Gene expression in developing ears of ra3;tpp4 maize mutants compared to wild-type
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE123147 | GEO | 2018/11/29
REPOSITORIES: GEO
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Project description:Gene expression in developing ears of ra3 tpp4 maize mutants compared to wild-type
| PRJNA507641 | ENA
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:In this study we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. These are the RNA-seq datasets used in this study. We profiled changes in gene expression during normal maize ear and tassel development and in developing maize ear primordia upon genetic perturbation of the RAMOSA branching pathway. For the wild-type ear and tassel developmental series, greenhouse-grown B73 inbred plants were used. 10mm ears were collected and sectioned as follows from tip to base along the developmental gradient: tip 1mm sampled (tip; Inflorescence Meristem/Spikelet Pair Meristem), next 1mm discarded, next 1mm sampled (mid; Spikelet Meristem), next 2mm discarded, next 2 mm sampled (base; Floral Meristem), and immediately frozen in liquid nitrogen. Sections from ~30 sampled ears were pooled for each of 2 biological replicates to represent tip, mid, and base stages. Tassels were hand-dissected, measured, separated by stage: 1-2mm (stg1), 3-4mm (stg2), and 5-7mm (stg3), and immediately frozen in liquid N. For each stage, ~20-30 tassels were pooled for each of 2 biological replicates. For ramosa mutant series, segregating families (1:1) of ra1-R, ra2-R, and ra3-fea1 mutant alleles, all introgressed at least 6 times into the B73 inbred background, were grown at CSHL Uplands Farm. Field-grown plants were genotyped and collected 6-7 weeks after germination (V7-V8 stage). First and second ear primordia were immediately hand-dissected, measured, and frozen in liquid nitrogen. For ra1, ra2 and ra3 mutants and wild-type controls, ears were pooled into two size classes: 1) 1mm class included a range of 0.7-1.5mm sized ears and nine ears were pooled for each of 2 biological replicates; 2) 2mm class included a range of 1.8-2.5mm sized ears and six ears were pooled for each of three biological replicates. Wild-type samples were proportional mixtures of heterozygote siblings segregating in ra1, ra2, and ra3 populations. Variability factors (e.g. ear size within class, ear rank on the plant, and time of collection) were distributed evenly across pooled samples.
2013-11-27 | E-GEOD-51047 | 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: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:Purpose: The goal of this study is to identify differentially expressed genes (DEGs) in immature ears between Barren inflorescence3 (Bif3) mutant and its wild-type siblings in maize. Methods: the 3-4 mm ear primordia of maize wild-type and Bif3 mutant were dissected from maize plant at the reproductive stage, and samples were snap freeze using liquid nitrogen. The total RNAs were prepared using RNeasy mini kit (Qiagen). All those RNA samples of wild-type and Bif3 mutant were submitted for RNA-Seq. Conclusions: Our RNA-seq experiments identified 1380 up- and 242 down-regulated genes (P < 0.05, FDR < 0.1, fold-change > 1.5).
2021-03-17 | GSE158330 | 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:Dark-grown maize seedlings with primary roots 12-20 mm in length were transplanted to high (-0.03 MPa) water potential vermiculite. About 1,000 roots were collected. Each root was divided into 4 segments (distances are from the junction of the root apex and root cap): segment 1, 0-3 mm plus the root cap; segment 2, 3-7 mm; segment 3, 7-12 mm; segment 4, 12-20 mm. Details of the conditions and nutrient modifications have been described before (Sharp et al., 1988; Spollen et al, 2000). From each segment, 250 mg of material was used and RNA was isolated form the combined sample containing all four segments. RNA was isolated using the RNeasy Maxi Kit (Qiagen). RNA integrity was verified by denaturing agarose gel electorphoresis and spectrophotometry.
2010-12-01 | GSE25761 | GEO
Project description:Microbial community diversity of gut from three Lepidopteran larvae damaging maize ears Raw sequence reads
| PRJNA819209 | ENA
Project description:S. reilianum triggered loss of organ and meristem identity, and loss of meristem determinacy in male and female inflorescences and flowers. Microarray analysis showed that these developmental changes were accompanied with transcriptional regulation of genes proposed to regulate floral organ and meristem identity, and meristem determinacy in maize. Infected ears were compared with mock infected ears. Each treatment had 3 biological replicates Disease: S. reilianum-infected ears with elongated kernel: Zm_Sr5_15_2_Leafy ears4weeks_I, Zm_Sr5_15_2_Leafy ears4weeks_II, Zm_Sr5_15_2_Leafy ears4weeks_III Disease: Mock infected ears at: Zm_Sr5_15_2_Mock4weeks_I, Zm_Sr5_15_2_Mock4weeks_II, Zm_Sr5_15_2_Mock4weeks_III biological replicate: Zm_Sr5_15_2_Leafy ears4weeks_I, Zm_Sr5_15_2_Leafy ears4weeks_II, Zm_Sr5_15_2_Leafy ears4weeks_III biological replicate: Zm_Sr5_15_2_Mock4weeks_I, Zm_Sr5_15_2_Mock4weeks_II, Zm_Sr5_15_2_Mock4weeks_III
2011-08-31 | E-GEOD-29747 | biostudies-arrayexpress