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| Status |
Public on Jul 08, 2021 |
| Title |
Direct and indirect transcriptional effects of abiotic stress in Zea mays plants defective in RNA-directed DNA methylation |
| Organism |
Zea mays |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
MOP1-mediated regulation of gene expression of plant responses to early ABA induction has transcriptionally and physiologically relevant roles. Homozygous mop1-1 plants are compromised in their ability to recover from water deprivation.
Purpose: Genome-wide identification of immediate and direct MOP1-dependent ABA transcriptional responses
Methods: mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings were subjected to ABA and MS treatments for 1 hour. The trimmed sequence reads were analyzed at the gene level using HISAT2, stringite, and edgeR.
Results: we mapped ~33 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 1,856 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a log2FC ≥ 0.95 and FDR <0.05, 1,119 DEGs were found to be unique to one genotype/treatment comparison.
Conclusions: MOP1-mediated regulation of gene expression in maize seedlings in the RdDM (mop1-1) mutant has relevant transcriptional and physiological roles in plants subjected to stress. Our study generated by RNA-seq technology identified genes and biological processes regulated by RdDM and ABA-mediated stress responses, including MOP1-dependent and immediate response genes (MIMs).
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| Overall design |
RNA-seq was preformed on homozgyous Mop1 wildtype and mop1-1 mutant V3 seedling shoots with and without exogenous 50 µM ABA treatment for 1 hour.
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| Web link |
https://doi.org/10.3389/fpls.2021.694289
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| Contributor(s) |
McGinnis KM, Madzima TF, Vendramin S, Lynn J, Lemert P, Lu KC |
| Citation(s) |
34489998 |
| Submission date |
Jul 07, 2021 |
| Last update date |
Sep 15, 2021 |
| Contact name |
Thelma F Madzima |
| E-mail(s) |
madzima@uw.edu
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| Phone |
425-352-5176
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| Organization name |
University of Washington Bothell
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| Department |
Division of Biological Sciences
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| Street address |
18115 Campus Way NE
|
| City |
Bothell |
| State/province |
WA |
| ZIP/Postal code |
98011-8246 |
| Country |
USA |
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| Platforms (1) |
| GPL25410 |
Illumina NovaSeq 6000 (Zea mays) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA744417 |
| SRA |
SRP327318 |
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