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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #321131

Research Project: Small Grains Database and Bioinformatics Resources

Location: Crop Improvement and Genetics Research

Title: GSP: A web-based platform for designing genome-specific primers in polyploids

item WANG, Y - University Of California
item TIWARI, T - Kansas State University
item Coleman-Derr, Devin
item RAWDA, N - Kansas State University
item GILL, B - Kansas State University
item HUO, NAXIN - University Of California
item YOU, FRANK - Agriculture And Agri-Food Canada
item Gu, Yong

Submitted to: Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/4/2016
Publication Date: 3/9/2016
Citation: Wang, Y., Tiwari, T., Coleman-Derr, D.A., Rawda, N., Gill, B., Huo, N., You, F., Gu, Y.Q. 2016. GSP: A web-based platform for designing genome-specific primers in polyploids. Bioinformatics. doi: 10.1093/bioinformatics/btw/34.

Interpretive Summary: The presence of more than two copies of each chromosome (polyploidy) is a major evolutionary feature of many important crop plants including wheat and cotton. Because of the presence of more than one copy of each gene in polyploid species, it is difficult to identify which specific sequences of the genes are present in a variety using PCR (Polymerase Chain Reaction) technology. In the research reported here, we developed a user-friendly web-based application tool that allows users to easily and effectively design PCR primers that can distinguish sequences from different genomes within a polyploid species. The tool is very useful for crop improvement research that uses PCR-based technology, e.g. molecular marker development. It is freely available to the community at

Technical Abstract: The sequences among subgenomes in a polyploid species have high similarity. This makes difficult to design genome-specific primers for sequence analysis. We present a web-based platform named GSP for designing genome-specific primers to distinguish subgenome sequences in the polyploid genome background. 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. An interactive primer diagram, sequence alignment viewer and virtual electrophoresis images are displayed as parts of the primer design results. GSP also designs specific primers from multiple sequences uploaded by users. GSP is a user-friendly and efficient web platform freely available at