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| Status |
Public on Sep 28, 2016 |
| Title |
Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L [miRNA-seq] |
| Organism |
Solanum tuberosum |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Light is a major environmental factor that affects metabolic pathways and stimulates the production of secondary metabolites in potato. However, adaptive changes in potato metabolic pathways and physiological functions triggered by light are partly explained by gene expression changes. Regulation of secondary metabolic pathways in potato has been extensively studied at transcriptional level, but little is known about the mechanisms of post-transcriptional regulation by miRNAs. To identify light-responsive miRNAs/mRNAs and construct putative metabolism pathways regulated by the miRNA-mRNA pairs, an integrated omics (sRNAome and transcriptome) analysis was performed to potato under light stimulus. A total of 31 and 48 miRNAs were identified to be differentially expressed in the leaves and tubers, respectively. Among the DEGs, 1353 genes in the leaves and 1841 genes in the tubers were upregulated, while 1595 genes in the leaves and 897 genes in the tubers were downregulated by light. Mapman enrichment analyses showed that genes related to MVA pathway, alkaloids-like, phenlypropanoids, flavonoids, and carotenoids metabolism were significantly upregulated, while genes associated with major CHO metabolism were repressed in the leaves and tubers. Integrated miRNA and mRNA profiles revealed that light-responsive miRNAs are important regulators in alkaloids metabolism, UMP-salvage, lipid biosynthesis, and cellulose catabolism. Moreover, several miRNAs may participate in glycoalkaloids metabolism via JA signaling pathway, UDP-glucose biosynthesis and hydroxylation reaction. This study provides a global view of transcriptome response in potato response to light, our results suggest that miRNAs might play important roles in secondary metabolic pathways, especially in glycoalkaloid biosynthesis. The findings will enlighten us on the genetic regulation of secondary metabolite pathways and pave the way for future application of genetically engineered potato.
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| Overall design |
Four RNA samples were used in this experiment. Eight-week-old plantlets were shifted to the dark 3 day and subsequently exposed to red light (～19.7μmol m−2s−1, 630 nm). Then, the leaves of plantlets were collected and immediately frozen in liquid nitrogen after 12, 24, and 48 h, respectively. Equal amounts of total RNA were pooled at 12, 24 and 48 h time points to produce one sample. Dark-grown plantlets were collected as the control. In vitro generated microtubers were treated under the same conditions as described previously.
Please note that the leaves of plantlets were collected and immediately frozen in liquid nitrogen after 12, 24, and 48 h, respectively and equal amounts of total RNA from three time points were pooled to produce one sample. The pooling strategy was employed to reduce the effect of circadian regulation on genes expression. Microtubers were treated under the same conditions and strategy.
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| Contributor(s) |
Qiao Y, Zhang J, Zhang J, Wang Z, An R, Guo H, Wang D, Zhang J |
| Citation(s) |
27679507 |
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| Submission date |
Apr 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yan Qiao |
| Organization name |
Gansu Agricultural University
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| Department |
College of Agronomy
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| Street address |
No. 1 Yingmen village, Anning District
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| City |
Lanzhou |
| State/province |
Gansu Province |
| ZIP/Postal code |
730070 |
| Country |
China |
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| Platforms (1) |
| GPL16436 |
Illumina HiSeq 2000 (Solanum tuberosum) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE79986 |
Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L |
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| Relations |
| BioProject |
PRJNA317570 |
| SRA |
SRP072936 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE79984_leaf_miRNAs.txt.gz |
369 b |
(ftp)(http) |
TXT |
| GSE79984_tuber_miRNAs.txt.gz |
524 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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