Wheat
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA517367 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8494395_1.fastq.gz | Fastqsanger.gz | |||
| SRR8494395_2.fastq.gz | Fastqsanger.gz | |||
| SRR8494396_1.fastq.gz | Fastqsanger.gz | |||
| SRR8494396_2.fastq.gz | Fastqsanger.gz | |||
| SRR8494397_1.fastq.gz | Fastqsanger.gz |
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Project description:Water deficit stress between the booting and grain filling stages significantly affect grain yield and quality of hard red winter wheat. Several stress tolerant cultivars with different adaptation mechanisms have been released and are widely cultivated on the Southern Great Plains of the US. However, the physiological, molecular, and genetic basis of adaptation to drought stress for these cultivars remains unknown. Use of transcriptome profiling to identify drought responsive genes in hexaploid wheat is a challenging process given the quantitative nature of drought stress, genome complexity, and the intricacy of interaction effects. If the information generated from functional genomics studies is to be used in molecular breeding programs for cultivar development, it is highly desirable to use cultivars better adapted for the region. In the current study we used two well-adapted, drought-tolerant, high-yielding, cultivated varieties, TAM 111 and TAM 112, which appear to have different adaptation mechanisms, to identify drought stress induced transcripts during heading and early dough stages. A set of 24 Affymetrix GeneChip wheat genome arrays (2 cultivars; 2 water treatments; 2 sampling stages; 3 biological replicates) from plants subjected to water deficit stress under controlled glasshouse conditions. Differentially expressed genes were identified using a ANOVA (p<0.01) controlling false discovery rate (FDR, q<0.01) using Benjamini Hochberg approach.
2022-01-01 | GSE45262 | GEO
Project description:Fusarium head blight (FHB), caused by Fusarium graminearum is a devastating disease that affects global wheat production. F. graminearum encodes many effector proteins; however, its virulence mechanisms are poorly understood. In this study, we identified a secretory effector candidate protein (FgEC10) that is essential for the virulence of F. graminearum and suppresses the basal immune response. FgEC10 interacted strongly with wheat fumarylacetoacetate hydrolase (TaFAH) and accelerated its degradation via the 26S proteasome pathway. In addition, we showed that TaFAH interacted with TaPSMD, an important component of the 26S proteasome and that FgEC10 enhanced the interaction between TaFAH and TaPSMD. RNA silencing or overexpression of TaFAH in wheat plants showed that TaFAH positively regulated wheat FHB resistance, heading period, and grain yield. Transcriptomic analysis revealed that TaFAH promoted the expression of genes associated with disease resistance and the heading period. Metabolomic analysis revealed that overexpression of TaFAH increased the levels of several amino acids that inhibited F. graminearum growth and enhanced wheat resistance to FHB. Collectively, our study reveals a novel pathogenic mechanism and provides a valuable genetic resource for improving FHB resistance and grain yield in wheat.
2024-08-15 | GSE254427 | GEO
Project description:We report the transcriptome profile of different cultivars of Fusarium graminearum-infected wheat grains, aiming to search for some different expression genes and pathways to reveal the difference between wheat cultivars.
2021-11-18 | GSE188959 | GEO
Project description:The goals of this study are to compare transcriptome profiling (RNA-seq) between two wheat cultivars with different antioxidant actvity and to clarify the differences of these two wheat cultivars.
2021-12-31 | GSE192732 | GEO
Project description:Global gene expression analysis of 7,835 tentatively unique wheat genes during caryopsis development Keywords: Time-course study; developing wheat caryopsis
2009-09-30 | GSE8963 | GEO
Project description:The economic importance of wheat and its contribution to human and livestock diets has been already demonstrated. However, wheat production is impacted by pests that induce yield reductions. Among these pests, wheat curl mite (WCM, Aceria tosichella Keifer) impacts wheat all around the world. WCM are tiny pests that feed within the whorl of developing leaves and prevent the leaves from unfurling by causing leaves curling. The curling of the leaves provides a protective niche for the WCM. Additionally, WCM are also the vector of serious viruses in wheat. Little is known regarding the impact of the WCM on wheat transcriptome, and to date, only one article has been published describing the wheat transcriptomic changes after 1 day of WCM feeding. To better understand the wheat transcriptome variation after long-term feeding by WCM (10 days post infestation (dpi)), we used an RNA-seq approach. We collected leaves uninfested and infested with WCR from two wheat cultivars: Byrd (WCM resistant) and Settler CL (WCM susceptible) at 10 dpi. Our transcriptomic analysis revealed the common and specific transcriptomic variations in WCM resistant and susceptible wheat cultivars, chromosome specific location of the differentially expressed genes, and also identified the gene functions and pathways involved in WCM resistance. Collectively, our study provides important insights on wheat defense mechanisms against WCM after long-term feeding.
