An active Helitron transposon family identified in wheat
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PROVIDER: PRJEB75199 | ENA |
REPOSITORIES: ENA
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Project description:Take-all is a devastating soil-borne disease that affects wheat production. The continuous generation of disease-resistance germplasm is an important aspect of the management of this pathogen. In this study, we characterized the wheat-Psathyrostachys huashania Keng-derived progeny H139 that exhibits significantly improved resistance to wheat take-all disease compared with its susceptible parent 7182. GISH) and mc-FISH analyses revealed that H139 is a stable wheat-P. huashania disomic substitution line lacking wheat chromosome 2D.EST-STS marker and Wheat Axiom 660K Genotyping Array analysis further revealed that H139 was a novel wheat-P. huashania 2Ns/2D substitution line, and that the P. huashania 2Ns chromosome shares high sequence similarity to wheat chromosome 2D. These results indicate that H139, with its enhanced wheat take-all disease resistance and desirable agronomic traits, provides valuable genetic resources for wheat chromosome engineering breeding.
2020-01-07 | GSE143188 | GEO
Project description:Purpose: The present study aimed to investigate the anthocyanin components and identify relevant regulatory genes in purple wheat grain by carrying out transcriptome analyses. Methods: The seeds of purple grain wheat and white grain wheat were collected 30 days after flowering, and three biological replicates were set. Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000. Then synthesizing the fragmented RNA into cDNA through the action of reverse transcriptase, and finally obtaining acDNA library. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol. Results: A total of 10440 diferentially expressed genes were signifcantly enriched by RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed signifcantly enriched flavonoid biosynthesis and anthocyanin biosynthesis in CW_S versus W_S. And the ANS and UFGT genes were predicted as core genes in anthocyanin biosynthesis. Conclusions: Our study represents the detailed analysis of wheat grain transcriptomes, with biologic replicates, generated by RNA-seq technology. Through this study, we speculated that ANS and UFGT genes are the core genes of anthocyanin biosynthesis.The significant differences of these genes affect the synthesis of anthocyanins in wheat grains, and thus affect the grain color of wheat.
2023-04-24 | GSE198515 | 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:An untargeted liquid chromatography tandem mass spectrometry method was used to analyze the content of peptides with celiac disease (CD) active epitope in the five wheat species common wheat, spelt, durum wheat, emmer and einkorn. In total, 494 peptides with CD active epitope were identified. Relevant differences between the species concerning their CD immunoractive potential based on the distribution of CD-active epitopes and relative quantities of peptides with CD-active epitope were demonstrated.
2024-07-16 | PXD050917 | Pride
Project description:Differentially expressed kinase genes in Rhizoctonia cerealis resistant wheat lines CI12633/Shanhongmai compared with the susceptible wheat line Wenmai 6 via Agilent Wheat Gene Expression Microarray assay. Goal was to identify the kinase genes whose expression was higher in CI12633/Shanhongmai compared with the susceptible wheat line Wenmai 6
2015-08-06 | GSE69245 | GEO
Project description:Common wheat is one of the most widely cultivated staple crops worldwide. Elucidating the gene regulatory network will provide essential information for mechanism studies and targeted manipulation of gene activity for breeding. However, detecting cis-regulatory elements and transcription factor (TF) bindings in the extremely large intergenic regions of the wheat genome is challenging. Linking cis-regulatory elements and TF binding to target genes is even more difficult given that enhancers can function irrespective of the strand and distance from target genes. Combining genome-wide TF binding profiles, epigenomic patterns, and transcriptome analysis is a compelling approach to detect the hierarchical regulatory network. We generated and collected 189 TF binding profiles, 90 epigenomic datasets, and 2,356 transcriptomic datasets in common wheat, which were further integrated using machine learning approach to infer direct target genes and the hierarchical regulatory network. We developed a web-based platform, Wheat-RegNet, that provides four major functions: (i) to identify regulatory elements regulating input gene(s), and to infer the tissue and environmental response specificity; (ii) to identify the TFs responsible for regulating input gene(s) or locus/loci; (iii) to construct the hierarchical regulatory network regulating input gene(s); and (iv) to browse hundreds of TF binding, epigenomic, and transcriptomic profiles of an input region or gene(s). Well-organized results and multiple tools for interactive visualization are available through a user-friendly web interface, making Wheat-RegNet a highly useful resource for exploring gene regulatory information for hypothesis-driven studies and for targeted manipulation for breeding research in common wheat. Wheat-RegNet is freely available at http://bioinfo.sibs.ac.cn/Wheat-RegNet
2024-07-08 | GSE207939 | GEO
Project description:Identification of open chromatin in wheat spikes and seedlings using MH-seq
2024-10-08 | GSE186694 | 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: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:This phase I clinical trial tests the immune effects of fermented wheat germ in patients with advanced solid tumor cancers who are being treated with standard of care checkpoint inhibitors. Fermented wheat germ is a nutritional supplement that some claim is a "dietary food for special medical purposes for cancer patients" to support them in treatment. There have also been claims that fermented wheat germ is "clinically proven" and "recognized by medical experts" to "enhance oncological treatment" and boost immune response to cancer; however, there are currently no documented therapeutic effects of fermented wheat germ as a nutritional supplement. Checkpoint inhibitors, given as part of standard of care for advanced solid tumors, are a type of immunotherapy that may help the body’s immune system attack the cancer and may interfere with the ability of tumor cells to grow and spread. The information gained from this trial may allow researchers to determine if there is any value of giving fermented wheat germ with standard of care checkpoint inhibitors for patients with advanced solid tumor malignancies.
| 68011 | ecrin-mdr-crc