PEPIS

PEPIS estimates polygenic and epistatic genetic effects for quantitative trait loci (QTL) mapping using a linear mixed model framework to analyze genome-wide interactions.

Key Features:

• Linear mixed model: Implements a linear mixed model approach for modeling polygenic and epistatic genetic effects.
• Sub-pipelines: Provides two sub-pipelines: kinship matrix calculation and polygenic component analysis with genome-wide scanning for main and epistatic genetic effects.
• Kinship matrices: Computes kinship matrices used in mixed-model analyses.
• Genome scanning: Performs genome-wide scans for main genetic effects and epistatic interactions.
• C/C++ implementation: Implements mathematical matrix computations in C/C++ for computational efficiency.
• Parallel computing: Distributes computations across multiple computer nodes in a networked cluster via parallel computing.
• Performance example: Reduced analysis time for an immortalized F2 rice population genotypic dataset from over one month (original R prototype) to approximately five minutes.
• Application to hybrid rice: Has been applied to predicting hybrid rice performance.

Scientific Applications:

• QTL mapping of polygenic and epistatic effects: Supports detection of polygenic and epistatic QTL to investigate missing heritability in GWAS.
• Hybrid rice prediction: Used for prediction of hybrid rice performance based on estimated genetic effects.
• Genome-wide epistatic analysis: Enables genome-wide analysis of epistatic genetic effects in structured populations such as immortalized F2 rice populations.

Methodology:

Computational steps comprise a linear mixed model with separate sub-pipelines for kinship matrix calculation and for polygenic component analysis plus genome-wide scanning for main and epistatic effects, implemented in C/C++ with parallel execution across cluster nodes.