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Protocols

CerealsDB specifications

Information


Unique identifier OMICS_09707
Name CerealsDB
Restrictions to use None
Version 2.0
Maintained Yes

Taxon


  • Plants and Fungi
    • Triticum aestivum

Maintainer


  • person_outline Paul A. Wilkinson

Publication for CerealsDB

CerealsDB citations

 (28)
library_books

Inferring defense related gene families in Arabidopsis and wheat

2017
BMC Genomics
PMCID: 5738178
PMID: 29258426
DOI: 10.1186/s12864-017-4381-3

[…] ted for more than 5% of the environment-relationship matrix variance as fixed effects in the mixed-model analysis. The sequences of the significant SNPs from the GWAS analysis were obtained in T3 and CerealsDB []. The genomic or scaffold regions surrounded by these SNP markers were inferred following Approach 1. […]

call_split

Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum)

2017
Plant Biotechnol J
PMCID: 5866950
PMID: 28913866
DOI: 10.1111/pbi.12834
call_split See protocol

[…] rcentage of reads required to call a genotype (for this analysis it was 20%), for example the read count A(20), T(80) would be assigned an AT genotype. This pipeline is available to download from the CerealsDB website (http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/sequence_capture_pipeline.php).Axiom® data allele calling was carried out using Affymetrix Analysis Suite (version 1.1.0.616) an […]

library_books

The identification of new candidate genes Triticum aestivum FLOWERING LOCUS T3‐B1 (TaFT3‐B1) and TARGET OF EAT1 (TaTOE1‐B1) controlling the short‐day photoperiod response in bread wheat

2017
PMCID: 5669021
PMID: 28667827
DOI: 10.1111/pce.13018

[…] control for spurious associations, population structure and/or relatedness between individuals. The general linear model analysis was conducted on Axiom genotype data for chromosome 1B available from CerealsDB (http://www.cerealsdb.uk.net) together with the genotype scores for TaTOE1‐B1 and TaFT3‐B1. The Q matrices were based on discriminant analysis of principal components on the SSR data from Wi […]

library_books

Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.)

2017
BMC Plant Biol
PMCID: 5477749
PMID: 28633642
DOI: 10.1186/s12870-017-1056-9

[…] etaining 1090 QTLs in seedlings and 1542 QTLs in adult plants for subsequent analysis (Additional file ).The sequences of the SNP markers from the GWAS results described above were obtained in T3 and CerealsDB []. To predict their functional consequences, these SNPs were first converted into a VCF (Variant Call Format) and annotated with VEP []. Then, to better estimate the genomic position of eac […]

library_books

Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr16

2017
BMC Plant Biol
PMCID: 5311853
PMID: 28202046
DOI: 10.1186/s12870-017-0993-7

[…] sequences of previously mapped markers on chromosome arm 2BS was performed to identify putative SNP markers linked to the Lr16 locus. The wheat 90 K iSelect Infinium assay [] and the SNP database at CerealsDB [] were used to mine SNPs. Additional SNP markers were also developed through comparative synteny analysis using Brachypodium and rice genomes. Here, syntenic Brachypodium and rice genes wer […]

call_split

Tissue specific transcript profiling of wheat phosphate transporter genes and its association with phosphate allocation in grains

2016
Sci Rep
PMCID: 5172359
PMID: 27995999
DOI: 10.1038/srep39293
call_split See protocol

[…] sions were queried in Unigene (http://www.ncbi.nlm.nih.gov/unigene) for assigning unique Unigene ID to particular set of ESTs. These ESTs were mapped individually on cereal data base (DB) (http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/search_reads.php), ensemble plants (http://plants.ensembl.org/common/Tools/Blast?db=core) and the International Wheat Genome Sequencing Consortium (IWGSC) seq […]

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CerealsDB institution(s)
School of Biological Sciences, University of Bristol, Bristol, UK

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