Vietnam Academy of Science and Technology

Project's information

Project's title	Identification and expression analysis of functionally important microRNAs mediating salinity adaptation in rice (Oryza sativa L.) using next generation sequencing
Project’s code	THTETN.04/21-23
Research hosting institution	Institute of Genome Research
Project leader’s name	Nguyen Duc Quan, Ph.D
Project duration	01/06/2021 - 30/06/2023
Project’s budget	500 million VND
Classify	Grade B
Goal and objectives of the project	- Generate 8 miRNA sequencing datasets from the shoot and root of a salt tolerant and a salt sensitive rice cultivars under normal and salt stress conditions by the next generation sequencing method. - Identify 2 miRNAs involved in salt stress adaptation in rice. - Identify miRNA’s target genes that are involved in salt tolerance in rice.
Main results	- Theoretical results: + The study evaluated the salt tolerance of 2 rice cultivars, ĐP and IR28 at the seedling stage under salt stress of 150 mM NaCl for 5 days. Evaluation of physiological and biochemical characteristics determined that the ĐP and IR28 used in the study was salt tolerant and salt sensitive varieties, respectively. + The study sequenced miRNAs from the shoot and root tissues of 2 rice cultivar ĐP and IR28, and 8 sets of sequencing data, including ĐP-ĐC-T, ĐP-ĐC-R, ĐP-NaCl-T, ĐP-NaCl-R, IR28-ĐC-T, IR28-ĐC-R, IR28-NaCl-T and IR28-NaCl-R, were obtained with a high level of quality. Whole-miRNA sequencing quality scores: Q20 > 90% and Q30 > 80%. + Bioinformatics screening and analysis identified 4 potential miRNAs involved in salt stress tolerance in ĐP cultivar, including miR164d, miR168a, miR171h and miR398a. They are potential miRNAs involved in salt stress responses in rice by interfering with the expression of target genes such as SPL – a protein that regulates the biosynthesis of ROS scavenger, anthocyanin, transcription factors NAC21/22, AGO1 - a protein involved in miRNA-mediated gene silencing and growth control, and SCL6-II – a protein regulates the growth of primary roots in salt stressed ĐP rice. + Evaluation of the accuracy of 8 miRNA sequencing data sets was conducted by the RT-qPCR method. RT-qPCR results of 4 miRNAs, miR164d, miR169i, miR172d, miR398a, showed that their expressions are consistent with the results of the miRNA sequencing of 2 salt stressed rice cultivars. RT-qPCR results also showed that the selected miRNAs target NAC21/22, NTYF, AP2/ERF and CSD2. Together, our data prove that the miRNA dataset obtained from miRNA sequencing is accurate and highly reliable. - Applied results: The results obtained from this study provide insight on the salt tolerance mechanism of rice, especially the salt tolerant rice cultivar Doc Phung, at the molecular level. In addition, the obtained miRNA datasets also provide a powerful tool to facilitate the development of new rice cultivars with a higher level of salt tolerance.
Novelty and actuality and scientific meaningfulness of the results	- The topic has identified 4 potential miRNAs involved in salt tolerance in Doc Phung.
Products of the project	Scientific and technological products − Eight miRNA datasets: + One set of miRNA sequencing data from shoot tissues of Doc Phung in control conditions. Quality scores: Q20 > 90% and Q30 > 80%. + One set of miRNA sequencing data from root tissues of Doc Phung in control conditions. Quality scores: Q20 > 90% and Q30 > 80%. + One set of miRNA sequencing data from shoot tissues of Doc Phung in salt stress (150 mM NaCl) conditions. Quality scores: Q20 > 90% and Q30 > 80%. + One set of miRNA sequencing data from root tissues of Doc Phung in salt stress (150 mM NaCl) conditions. Quality scores: Q20 > 90% and Q30 > 80%. + One set of miRNA sequencing data from shoot tissues of IR28 in control conditions. Quality scores: Q20 > 90% and Q30 > 80%. + One set of miRNA sequencing data from root tissues of IR28 in control conditions. Quality scores: Q20 > 90% and Q30 > 80%. + One set of miRNA sequencing data from shoot tissues of IR28 in salt stress (150 mM NaCl) conditions. Quality scores: Q20 > 90% and Q30 > 80%. + One set of miRNA sequencing data from root tissues of IR28 in salt stress (150 mM NaCl) conditions. Quality scores: Q20 > 90% and Q30 > 80%. + These datasets are stored in the NCBI SRA library with BioProject ID: PRJNA892745 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA892745). − Four potential miRNAs involved in salt tolerance in Doc Phung rice, including miR164d, miR168a, miR171h and miR398a. Published articles: + Nguyen, Duc Quan, Nguyen, N.L., Nguyen, V.T., Tran, T.H.G., Nguyen, T.H., Nguyen, T.K.L., Nguyen, H.H. Comparative analysis of microRNA expression profiles in shoot and root tissues of contrasting rice cultivars (Oryza sativa L.) with different salt stress tolerance. PloS one, 2023, vol. 18, p. e0286140. http://doi.org/10.1371/journal.pone.0286140. (Impact factor: 3.75, Journal rank: Q1). + Nguyen, Duc Quan, Nguyen, N.L., Nguyen, V.T., Nguyen, T.H.G., Nguyen, T.H., Nguyen, T.K.L., Nguyen, H.H. Reliable reference genes for accurate gene expression profiling across different tissues and genotypes of rice seedlings (Oryza sativa L.) under salt stress. Russ J Plant Physiol, 2023, vol. 70, p. 104-114. http://doi.org/10.1134/S102144372360068X. (Impact factor: 1.4). + Nguyen, Duc Quan, Tran, T.H.G., Do, H. D. and Nguyen, H. H. Expression analysis of genes encoding salt induced transport proteins in two contrasting rice cultivars with different salt stress tolerance. J Biol, 2023, vol. 45(3), p. 59-67. http://doi.org/10.15625/2615-9023/18301.
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