Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GBS-based identification of Dasypyrum villosum introgressions in a wheat pre-breeding population

ABSTRACT: A wheat × D.villosum pre-breeding population was analyzed using Genotyping-by-sequencing (GBS) combined with a skim-seq pipeline to identify and characterize D.villosum introgressions. Read coverage analysis based on a combined T. aestivum– D.villosum reference genome enabled high-resolution detection of major chromosomal introgressions and copy-number changes. To identify wheat- D.villosum introgressions, the Chinese Spring reference genome (IWGSC RefSeq v2.1) (IWGSC, 2021) and the Dasypyrum villosum (Zhang et al., 2023) reference genome were used as a reference during read coverage analyzis. During the assembly process, unique identifiers were assigned to all chromosomes or pseudomolecules to maintain distinctiveness. Prior to alignment, the Illumina short reads from 33 lines, were demultiplexed and adapter-trimmed with Stacks v2.68 (Rochette et al., 2019). The processed paired-end reads were then mapped separately to the combined reference genome using HISAT v2.2.1 (Kim et el., 2019) with the – no-spliced-alignment and – no-unal parameters. Following alignment, concordant unique reads were retrieved by filtering the sequence alignment map (SAM) outputs for the YT:Z:CP and NH:i:1 tags.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Triticum aestivum

SUBMITTER: Balázs Kalapos

PROVIDER: E-MTAB-17546 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

GBS-based identification of Triticum timopheevii introgressions in a wheat pre-breeding population

Project description:A wheat × T. timopheevii pre-breeding population was analyzed using Genotyping-by-sequencing (GBS) combined with a skim-seq pipeline to identify and characterize T. timopheevii introgressions. Read coverage analysis based on a combined T. aestivum–T. timopheevii reference genome enabled high-resolution detection of major chromosomal introgressions and copy-number changes. Sequencing reads were aligned to this combined assembly, and chromosome identity and physical position could be extracted. An \"in silico wheat × T. timopheevii hybrid\" reference genome was constructed by combining the reference sequences of the donor and the recipient species. To identify wheat-T. timopheevii introgressions, we combined the Chinese Spring reference genome (IWGSC RefSeq v1.0) (IWGSC, 2018) with the draft genome assembly of T. timopheevii (GCA_963921465.1) (Grewal et al., 2024). During the assembly process, unique identifiers were assigned to all chromosomes or pseudomolecules to maintain distinctiveness. Prior to alignment, the Illumina short reads from 42 lines, along with the previously described control genotypes, were demultiplexed and adapter-trimmed with Stacks v2.68 (Rochette et al., 2019). The processed paired-end reads were then mapped separately to the combined reference genome using HISAT v2.1.0 (Kim et el., 2019) with the – no-spliced-alignment and – no-unal parameters. Following alignment, concordant unique reads were retrieved by filtering the sequence alignment map (SAM) outputs for the YT:Z:CP and NH:i:1 tags.

2026-05-28 | E-MTAB-17094 | biostudies-arrayexpress

GBS-based genomic characterization of a wheat–Thinopyrum 3J(3D) chromosome substitution line (GLA3)

Project description:A wheat–Thinopyrum chromosome substitution line (GLA3) was characterized at the genomic level using genotyping-by-sequencing (GBS). In the GLA3 line, a Thinopyrum-derived group 3 chromosome (3J) replaces wheat chromosome 3D. To confirm the chromosomal composition, identify the homoeologous relationships of the alien chromosome, and detect potential chromosomal rearrangements or deletions, GBS read coverage analysis was performed. Short reads from the GLA3 introgression line were aligned to the wheat (Triticum aestivum IWGSC RefSeq v2.1) and Thinopyrum intermedium (v3.1) reference genomes, revealing the absence of chromosome 3D and the presence of Thinopyrum group 3 chromatin predominantly of J-genome origin.

2026-05-19 | E-MTAB-17093 | biostudies-arrayexpress

Genome-wide profiling of the meiotic recombinase DMC1, the chromosome axis protein ASY1 and chromatin states in hexaploid wheat (MNase-seq)

Project description:We performed ChIP-seq for the meiotic strand exchange protein DMC1, which marks an early stage in the meiotic recombination pathway, and the chromosome axis protein ASY1, which promotes interhomolog synapsis and recombination in plants, using tissue collected from immature pre-emergence spikes from wild type bread wheat cultivar Chinese Spring plants. To investigate connections between meiotic recombination and chromatin states in wheat, we also performed ChIP-seq for euchromatic (H3K4me3) and constitutive heterochromatic (H3K9me2 and H3K27me1) marks, and mapped genome-wide nucleosome occupancy via micrococcal nuclease sequencing (MNase-seq) using leaf tissue from Chinese Spring.

