Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE49805 | GEO | 2015/04/30
SECONDARY ACCESSION(S): PRJNA214978
REPOSITORIES: GEO
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Project description:The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutants analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development. Seeds of the maize inbred line 18-599 (Maize Research Institute, Sichuan Agricultural University, Chengdu, China) were grown in a growth chamber at 24°C/18°C (day/night) with 12 h illumination per day. Ears were collected as described previously [10] at four developmental stages: the growth point elongation, spikelet differentiation, floret primordium differentiation, and the floret organ differentiation phases. In brief, ears were manually collected at the four developmental stages. All the samples were harvested and immediately frozen in liquid nitrogen, and stored at -80°C until used for RNA isolation.
2015-04-30 | E-GEOD-49805 | biostudies-arrayexpress
Project description:In plants, MicroRNAs (miRNAs) are a new class of endogenous small RNAs that play essential regulatory roles in plant growth, development and stress response. Extensive studies of miRNAs have been performed in model plants such as rice, Arabidopsis thaliana and other plants. However, the number of miRNAs discovered in maize is relatively low and little is known about miRNAs involved in the four stages during maize ear development. Here, we use deep-sequencing, miRNA microarray assays and computational methods to identify, proM-oM-,M-^Ale, and describe conserved and non-conserved miRNAs at four developmental stages. A total of 27 conserved miRNA families were identiM-oM-,M-^Aed in all four stages, In addition to known miRNAs, we also found 23 new maize-specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. We have found that many known and new miRNAs showed temporally expression. Finally, a total of 251 transcripts (140 genes) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs.This study led to the confirmation of the authenticity of 27 conserved miRNA families and the discovery of 23 novel miRNAs in maize. In addition, we have identified 130 targets of known and new miRNAs and ta-siRNA using recently developed tools for the global identification of miRNA targets. Identification and characterization of this important class of regulatory genes in maize may improve our understanding of molecular mechanism controlling flower development. The seeds of maize inbred line B73 were first sterilized and germinated in an incubator, then grown in a controlled environment with 28M-BM-0C/21M-BM-0C (day/night) under a 16-h day/8-h night photoperiod with a relative humidity of 70%. Ear development can be divided into four stages: the growth point elongation phase, spikelet differentiation phase, the floret primordium differentiation phase and floret organ differentiation phase. Plant materials (ears) were collected as described previously. In brief, ears were manually collected at the four developmental stages according to the plant features (number of visible leaves, leaf age index, and number of unfolded and folded leaves) combined with microscopic observation.
2014-10-22 | E-GEOD-47837 | biostudies-arrayexpress
Project description:Agilent oligonucleotide arrays were used to profile gene expression in dissected maize anthers of 3 types of male-sterile plants and their fertile siblings at four stages of development: after anther initiation, at the rapid mitotic proliferation stage, pre-meiosis, and meiotic prophase I. The male-sterile mutants (ms23, msca, and mac1) lack a range of normal cell types resulting from a temporal progression of anther failure. By combining the data sets from the comparisons between individual sterile and fertile anthers, candidate genes predicted to play important roles during maize anther development were assigned to stages and to likely cell types. Keywords: anther development, maize, male sterility
2008-09-16 | GSE12756 | GEO
Project description:In plants, MicroRNAs (miRNAs) are a new class of endogenous small RNAs that play essential regulatory roles in plant growth, development and stress response. Extensive studies of miRNAs have been performed in model plants such as rice, Arabidopsis thaliana and other plants. However, the number of miRNAs discovered in maize is relatively low and little is known about miRNAs involved in the four stages during maize ear development. Here, we use deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four developmental stages. A total of 27 conserved miRNA families were identified in all four stages, In addition to known miRNAs, we also found 23 new maize-specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. We have found that many known and new miRNAs showed temporally expression. Finally, a total of 251 transcripts (140 genes) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs.This study led to the confirmation of the authenticity of 27 conserved miRNA families and the discovery of 23 novel miRNAs in maize. In addition, we have identified 130 targets of known and new miRNAs and ta-siRNA using recently developed tools for the global identification of miRNA targets. Identification and characterization of this important class of regulatory genes in maize may improve our understanding of molecular mechanism controlling flower development.
2014-10-22 | GSE47837 | GEO
Project description:Transformation of the Arabidopsis ATHB17 gene into maize results in the expression of a truncated protein (smaller by 113 amino acids) that functions as a dominant-negative regulator that can modify activity of endogenous maize HD-Zip II transcription factors. This RNASeq experiment indicates that the observed effects of ATHB17d113 on the maize ear inflorescence and ear transcriptome are very small. Expression of ATHB17delta113 protein in maize leads to changes in ear growth resulting in increased ear size at early reproductive stages and, potentially increased sink size.
