Hot Topics

Genome-Specific Primers in Polyploid Species

The sequences among subgenomes in a polyploid species share high similarity. This makes it difficult to design genome-specific primers for sequence analysis. GSP, a web-based platform to design genome-specific primers that distinguish subgenome sequences in the polyploid wheat genome. GSP uses BLAST to extract homeologous sequences of the subgenomes in the existing databases, performs a multiple sequence alignment, and designs primers based on sequence variants in the alignment.

WheatExp : A Tool to Visualize Gene Expression in Wheat

Presented is WheatExp, an expression database and visualization tool to analyze and compare homoeologue-specific transcript profiles across a broad range of tissues from different developmental stages in polyploid wheat. Beginning with publicly-available RNA-seq datasets, a pipeline was developed to distinguish between homoeologous transcripts from each annotated gene in the hexaploid bread wheat genome. We have processed and compiled data from multiple studies into a database which can be queried either by BLAST or by searching for a known gene of interest by name or functional domain.

The Fusarium Head Blight (FHB) Scab Alert is now operational

The Fusarium Head Blight (FHB) Scab Alert is now operational for the 2015 growing season. Offered through the U.S. Wheat & Barley Scab Initiative, the real-time alert system, based on commentary from small grains disease specialists around the country, is part of the disease prediction and outreach efforts sponsored by the USWBSI. New models in place for the 2015 season are expected to enhance the system’s accuracy.

820K wheat Axiom genotyping data

The BBSRC funded WISP partners are pleased to announce that the 820K wheat Axiom array data set, consisting of over 380 million data points, is now available for download from the Cerealsdb web site.

The genotype dataset consist of data derived from screening a range of hexaploid lines mapping populations, nullisomic lines, Kansas deletion lines, progenitors and ancestral species against the 820K SNP array.

Mapping is in progress for the three populations included in the data set, and will be published in due course.

BLAST site for barley genetic markers on physical map

BLAST site for barley genetic markers on physical map. Barleymap was designed to search the position of barley genetic markers on the Barley Physical Map (IBSC[1]) and the POPSEQ map (Mascher et al.[2]).

BLAST or search by name.

Find Markers and Align Sequences.


This resource has updated information on:

SNPs databases, divided by platform:

Axiom® 820K and 35K SNP Arrays: Along with researchers at Affymetrix, we have developed a '820,000' featured wheat SNP array. The background information for all these SNPs (Affymetrix code, Bristol SNP code and probe sequence containing the SNP ambiguity code) can be downloaded here.

iSelect Array: The iSelect Array contains over 80,000 SNP loci of which 44,000 have been mapped.

USDA wheat SNP database, KS

Single Nucleotide Polymorphism (SNP) markers for high-throughput genotyping to advance genomic, genetic and breeding research in wheat.