Sweet corn: low vs. high plant density
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE72434 | GEO | 2021/06/01
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptional profiling of sweet corn plant density (crowding stress) tolerance influencing yield. Tolerance to crowding stress has played a crucial role in improving agronomic productivity in field corn; however, commercial sweet corn hybrids vary greatly in crowding stress tolerance. The experiment was conducted to 1) explore transcriptional changes among sweet corn hybrids with differential yield under crowding stress, 2) identify relationships between phenotypic responses and gene expression patterns, and 3) identify groups of genes associated with yield and crowding stress tolerance. Under conditions of crowding stress, three high-yielding and three low-yielding sweet corn hybrids were grouped for transcriptional and phenotypic analyses. Transcriptional analyses identified from 372 to 859 common differentially expressed genes (DEGs) for each hybrid. Large gene expression pattern variation among hybrids and only 26 common DEGs across all hybrid comparisons were identified, suggesting each hybrid has a unique response to crowding stress. Over-represented biological functions of DEGs also differed among hybrids. Strong correlation was observed between: 1) modules with up-regulation in high-yielding hybrids and yield traits, and 2) modules with up-regulation in low-yielding hybrids and plant/ear traits. Modules linked with yield traits may be important crowding stress response mechanisms influencing crop yield. Functional analysis of the modules and common DEGs identified candidate crowding stress tolerant processes in photosynthesis, glycolysis, cell wall, carbohydrate/nitrogen metabolic process, chromatin, and transcription regulation. Moreover, these biological functions were greatly inter-connected, indicating the importance of improving the mechanisms as a network. 3 high-and 3 low-yielding hybrids with 2-3 biological replications grown under high population density (crowding stress)
2016-01-05 | E-GEOD-73435 | biostudies-arrayexpress
Project description:Transcriptional profiling of sweet corn plant density (crowding stress) tolerance influencing yield. Tolerance to crowding stress has played a crucial role in improving agronomic productivity in field corn; however, commercial sweet corn hybrids vary greatly in crowding stress tolerance. The experiment was conducted to 1) explore transcriptional changes among sweet corn hybrids with differential yield under crowding stress, 2) identify relationships between phenotypic responses and gene expression patterns, and 3) identify groups of genes associated with yield and crowding stress tolerance. Under conditions of crowding stress, three high-yielding and three low-yielding sweet corn hybrids were grouped for transcriptional and phenotypic analyses. Transcriptional analyses identified from 372 to 859 common differentially expressed genes (DEGs) for each hybrid. Large gene expression pattern variation among hybrids and only 26 common DEGs across all hybrid comparisons were identified, suggesting each hybrid has a unique response to crowding stress. Over-represented biological functions of DEGs also differed among hybrids. Strong correlation was observed between: 1) modules with up-regulation in high-yielding hybrids and yield traits, and 2) modules with up-regulation in low-yielding hybrids and plant/ear traits. Modules linked with yield traits may be important crowding stress response mechanisms influencing crop yield. Functional analysis of the modules and common DEGs identified candidate crowding stress tolerant processes in photosynthesis, glycolysis, cell wall, carbohydrate/nitrogen metabolic process, chromatin, and transcription regulation. Moreover, these biological functions were greatly inter-connected, indicating the importance of improving the mechanisms as a network.
2016-01-05 | GSE73435 | GEO
Project description:Shotgun metagenomics of phyllosphere and rhizosphere of commercial sweet corn in Thailand
| PRJNA1105040 | ENA
Project description:Globally, gains in sweet corn [Zea mays L.var. rugosa (or saccharata)] are a fraction of the yield advances made in field corn (Zea mays L.) in the last half-century. Grain yield improvement of field corn is associated with increased tolerance to higher plant densities (i.e., crowding stress). Processing sweet corn hybrids that tolerate crowding stress have been identified; however, such hybrids appear to be under-planted in the processing sweet corn. Using crowding stress tolerant (CST) hybrids, the objectives of this study were to: (1) identify optimum plant densities for a range of growing conditions; (2) quantify gaps in production between current and optimum plant densities; and (3) enumerate changes in yield and ear traits when shifting from current to optimum plant densities. Using a CST shrunken-2 (sh2) processing sweet corn hybrid, on-farm plant density trials were conducted in thirty fields across the states of Illinois, Minnesota and Wisconsin, from 2013 to 2017 in order to capture a wide variety of growing conditions. Linear mixed-effects models were used to identify the optimum plant density corresponding to maximum ear mass (Mt ha-1), case production (cases ha-1), and profitability to the processor ($ ha-1). Kernel moisture, indicative of plant development, was unaffected by plant density. Ear traits, such as ear number and ear mass per plant, average ear length, and filled ear length declined linearly with increasing plant density. Nonetheless, there was a large economic benefit to the grower and processor by shifting to higher plant densities in most environments. This research shows that increasing plant densities of CST hybrids from current (58,475 plants ha-1) to optimum (73,075 plants ha-1) could improve processing sweet corn green ear yield and processor profitability on average of 1.13 Mt ha-1 and $525 ha-1, respectively.
