Phenotypic and molecular characterisation of a novel Bt2 allele in maize
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE7030 | GEO | 2007/07/01
SECONDARY ACCESSION(S): PRJNA98387
REPOSITORIES: GEO
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Project description:At 35 DAP whole kernels (pericarp + endosperm + embryo) without glumes of green house grown ears of heterozygous (+/bt2-H2328), self-pollinated plants were visually divided into pools of phenotypically normal looking kernels (small indentation, slightly smaller than mutant kernels, genotype +/+ or +/bt2-H2328) and pools of phenotypically mutant kernels (plump, round kernels, slightly larger than normal kernels, genotype bt2-H2328/bt2-H2328). Pools consisted of 4 kernels. 3 different ears were used for a biological duplicate. Experiment Overall Design: 4 arrays - maize
2008-06-15 | E-GEOD-7030 | biostudies-arrayexpress
Project description:The experiment consisted of a field design containing two maize inbred lines Va35 and Mp313E. Va35 has yellow kernels and is susceptible to kernel infection by Aspergillus flavus (A. flavus). Mp313E is a white dent maize inbred line and was released primarily as a source of resistance to kernel infection by A. flavus. The test ears were inoculated with Aspergillus flavus and collected two days after inoculation. Non-inoculated ears collected 16 days after pollination were also used as a control. The microarray experimental design was a randomized complete block design with three replications. One microarray slide was used for each field plot. Each slide contained the inoculated and non-inoculated sub-treatments. A second slide for one replication of each genotype contained a dye swap for the inoculation treatment and three subsamples (dots) within the slide represented each contig. Keywords: Direct comparison
2007-11-09 | GSE9546 | GEO
Project description:Maize kernel is an important source of food, feed and industrial raw materials. The illustration of the molecular mechanisms of maize kernel development will be helpful for the manipulation of maize improvements. Although a great many researches based on molecular biology and gecetics have greatly increased our understanding on the kernel development, many of the mechanisms controlling this important process remain elusive. In current study, a microarray with approximately 58,000 probes was used to study the dynamic gene expression during kernel development from the fertilization to physiological maturity. Samples from two consecutive time-points were paired and labeled using different fluorescent dyes (Cy3 and Cy5) and hybridized in the same array. Hybridization of slides was performed according to the manufacturer’s instructions (http://www.maizearray.org/). The hybridized slides were scanned by a Genepix 4000B (Axon, USA). A loop design was applied for running the microarray. Two replicates of each pair of samples were carried out to test both the reproducibility and quality of the chip hybridizations. By comparing six consecutive time-points, namely 1, 5, 10, 15, 25 and 35 days after pollination (DAP), 3,445 differentially expressed genes were identified. These genes were then grouped into 10 clusters showing specific expression patterns using a K-means clustering algorithm. An investigation of function and expression patterns of genes expanded our understanding of the regulation mechanism underlying the important developmental processes, cell division and kernel filling. The differential expression of genes involved in plant hormone signaling pathways suggested that phytohormone might play a critical role in the kernel developmental process. Moreover, regulation of some transcription factors and protein kinases might be involved in the whole developmental process. To obtain the global gene expression profile during maize kernel development, a microarray with approximately 58,000 probes was used. The maize inbred line X178 was planted on the field. Each plant was self-pollinated by hand. The ears were harvested from healthy plants at 1, 5, 10, 15, 25 and 35 days after pollination (DAP), respectively. In order to increase the consistency & uniformity of the isolated kernels, the upper half and about one sixth of ears from the bottom were cut and discarded, the kernels were isolated from the rest part of the ears. Samples at each time-point were collected from at least thirty ears and pooled to represent the line characteristics of X178. Two sub-samples for replication in the microarray analysis were randomly drawn. Samples from two consecutive time-points were paired and labeled using different fluorescent dyes (Cy3 and Cy5) and hybridized in the same array. A loop design was applied for running the microarray. Two replicates of each pair of samples were carried out to test both the reproducibility and quality of the chip hybridizations.
2008-04-09 | E-GEOD-9386 | biostudies-arrayexpress
Project description:To provide insights into how SUN regulates shape and whether this is accompanied with shifts in transcript profiles, we identified differentially expressed genes in eight pairwise comparisons of SUN and wild-type fruit tissues and time points. Lines nearly isogenic for SUN in the cultivated background Solanum lycopersicum c.v. SUN1642 were grown in the greenhouse in a completely randomized design. SA4 is like SUN1642 and SA3 is like WT LA1589 at SUN locus. Flowers at anthesis were tagged and self-pollinated on successive days. Anthesis is defined as when the flower opens. Pollination of flowers was staggered so fruit of all developmental stages would be harvested on the same day. Fruits at stage four, seven, and ten days post anthesis (dpa) were harvested and brought back to the laboratory. Septum, seed, and pericarp tissue were isolated and frozen in liquid nitrogen. Four dpa septum tissues is a mixture of septum and seed tissue. Four dpa pericarp is a mixture of pericarp and exocarp tissue due to small size of four dpa fruits. Seven and 10 dpa pericarp dont contain the exocarp (epidermal) tissues. Four replicates were collected. RNA was extracted using Trizol and Stand-specific libraries were prepared from total RNA and sequences of 51 bp were generated on an Illumina HiSeq2000.
