Similar Datasets
Project description:Find differentially expressed genes under low temperature (10℃) and normal conditions (25℃) during maize germination
2023-02-10 | GSE183230 | GEO
Project description:High temperature is increasingly becoming one of the prominent environmental factors affecting the growth and development of maize (Zea mays L.). Therefore, it is critical to identify key genes and pathways related to heat stress (HS) tolerance in maize. Here, we identified a heat-resistant (Z58D) and heat-sensitive (AF171) maize inbred lines at seedling stage. Transcriptomic analysis identified 3,006 differentially expressed genes (DEGs) in AF171 and 4,273 DEGs in Z58D under HS treatments, respectively. Subsequently, GO enrichment analysis showed that shared upregulated genes in AF171 and Z58D involved in response to HS, protein folding, abiotic and temperature stimulus pathway. Moreover, the comparison between the two inbred lines under HS showed that response to heat and response to temperature stimulus significantly overrepresented for the 1,234 upregulated genes. Furthermore, commonly upregulated genes in Z58D and AF171 had higher expression level in Z58D than AF171. In addition, maize inbred CIMBL55 had been verified to be more tolerant than B73 and commonly upregulated genes had higher expression level in CIMBL55 than B73 under HS. The consistent results indicated that heat-resistant inbred lines may coordinate the remarkable expression of genes in order to recover from HS. Additionally, 35 DEGs were conserved among 5 inbred lines by a comparative transcriptomic analysis. Most of them were more pronounced in Z58D than AF171 at expression level. Those candidate genes may confer thermotolerance in maize.
2024-03-01 | GSE254852 | GEO
Project description:RNA-seq for two maize inbred lines
| PRJNA611589 | ENA
Project description:Rapid and uniform seed germination is required for modern cropping system. Thus, it is important to optimize germination performance through breeding strategies in maize, in which identification for key regulators is needed. Here, we characterized an AP2/ERF transcription factor, ZmEREB92, as a negative regulator of seed germination in maize. Enhanced germination in ereb92 mutants is contributed by elevated ethylene signaling and starch degradation. Consistently, an ethylene signaling gene ZmEIL7 and an α-amylase gene ZmAMYa2 are identified as direct targets repressed by ZmEREB92. OsERF74, the rice ortholog of ZmEREB92, shows conserved function in negatively regulating seed germination in rice. Importantly, this orthologous gene pair is likely experienced convergently selection during maize and rice domestication. Besides, mutation of ZmEREB92 and OsERF74 both lead to enhanced germination under cold condition, suggesting their regulation on seed germination might be coupled with temperature sensitivity. Collectively, our findings uncovered the ZmEREB92-mediated regulatory mechanism of seed germination in maize and provide breeding targets for maize and rice to optimize seed germination performance towards changing climates.
2023-11-09 | GSE234833 | GEO
Project description:This SuperSeries is composed of the following subset Series:; GSE8174: Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Seedling data; GSE8176: Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data; GSE8179: Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Embryo data Experiment Overall Design: Refer to individual Series
2008-06-17 | E-GEOD-8194 | biostudies-arrayexpress
Project description:Analysis of whole genome bisulfite data for 3 maize inbred lines (B73, PH207, and W22) with data aligned to the corresponding genome for determination of methylation level (CG, CHG, and CHH) across 100bp windows of the maize genome.
2020-03-01 | GSE128859 | GEO
Project description:Among the mineral elements necessary for plant growth, nitrogen (N) is the macronutrient required in larger amounts. The optimization of N use efficiency (NUE) in maize could be obtained through both genetic improvement and agronomic practices in order to enhance production and reduce the negative impact of the N fertilizer use on the environment. Physiological characterizations of inbred lines with different NUE are available in maize.
