Transcriptome and differential gene expression analysis for nacRNAi and non-transgenic sibling
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE127525 | GEO | 2019/05/04
REPOSITORIES: GEO
Similar Datasets
Project description:The cereal endosperm consists of starchy endosperm (ST) cells, which accumulate storage proteins and starch, the peripheral aleurone (AL) cells, which mobilize these storage compounds during germination, and transfer cells in contact with the maternal vascular tissues, and the embryo-surrounding region. We conducted RNA-sequencing and analyzed transcript profiles of AL and ST tissues at 18 and 22 days after pollination (DAP), when storage compounds such as proteins, starch, triacylglycerols, specialized metabolites, and minerals are actively synthesized in the maize endosperm. We combined published RNA-seq datasets from other kernel tissues at different developmental stages to analyze gene expression connected to synthesis and accumulation of storage compounds and metabolites. Using weighted correlation network analysis (WGCNA), we identified gene modules associated with metabolic pathways related to nutritional properties of the maize endosperm. We also provide information of novel marker genes specifically expressed in AL and ST, at either early or late developmental stages. This study is important for understanding maize endosperm development and for developing strategies to improve nutritional quality of maize kernels.
2017-05-02 | GSE95678 | GEO
Project description:Starch synthesis is an essential feature for crops, but its regulatory mechanism has been largely restricted to transcription factors. Starch synthesis parallels the endosperm development in maize. we obtained transcriptome, small RNAome and DNA methylome data from the multiple developing stages of endosperms, as well as kernel and leaf, via applying RNA-seq, sRNA-seq and BS-seq technologies. We demonstrated that genome-wide gene expression makes a sharp transition at the point when starch accumulation speeds between DAP 10-13, while the enriched up-regulation of starch and sucrose metabolism genes occurs earlier at DAP 9-10. Expression pattern analysis establishes a comprehensive network between starch synthesis genes and transcription factors. MiRNAs negatively regulating TF expression were extensively downregulated during maize endosperm development. We showed that TF ZmMYB33 and ZmMYB65 promotes the transcription of the GUS reporter under the control of Wx and Sbe2b/Bt2 gene promoters containing their binding motifs, respectively. We further showed that the abundantly expressed miR159k-3p negatively regulate the expression of these two transcription factors, suggesting that miRNAs are important regulators of starch synthesis. In addition, we showed that both starch synthesis genes and miRNAs are globally repressed by DNA methylation, while transcription factors are not. Taken together, the presented results establish the regulatory functions of miRNAs and DNA methylation in starch synthesis, and indicates DNA methylation as the master switch.
2020-11-04 | GSE106684 | GEO
Project description:Starch synthesis is an essential feature for crops, but its regulatory mechanism has been largely restricted to transcription factors. Starch synthesis parallels the endosperm development in maize. we obtained transcriptome, small RNAome and DNA methylome data from the multiple developing stages of endosperms, as well as kernel and leaf, via applying RNA-seq, sRNA-seq and BS-seq technologies. We demonstrated that genome-wide gene expression makes a sharp transition at the point when starch accumulation speeds between DAP 10-13, while the enriched up-regulation of starch and sucrose metabolism genes occurs earlier at DAP 9-10. Expression pattern analysis establishes a comprehensive network between starch synthesis genes and transcription factors. MiRNAs negatively regulating TF expression were extensively downregulated during maize endosperm development. We showed that TF ZmMYB33 and ZmMYB65 promotes the transcription of the GUS reporter under the control of Wx and Sbe2b/Bt2 gene promoters containing their binding motifs, respectively. We further showed that the abundantly expressed miR159k-3p negatively regulate the expression of these two transcription factors, suggesting that miRNAs are important regulators of starch synthesis. In addition, we showed that both starch synthesis genes and miRNAs are globally repressed by DNA methylation, while transcription factors are not. Taken together, the presented results establish the regulatory functions of miRNAs and DNA methylation in starch synthesis, and indicates DNA methylation as the master switch.
2020-11-04 | GSE106642 | GEO
Project description:Starch synthesis is an essential feature for crops, but its regulatory mechanism has been largely restricted to transcription factors. Starch synthesis parallels the endosperm development in maize. we obtained transcriptome, small RNAome and DNA methylome data from the multiple developing stages of endosperms, as well as kernel and leaf, via applying RNA-seq, sRNA-seq and BS-seq technologies. We demonstrated that genome-wide gene expression makes a sharp transition at the point when starch accumulation speeds between DAP 10-13, while the enriched up-regulation of starch and sucrose metabolism genes occurs earlier at DAP 9-10. Expression pattern analysis establishes a comprehensive network between starch synthesis genes and transcription factors. MiRNAs negatively regulating TF expression were extensively downregulated during maize endosperm development. We showed that TF ZmMYB33 and ZmMYB65 promotes the transcription of the GUS reporter under the control of Wx and Sbe2b/Bt2 gene promoters containing their binding motifs, respectively. We further showed that the abundantly expressed miR159k-3p negatively regulate the expression of these two transcription factors, suggesting that miRNAs are important regulators of starch synthesis. In addition, we showed that both starch synthesis genes and miRNAs are globally repressed by DNA methylation, while transcription factors are not. Taken together, the presented results establish the regulatory functions of miRNAs and DNA methylation in starch synthesis, and indicates DNA methylation as the master switch.
