SoyBase

SoyBase provides an integrated repository of curated soybean genetic, physical, and genomic sequence maps linked to qualitative and quantitative trait data, including quantitative trait loci (QTL) mappings spanning over 18 years for more than 90 soybean traits.

Key Features:

• Genetic, physical, and genomic maps: Integrates current genetic, physical, and genomic sequence maps linked to qualitative and quantitative traits.
• Quantitative trait loci (QTL) collection: Contains a comprehensive QTL dataset representing over 18 years of mapping for more than 90 unique soybean traits.
• 'Williams 82' reference genome: Provides a well-annotated genomic sequence of the 'Williams 82' soybean cultivar as a reference.
• Chromosome-level integration: Offers an integrated view of soybean chromosomes linking genetic and sequence information.
• Controlled vocabularies and ontologies: Hosts controlled vocabularies for soybean growth, development, and trait terms interconnected with broader plant ontologies.
• Analytical tools: Supports data mining and analysis via associated analytical tools.

Scientific Applications:

• QTL mapping and trait analysis: Enables identification and analysis of loci underlying qualitative and quantitative soybean traits by linking maps and trait data.
• Reference-based genomic analyses: Provides the 'Williams 82' reference for sequence-based analyses and comparative genomics.
• Ontology-driven annotation and comparison: Standardizes terminology and enables cross-study comparisons using controlled vocabularies linked to plant ontologies.
• Integrative chromosome-level studies: Facilitates integration of genetic, physical, and sequence data for chromosome-scale analyses.

Methodology:

Integration of genetic, physical, and genomic sequence maps and linkage with qualitative and quantitative trait data; curation of QTL mapping data spanning over 18 years; annotation of the 'Williams 82' reference genome; and linking of controlled vocabularies to plant ontologies.