Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification and Comparative Analysis of Genes and MicroRNAs Involved in the Floral Transition of the Xinjiang Early-Flowering Walnut (Juglans regia L.)

ABSTRACT: For tree crops, shortening juvenile phase is a vital strategy for early flowering that ensure to bear fruits in advance to enhance breeding efficiency. In walnut (Juglans regia L.), it usually takes 3-5 years for blooming, but the early flowering (EF) walnut can even flower in a year after planted. The juvenile phase of EF walnut is shorter than the late flowering (LF) walnut, which is more propitious to breeding efficiency. In this study, using RNA sequencing (RNA-seq) and microRNA-seq, we profiled transcriptome-wide identification of gene expression and microRNAs between EF and LF walnuts.

ORGANISM(S): Juglans regia

PROVIDER: GSE193061 | GEO | 2022/07/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

A Preliminary Study for Identifying Genes Associated with Pellicle Development in Xinjiang Walnut (Juglans regia L.)

Project description:Walnut (Juglans regia L.) is an important nut fruit crop mainly grown for its high nutritional and medicinal value. In walnut fruit, the pellicle is the main source of polyphenols (such as proanthocyanidins), which are natural bioactive compounds but also cause astringency and bitterness for walnut fruit consumption. However, the gene regulatory networks of phenolic biosynthetic pathways remain largely unknown in walnut pellicles. Here, we performed RNA sequencing (RNA-seq) to identify differentially expressed genes (DEGs) associated with pellicle development in walnut. In this study, seven developmental stages (8-, 9-, 11-, 13-, 15-, 17-, and 19-week after pollination) of ‘Xinwen179’ pellicle tissues were harvested to conduct further transcriptome-wide profiles. Via RNA-seq, we explored several key DEGs involved in the phenolic biosynthetic pathway, such as dihydroflavonol-4-reductase (DFR), leucoanthocyanidin reductase (LAR), anthocyanidin synthase (ANS) and anthocyanidin reductase (ANR), which are dynamically expressed at developmental stages of the walnut pellicle. Taken together, our preliminary investigation on DEGs associated with pellicle development will not only elucidate the gene regulatory networks of the phenolic biosynthetic pathway for pellicle development, but also contribute to the broad spectrum of RNA-seq data resources for further genetic improvement of walnut.

2022-08-30 | GSE209790 | GEO

Expression profile from anthrax edema toxin (ET) treated murine bone marrow derived macrophages (BMDM)

Project description:Bacillus anthracis, the causative agent of anthrax, secretes three toxin proteins: protective antigen (PA), lethal factor (LF), and edema factor (EF). PA is a transporter of LF and EF into host cells by receptor-mediated endocytosis. LF is a metalloprotease that cleaves mitogen-activated protein kinase (MAPK) kinases (MKK), while EF is an adenylate cyclase, which converts ATP to cAMP. We used microarrays to decipher the specific gene regulation in edema toxin (ET), the complex of EF and PA, treated mouse bone marrow derived macrophages. Keywords: Time course

2007-09-28 | GSE9184 | GEO

Transcription profiling of mouse bone marrow derived macrophages (BMDM) treated with anthrax edema toxin (ET)

2008-06-16 | E-GEOD-9184 | biostudies-arrayexpress

Proteomic study of walnut oleosome and first evidence on oleosinsensitization in allergic patients

Project description:The research project aims to investigate the walnut oleosome sub-proteome of raw, boiled, and roasted kernels. To achieve this goal both off-gel and in-gel approaches were used. Moreover, the immunoblotting experiments were performed to characterize the walnut OB proteins as potential allergens by demonstrating that the sera collected from walnut allergic patients’ immune-recognized walnut oleosins.

2023-05-18 | PXD038199 | Pride

Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)

Project description:Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is a major disease affecting walnut production in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease resistance , the molecular mechanisms underlying resistance to C. gloeosporioides in walnut remain poorly understood.The anthracnose-resistant F26 fruits from the B26 clone and the anthracnose susceptible F423 fruits from the 4-23 clone of walnut were used as the test materials. Specifically, we performed a comparative transcriptome analysis of F26 fruit bracts and F423 to identify differentially expressed LncRNAs (DELs) at five time-points (tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi). Compared with F423, a total of 14525 DELs were identified, including 10645 upregulated lncRNAs and 3846 downregulated lncRNAs in F26. The number of upregulated lncRNAs in F26 compared to in F423 was significantly higher at the early stages of C. gloeosporioides infection. A total of 5 modules related to disease resistance were screened by WGCNA and the target genes of lncRNAs were obtained. Bioinformatic analysis showed that the target genes of upregulated lncRNAs were enriched in immune-related processes during the infection of C. gloeosporioides , such as activation of innate immune response, defense response to bacterium, incompatible interaction and immune system process, and enriched in plant hormone signal transduction, phenylpropanoid biosynthesis and other pathways. And 124 known target genes for 96 hub lncRNAs were predicted, including 10 known resistance genes. The expression of 5 lncRNAs and 5 target genes was confirmed by qPCR, which was consistent with the RNA-seq data.The results of this study provide the basis for future functional characterizations of lncRNAs regarding the C. gloeosporioides resistance of walnut fruit bracts.