2020-11-04 | GSE106627 | GEO
Project description:Maize plants were transformed with endosperm-specific PPDK RNAi knockout constructs to alter starch/protein ratios. Metabolite pool comparisons will be examined from sibling kernels harvested from segregating ears.
2015-08-17 | ST000289 | MetabolomicsWorkbench
Project description:Cereal crops accumulate starch in seeds as an energy reserve. Sucrose synthase (SuSy) plays an important role in grain starch synthesis. In this study, ZmSUS1 was transformed into maize inbred line KN5585, and transgenic plants were obtained. Compared with the control, the content and activity of SuSy were significantly increased, the amylose content in mature seeds of transgenic maize increased by 41.1-69.2%, the total starch content increased by 5.0-13.5%, The 100-grain weight increased by 19.0-26.2% and the average diameter of starch granules increased by 10.8-17.2%. These results indicated that overexpression of ZmSUS1 can significantly improve the traits of maize kernels and obtain new lines with high amylose content. It was also found that ZmSUS1 may increase the amylose content by regulating the expression of Shrunken2 (Sh2) and Brittle2 (Bt2) which encodes endosperm ADP-glucose pyrophosphorylase (AGPase) size subunits, and the expression of Granule bound starchsynthase1 (GBSS1) and Starch synthase1 (SS1) which encodes starch synthase. This study proved the important role of ZmSUS1 in maize starch synthesis, and provided a new technology strategy for improving corn starch content and yield.
2022-09-07 | GSE212465 | GEO
Project description:Endosperm is a product of double fertilization, and provides nutrients and signals to the embryo during seed development in flowering plants. Early stages of endosperm development are critical for the development of its storage capacity through synthesis and accumulation of starch and storage proteins. Here we report on the isolation and sequencing of mRNAs from the central portion of the starchy endosperm of Zea mays (maize) B73 at 6 days after pollination. We detected high correlation among the four biological replicates of RNAs isolated using laser-capture microdissection of the cell type. Because the assayed stage of development precedes the synthesis and accumulation of the major storage proteins and starch in the endosperm, our dataset likely include mRNAs for genes that are involved in control and establishment of these developmental programs.
2014-06-17 | GSE58504 | GEO
Project description:The kernel serves as a storage organ for various nutrients and determines the yield and quality of maize. Understanding the mechanisms regulating kernel development is important for maize production. In this study, a small kernel mutant smk7a of maize was characterized. Cytological observation suggested that the development of the endosperm and embryo was arrested in smk7a in the early development stage. Biochemical tests revealed that the starch, zein protein, and indole-3-acetic acid (IAA) contents were significantly lower in smk7a compared with wild-type (WT). Consistent with the defective development phenotype, transcriptome analysis of the kernels 12 and 20 days after pollination (DAP) revealed that the starch, zein, and auxin biosynthesis related genes were dramatically downregulated in smk7a. Genetic mapping indicated that the mutant was controlled by a recessive gene located on chromosome 2. Our results suggest that disrupted nutrition accumulation and auxin synthesis cause the defective endosperm and embryo development of smk7a.
2023-01-25 | GSE221594 | GEO
Project description:We performed a molecular characterization of the maize small kernel mutant with endosperm developmental deficiency phenotypes.To elucidate how SMK8 affects kernel development, we performed RNA sequencing (RNA-seq), and the results revealed numerous differentially expressed genes related to storage proteins and starch biosynthesis and biosynthesis of amino acids.
2020-07-09 | GSE154016 | GEO
Project description:Endosperm is a product of double fertilization, and provides nutrients and signals to the embryo during seed development in flowering plants. Early stages of endosperm development are critical for the development of its storage capacity through synthesis and accumulation of starch and storage proteins. Here we report on the isolation and sequencing of mRNAs from the central portion of the starchy endosperm of Zea mays (maize) B73 at 6 days after pollination. We detected high correlation among the four biological replicates of RNAs isolated using laser-capture microdissection of the cell type. Because the assayed stage of development precedes the synthesis and accumulation of the major storage proteins and starch in the endosperm, our dataset likely include mRNAs for genes that are involved in control and establishment of these developmental programs. Four replicates of mRNAs from the central portion of starchy endopserm were isolated using laser-capture microdissection and sequenced using the Illumina GAIIx platform.
2014-06-17 | E-GEOD-58504 | biostudies-arrayexpress