Identification of Cold-Responsive miRNAs and Their Target Genes in Nitrogen-Fixing Nodules of Soybean
Abstract
:1. Introduction
2. Results and Discussion
2.1. Results
2.1.1. The Nitrogen Use Efficiency of Nitrogen-Fixing Nodules Was Decreased in Response to Low Temperature Treatment
2.1.2. Identification and Validation of Low Temperature-Responsive miRNAs in Functional Nodules
2.1.3. Target Prediction and Validation for the Identified Low Temperature-Responsive miRNAs
miRNA | Target Gene | Target Annotation |
---|---|---|
gma-miR397a | Glyma01g26750 a,b | Multicopper oxidase, oxidation/reduction |
Glyma18g07240 b | Multicopper oxidase, oxidation/reduction | |
Glyma03g15800 a,b | Multicopper oxidase, oxidation/reduction | |
Glyma03g14450 b | Multicopper oxidase, oxidation/reduction | |
Glyma06g43700 b | Multicopper oxidase, oxidation/reduction | |
Glyma12g14230 b | Multicopper oxidase, oxidation/reduction | |
gma-miR166u | Glyma08g21620 a,c | bZIP transcription factor |
Glyma07g01940 a,c | Homeobox-leucine zipper protein | |
gma-miR171p | Glyma01g18040 a,b,c | GRAS family transcription factor |
Glyma11g17490 a,c | GRAS family transcription factor | |
gma-miR2111f | Glyma19g01430 a,b | EamA-like transporter family |
Glyma15g34831 a,b | EamA-like transporter family | |
Glyma16g06160 b,c | Kelch motif; Protin Binding; Kelch-related protein | |
Glyma19g25770 b,c | Kelch motif; Protin Binding; Kelch-related protein | |
gma-miR169c | Glyma02g35190 a,b,c | HAP2 like transcription factor |
Glyma19g38800 a,b | HAP2 like transcription factor | |
Glyma13g16770 a,b | HAP2 like transcription factor | |
Glyma07g04050 a,b | HAP2 like transcription factor | |
Glyma13g27230 a,b | HAP2 like transcription factor | |
gma-miR5037a | Glyma17g13680 a,b | GRAS family transcription factor |
Glyma05g03020 a,b | GRAS family transcription factor | |
gma-miR167c | Glyma11g31940 a,b | Auxin response factor |
Glyma18g05330 a,b | Auxin response factor | |
Glyma02g40650 a,b | Auxin response factor | |
Glyma14g03650 a,b | Auxin response factor | |
Glyma14g38940 a,b | Auxin response factor | |
Glyma08g10550 a,b | Auxin response factor | |
gma-miR319a/b | Glyma13g04030 a,b | MYB family transcription factor |
Glyma13g25720 a,b | MYB family transcription factor | |
Glyma15g35860 a,b | MYB family transcription factor | |
Glyma20g11040 a,b | MYB family transcription factor | |
Glyma06g43720 a,b | TCP family transcription factor | |
Glyma12g14200 a,b | TCP family transcription factor | |
gma-miR399i | Glyma10g04230 a,b | Inorganic phosphate and sugar transporter |
Glyma14g36650 b | Inorganic phosphate and sugar transporter | |
Glyma19g34710 a | Inorganic phosphate and sugar transporter | |
Glyma20g34620 a | Inorganic phosphate and sugar transporter | |
gma-miR1523a | Glyma13g25040 b | Putative lysophospholipase |
Glyma13g25050 b | Putative lysophospholipase | |
gma-miR5559 | Glyma20g34670 b | Mediator complex subunit 28 |
Glyma02g19340 b | No functional annotation | |
Glyma14g02030 b | Protein binding | |
Glyma02g46640 b | Protein binding |
2.1.4. Correlation between the Expression of miRNAs and Their Targets in Response to Low Temperature Stress in Mature Nodules
2.2. Discussion
3. Experimental Section
3.1. Plant Materials and Low Temperature Treatment
3.2. Analysis of the Leghemoglobin (Lb) Concentration
3.3. Analysis of the Acetylene Reduction Activity (ARA) Level
3.4. Small RNA Library Construction, Solexa Sequencing and Data Analysis
3.5. Quantitative Reverse Transcription PCR (RT-qPCR)
3.6. miRNA Target Gene Prediction and Experimental Validation
4. Conclusions
Supplementary Files
Supplementary File 1Acknowledgments
Author Contributions
© 2014 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
Share and Cite
Zhang, S.; Wang, Y.; Li, K.; Zou, Y.; Chen, L.; Li, X. Identification of Cold-Responsive miRNAs and Their Target Genes in Nitrogen-Fixing Nodules of Soybean. Int. J. Mol. Sci. 2014, 15, 13596-13614. https://doi.org/10.3390/ijms150813596
Zhang S, Wang Y, Li K, Zou Y, Chen L, Li X. Identification of Cold-Responsive miRNAs and Their Target Genes in Nitrogen-Fixing Nodules of Soybean. International Journal of Molecular Sciences. 2014; 15(8):13596-13614. https://doi.org/10.3390/ijms150813596
Chicago/Turabian StyleZhang, Senlei, Youning Wang, Kexue Li, Yanmin Zou, Liang Chen, and **a Li. 2014. "Identification of Cold-Responsive miRNAs and Their Target Genes in Nitrogen-Fixing Nodules of Soybean" International Journal of Molecular Sciences 15, no. 8: 13596-13614. https://doi.org/10.3390/ijms150813596