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Zea mays

ABSTRACT: Gene expression in B73 maize aleurone and starchy endosperm at 18 and 22 day after pollination

PROVIDER: PRJNA377908 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5312210.fastq.gz	Fastqsanger.gz
	SRR5312211.fastq.gz	Fastqsanger.gz
	SRR5312204.fastq.gz	Fastqsanger.gz
	SRR5312205.fastq.gz	Fastqsanger.gz
	SRR5312206.fastq.gz	Fastqsanger.gz

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The naked endosperm genes encode duplicate ID domain transcription factors required for maize endosperm differentiation

Project description:The objective of the current study is to unravel the gene regulatory networks controlled by the nkd genes during maize endosperm development. We compared wild type (B73) vs. nkd mutant (introgressed into B73 background) transcriptomes in aleurone vs. starchy endosperm cell types captured by laser capture microdissection technology. We performed RNA seq analysis of mid-mature (15DAP) endosperm in two cell types [aleurone (A) and starchy endosperm (S)] of wild type B73 (B) and nkd mutant (N) kernels with three independent biological replicates.

2015-01-28 | E-GEOD-61057 | biostudies-arrayexpress

The naked endosperm genes encode duplicate ID domain transcription factors required for maize endosperm differentiation

Project description:The objective of the current study is to unravel the gene regulatory networks controlled by the nkd genes during maize endosperm developent. We compared wild type (B73) vs. nkd mutant (introgressed into B73 background) transcriptomes in aleurone vs. starchy endosperm cell types captured by laser capture microdissection technology.

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E-GEOD-95678

Project description:Gene expression in B73 maize aleurone and starchy endosperm at 18 and 22 day after pollination

2023-06-15 | E-GEOD-95678 | ExpressionAtlas

Gene expression in B73 maize aleurone and starchy endosperm at 18 and 22 day after pollination

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.

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Developing rice endosperm at seven days after flowering: Aleurone layers vs central starchy endosperm

Project description:Transcriptional profiling of developing rice endosperm at seven days after flowering comparing aleurone layers with central starchy endosperm. Cereal productivity is dependent on the accumulation of storage compounds in the endosperm, a nutritive tissue that is composed of aleurone cells in the outermost regions and starchy endosperm in the inner region. The transcriptional analyses provides clues to the molecular basis for different metabolic pathways in response to the spatial and nutritional differences between rice aleurone cells and starchy endosperm.

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Project description:Here we report genome-wide high resolution allele-specific maps of DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3) in maize endosperm. To investigate the allele-specific DNA methylation pattern of maize endosperm on a genome-wide scale, we performed MethylC-seq for shoot, embryo, and endosperm tissue 12 d after pollination (DAP) of inbred B73, and the endosperm tissue 12 DAP of reciprocal crosses B73 Ã Mo17 (BM) and Mo17 Ã B73 (MB). We also performed additional RNA-seq for samples from 12-DAP and 10-DAP endosperm of both reciprocal crosses between inbreds B73 and Mo17

2013-10-17 | E-MTAB-4206 | biostudies-arrayexpress

RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation

Project description:Endosperm is an absorptive structure that supports embryo development or seedling germination in angiosperms. The endosperm of cereals is a main source of food, feed, and industrial raw materials worldwide. However, the gene regulatory networks that control endosperm cell differentiation remain largely unclear. As a first step toward characterizing these networks, we profiled the mRNAs in five major cell types of the differentiating endosperm and in the embryo and four maternal compartments of the kernel. Comparisons of these mRNA populations revealed the diverged gene expression programs between filial and maternal compartments, and an unexpected close correlation between embryo and the aleurone layer of endosperm. Gene co-expression network analysis identified co-expression modules associated with single or multiple kernel compartments including modules for the endosperm cell types, some of which showed enrichment of previously identified temporally activated and/or imprinted genes. Detailed analyses of a co-expression module highly correlated with the basal endosperm transfer layer (BETL) identified a regulatory module activated by MRP-1, a regulator of BETL differentiation and function. These results provide a high-resolution atlas of gene activity in the compartments of the maize kernel and help to uncover the regulatory modules associated with the differentiation of the major endosperm cell types. RNAs from ten compartments of the maize kernel including the central starchy endosperm (CSE), conducting zone (CZ), aleurone (AL), basal endosperm transfer layer (BETL), embryo-surrounding region (ESR), nucellus (NU), pericarp (PE), placenta-chalazal region (PC), the vascular region of the pedicel (PED), and the embryo (EMB) were isolated at 8 days after pollination (DAP) using laser-capture microdissection and sequenced using an Illumina HiSeq 2000 platform.

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