| S-EPMC6762085 | biostudies-literature
Project description:Over the last six decades, steady improvement in plant density tolerance (PDT) has been one of the largest contributors to genetic yield gain in field corn. While recent research indicates that PDT in modern sweet corn hybrids could be exploited to improve yield, historical changes in PDT in sweet corn are unknown. The objectives of this study were to: (a) quantify the extent to which PDT has changed since introduction of hybrid sweet corn and (b) determine the extent to which changes over time in PDT are associated with plant morpho-physiological and ear traits. An era panel was assembled by recreating 15 sugary1 sweet corn hybrids that were widely used at one time in the United States, representing hybrids since the 1930s. Era hybrids were evaluated in field experiments in a randomized complete block design with a split-plot arrangement of treatments, including hybrid as the main factor and density as the split-plot factor. Plant density treatments included "Low" plant density (9,900 plants/ha) free of crowding stress or "High" plant density (79,000 plants/ha) with crowding stress. On average, per-area marketable ear mass (Mt/ha) increased at a rate of 0.8 Mt/ha/decade at High densities, whereas per-plant yield (i.e., kg/plant) remained unchanged over time regardless of the density level. Crate yield, a fresh market metric, improved for modern hybrids. However, processing sweet corn yield metrics like fresh kernel mass and recovery (amount of kernel mass contributing to the fresh ear mass) showed modest or no improvement over time, respectively. Modern sweet corn hybrids tend to have fewer tillers and lower fresh shoot biomass, potentially allowing the use of higher plant density; however, plant architecture alone does not accurately predict PDT of individual hybrids.
| S-EPMC8492913 | biostudies-literature
Project description:This study was designed to identify changes in gene expression when corn was placed under various related stresses including being grown with a competing weed (canola) to the V4 or V8 stage, or when 40% shade cloth was present to the V4 or V8 stage, or under low nitrogen (no added nitrogen fertilizer), or under weed/shade free fertilized control conditions. In all 5 treatments and the control, samples were harvested at V8. Mechanisms underlying early season weed stress on crop growth are not well described. Corn vegetative growth and development, yield, and gene expression response to nitrogen (N), light (40% shade), and weed stresses were compared with the response of nonstressed plants. Vegetative parameters, including leaf area and biomass, were measured from V2 toV12 corn stages. Transcriptome (2008) or quantitative Polymerase Chain Reaction (q PCR) (2008/09) analyses examined differential gene expression in stressed versus nonstressed corn at V8. Vegetative parameters were impacted minimally by N stress although grain yield was 40% lower. Shade, present until V2, reduced biomass and leaf area > 50% at V2 and, at V12, recovering plants remained smaller than nonstressed plants. Grain yields of shade-stressed plants were similar to nonstressed controls, unless shade remained until V8. Growth and yield reductions due to weed stress in 2008 were observed when weeds remained until V6. In 2009, weed stress at V2 reduced vegetative growth, and weed stress until V4 or later reduced yield. Principle component analysis of differentially expressed genes indicated that shade and weed stress had more similar gene expression patterns to each other than to nonstressed or low N stressed tissues. Weed-stressed corn had 630 differentially expressed genes compared with the nonstressed control. Of these genes, 259 differed and 82 were shared with shade-stressed plants. Corn grown in N-stressed conditions shared 252 differentially expressed genes with weed-stressed plants. Ontologies associated with light/photosynthesis, energy conversion, and signaling were down-regulated in response to all three stresses. Although shade and weed stress clustered most tightly together, only three ontologies were shared by these stresses, O-methyltransferase activity (lignification processes), Poly U binding activity (post-transcriptional gene regulation), and stomatal movement. Based on both morphologic and genomic observations, results suggest that shade, N, and weed stresses to corn are regulated by both different and overlapping mechanisms.
2011-05-09 | GSE29132 | GEO
Project description:The N6-methyladenosine (m6A) modification is the most common internal post-transcriptional modification, with important regulatory effects on RNA export, splicing, stability，and translation. However, the effects of m6A modifications on the resistance of sweet sorghum to salt stress remain unclear. In this study, we mapped the m6A modifications in two sorghum inbred lines (salt-tolerant M-81E and salt-sensitive Roma) that differ regarding salt tolerance. Dynamic changes to m6A modifications in sweet sorghum were identified in response to salt stress. Our data suggest that the differences in the m6A modifications between salt-tolerant and salt-sensitive sweet sorghum might contribute to the diversity in salt tolerance.
2022-05-02 | GSE146936 | GEO
Project description:We report transcriptome profiling from three developing stages of middle internode in Hybrid sweet sorghum. Samples were harvested at Booting, milky stages and physiological maturity.
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Project description:miRNAs-mediated gene silencing pathway plays vital roles in plant development, abiotic and biotic stress responses. Here, we carried out a high-throughput sequencing approach to identify miRNAs in leaves and flowers of sweet orange. Consequently we identified genome-wide 183 known miRNAs and 38 novel miRNAs. Small RNA sequencing of the leaves and flowers in sweet orange
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