statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of...

Area of Science:

• Genetics
• Bioinformatics
• Statistical Genetics

Background:

• Multi-parent populations (MPPs) offer significant genetic diversity for quantitative trait loci (QTL) mapping.
• Existing software for QTL analysis in MPPs is limited, particularly for diverse MPP designs.

Purpose of the Study:

• To develop a user-friendly R package for QTL mapping in general multi-parent populations.
• To provide a unified identity-by-descent (IBD)-based mixed model approach for QTL analysis.

Main Methods:

• Development of the R package statgenMPP.
• Implementation of IBD calculations and mixed model solutions within the package.
• Integration of visualization tools for QTL mapping.

Main Results:

• The statgenMPP package facilitates QTL analysis across various MPP designs (diallele, NAM, MAGIC, etc.).
• It offers integrated functionalities for IBD estimation, mixed model analysis, and result visualization.
• The package supports complex MPP designs with known crossing schemes.

Conclusions:

• statgenMPP addresses the need for specialized QTL mapping software for MPPs.
• The package enhances the analysis of genetic diversity and trait-associated loci in complex breeding designs.
• Open-source availability promotes wider adoption in genetic research.