Investigation of Gene Network of NKD1, NKD2 and OPAQUE-2 Associated with Maize Endosperm Development
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ABSTRACT:
PROVIDER: PRJNA728077 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14466100_1.fastq.gz | Fastqsanger.gz | |||
| SRR14466100_2.fastq.gz | Fastqsanger.gz | |||
| SRR14466101_1.fastq.gz | Fastqsanger.gz | |||
| SRR14466101_2.fastq.gz | Fastqsanger.gz | |||
| SRR14466102_1.fastq.gz | Fastqsanger.gz |
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Project description:The maize NAKED ENDOSPERM (NKD) genes Nkd1 and Nkd2 encode paralogous INDETERMINATE DOMAIN (IDD) transcription factors (TFs) that have previously been shown to play critical roles in regulating endosperm gene expression and development. However, the function of each individual NKD protein is unclear. To elucidate this, we performed a transcriptome analysis for nkd1-Ds and nkd2-Ds single mutant endosperm. We found that in nkd1-Ds single mutant, nkd2 gene expression is significantly lower than WT, and similar to the nkd2-Ds mutant.
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Project description:Transcription factors (TFs) play an important role in maize endosperm development regulation. The temporal RNA-seq and co-expression network analysis of maize endosperm reveals a hiararchical regulatory network architechture modulating the endosperm development. In the network, NKD1 and NKD2 are central regulators, and GBF1, HSFTF10, NACTF49 and HB115 are secondary regulators downstream of NKD1 and 2. To further test the relationship between these TFs, a DNA affinity purification and sequencing (DAP-seq) assay was performed. The result shows that the assay on NKD1 and NKD2 called 1,951 and 56,855 peaks, and 93 and 1,692 peaks are located within 3 kb distance to transcription starting site (TSS), respectively. And assays on GBF1, HSFTF10, NACTF49 and HB115 called 15,543; 38,147; 7,388 and 936 peaks, respectively.
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Project description:Quality Protein Maize (QPM) was created by selecting for genetic modifiers that convert the starchy endosperm of an opaque2 (o2) mutant to a hard, vitreous phenotype. Genetic analysis has shown there are multiple, unlinked o2 modifiers (Opm), but their identity and mode of action are unknown. A microarray hybridization performed with RNA obtained from true breeding o2 progeny with vitreous and opaque kernel phenotypes identified a small group of differentially expressed genes, some of which map at or near the Opm QTLs. Keywords: Genetic modification
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Project description:Opaque-2 regulates a complex gene network associated with cell differentiation and storage function of maize endosperm
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