Small RNA Differential Expression Analysis Reveals miRNAs Involved in Dormancy Progression in Sweet Cherry Floral Buds
Abstract
:1. Introduction
2. Results
2.1. Identification and Annotation of miRNAs during Dormancy in Prunus avium L. var. Bing by Next-Generation Sequencing
2.2. Expression Profiles of miRNAs during Dormancy in Prunus avium L. var. Bing
2.3. Effect of Environmental Fluctuations on the Levels of miR156e, miR172d, miR482c, miRn1, miRn2, and miRn3
2.4. Identification of the Target Genes of miRNAs in Prunus avium L. var. Bing
2.5. Functional Validation of miR156 and Its Target Genes SPL2, SPL6, and SPL13
3. Discussion
3.1. CR Determination of Prunus avium L. var. Bing
3.2. Identification of Dormancy Sensitive microRNAs in Prunus avium L. var. Bing by Massive Sequencing
3.3. Identification and Characterization of microRNAs and Target Genes during Dormancy in Prunus avium L. var. Bing
3.4. Effect of Environmental Fluctuations on the Expressions of miR156e, miR172d, miR482c, miRn1, miRn2, and miRn3 during Dormancy in Prunus avium L. var. Bing
3.5. Inverse Correlation between miR156e and the Target Genes SPL2, 6, and 13 under Field Chilling and Non-Stop Chilling Conditions during Dormancy in Prunus avium
3.6. Future Perspectives
3.7. Conclusions
4. Materials and Methods
4.1. Plant Material
4.2. Dormancy Analyses
4.3. Field Chilling (FC) Experiments and Temperature Data Collection
4.4. Chilling Requirement Determination under Forcing Conditions
4.5. Non-Stop Chilling (NC) Experiments
4.6. RNA Isolation
4.7. Genome-Wide Identification of Cherry miRNAs and Their Expression
4.8. Prediction of Target Genes
4.9. Experimental Determination of microRNAs and Target Genes
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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FC 1 | NC 2 | ||
---|---|---|---|
Chilling Hours | Observed Bud Burst | Chilling Hours | Observed Bud Burst |
0 (T0) | 0% | 0 (T0) | 0% |
254 | 0% | 218 | 0% |
356 | 0% | 386 | 0% |
545 | 0% | 530 | 0% |
693 | 0% | 698 | 0% |
853 (T1) | 14% | 890 (T1) | 36% |
909 (T2) | 58% | 914 (T2) | 58% |
989 | 83% | 1250 | 87% |
Name | Best Match miRBase | Mature Sequence (5’-3’) | miRNA Levels | Target(s) (psRNAtarget) | GO-Molecular Function | GO-Biological Process | Function |
---|---|---|---|---|---|---|---|
miR156e | ppe-miR156e | UGACAGAAGAGAGUGAGCAC | Increased | Squamosa promoter-binding-like protein | DNA binding; DNA binding transcription factor activity; metal ion binding | Defense response to bacterium; regulation of gene expression; regulation of transcription, DNA-templated; anther development (SPL13) | Trans-acting factor that binds specifically to the consensus nucleotide sequence 5’-TNCGTACAA-3’. |
miR166c | ppe-miR166c | UCGGACCAGGCUUCAUUCCCC | Decreased | Homeobox-leucine zipper protein ATHB-15 | DNA binding; lipid binding | Cell differentiation; regulation of transcription, DNA-templated | Probable transcription factor involved in the regulation of meristem development to promote lateral organ formation. May regulate procambial and vascular tissue formation or maintenance and vascular development in inflorescence stems. |
miR172d | ppe-miR172d | GGAAUCUUGAUGAUGCUGCAG | Decreased | AP2-like ethylene-responsive transcription factor | DNA binding; DNA binding transcription factor activity | Ethylene-activated signaling pathway; multicellular organism development; transcription, DNA templated | Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways (by similarity). May negatively regulate the transition to flowering time and confers flowering time delay. |
