Wheat Expression Database

The wheat expression database is now hosted by Graingenes and can be found here.

The database currently contains six published RNA-seq datasets:

1) Developmental timecourse in five tissues - Five different wheat tissues (Spike, root, leaf, grain and stem) each sampled at three different developmental stages, providing a broad overview of gene expression during development. Data generated from hexaploid bread wheat (var. Chinese Spring) by Choulet et al. 2014 Science 345:1249721.

2) Grain layer developmental timecourse - Tissues from different layers of the wheat grain at three different stages of development (10, 20 and 30 days after anthesis). Data generated from hexaploid wheat (var. Chinese Spring) by Pfiefer et al. 2014,Science 346:1250091.

3) Grain layers - A complementary set of grain tissue data taken from three layers of the developing grain (Outer pericarp, inner pericarp and endosperm) at 12 days after anthesis. Data generated from hexaploid bread wheat (var. Holdfast) by Pearce et al. 2015 BMC Plant Biology 15:130

4) Senescing leaf timecourse - A timecourse of early leaf senescence, from flag leaves at three stages (Heading date, 12 and 22 days after anthesis). Data generated from tetraploid durum wheat (var. Kronos) by Pearce et al. 2014 BMC Plant Biology 14:368.

5) Drought and heat stress - One-week-old seedlings were treated either with heat (40 deg C), drought, or combined heat and drought stress.  Whole seedlings were harvested at two timepoints in each treatment. Data generated from hexaploid bread wheat (var. TAM 107) by Liu et al. 2015 BMC Plant Biology 15:152.

6) Seedling photomorphogenesis - From two diploid wheat species, samples were harvested from dark-grown etiolated seedlings and light-exposed green seedlings. Data was generated from wild T. monococcum spp. aegilopides (accession G3116) and domesticated T. monococcum spp. monococcum (accession DV92), by Fox et al. 2015 PLoS ONE 9:e96855.

For all datasets, RNA-seq reads were trimmed for quality and adapter contamination and mapped to the Ensembl collection of wheat cDNAs (Release 27). To calculate relative expression levels, reads were counted only when both forward and reverse reads from a paired end fragment were mapped unambiguously. Counts were normalized based on library size and transcript length (FPKM), so are directly comparable across samples, tissues and genes.

For more information, please contact either:

Stephen Pearce sppearce@ucdavis.edu or Hans Vazquez-Gross havasquezgross@ucdavis.edu

Wheat Expression ID and Term search
Wheat Expression BLAST search