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KnowPulse: A Web-Resource Focused on Diversity Data for Pulse Crop Improvement
Lacey-Anne Sanderson1, Carolyn T Caron1, Reynold Tan1
1Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
Frontiers in Plant Science
|August 21, 2019
Summary
KnowPulse is a web portal offering genetic diversity data for pulse crops. It provides tools for breeders and geneticists to access and visualize genotypic and phenotypic information for improved crop development.
Area of Science:
- Plant genetics and breeding
- Bioinformatics
- Agricultural science
Background:
- Pulse crops like chickpea, common bean, field pea, faba bean, and lentil are vital global food sources.
- Effective breeding programs require comprehensive access to genetic diversity data.
- Existing data resources may be fragmented or lack user-friendly visualization tools.
Purpose of the Study:
- To introduce KnowPulse, a centralized web portal designed for pulse breeders and geneticists.
- To provide integrated access to diverse genetic and phenotypic data for key pulse species.
- To offer advanced tools for data visualization and analysis to support crop improvement.
Main Methods:
- Development of a breeder-focused web portal utilizing the open-source Tripal toolkit.
- Integration of genotypic data (markers, variants) and phenotypic data (traits, germplasm).
- Implementation of visualization tools including genotype matrix, trait distribution plots (violin plots, histograms), JBrowse, BLAST, and CViTjs.
Main Results:
- KnowPulse offers searchable access to genetic markers, sequence variants, phenotypic traits, and germplasm for five pulse crops.
- Genotypic data is available via a genotype matrix tool and summarized on dedicated pages.
- Phenotypic data is visualized through interactive plots accessible via multiple search and browsing functionalities.
- The portal is built on open-source technologies, ensuring flexibility and community contribution.
Conclusions:
- KnowPulse serves as a valuable, evolving resource for the pulse breeding community.
- The portal facilitates data-driven decision-making in crop improvement by providing integrated genetic information.
- Future development includes integrating genetic maps, quantitative trait loci, and exploring structural variation analysis.
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