2023-02-01 | GSE195958 | GEO
Project description:Global expression analysis of transcripts in response to salt treatment was carried out for common wheat using oligo-DNA microarrays. Microarrays have been designed from unique wheat genes classified from a large number of expressed sequence tags (ESTs). Two-week-old seedlings of common wheat were treated with 150 mM NaCl for 1, 6 and 24 hours and their roots and shoots were separately subjected to microarray analyses. Consequently, 5996 genes showed changes in expression of more than two-fold, and were classified into 12 groups according to correlations in gene expression patterns. These salt-responsive genes were assigned functions using Gene Ontology (GO) terms. Genes assigned to transcription factor, transcription-regulator activity and DNA binding functions were preferentially classified into early response groups. On the other hand, those assigned transferase and transporter activity were classified into late response groups. These data on gene expression suggest that multiple signal transduction pathways in response to salt treatment exist in wheat. Salt-responsive transcription factors (TFs), namely AP2/EREBP, MYB, NAC and WRKY, were selected and their expression patterns compared with those of rice. Most showed different expression patterns in wheat and rice in response to salt treatment. Furthermore, comparing the microarray data for wheat and rice, only a small number of genes were up- or down-regulated in common in response to salt treatment. These findings suggest that salt-responsive mechanisms distinct from rice might be present in wheat, and wheat genes can contribute to providing novel gene resources for breeding of salt-tolerant crops. Keywords: time cource, stress response
2007-10-02 | GSE8064 | GEO
Project description:The wheat gene Lr34 confers partial resistance to all races of Puccinia triticina, the causal agent of wheat leaf rust. However, the biological basis for the exceptional durability of Lr34 is unclear. The Affymetrix wheat genome array was used to identify wheat genes differentially expressed in a compatible interaction (Tc), an R-gene mediated incompatible interaction (Tc-Lr1), and a race non-specific resistance interaction (Tc-Lr34) in response to infection challenge by P. triticina race 1 at anthesis. Transcriptome interrogation was conducted by comparing mock- and P. triticina-inoculated leaves harvested at 3 and 7 days post inoculation (dpi). Keywords: Time course
2008-11-01 | GSE9915 | GEO
Project description:TaGPC1 and TaGPC2 are NAC-domain transcription factors which accelerate the onset of senescence and facilitate nutrient translocation in wheat. We developed knockout mutants of these genes in tetraploid wheat and used RNA-seq to identify the effect of these mutations on the wheat flag leaf transcriptome during monocarpic senescence. Several transporter-related genes were identified which were upregulated during senescence and differentially expressed between genotypes. Illumina cDNA libraries were constructed from four biological replicates of three genotypes (WT, gpc-a1 and gpc-a1/gpc-b2) at three timepoints (Heading date, 12 days after anthesis and 22 days after anthesis). Reads were aligned to a collection of assembled genomic contigs from flow-sorted chromosome arms (A and B genomes only) provided by the International Wheat Genome Sequencing Consortium. A custom GTF file was generated to identify 139828 gene loci corresponding to transcribed regions of this reference sequence. Please note that the contig names provided by URGI (http://wheat-urgi.versailles.inra.fr/Seq-Repository) were used in the analysis. Most, but not all, of these loci are present in Ensembl (With a modified name, but the same basic information, chromosome arm and unique contig ID) at ftp://ftp.ensemblgenomes.org/pub/plants/release-22/fasta/triticum_aestivum/dna/ Therefore, the contig IDs from URGI (which are available for all our sequences) were used in the processed data file (i.e. the count table and GFF file) and an additional file describing the corresponding Ensembl names for these was provided (Additional_file_2.xlsx).
2014-12-23 | E-GEOD-60635 | biostudies-arrayexpress
Project description:To study the expression profiles of hexaploid wheat chromosome 3B genes during the life cycle of a wheat plant and establish a transcriptome atlas for this chromosome, deep transcriptome sequencing was conducted in duplicates in 15 wheat samples corresponding to five different organs (leaf, shoot, root, spike, and grain) at three developmental stages each. Strand-non-specific and strand-specific libraries were used to produce 2.52 billion paired-end reads (232 Gb) and 615.3 single-end reads (62 Gb), respectively.
2014-09-08 | E-MTAB-4484 | biostudies-arrayexpress