KnowPulse

KnowPulse provides access to genetic, genomic, and phenotypic data and tools for pulse crops (chickpea, common bean, field pea, faba bean, and lentil) to support crop improvement research.

Key Features:

• Genotypic Data Access: A genotype matrix presents marker-by-germplasm genotype calls and provides summaries on genetic marker and sequence variant records.
• Phenotypic Data Visualization: Visualization tools include violin plots for quantitative traits and histograms for qualitative traits to represent phenotypic distributions.
• Integration of Open-Source Tools: The platform integrates the Tripal toolkit, species-specific JBrowse instances for genome browsing, a BLAST interface for sequence alignment searches, and whole-genome CViTjs visualizations.
• Genetic maps, QTL, and Structural Variation (planned): Planned features include full integration of genetic maps and quantitative trait loci (QTL) and exploration of structural variation analysis tools.

Scientific Applications:

• Pulse crop improvement: Integrates genotypic and phenotypic data for chickpea, common bean, field pea, faba bean, and lentil to inform selection for traits such as yield, disease resistance, and environmental adaptability.
• Breeding program support: Enables analysis of genotype–phenotype relationships to support selection decisions in breeding programs.
• Genetic and genomic research: Supports basic genetic studies and advanced genomic analyses using genetic markers, sequence variant data, and genome visualizations.
• Germplasm characterization: Facilitates characterization of germplasm collections using genotype matrices and phenotypic distribution visualizations.

Methodology:

Implements the open-source Tripal toolkit and integrates species-specific JBrowse instances, a BLAST interface for sequence alignment searches, genotype matrices (marker-by-germplasm genotype calls), violin plots and histograms for phenotypic visualization, and whole-genome CViTjs visualizations.