2013-12-10 | E-MTAB-4837 | biostudies-arrayexpress
Project description:Seedlings grown from seeds from open-pollinated mother trees of genotype UF12 were grown and at two months of age used to analyze response to treatment with the fungal pathogen Colletotrichum theobromicola and the oomycete pathogen Phytophthora palmivora.
2015-11-16 | GSE73804 | GEO
Project description:Quality Protein Maize (QPM) was created by selecting for genetic modifiers that convert the starchy endosperm of an opaque2 (o2) mutant to a hard, vitreous phenotype. Genetic analysis has shown there are multiple, unlinked o2 modifiers (Opm), but their identity and mode of action are unknown. A microarray hybridization performed with RNA obtained from true breeding o2 progeny with vitreous and opaque kernel phenotypes identified a small group of differentially expressed genes, some of which map at or near the Opm QTLs. Compared 18 days after pollination endosperm transcript profiles in true breeding modified (vitreous; V) and non-modified (opaque; O) opaque 2 kernels. Used four vitreous biological reps (V1-V4) and four opaque biological reps (O1-O4). Each biological rep is a pool of 25 kernels representing 5 kernels form each of 5 uniform phenotype ears (vitreous or opaque). Four arrays used: Array 1= V1 vs O1, Array 2 = V2 vs O2, Array 3 = V3 vs O3, Array 4 = V4 vs O4
2010-05-26 | E-GEOD-10449 | biostudies-arrayexpress
Project description:Effect of high grain protein locus on barley grain protein accumulation. Gene expression levels were analysed in Karl, a low grain protein variety with its near-isogenic line 10_11(has high grain protein locus, chromosome 6)using Barley1 22k affymetrix chip. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Aravind Jukanti. The equivalent experiment is BB53 at PLEXdb.] developmental stage: 14 days past anthesis - genotype: Karl - tissue type: Leaves(3-replications); developmental stage: 14 days past anthesis - genotype: Karl - tissue type: Kernels(3-replications); developmental stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves(3-replications); developmental stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels(3-replications); developmental stage: 21 days past anthesis - genotype: Karl - tissue type: Leaves(3-replications); developmental stage: 21 days past anthesis - genotype: Karl - tissue type: Kernels(3-replications); developmental stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves(3-replications); developmental stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels(3-replications)
2011-11-22 | E-GEOD-33413 | biostudies-arrayexpress
Project description:Lines nearly isogenic for fw3.2 in the cultivated background Solanum lycopersicum c.v. Yellow Stuffer were grown in the greenhouse in a completely randomized design. fw3.2(ys) and fw3.2(wt) are NILs carrying cultivated and wild alleles for fw3.2 locus. Flowers were tagged a day before anthesis and self-pollinated at anthesis. Fruits at stage five, seven, and ten days post anthesis (dpa) were harvested. Pericarp and seed tissues were separately isolated. Four replicates were collected for each sample. RNA was extracted using Trizol and Stand-specific libraries were prepared from total RNA and sequences of 51 bp were generated on an Illumina HiSeq2000.
2013-03-11 | E-MTAB-4792 | biostudies-arrayexpress
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:Results: In this study, the ears at the V9 stage, kernels and ear leaf at the 5DAP (days after pollination) stage of maize were used for morphological, physiological and comparative transcriptomics analysis to understand the different features of “sink” or “source” organs and the effects on kernel yield under drought stress conditions. The ABA-, NAC-mediate signaling pathway, osmotic protective substance synthesis and protein folding response were identified as common drought stress response in the three organs. Tissue-specific drought stress responses and the regulators were identified, they were highly correlated with growth, physiological adaptation and yield loss under drought stress. For ears, drought stress inhibited ear elongation, led to the abnormal differentiation of the paired spikelet, and auxin signaling involved in the regulation of cell division and growth and primordium development changes. In the kernels, reduced kernel size caused by drought stress was observed, and the obvious differences of auxin, BR and cytokine signaling transduction appeared, which indicated the modification in carbohydrate metabolism, cell differentiation and growth retardation. For the ear leaf, dramatically and synergistically reduced the expression of photosynthesis genes were observed when suffered from drought stress, the ABA- and NAC- mediate signaling pathway played important roles in the regulation of photosynthesis. Conclusions: Transcriptomic changes caused by drought were highly correlated with developmental and physiological adaptation, which was closely related to the final yield of maize, and a sketch of tissue- and developmental stage-specific responses to drought stress in maize was drafted.
2019-06-04 | GSE132113 | GEO