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| Status |
Public on Mar 22, 2020 |
| Title |
Abscisic acid transcriptional response of the maize epigenetic mutant, mop1-1 |
| Organism |
Zea mays |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
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| Summary |
MOP1-dependent and ABA-responsive pathways act within complex, connected transcriptional regulatory networks to mediate tissue-specific growth and responses to abiotic stress in maize
Purpose: To identify genome-wide ABA-induced, MOP1-dependent and independent transcriptional responses
Methods: mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings were subjected to ABA and MS treatments for 8 hours. The trimmed sequence reads were analyzed at the gene level using HISAT2, stringite, and edgeR.
Results: we mapped ~23 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 3,242 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a fold change ≥2 and FDR <0.05, 1,561 DEGs were found to be unique to one genotype/treatment comparison.
Conclusions: Our study represents the first analysis of ABA in maize seedlings in the RdDM (mop1-1) mutant, with biological replicates, and generated by RNA-seq technology. We identified common targets of MOP1 and ABA transcriptional regulation.
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| Overall design |
RNA-seq and Sequence Capture Bisulfite-seq was preformed on homozgyous Mop1 wildtype and mop1-1 mutant V3 seedling shoots with and without exogenous 50 µM ABA treatment for 7 (SeqCap) or 8 hours (RNA-seq).
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| Contributor(s) |
McGinnis KM, Madzima TF, Vendramin S, Huang J, Crisp P |
| Citation(s) |
32179621 |
| |
| Submission date |
Jun 04, 2019 |
| Last update date |
Mar 22, 2020 |
| 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 (2) |
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| Samples (17)
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| Relations |
| BioProject |
PRJNA546250 |
| SRA |
SRP200396 |
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