2021-07-07 | E-MTAB-9633 | biostudies-arrayexpress

iTRAQ-based proteomic analysis reveals genome-wide protein expression patterns in allohexaploid bread wheat in adaptation to potassium deficiency and an important role of jasmonic acid

Project description:Two-week old bread wheat seedlings hydroponically grown Hoagland solution were transferred to potassium (K+)-free conditions for 8 d, their root and leaf proteome profiles were assessed using iTRAQ proteome method, and NCBInr database combined with the recently published bread wheat genome information were used to analyze the identified protein species. Over 4,000 unique proteins were identified, 818 K+-responsive protein species showed significant abundance regulation. The most majority of the identified K+-responsive protein species had exact gene loci, and showed no global but tissue- and chromosome- dependent genome distributions. The identified protein species were associated with diverse functions and exhibited organ-specific differences. Most of identified protein species associated with hormone synthesis were the enzymes involved in the synthesis of jasmonic acid (JA). Allene oxide synthase (AOS), a key JA synthesis-related enzyme, was significantly induced in both root and leaf organs of K+-deficient wheat seedlings, and its overexpression in rice enhanced the tolerance to low K+ or K+ deficiency, increased contents of K+ and JA and transcription levels of some K+-responsive genes. However, rice AOS T-DNA inserted mutant (osaos) exhibited more sensitivity to K+ deficiency. K+ deficiency significantly increased abundance of a high affinity K+ transporter (TaAHAK1), TaAHAK1 transgenic rice seedlings markedly alleviated sensitivity to K+ deficiency, and K+ deficiency also upregulated expression of homologous OsHAK1 gene in TaAOS transgenic rice plants. These results suggested an essential role of JA in K+ deficiency and gave molecular insight into the responses of plant to K+ deficiency.

2017-10-09 | PXD003570 | Pride

Heat tolerance mechanisms in bread wheat: Insights from flag leaves and spike tissues.

Project description:Heat stress adversely affects global bread wheat (Triticum aestivum L.) productivity. This study aimed to uncover the mechanisms underlying heat tolerance in wheat flag leaves and spike tissues. We compared protein abundance in flag leaves and spikes among wheat genotypes with contrasting heat tolerance—two tolerant (RAJ3765 and HD2932 )and two susceptible (HD2329 and HD2733)—under short-term heat stress (32°C) at ear peep. We identified 31 and 60 changes in protein abundance within flag leaves and spike tissues, respectively.

2025-05-03 | PXD048499 | Pride

Genome-wide profiling of the meiotic recombinase DMC1, the chromosome axis protein ASY1 and chromatin states in hexaploid wheat (ChIP-seq)

2021-07-07 | E-MTAB-9632 | biostudies-arrayexpress

Developmental transcriptional profiling of Triticeae reproductive development

Project description:Despite their importance, there remains a paucity of large scale expression-based studies of reproductive development in the species belonging to the Triticeae. As a first step to address this deficiency, a gene expression atlas of triticale reproductive development was generated using the 55K Affymetrix GeneChipÂ® Wheat Genome Array. The global transcriptional profiles of the anther/pollen, ovary and stigma were analyzed at concurrent developmental stages and co-regulated as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae floral development and function. Triticale reproductive tissues (anther, ovary, stigma) were collected at 4 successive stages using pollen development as a developmental reference: tetrad (TET), uninucleate microspore (UNM), bi-cellular pollen (BCP), and tri-cellular pollen (TCP). Mature pollen grains (MPG) were also collected. Three biological replicates were analyzed for each tissue using the 55K Affymetrix GeneChipÂ® Wheat Genome Array.

2012-11-01 | E-GEOD-41984 | biostudies-arrayexpress

gene mapping in the physical map of the Triticum aestivum chromosome arm 1BL

Project description:To improve our understanding of the organization and evolution of the wheat gene space, we established the first map of genes of the wheat chromosome 1BL by hybridizing the newly developed INRA GDEC Triticum aestivum NimbleGen 12x40k unigenes microarray (A-MEXP-2314) with BAC pools from the 1BL physical map as well as with genomic DNA of the sorted chromosome 1BL. By hybridizing the BAC pools with the wheat NimbleGen 40K unigenes chip we managed to map almost 1615 unigenes on the wheat chromosome 1BL BACs. By hybridizing the genomic DNA of the 1BL sorted chromosome and by comparison with 454 sequences from the sorted chromosome 1BL, we confirmed the assignation of 1223 unigenes in individual BACs from the chromosome 1BL. This data allowed us to study the organization of the wheat gene space along chromosome 1BL. The sequences of the unigenes helped to perform synteny and evolutionary analyses of these unigenes.

2013-06-01 | E-MTAB-1650 | biostudies-arrayexpress

Expression data from wheat cultivar TAM 107 flag leaf

Project description:We used microarray to study the transcriptome response of wheat flag leaves to heat stress (40℃) In order to study the transcriptome response of wheat flag leaf to heat stress, wheat cultivar ‘TAM 107’ plants were subjected to heat stress (40℃). After 1 hour of stress, flag leaves were sampled from both stressed and control plants and were used for microarray analysis.

2015-08-13 | E-GEOD-60351 | biostudies-arrayexpress

Proteomics-based data integration of wheat cultivars facing Fusarium graminearum strains revealed a core-responsive pattern driving the fate of the interaction

Project description:The aim of this work is to dissect the plant component of the dual-proteome established during the FHB process using the same three wheat cultivars facing the three fungal strains as described in Fabre et al. (2019b). Qualitative and quantitative dissection of the three wheat cultivar proteomes was devoted to identify molecular events that drive the FHB-susceptibility differences. This included, the identification of (i) the generic molecular adjustments taking place during FHB progress, (ii) the cultivar-specific responses and their accommodation with different F. graminearum strains inducing FHB and (iii) the range of wheat proteins that basically discriminate the three wheat cultivars of contrasted susceptibility. The joint analysis of all these data with the fungal protein information was carried out to identify relationship between wheat protein abundance changes and fungal effectors differentially accumulated between the three F. graminearum strains (Fabre et al., 2019b).

2021-05-28 | PXD023212 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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