Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods
Abstract
:1. Introduction
2. Results
2.1. Root Growing in TPG and IPG Culture Methods
2.2. Differentially-Expressed Genes (DEGs) in the Roots Grown in IPG and IPG Conditions
2.3. GO Enrichment Analysis of DEGs between IPG and TPG Roots
2.4. Identification and Classification of the DEGs in the KEGG Pathways
2.5. Different Expression Pattern of Plant Photoreceptor Genes
3. Discussion
4. Materials and Methods
4.1. Plant Sampling
4.2. Library Preparation for Transcriptome Sequencing
4.3. Clustering and Sequencing
4.4. Quality Control
4.5. Differential Expression Analysis
4.6. Reads Mapping to the Reference Genome and Functional Annotation
4.7. GO and KEGG Enrichment Analysis of Differentially Expressed Genes
4.8. Total RNAs Extraction
4.9. cDNA Synthesis
4.10. Primer Design
4.11. Quantitative Real-Time PCR (qRT-PCR)
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Main GO Categories | GO Accession | Description |
---|---|---|
Biological Process(BP) | GO:0044710 | Single-organism metabolic process |
GO:0008150 | Biological process | |
GO:0008152 | Metabolic process | |
GO:0055114 | Oxidation-reduction process | |
GO:0005975 | Carbohydrate metabolic process | |
Molecular Function(MF) | GO:0016491 | Oxidoreductase activity |
GO:0003824 | Catalytic activity | |
GO:0050662 | Co-enzyme binding | |
GO:0048037 | Cofactor binding | |
GO:0020037 | Heme binding |
KEGG Pathways | Pathways ID | Rich Factor | Genes ID | Gene Name | Log2 Fold Change (TPG vs. IPG) | q-Value |
---|---|---|---|---|---|---|
Flavone and flavonol biosynthesis | ath00944 | 0.6 | AT5G17050 | UGT78D2 | 1.3328 | 1.85 × 10−16 |
AT1G30530 | UGT78D1 | 1.5333 | 7.23 × 10−5 | |||
AT5G07990 | CYP75B1 | 2.1337 | 6.72 × 10−57 | |||
α-Linolenic acid metabolism | ath00592 | 0.22 | AT5G48880 | KAT5 | 1.5858 | 1.68 × 10−29 |
AT1G20510 | OPCL1 | −1.0607 | 4.72 × 10−7 | |||
AT2G06050 | ATOPR3 | −1.0431 | 0.0044624 | |||
AT1G17420 | ATLOX3 | −2.0906 | 0.00038411 | |||
AT5G42650 | AOS | −1.2413 | 1.74 × 10−6 | |||
Flavonoid biosynthesis | ath00941 | 0.16 | AT5G07990 | CYP75B1 | 2.1337 | 6.72 × 10−57 |
AT5G13930 | ATCHS | 1.0895 | 5.86 × 10−28 | |||
AT5G08640 | FLS1 | 1.2799 | 3.77 × 10−85 | |||
AT3G55120 | ATCHI | 1.5173 | 1.7 × 10−49 |
KEGG Pathways | DEG Number | Gene ID | Gene Name | Log2 Fold Change (TPG vs. IPG) | q-Value |
---|---|---|---|---|---|
Jasmonic Acid | 5 | AT1G19180 | ATJAZ1 | −1.0859 | 2.99 × 10−26 |
AT1G32640 | ATMYC2 | −1.005 | 3.77 × 10−19 | ||
AT1G72450 | JAZ6 | −1.5942 | 2.76 × 10−9 | ||
AT1G74950 | JAZ2 | −2.4038 | 5.14 × 10−20 | ||
AT5G13220 | JAS1 | −2.861 | 0.002773 | ||
Abscisic Acid | 1 | AT1G78290 | SRK2C | 1.2903 | 2.06 × 10−5 |
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Qu, Y.; Liu, S.; Bao, W.; Xue, X.; Ma, Z.; Yokawa, K.; Baluška, F.; Wan, Y. Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods. Int. J. Mol. Sci. 2017, 18, 951. https://doi.org/10.3390/ijms18050951
Qu Y, Liu S, Bao W, Xue X, Ma Z, Yokawa K, Baluška F, Wan Y. Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods. International Journal of Molecular Sciences. 2017; 18(5):951. https://doi.org/10.3390/ijms18050951
Chicago/Turabian StyleQu, Yanli, Shuai Liu, Wenlong Bao, Xian Xue, Zhengwen Ma, Ken Yokawa, František Baluška, and Yinglang Wan. 2017. "Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods" International Journal of Molecular Sciences 18, no. 5: 951. https://doi.org/10.3390/ijms18050951
APA StyleQu, Y., Liu, S., Bao, W., Xue, X., Ma, Z., Yokawa, K., Baluška, F., & Wan, Y. (2017). Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods. International Journal of Molecular Sciences, 18(5), 951. https://doi.org/10.3390/ijms18050951