2015-10-26 | GSE51742 | GEO
Project description:Agilent oligonucleotide arrays were used to profile gene expression in dissected maize anthers of 3 types of male-sterile plants and their fertile siblings at four stages of development: after anther initiation, at the rapid mitotic proliferation stage, pre-meiosis, and meiotic prophase I. The male-sterile mutants (ms23, msca, and mac1) lack a range of normal cell types resulting from a temporal progression of anther failure. By combining the data sets from the comparisons between individual sterile and fertile anthers, candidate genes predicted to play important roles during maize anther development were assigned to stages and to likely cell types. Keywords: anther development, maize, male sterility 3 biological replicates of 3 different male-sterile mutants and their fertile siblings at 4 stages of anther development (36 arrays). Comparisons were done between male-sterile and fertile sibs at the same development stage.
2008-09-16 | E-GEOD-12756 | biostudies-arrayexpress
Project description:Transformation of the Arabidopsis ATHB17 gene into maize results in the expression of a truncated protein (smaller by 113 amino acids) that functions as a dominant-negative regulator that can modify activity of endogenous maize HD-Zip II transcription factors. This RNASeq experiment indicates that the observed effects of ATHB17d113 on the maize ear inflorescence and ear transcriptome are very small. Expression of ATHB17delta113 protein in maize leads to changes in ear growth resulting in increased ear size at early reproductive stages and, potentially increased sink size. Two ATHB17delta113 expressing events (Event 1 and Event 2) were compared to control plants (herein referred to as WT) in the context of Monsanto Elite Maize hybrid line NN6306. Three bioreps of both Ear inflorescence and Ear tissues were sampled for the WT and each of the two transgenic events.
2015-10-26 | E-GEOD-51742 | biostudies-arrayexpress
Project description:affy_zeawall_ril_maize - Four major QTL explaining lignin content and cell wall degradability variation have been identified in the F288 x F271 RIL progeny (Roussel et al., 2002, Maydica 47: 9-20). Gene expression has been considered as a way in identification of candidate gene underlying QTL. Five lines chosen for their allelic pattern at four main QTL were considered for expression studies, two lines with all four favorable alleles (RIL99, RIL54), two lines with the unfavorable allele at bin 6.06 QTL position (RIL39 , RIL71), and one line with the unfavorable allele at bin 9.02 QTL position (RIL118). Expression study will be investigated in ear internode at two stages emerging tassel and early silking stages with two replicates. Plants were cropped at INRA Lusignan (Vienne, France) in 2009 in a bloc design with two four-row replicates. Below-ear internodes of five representative RIL plants of one row in each replicate were harvested at the two stages and pooled. Keywords: genotype comparison, time course 20 arrays - maize
2012-06-16 | E-GEOD-22439 | biostudies-arrayexpress
Project description:Non-additive gene regulation has been recently suggested as an important factor promoting phenotypic variation and plasticity. In order to obtain a description of gene expression status at an early stage of ear development in a maize (Zea mays L.) F1 hybrid as relative to its parental inbreds, we compared gene expression profiles in immature ears of elite inbred lines B73 and H99 to one of their F1 hybrids (B73xH99) using cDNA microarray technology. Results show several genes expressed at a significantly different level between both inbred lines and their hybrid. In addition, gene expression non-additivity in the hybrid was detected on a broad scale, consisting of both dominance and over-dominance components, indicating that complex non-additive interactions at the molecular level exist in the developing ear of the studied maize hybrid. Non-additively regulated genes belong to a wide range of molecular functions, indicating that several regulatory and metabolic patterns are possibly affected during ear development in the investigated hybrid. We discuss the possibility that observed gene expression non-additivity in immature ear might be an early molecular manifestation of hybrid vigor, the most exploited factor for maize agronomic improvement.
2007-10-01 | GSE2771 | GEO
Project description:Maize (Zea mays L.) is one of the major cereal crops worldwide. Increasing planting density is an effective way to improve crop yield. However, plants grown under high-density conditions compete for water, nutrients, and light, which often leads to changes in productivity. To date, few studies have determined the transcriptomic differences in maize leaves in response to different planting densities. This study examined the whole-genome expression patterns in the leaves of maize planted under high and low densities to identify density-regulated genes. Leaves at upper, ear, and lower stem nodes were collected at the grain-filling stage of the maize hybrid Xianyu335 grown under low-density planting and high-density planting. In total, 72, 733, and 1,739 differentially expressed genes (DEGs) were identified in the respective upper, ear, and lower leaves under HDP. Upregulated and downregulated DEGs in the upper and lower leaves were similar in number, whereas upregulated DEGs in the ear leaves were significantly higher in number than the downregulated DEGs. Functional analysis indicated that genes responding to HDP-related stresses were mediated by pathways involving four phytohormones responsible for metabolism and signaling, osmoprotectant biosynthesis, transcription factors, and fatty acid biosynthesis and protein kinases, which suggested that these pathways are affected by the adaptive responses mechanisms underlying the physiological and biochemical responses of the leaves of maize planted at high density.
2020-06-29 | GSE152107 | GEO