2020-03-18 | GSE147083 | GEO

H3K36me3 ChIP-seq of 2 rice lines D248 and SH881

Project description:A major maturity duration-regulatory gene, Early flowering-completely dominant (Ef-cd) was cloning in this study. The Ef-cd locus gives rise to a long noncoding RNA (lncRNA) antisense transcript overlapping the OsSOC1 gene. Ef-cd lncRNA expression positively correlates with the expression of OsSOC1 and H3K36me3 deposition.

2019-07-10 | GSE134021 | GEO

Discovery, Verification, and Validation of Walnut Protein Marker Peptides Using LC-MS/MS Approaches

Project description:A key requirement of liquid chromatography-mass spectrometry (LC-MS)-based allergenic food protein analysis methods is to use protein marker peptides with good analytical performances in LC-MS analysis of commercial processed foods. In this study, we developed a multistage walnut protein marker peptide selection strategy involving marker peptide discovery and verification and LC-MS validation of chemically equivalent stable isotope-labeled peptides. This strategy proposed three walnut protein marker peptides, including two new marker peptides. Our LC-MS-based walnut protein analysis method using the three stable isotope-labeled peptides showed acceptable linearity (R2 >0.99), matrix effects (coefficient of variation <±15%), sensitivity (limit of detection >0.3 pg/μL, limit of quantification >0.8 pg/μL), recovery (85.1–103.4%), accuracy, and precision (coefficient of variation <10%). In conclusion, our multistage marker peptide selection strategy effectively selects specific protein marker peptides for sensitive detection and absolute quantification of walnut proteins in LC-MS analysis of commercial processed foods.

2023-07-31 | PXD043010 | Pride

Expression profiling by RNA-Seq of breast cancer samples from patients in walnut-consuming and control groups

Project description:Consumption of walnuts has slowed breast cancer growth and/or reduced the risk of breast cancer in mice. The significantly reduced mean tumor size or numbers of tumors was associated with changing the expressions of many genes that are associated with cancer growth, survival and metastasis. Many women treated for breast cancer are interested in reducing the risk for recurrence. The study was a non-placebo, two-arm, clinical trial. Women with lumps large enough for research and pathology biopsies were recruited to the trial. One or two additional biopsies were taken for gene expression analyses using next generation RNA Sequencing methods. The subjects randomized to the walnut group immediately began to consume 2 ounces of walnuts per day until follow-up surgery, if surgery were needed. At follow up surgery, additional biopsies were taken from the surgically removed, cancerous tissue for additional gene expression analyses. Changes in gene expression compared to baseline were determined in tumors of each individual woman in walnut-consuming and control groups.

2019-03-10 | GSE111073 | GEO

Transcriptomic profiling of the walnut endopleura during its development

Project description:The color of endopleura is one of the most commercially important characteristics of walnut. There exists one major loci on chromosome 9 significantly associated with the color trait. Zooming in on the GWAS peak region, we found a gene JreChr09G12363 homologous to ANR (BAN) located within this region. ANR encodes an anthocyanidin reductase, which functions as a negative regulator of flavonoid biosynthesis and is involved in procyanidin accumulation in the seed. We further examined the transcriptomic profile of this gene in the endopleura, and found that during the development of endopleura, the expression level of JreChr09G12363 (JrANR) showed a continuously increasing trend, and FPKM value could reach up to ~800, providing support for a role of JrANR playing in the endopleura development.

2021-10-04 | GSE185230 | GEO

Ef-cd locus shortens rice maturity duration without yield penalty

Project description:The contradiction between ‘high-yielding’ and ‘early-maturing’ hampers further improvement on annual rice yield. Here we reported the positional cloning of a major maturity duration-regulatory gene, Early flowering-completely dominant (Ef-cd), and demonstrated that natural variation in Ef-cd could be used to overcome the above contradictory. The Ef-cd locus gives rise to a long noncoding RNA (lncRNA) antisense transcript overlapping the OsSOC1 gene. Ef-cd lncRNA expression positively correlates with the expression of OsSOC1 and H3K36me3 deposition. Field test comparisons of early-maturing Ef-cd near-isogenic lines (NILs) with their wild types as well as the derivative early-maturing hybrids with their wild-type hybrids conducted under different latitudes determined that early-maturing Ef-cd allele shortens maturity duration (ranging from 7 to 20 days) without a concomitant yield penalty. Ef-cd facilitates nitrogen utilization and also improves the photosynthesis rate. Analysis of 1,439 elite hybrid rice varieties revealed that the 16 homozygotes and 299 heterozygotes possessing Ef-cd matured significantly earlier. Therefore, Ef-cd could be a vital contributor of elite early-maturing hybrid varieties in balancing grain yield with maturity duration.

2019-07-03 | GSE133746 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data