miR391 | mdm-miR391 | UACGCAGGAGAGAUGGCGCUG | Increased | Profilin | Actin monomer binding | Actin polymerization or depolymerization; inflorescence development; lateral root development; leaf development; sequestering of actin monomers; unidimensional cell growth | Binds to actin and affects the structure of the cytoskeleton. At high concentrations, profilin prevents the polymerization of actin, whereas it enhances it at low concentrations. By binding to PIP2, it inhibits the formation of IP3 and DG (by similarity). |
miR482a | ppe-miR482a-3p | UUUCCGAAACCUCCCAUUCCAA | unchanged | Disease resistance protein At4g27190-like | ADP binding; ATP binding | Defense response; signal transduction | Disease resistance protein |
miR482c | ppe-miR482c-3p | UUGCCAACCCCGCCCAUUCCAA | Increased | Putative disease resistance RPP13-like protein 1 | ATP binding | Plant-type hypersensitive responser; signal transduction | Potential disease resistance protein |
miR535b | ppe-miR535d | UUGACGACGAGAGAGAGCACG | Increased | Periodic tryptophan protein 2 homolog | RNA binding; snoRNA binding | Maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); ribosomal small subunit assembly; rRNA processing | Not in plants |
miR1309 | pta-miR1309 | UUGAUGGACCAUUUGAAUGAA | not validated | WD repeat-containing protein 7 | Hematopoietic progenitor cell differentiation | / | Not present in plants |
miRn51 | / | UUUGGCGCGUUGCUGUGGAUU | Increased | Metal transporter Nramp5-like | / | Metal ion transmembrane transporter activity | / |
miRn1 | / | CAUAGGAUGCUUAGGAAACUU | Increased | Putative receptor protein kinase | ATP binding; protein serine/threonine kinase activity | Recognition of pollen, self-incompatibility | Probable receptor. Interaction with a ligand in the extracellular domain triggers the protein kinase activity of the cytoplasmic domain. |
miRn2 | / | UAGUCAAUUAAUGAGGAUUAGU | unchanged | n.a | / | / | / |
miRn3 | / | UUUUCUGAAGCAUUUGGCAUC | Decreased | Ninja-family protein [AFP3] | / | Signal transduction; protein binding | Acts as a negative regulator of abscisic acid (ABA) response and stress responses. |
miRn4 | / | UUCUUGGAGGCAUGAAGCACC | Increased | Arabinosyltransferase RRA3-like | Transferase, transfering glycosyl groups | Cell wall biogenesis; cell wall organization; root hair cell development | Plays a role in the arabinosylation of cell wall components. Involved in the arabinosylation of extensin proteins in root hair cells. Extensins are structural glycoproteins present in cell walls, and their arabinosylation is important for root hair cell development and root hair tip growth. |
miRn5 | / | UGGCAUCGAGGACGAACAGCU | not validated | psbP domain-containing protein 7, chloroplastic | Calcium ion binding | Photosynthesis | / |
miRn6 | / | UUACAAAGUAUCUUAUGGGUCU | not validated | Pentatricopeptide repeat-containing protein At1g32415, mitochondrial | Endonuclease activity; RNA binding | RNA modification | / |
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Soto, E.; Sanchez, E.; Nuñez, C.; Montes, C.; Rothkegel, K.; Andrade, P.; Prieto, H.; Almeida, A.M. Small RNA Differential Expression Analysis Reveals miRNAs Involved in Dormancy Progression in Sweet Cherry Floral Buds. Plants 2022, 11, 2396. https://doi.org/10.3390/plants11182396
Soto E, Sanchez E, Nuñez C, Montes C, Rothkegel K, Andrade P, Prieto H, Almeida AM. Small RNA Differential Expression Analysis Reveals miRNAs Involved in Dormancy Progression in Sweet Cherry Floral Buds. Plants. 2022; 11(18):2396. https://doi.org/10.3390/plants11182396
Chicago/Turabian StyleSoto, Esteban, Evelyn Sanchez, Carlos Nuñez, Christian Montes, Karin Rothkegel, Paola Andrade, Humberto Prieto, and Andrea Miyasaka Almeida. 2022. "Small RNA Differential Expression Analysis Reveals miRNAs Involved in Dormancy Progression in Sweet Cherry Floral Buds" Plants 11, no. 18: 2396. https://doi.org/10.3390/plants11182396