterization of miRNA family members responsive to potassium deprivation in wheat (Triticum aestivum L.). Scientific Reports 10(1): 15812. DOI: https://doi.org/10.1038/s41598-020-72642-y