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| Status |
Public on Dec 01, 2023 |
| Title |
Cis and Trans Gene Transcription Regulatory Mechanisms Underpin Variation of a Maize Agronomic Trait |
| Organism |
Zea mays |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
P1 is the major QTL for maysin and chlorogenic acid accumulation in silk. Both compounds were important for plant defenses. Silk is an important reproductive organ that is critical for good seed setting in corn ear and needs to be protected against various stresses, therefore, metabolics compounds (ex: phenolics) were highly enriched in silk. Here we characterize transcriptome changes in maize protoplast, and natural variants of P1 silks, and pericards to characterize the regulatory landscape. Also we evaluated profiles of silk in B73 x A632 hybrids in order to cis and trans specific effect driven by P1 in maize. Our study identifies new P1 targets in the silk and protoplast. Together with the RNA-seq data (P1-rr vs P1-ww in silk and pericarp and protoplast 35S:P1 vs empty vector control), we observed new P1 functions in silk that were not observed in pericarp. Also, Protoplast and silk ChIP-seq in F1 silk, as well as DAP-seq analysis of P1 - shows specific P1 targets with highlight cis and trans effect on the F1 hybrids.
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| Overall design |
DAP-seq: We generated Maize genomic DNA library through collecting leaves of Maize 2-week-old young seedlings of B73xA632 F1 hybrid. gDNA is fragmented to 200-300 bp. and sent for either Illumina Hiseq 4000 SE50 sequencing (MSU genomic core facility). Halo-TF was compared to the Halo negative control. The TFs have 2 replicates. Ideally, each TF will have 2 replicates for both demethylated and methylated gDNA libraries (when required). ChIP-seq protoplast: For protoplast 35S:P1 ChIP-seq, 3 biological reps of pooled 35S:P1 transformed cells as well as the input were used to make ChIP-seq libraries. ChIP-seq Silks: For silk ChIP-seq, 3 biological reps of P1-ww, F1 (B73xA632) as well as their inputs were used to make ChIP-seq libraries. All ChIP were processed using P1 specific Antibody (serum), ID:344-3 (Erich Grotewold lab, Michigan State University). All ChIP-seq libraries were made using NEBNext Ultra II DNA library Prep kit for Illumina (NEB#7645 S/L, $E7103 S/L). Hiseq4000 were used for all SE50 sequencing. RNA-seq protoplast: RNAseq of 12-day-old maize hybrid (B73xA632) transformed with 35S:P1-rr vector (DP2019) as well as empty vector control(DP611), in triplicate, using Illumina Hiseq4000 SE50. Protoplast was collected ~18 hrs after transformation. RNA-seq silks and pericarp: 2 individual plants in the field were collected per replicate, and a total of 3 replicates were collected. For pericarp, 14 DAP ears were used to collect pericarps. More than 10 kernels were collected per individual and 2 individual plants were used per replicate. A total of 3 replicates were collected for the pericarp experiment. Sequencing was completed using Illumina Hiseq4000 SE50.
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| Contributor(s) |
Grotewold E, Chu Y, Gomez-Cano F |
| Citation missing |
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| Submission date |
Jan 31, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Erich Grotewold |
| E-mail(s) |
grotewol@msu.edu
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| Organization name |
Michigan State University
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| Department |
Biochemistry and Molecular Biology
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| Lab |
Grotewold Lab
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| Street address |
603 Wilson Rd.
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| City |
East Lasing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
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| Platforms (2) |
| GPL20156 |
Illumina NextSeq 500 (Zea mays) |
| GPL24163 |
Illumina HiSeq 4000 (Zea mays) |
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| Samples (46)
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| Relations |
| BioProject |
PRJNA930042 |
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