Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting Indica Rice Cultivars under Reproductive-Stage Drought
Abstract
:1. Introduction
2. Results
2.1. Processing and Analysis of Small RNA-Seq Data
2.2. Identification of miRNAs Expressed in the Rice Cultivars
2.3. Differential Expression of miRNA in Root
2.4. Target Prediction for Known and Novel miRNAs in Rice
2.5. Expression Analysis of miRNA Target Gene
2.6. Gene Ontology Network Analysis of miRNA Targeted Genes
2.7. Functional Validation of miRNAs by RT-qPCR Assay
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Drought Stress Imposition
4.2. RNA Isolation, Small RNA Library Construction, and Sequencing
4.3. Small RNA Sequencing Reads Analysis
4.4. Differential Expression of Known and Novel miRNAs
4.5. Target Gene Prediction and Functional Enrichment Analysis of Targets
4.6. Whole-Genome Transcriptome Analysis for Functional Validation of miRNA
4.7. Validation of Differential Expression of miRNA by RT-qPCR
4.8. RT-qPCR Validation of Target Gene Expression
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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miRNA Family | Known miRNAs (Total Count) | Description of Target Gene |
---|---|---|
miR812 | osa-miR812a, b, c, d, e, f, g, h, i, j, k, l, m, n-5p, n-3p, o-5p, o-3p, p, s, t, u, and v (22) | GRAS family nuclear protein, Control of tillering (MOCI), Similar to serine/threonine protein kinase (OsCIPK10), Leucine-rich repeat, plant-specific protein, Similar to Na+/H+ antiporter, probable CP0838, Similar to 1-aminocyclopropane-1-carboxylate oxidase (Fragment) (ACO3), Similar to PDR-like ABC transporter (PDR4 ABC transporter). |
miR166 | osa-miR166a-5p, a-3p, b-5p, b-3p, c-5p, c-3p, d-5p, d-3p, e-5p, f, g-3p, h-5p, h-3p, i-3p, j-5p, j-3p, k-3p, l-5p, l-3p, and m (20) | Class III homeodomain Leu zipper (HD-Zip III) family member, Control of plant type architecture and leaf development (OsHB4), Leucine-rich repeat, N-terminal domain-containing protein, Similar to Rolled leaf1 (OsHox1), Serine/threonine protein kinase domain-containing protein (OsWAK105), Chloroplast-targeted Deg protease protein, Chloroplast development and maintenance of PSII function under high temperature (OsDeg10). |
miR156 | osa-miR156a, b-5p, b-3p, c-5p, c-3p, d, e, f-5p, f-3p, g-5p, g-3p, h-5p, h-3p, i, j-5p, j-3p, k, l-5p, and l-3p (19) | Positive regulator of cell proliferation, Control of grain size, shape, and quality (GW8), Squamosa promoter-binding-like transcription activator, Regulation of branching in panicles and vegetative shoots, Semi-dominant regulator of plant architecture (OsSPL). |
miR1861 | osa-miR1861b, c, e, f, g, h, I, j, k, l, and m (11) | Glyoxalase I, Abiotic stress response (GLYI-11), Glycoside hydrolase, carbohydrate-binding domain-containing protein, pentatricopeptide repeat protein, Chloroplast development (YSA), Similar to guanine nucleotide-binding protein α-1 subunit, Similar to GTP-binding protein-like; root hair defective 3 protein-like, Leucine-rich repeat, N-terminal domain-containing protein. |
miR167 | osa-miR167 a-5p, b, c-5p, d-5p, e-5p, f, g, h-5p, h-3p, i-5p, and j (11) | NB-ARC domain-containing protein, Similar to glutamate-gated kainate-type ion channel receptor subunit GluR5, pentatricopeptide repeat domain-containing protein, Short-chain dehydrogenase/reductase SDR family protein. |
