Transcriptome profile for spikelets of rice plants subjected to severe reproductive stage drought stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
SUBMITTER: Manish Raorane
PROVIDER: E-GEOD-78777 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To understand how the qDTY12.1 interacts with other genes within the genome to give better physiological adaptations and better yield; the leaves transcriptome of DTY12.1 parents (Vandana , Way Rarem) and DTY12.1 NIL (481-B) were compared under control and drought conditions. Drought induced gene expression was studied in the leaves of the rice plants subjected to severe reproductive stage drought. Seeds of Vandana, Way Rarem, and 481-B were sown into rotovated soil at a rate of 2.0 g m-1 into plots of 3 rows X 3 m. The three genotypes were sown in three replications in a randomized complete block design.
2016-03-01 | E-GEOD-78776 | biostudies-arrayexpress
Project description:To understand how OsNAM12.1 over-expression influences the target genes within qDTY12.1 and across the genome to affect root growth, the root transcriptome of Vandana, 481-B, IR64-Tr-E2, and IR64-WT were compared under control and drought conditions. Drought induced gene expression was studied in the roots of the rice plants subjected to severe drought. Seeds of Vandana, 481-B, IR64 and the OsNAM12.1 overexpression line (OsNAM Event 2) were sown in 5 biological replicates in a randomized complete block design for both the well watered and drought stress treatments.
2016-02-25 | E-GEOD-78504 | biostudies-arrayexpress
Project description:To understand how the qDTY12.1 interacts with other genes within the genome to give better yield under drought; the spikelets transcriptome of DTY12.1 parents (Vandana , Way Rarem) and DTY12.1 NIL (481-B) were compared under control and drought conditions.
2016-03-01 | GSE78777 | GEO
Project description:The biological functions of differently expressed proteins between superior and inferior spikelet grains were investigated based on the isobaric tags for relative and absolute quantification to further clarify the mechanism of rice grain filling at the proteomic level, as well as the response of inferior spikelets to drought dress (-20 kPa or -40 kPa). Compared with superior spikelets, inferior ones had lower sink strength due to the lower sink activities (lower expressions of ADP-glucose pyrophosphorylase, granule-bound starch synthase, starch branching enzyme and pullulanase) and smaller sink sizes (lower abundances of structural proteins). The slower and later grain filling resulted from the weaker decomposition and conversion of photoassimilate and the slower cell division. Moderate drought stress (-20 kPa) promoted the grain filling of inferior spikelets through regulating the proteins associated with photoassimilate supply and conversion. These proteins may be important targets for rice breeding programs that raise the rice yield under drought condition. The findings offer new insights into rice grain-filling and provide theoretical evidences for better quality control and scientific improvement of super rice in practice.
2015-08-05 | PXD001046 | Pride
Project description:Fusarium Head Blight (FHB) is a disease of wheat and other cereal crops, where Fusarium graminearum and related species infects the wheat inflorescence during and post-anthesis. The fungus produces trichothecene toxins that accumulate in the grain of infected head, and are required for disease spread. Microarrays were used to observe differential gene expression in the uninoculated spikelets of FHB-challenged wheat spikes in three wheat genotypes. A summary of our findings will be published in Plant Pathology. Three wheat genotypes were used: (1) 'Superb', an FHB-susceptible Canadian wheat cultivar; (2) GS-1-EM0040 (CIMMYT11x'Superb'*2), a double haploid line with good resistance to initial infection (Type 1 resistance), and moderate resistance to disease spread (Type 2 resistance); and (3) GS-1-EM0168 (CM82036x'Superb'*2), a double haploid line with moderate Type 1 resistance, and good Type 2 resistance. Five inocula were used: (A) water, (B) FgTri5+ (GZ3639, a trichothecene-producing F. graminearum strain); (C) FgTri5- (GZT40, a trichothecene-non-producing mutant of the F. graminearum strain GZ3639); (D) FgTri5 supplemented with deoxynivalenol (DON), which is the main trichothecene produced by FgTri5+; and (E) DON. The inocula were injected into two spikelets near the center of the spike during early stages of anthesis, and spikelets above and below the inoculation point were collected at 3, 8, and 24 h after inoculation. A zero-hour un-inoculated control was also collected from each line. Total RNA was extracted from collected spikelets, and microarray analysis was perfomed using the Affymetrix Wheat GeneChip.
