About WheatExp

Mapping Reference

Quality and adapter-trimmed RNA-seq reads were mapped to the full cDNA set of wheat transcripts from the International Wheat Genome Sequencing Consortium which are hosted by the Ensembl database. Diploid datasets were mapped to A-genome (32,091 cDNAs), tetraploid datasets were mapped to the A- and B-genomes (68,166 cDNAs) and hexaploid datasets were mapped to the A-, B- and D- genomes (101,245 cDNAs). Current expression data is generated from Ensembl release 26. Reference FASTA and GTF files, as well as all expression data in tabular format, are available for download from the following FTP site.

Ensembl Release 26 mapping rates


Wheat species


Developmental stage/treatment

RNA-seq reads

% uniquely mapped reads

Data source


Wheat development timecourse

T. aestivum cv. Chinese Spring

Shoot, root, grain, spike and stem.

Three stages for each tissue

101bp Paired End (PE)


ENA: ERP004714

Choulet et al. 2014



T. monococcum ssp. monococcum Acc. DV92

Whole seedlings


Etiolated and light-exposed seedlings.

50bp Single end (SE)




SRA: SRX283514


Fox et al. 2015

T. monococcum ssp. aegilopoides Acc. G3116

Whole seedlings

Etiolated and light-exposed seedlings.

101bp PE


SRA: SRX257915

Drought and heat stress

T. aestivum cv. TAM 107

Whole seedlings

Drought, heat and combined stress.

101bp PE


SRA: SRP045409

Liu et al. 2015


Grain layers

T. aestivum cv. Holdfast

Endosperm, inner pericarp, outer pericarp.

12 days after anthesis

50bp SE


ENA: ERP008767

Pearce et al. 2015


Senescing leaf timecourse

T. turgidum ssp. durum L. cv. Kronos

Flag leaves

Heading date, 12 and 22 days after anthesis

50bp SE


GEO: GSE60635

Pearce et al. 2014

Grain development timecourse

T. aestivum cv. Chinese Spring

Grain layers

10, 20 and 30 days after anthesis

101bp PE


ENA: ERP004505

Pfiefer et al. 2014



The main application of WheatExp is to compare the relative expression levels of the different homoeologues of a single gene across different tissues, developmental stages, environmental conditions and genetic backgrounds. Comparisons among genes are valid only when the genes being compared have the same number of homoeologues in the reference genome. In a simulated RNA-seq experiment using a set of confirmed homoeologous triplets, 98.4% of reads map uniquely to their transcript of origin when their homoeologous genes are absent from the reference. When mapping to the full reference, unique mapping rates fall to 82.2% due to the loss of reads which map equally well to different homoeologues. Consequently, genes where one homoeologue is absent from the reference will exhibit a higher proportion of uniquely-mapped reads and the expression levels of the two remaining homoeologues may also be inflated by the incorrect mapping of reads from the absent homoeologue. Additionally, no expression data will be reported for any genes which lack annotation within the current IWGSC release and any contig assemblies which are duplicated in the reference assembly will exhibit a reduced number of uniquely mapped reads. Therefore, caution is advised when comparing the expression levels of different genes.


Pearce S, Vazquez-Gross H, Herin SY, Hane D, Wang Y, Gu YQ, Dubcovsky J. WheatExp: an RNA-seq expression database for polyploid wheat. BMC Plant Biol. 2015;15:299. PDF available here WheatExp: an RNA-seq expression database for polyploid wheat

Database Implementation and System Architecture

WheatExp database implementation uses a flexible storage schema to house the data. The storage table has the following MySQL (https://www.mysql.com/) storage datatypes: study_id (varchar), seq_id (varchar), tissue (varchar), mean (float), se (float), se_low (float) and se_high (float). Binary search tree indices (BTREE) were implemented to increase the speed of queries using the study_id and seq_id columns. The web and database is running on a ThinkMate ThinkTank IQ4 system with four Intel Xeon E7-4820 at 2.00 GHz with 52 GB of RAM. It is currently running Linux Kernel 3.13 distribution Ubuntu 14.04 long term support with PHP version 5.5.9 and MySQL version 5.5.43.