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Expression profile of Maize (Zea mays L.) Embryonic Axes During Germination: Regulation of Ribosomal Protein mRNAs.

ABSTRACT: Seed germination is a critical developmental process in plant propagation. Knowledge of the gene expression patterns in this critical process is important in order to understand the main biochemical reactions involved in successful germination, specially for economically relevant plants such as Maize. The purpose of this study is the gene expression analysis of quiescent and germinated maize embryonic axes to determine the regulatory mechanism for (r)-protein expression during the maize development process.

ORGANISM(S): Zea mays

PROVIDER: GSE27648 | GEO | 2011/08/01

SECONDARY ACCESSION(S): PRJNA138513

REPOSITORIES: GEO

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Expression profile of Maize (Zea mays L.) Embryonic Axes During Germination: Regulation of Ribosomal Protein mRNAs.

Project description:Seed germination is a critical developmental process in plant propagation. Knowledge of the gene expression patterns in this critical process is important in order to understand the main biochemical reactions involved in successful germination, specially for economically relevant plants such as Maize. The purpose of this study is the gene expression analysis of quiescent and germinated maize embryonic axes to determine the regulatory mechanism for (r)-protein expression during the maize development process. This study analyzed samples of total and polysomal RNA from maize embryonic axes at different time periods during the germination process and under the influence of a specific growth factor. For each condition a biological replicate was included and for the time periods, a technical replicate was also included.

2011-07-31 | E-GEOD-27648 | biostudies-arrayexpress

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Project description:Through hierarchical clustering of transcript abundance data across a diverse set of tissues and developmental stages in maize, we have identified a number of coexpression modules which describe the transcriptional circuits of maize development. We examined transcript abundance data at 50 developmental stages/tissues of maize, from embryogenesis to senescence, using a custom Affymetrix Unigene array. The VE stage is germination and emergence Vn leaf stage refers to when the collar of the nth leaf is visible.

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Project description:In this study a transcriptomic approach (RNA-sequencing) was utilized to elucidate molecular responses of maize (Zea mays L.) primary roots of the inbred line B73 to water deficit to gain a better understanding of the mechanisms underlying drought tolerance. Kernels of the maize inbred line B73 were germinated in paper rolls soaked with distilled water until seedlings had a primary root length of 2 to 4 cm. For mild and severe water deficit conditions, seedlings were transferred to PEG8000 solution with water potentials of -0.2 MPa and -0.8 MPa, respectively. Water deficit treatment was applied for 6 h and 24 h. Each treatment was performed in four biological replicates each consisting of 10 roots.

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Project description:Purpose: To identify the potential genes that regulate seed germination speed in maize, we performed a time-series transcriptome analysis with two inbred maize lines (72-3 fast germination, F9721 slow germination) during the seed germination and compared the differentially expressed genes (DEGs) in transcriptome with genes identified by GWAS Methods: Methods: mRNA profiles of two maize inbred lines 72-3 and F9721 showing divergent seed germination at six stages during germination were generated by deep sequencing, in triplicate, using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed at the gene level. Hisat2 was used to align clean reads to maize B73 reference genome, and HTSeq was used to count transcript abundance. DESeq2 models were used to compare DEGs at each germination stage within or between samples Results: Comparative transcriptome study identified 12 hours after imbibition (HAI) as the critical stage responsible for the variation of germination speed. The DEGs between 72-3 and F9721 were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, oxidoreductase activity pathways, hormone signal transduction, and amino acid transporter activity pathways Conclusions: Combined with evidence from gene expression data, GWAS, and gene synteny with other model species, we finally anchored three genes as the likely candidate genes regulating germination speed in maize

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