In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

VIEWgenome - Results Description

QTL Genomic Context

Integrated View: - QTL positions mapped to genome assembly - Genetic and physical positions aligned - Confidence intervals visualized on genome

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Gene Annotation Results

Candidate Genes: - All genes within QTL confidence intervals listed - Functional annotations displayed (when available) - Gene structure visualized in browser

Annotation Details: - Gene ID (systematic name) - Gene symbol/common name - Product description - Genomic coordinates - Strand orientation - Number of exons/introns

Functional Categories: - GO terms (when available) - KEGG pathways - InterPro domains - Protein families

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Recombination Landscape

Physical vs Genetic Distance: - Recombination rate variation across chromosomes - Hotspots and coldspots identified

Interpretation: - Steep slopes = high recombination - Flat regions = suppressed recombination - Non-monotonic patterns = structural variants

Breeding Implications: - Difficult to break linkage in low-recombination regions - High-recombination regions allow fine mapping - Affects marker-assisted selection strategies

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Candidate Gene Prioritization

Evidence Integration: - Genes within QTL intervals - Expression patterns - Functional annotations

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Troubleshooting

If genes don't appear: - Check GFF3 file format - Verify chromosome naming matches assembly - Ensure proper indexing (.tbi files)

If positions don't match: - Verify same genome version for all files - Check coordinate system (0-based vs 1-based) - Validate marker positions

Performance issues: - Use hosted URLs for large files - Reduce number of active tracks - Zoom to specific regions - Clear browser cache

Additional Resources

JBrowse Documentation: https://jbrowse.org/jb2/

VIEWpoly Tutorial: https://cristianetaniguti.github.io/viewpoly_vignettes/

viewpoly documentation built on July 11, 2026, 1:08 a.m.