2014-05-19 | GSE49681 | GEO
Project description:The phenomenon of heterosis describes the increased agronomic performance of heterozygous F1-plants compared to their homozygous parental inbred plants. Heterosis is already manifested during the early stages of root development in maize. The goal of this study was to identify non-additive gene expression in primary roots of maize hybrids compared to the average expression levels of their parental inbred lines. To achieve this goal a two step strategy was selected. First, a microarray preselection of non-additively expressed candidate genes was performed. Subsequently, gene expression levels in a subset of genes were determined via high throughput qRT-PCR experiments. Initial microarray experiments identified 1941 non-redundant genes which displayed non-additive gene expression in at least one of the twelve analyzed hybrids compared to the midparent value of their parental inbred lines. Comparison of these 1941 genes with non-additively expressed genes identified in maize shoot apical meristems via the same experimental procedure in the same genotypes revealed significantly less overlap than expected by pure chance supporting. This supports the notion of organ specific patterns of non-additively expressed genes. qRT-PCR analyses of 64 of the 1941 non-additively expressed genes in four different hybrids revealed that the majority of non-additively expressed genes were expressed between the high and low parent expression values and only a small fraction of genes was expressed below low or above high parent levels. Subsequently, 22 of the 64 genes that displayed non-additive expression in all four hybrids were analyzed in twelve hybrids that were generated from four inbred lines. Among those genes a superoxide dismutase 2 was expressed significantly above the midparent value in all twelve hybrids and might thus play a protective role in antioxidative defense in the primary root of maize hybrids. These findings are consistent with the hypothesis that global expression trends but also the consistent differential expression of key genes might be relevant during the organ-specific manifestation of heterosis. Keywords: Comparative genomic hybridization
2008-02-16 | GSE10539 | GEO
Project description:To understand the transcriptome changes during drought tolerance in maize, the drought-tolerant line Han21 and drought-sensitive line Ye478, which show substantial differences in drought tolerance at the seedling stage, were selected for this study. Using the GeneChip Maize Genome Arrays, we applied genome-wide gene expression analysis to the two genotypes under gradual drought stress and re-watering. We identified 2172 common regulated transcripts in both lines under drought stress, with 1084 common up-regulated transcripts and 1088 common down-regulated transcripts. Among the 2172 transcripts, 58 potential protein kinases and 117 potential transcription factors were identified. The potential components of the ABA signaling pathway were identified from the common regulated transcripts. We also identified 940 differentially regulated transcripts between the two lines. Among the 940 transcripts, the differential expression levels of 29 transporters and 15 cell wall-related transcripts may contribute to the different tolerances of the two lines. Additionally, we found that the drought-responsive genes in the tolerant Han21 line recovered more quickly when the seedlings were re-watered, and 311 transcripts in the tolerant Han21 line were exclusively up-regulated at the re-watering stage compared to the control and stress conditions. Our study provides a global characterization of two maize inbred lines during drought stress and re-watering and will be valuable for further study of the molecular mechanisms of drought tolerance in maize.
2010-06-03 | GSE16567 | GEO
Project description:Genome-wide gene expression atlas of maize inbred line B73. Maize inbred B73 was used for constructing the gene atlas. Plants were grown in Plano silt loam soil at the West Madison Agricultural Research Station, Verona, WI during Summer 2008. During field preparation, 200 kg/acre of Urea (46-0-0) was applied. One day after planting, herbicides including Callisto (142 g/acre), Dual II (710 ml/acre), and Simazine (227 g/acre) were applied. For collection of seed tissues, shoots were covered before silk emergence avoiding any injury to the plants. Plants were self-pollinated on the same day to establish a common time initiation point for the harvest timeline. Greenhouse-grown plants were propagated by growing five plants per pot (30 cm top diameter, 28 cm height, 14.5 L volume) containing Metro-Mix 300 (Sun Gro Horticulture, Bellevue, WA, USA) with no additional fertilization. The growing conditions were 27 deg. C day and 24 deg. C night temperature with a 16h light (5:00am to 9:00pm) and 8h dark regime. Germinating seed tissue was generated by soaking seeds in distilled water in a Petri dish for 12h and then placing seeds between layers of moist paper towels for another 12h to allow germination. The field samples were collected between 8:00am and 10:00am, approximately 3 hours after sunrise. The greenhouse samples were collected between 8:00am and 9:00am, three hours after turning on the lights. Three biological replicates were collected for each tissue type. For all the tissues except germinating seeds, a biological replicate was constituted by collecting and pooling samples from three competitive randomly chosen plants. For germinating seed, ten randomly chosen seeds were pooled to form a biological replicate. The harvested tissues were immediately frozen in liquid nitrogen and stored at -80 deg. C. Total RNA was extracted using TRIZOL reagent (Invitrogen, http://www.invitrogen.com) following the manufacturer's protocol, and purified using RNeasy MinElute Cleanup Kit (Qiagen, http://www.qiagen.com) following the manufacturer's instructions. PLEXdb (http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rajandeep S Sekhon. The equivalent experiment is ZM29 at PLEXdb.
2011-02-11 | GSE27004 | GEO