miR396 | osa-miR396 a-5p, a-3p, b-5p, b-3p, c-5p, d, e-5p, f-5p, g, and h (10) | Growth regulating factor members (OsGRF), WD40/YVTN repeat-like domain-containing protein, Transcription activator, Gibberellin (GA)-induced stem elongation, Growth-regulating factor, Regulation of grain shape and panicle length, Negative regulation of seed shattering, Auxin efflux carrier protein, Auxin transport, Drought tolerance |
miR444 | osa-miR444 a-3p.2, b.2, b.1, c.2, c.1, d.3, d.2, e, and f (9) | MADS-box transcription factor, Cold tolerance, Control of tillering (OsMADS57), MADS-box transcription factor, Homologue of the AGL17-clade MADS-box genes, Regulation of root system development via auxin signaling (OsMADS25), Zinc finger, RING/FYVE/PHD-type domain-containing protein, pentatricopeptide repeat domain-containing protein. |
miR159 | osa-miR159a.2, a.1, b, c, d, e, and f (7) | GAMYB-like protein, Flower development and stem elongation at the reproductive stage (OsGAMYBL1), Transcriptional activator of gibberellin-dependent α-amylase expression, Regulation of nutrient mobilization in germination (GAMYB), Similar to Coatomer protein complex, β prime; β′-COP protein (OsWD40-125). |
miR395 | osa-miR395b, d, e, g, s, and y (6) | Similar to ATP sulfurylase (OsATPS), Similar to low-affinity sulfate transporter 3 (OsSultr2), Similar to Thioredoxin peroxidase (OsPrxII), Cytochrome b5 domain-containing protein (OsMSBP2), Sulphate permease. |
miR160 | osa-miR160a-5p, b-5p, c-5p, d-5p, and e-5p (5) | Auxin response factors (OsARF10, 13), Transcriptional factor B3 family protein (OsARF22). |
miR164 | osa-miR164a, b, d, e, and f (5) | NAC transcription factor is a positive regulator of heading and senescence during the reproductive phase (OsY37). Sugar transporter protein, Similar to Pollen-specific kinase partner protein. |
miR393 | osa-miR393a and b-5p (2) | Auxin receptor, Flag leaf inclination, Primary root growth, Crown root initiation, Seed development, Tillering (OsAFB2), F-Box auxin receptor protein, Nuclear protein, Flag leaf inclination, Primary root growth, Crown root initiation, Seed development, Tillering (TIR1), Protein kinase, catalytic domain-containing protein (OsWAK7/8). |
miR397 | osa-miR397a and b (2) | Heat shock protein (HSP40), Putative tetratricopeptide repeat (TPR)-containing protein, Growth and development, salt tolerance, abiotic stress tolerance (OsHsp40), Laccase (OsLAC2, 5, 7, 9, and 29). |
miR398 | osa-miR398a and b (2) | Similar to Superoxide dismutase [Cu-Zn] (Cu/Zn-SOD), Selenium binding protein. |
miR408 | osa-miR408-5p and 3p (2) | Similar to Auxin-responsive protein (Aux/IAA) (Fragment) (OsIAA30), Cupredoxin domain-containing protein (OsUCL30). |
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Kaur, S.; Seem, K.; Kumar, S.; Kaundal, R.; Mohapatra, T. Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting Indica Rice Cultivars under Reproductive-Stage Drought. Genes 2023, 14, 1390. https://doi.org/10.3390/genes14071390
Kaur S, Seem K, Kumar S, Kaundal R, Mohapatra T. Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting Indica Rice Cultivars under Reproductive-Stage Drought. Genes. 2023; 14(7):1390. https://doi.org/10.3390/genes14071390
Chicago/Turabian StyleKaur, Simardeep, Karishma Seem, Suresh Kumar, Rakesh Kaundal, and Trilochan Mohapatra. 2023. "Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting Indica Rice Cultivars under Reproductive-Stage Drought" Genes 14, no. 7: 1390. https://doi.org/10.3390/genes14071390
APA StyleKaur, S., Seem, K., Kumar, S., Kaundal, R., & Mohapatra, T. (2023). Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting Indica Rice Cultivars under Reproductive-Stage Drought. Genes, 14(7), 1390. https://doi.org/10.3390/genes14071390