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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
PubMed
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.

Keywords:
diversitygenotypic datalegumesphenotypic datapulsesweb resource

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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.