statgenMPP

statgenMPP implements identity-by-descent (IBD)-based mixed-model QTL mapping in R to detect quantitative trait loci (QTL) in multi-parent populations (MPPs).

Key Features:

• Unified IBD-based mixed model: Implements an identity-by-descent (IBD)-based mixed-model framework for QTL mapping across MPP designs.
• IBD calculations: Performs identity-by-descent calculations tailored to multi-parent crossing schemes.
• Mixed-model solutions: Provides mixed-model inference and solution routines for QTL effect estimation.
• Support for diverse MPP designs: Handles diallel populations, nested-association mapping (NAM) populations, multi-parent advanced genetic inter-cross (MAGIC) populations, and other complex MPPs with known crossing schemes.
• Visualization: Generates visualizations to aid interpretation of QTL mapping results.

Scientific Applications:

• QTL mapping in MPPs: Detection and localization of quantitative trait loci in multi-parent populations.
• Cross-design analysis: Comparative QTL analysis across diallel, NAM, MAGIC, and other complex crossing schemes.
• Result interpretation: Interpretation and exploration of QTL mapping outputs via visualization.

Methodology:

Performs identity-by-descent (IBD) calculations followed by an IBD-based mixed-model approach for QTL inference and provides visualization of mapping results.