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Effects of drought on gene expression in Maize reproductive and leaf meristem tissue revealed by RNA-seq

ABSTRACT: Purpose: To study the effects of drought at the transcriptomic level on two different actively dividing maize tissue: the ovaries, and the leaf meristem Methods: The Illumina reads were mapped to the maize B73 reference genome using Tophat followed by transcriptome reconstruction using Cufflinks. The FPKM valuse were extracted from cufflinks output and an R package called Limma was used to identify differentially expressed genes under drought under both tissues Results and Conclusions: Different processes which were differentially expressed under drought in both tissues were identified and analyzed in detail. A working hypothesis was formulated to account for the observed susceptibility of the reproductive tissue when compared to the robust response of the vegetative tissue. This analysis also servers as a basis for future study on drought-induced embryo abortion.

ORGANISM(S): Zea mays

PROVIDER: GSE40070 | GEO | 2012/08/14

SECONDARY ACCESSION(S): PRJNA172724

REPOSITORIES: GEO

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Effects of drought on gene expression in Maize reproductive and leaf meristem tissue revealed by RNA-seq

Project description:Purpose: To study the effects of drought at the transcriptomic level on two different actively dividing maize tissue: the ovaries, and the leaf meristem Methods: The Illumina reads were mapped to the maize B73 reference genome using Tophat followed by transcriptome reconstruction using Cufflinks. The FPKM valuse were extracted from cufflinks output and an R package called Limma was used to identify differentially expressed genes under drought under both tissues Results and Conclusions: Different processes which were differentially expressed under drought in both tissues were identified and analyzed in detail. A working hypothesis was formulated to account for the observed susceptibility of the reproductive tissue when compared to the robust response of the vegetative tissue. This analysis also servers as a basis for future study on drought-induced embryo abortion. Maize (Zea mays) plants of inbred line B73 were grown in the green house under well watered and drought stress conditions until they reached the reproductive stage (at the onset of silk emergence). For the drought stress two to three days after irrigation was withheld, the plants were hand pollinated, and 24 hours after pollination measurements and samples were collected for transcriptome analysis. At the end of the drought period (1DAP) the basal leaf meristem of the three youngest leaves and the ovary tissues were sampled for Illumina deep sequencing. Samples were labeled as well watered control leaf meristem (MLC), well watered control ovaries/ "cob" (MCC), drought stressed leaf meristem (MLD) and drought stressed ovary tissue (MCD). There are 8 libraries in total including one biological replicate for each condition.

2012-08-14 | E-GEOD-40070 | biostudies-arrayexpress

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Phenotypic and Proteomic Insights into Differential Cadmium Accumulation in Maize Kenerls

Project description:The contamination of agricultural soil by heavy metal cadmium (Cd) poses a significant environmental challenge, affecting crop growth, development and, human health. Previous studies have established the pivotal role of the ZmHMA3 gene, a P-type ATPase heavy metal transporter, in determining variable Cd accumulation in maize grains among 513 inbred lines. To decipher the molecular mechanism underlying mutation-induced phenotypic differences mediated by ZmHMA3, we conducted a quantitative Tandem Mass Tag (TMT)-based proteomic analysis of immature maize kernels. This analysis aimed to identify differentially expressed proteins (DEPs) in wild-type B73 and zmhma3 null mutant under Cd stress. The findings demonstrated that zhma3 accumulated higher levels of Cd compared to B73 when exposed to varying Cd concentrations in the soil. In comparison to low Cd concentration soil, B73 and zmhma3 exhibited 75 and 142 DEPs, respectively, with 24 common DEPs shared between them. Zmhma3 showed a higher induction of upregulated genes related to Cd stres than B73. Amino sugar and nucleotide sugar metabolism were specifically enriched in B73, while phenylpropanoid biosynthesis, nitrogen metabolism, and glyoxylate and dicarboxylate metabolism appeared to play a more significant role in zmhma3. This study provides proteomics insights into unraveling the molecular mechanism underlying the differences in Cd accumulation in maize kernel.

2024-01-26 | PXD047578 | Pride

Expression analysis of maize (Zea mays L.) genes in continuous light

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2014-03-04 | GSE55524 | GEO

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Project description:The shoot apical meristem (SAM) of plants, a specialized stem cell niche at the growing shoot tip, integrates developmental and environmental signals to direct the initiation and patterning of new organs such as leaves. Its activity throughout the plant's lifetime is tightly controlled. To gain insight into gene regulatory networks behind stem cell maintenance and organogenesis, we generated a high-resolution gene expression atlas of distinct domains and cell types within the vegetative shoot apex of 14 day-old maize B73 seedlings using laser microdissection and RNA deep sequencing. Data for 9 domains was previously released under SRA: SRP101301. This release adds data for biological duplicate samples collected for the SAM central zone, and the adaxial and abaxial sides of leaf primordia.

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Zea mays Transcriptome or Gene expression

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Project description:Band9 maize B73 leaf, Bundle sheath strand section1(0-1.5cm) biological replica1 SDS-PAGE trypsin Orbitrap

2011-04-15 | PRD000190 | Pride