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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Publications at this Location » Publication #327067

Research Project: Enabling Improved Environmental Stress Tolerance in Crops through Novel Computational Strategies and Tool Development

Location: Plant Gene Expression Center

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

Author
item WANG, YI - University Of California
item TIWARI, VIJAY - Kansas State University
item RAWAT, NIDHI - Kansas State University
item GILL, BIKRAM - Kansas State University
item HUO, NAXIN - Kansas State University
item YOU, FRANK - Agri Food - Canada
item Coleman-Derr, Devin
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, V.K., Rawat, N., Gill, B.S., Huo, N., You, F.M., Coleman-Derr, D.A., Gu, Y.Q. 2016. GSP: a web-based platform for designing genome-specific primers in polyploids. Bioinformatics. 32(15):2382-2383.

Interpretive Summary: Polyploidy is a major evolutionary feature of many plants and some animals (Chen, et al., 2007). Development of genome-specific primers for polyploids will facilitate not only the study of sequence diversity and association mapping of genes, but also the development of gene-based functional markers (Huang and Brule-Babel, 2010). However, polyploid genome contains two or more homeologous subgenomes with high sequence similarities, especially in the coding regions. This presents a particular problem with respect to design genome-specific primers to amplify individual genes. To our knowledge, only one pipeline named PolyMarker can generate genome specific primers. Here, we present a web-based, user-friendly primer design tool named GSP, which employs a BLAST search and multiple sequence alignment (MSA) to identify sequence variant sites among the homeologous sequences retrieved and then designs specific primers.

Technical Abstract: The primary goal of this research was to develop 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, performed a multiple sequence alignment, and design primers based on sequence variants in the alignment. An interactive primer diagram, sequence alignment viewer and virtual electrophoresis are displayed as parts of the primer design result. GSP also designs specific primers from multiple sequences uploaded by users. . GSP is a time-saving, user-friendly and easy-to-use web tool for designing genome-specific primers to distinguish sequences among the subgenomes in polyploid species. This web application tool can be easily extended to other polyploids when their genome sequences become available