2011-08-31 | E-GEOD-28973 | biostudies-arrayexpress
Project description:Drought stress is a major problem around the world and although progress in understanding how vegetable crops and model plants adapt to drought have been made, there is still little information about how fruit crops deal with moderate drought stress. In this study, we investigated the response of two apple genotypes: a drought-sensitive genotype (M26) and a drought-tolerant genotype (MBB). Our results of the morphology, physiology and biochemistry under moderate drought stress, indicated that relative water content (RWC) and leaf area (LA) were not significant changes in two genotypes. However, it had larger leaf mass per area (LMA), and accumulated higher free proline (CFP), soluble sugars (CSS) and malonaldehyde (MDA) in the leaves. Thus, it appears that the MBB genotype could produce more osmosis-regulating substances. Phosphoproteomic was analyzed from leaves of both genotypes under moderate drought stress using the isobaric tags for relative and absolute quantification (iTRAQ) technology. A total of 595 unique phosphopeptides, 682 phosphorylated sites and 446 phosphoproteins were quantitatively analyzed in the two genotypes. Motif analyses of the phosphorylation sites showed that six motifs including [PxsP], [sP], [sD], [Rxxs], [sxP] and [sxs] were enriched. We identified 12 and 48 PLSC phosphoproteins in M26 and MBB, respectively. Among these, 9 PLSC phosphoproteins were common to both genotypes, perhaps indicating a partial overlaps of the mechanisms to moderate drought stress. Gene ontology analyses revealed that the PLSC phosphoproteins present a unique combination of metabolism, transcription, translation and protein processing, suggesting that the response in apple to moderate drought stress encompasses a new homeostasis of major cellular processes. The basic trend was an increase in protein abundance related to drought and organic substance upon moderate drought stress between two genotypes. These increases were higher in the drought-tolerant genotype (MBB) than in the drought-sensitive genotype (M26). The 23 differentially expressed mRNA encoding phosphoproteins were analysis by quantitative real-time PCR (qRT-PCR). Our study is the first to address the phosphoproteome of a major fruit crop, apple rootstocks, in response to moderate drought stress, and provide insights into the molecular regulation mechanisms of apple rootstock under moderate drought stress.
2016-11-08 | PXD005238 | Pride
Project description:We used microarray analysis to examine transcriptomic changes upon dreb1a under drought, identifying hundreds of genes that potentially function downstream of DREB1A and mediate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles. DREB1a mutant (CS872453) were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest. Unopened flower samples were collected from drought treated plants, at day 3, 4, 5.
2013-11-06 | E-GEOD-43724 | biostudies-arrayexpress
Project description:We aimed to identify differential expression of microRNAs between superior and inferior spikelets by using a deep sequencing approach developed by Solexa (Illumina). Two small RNA libraries were constructed from superior and inferior spikelets at 18 days after fertilization, and more than nine million small RNA sequence reads were generated for each library. Totals of 351 and 312 known miRNAs were obtained from the superior and inferior spikelets, respectively. Analysis of the expression profiles of these miRNAs showed that 189 miRNAs were differentially expressed between superior spikelets and inferior spikelets. In addition, 43 novel miRNAs were identified mostly by the accumulations of miRNA*s were also expressed differentially. Further analysis shows that these miRNAs may individually participate in regulating hormone metabolism, carbohydrate metabolic pathways, and cell division during rice grain development. These results indicate that slow grain filling and low grain weight of rice inferior spikelets probably relation to the expression and function differences between superior and inferior spikelet miRNAs. Examination of 2 different small RNA expression profilings in superior and inferior spikelets at 18 days after fertilization.
2011-03-19 | E-GEOD-28028 | biostudies-arrayexpress
Project description:We also used microarray analysis to examine transcriptomic changes under drought, identifying thousands of genes that potentially mediate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles. Arabidopsis were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest (about 50 days). For well-watered (control) plants, 90% of the soil water-holding capacity was maintained until tissue harvest or after seed maturation (pots were weighed and watered twice per day). Unopened flower samples were collected, from both treated and control plants, at day 0, 3, 4, 5, 10.
2013-11-06 | E-GEOD-40998 | biostudies-arrayexpress
Project description:Purpose: Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic expression patterns under water stress conditions. We used RNA sequencing (RNA-seq) to identify the candidate genes and alleles and to explore the evolutionary signatures of selection Methods: We studied the effect of water stress on gene expression in Eucalyptus camaldulensis seedlings derived from three natural populations. We used reference-guided transcriptome mapping to study gene expression. Reads mapping to predicted transcripts were analysed with edgeR pacakge to study differntial expression of genes under control and water-stress conditions. SNPs within the genes were obtained using pileup file generated with samtools and the SNP frequencies were analysed with VarScan package. SNPs were further characterised as sysnonymous and non-synonymous using popoolation2 pacakge. Results: Several genes showed differential expression between control and stress conditions. Gene ontology (GO) enrichment tests revealed up-regulation of 140 stress-related gene categories and down-regulation of 35 metabolic and cell wall organisation gene categories. More than 190,000 single nucleotide polymorphisms (SNPs) were detected and 2737 of these showed differential allelic expression. Allelic expression of 52% of these variants was correlated with total gene expression. Signatures of selection patterns were studied by estimating the proportion of nonsynonymous to synonymous substitution rates (Ka/Ks). The average Ka/Ks ratio among the 13,719 genes was 0.39 indicating that most of the genes are under purifying selection. Among the positively selected genes (Ka/Ks > 1.5) apoptosis and cell death categories were enriched. Of the positively selected genes, ninety genes showed differential expression and 27 SNPs from 17 positively selected genes showed differential allelic expression between treatments. Conclusions: Correlation of allelic expression of several SNPs with total gene expression indicates that these variants may be the cis-acting variants or in linkage disequilibrium with such variants. Enrichment of apoptosis and cell death gene categories among the positively selected genes reveals the past selection pressures experienced by the populations used in this study. Leaf mRNA of 12 samples were used to study the gene expression under control and water-stress conditions. Three samples under water-stress conditions and three samples under control conditions were used as biological replicates for differenctial gene expression between the treatments. High-throughput sequence reads from mRNA samples were generated by deep sequencing with Illumina GAIIx.
2012-07-17 | E-GEOD-39369 | biostudies-arrayexpress