Rqtl2

Rqtl2 performs quantitative trait loci (QTL) mapping in experimental multiparent populations to identify genetic loci underlying quantitative traits and to integrate high-density genotyping with high-dimensional molecular phenotypes.

Key Features:

• Multiparent population support: Handles multiparent populations including Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and Multiparent Advanced Generation Intercross (MAGIC) plant populations.
• High-density genotyping: Manages modern high-density genotyping data for genome-wide analyses.
• High-dimensional molecular phenotypes: Integrates molecular phenotypes such as gene expression profiles and proteomics data for QTL analysis.
• Linear mixed model genome scans: Performs genome scans using linear mixed models to account for population structure.
• SNP imputation and association mapping: Imputes single nucleotide polymorphisms (SNPs) based on founder strain genomes and performs association mapping.
• Implementation and extensibility: Implemented in R and C++ and extensible via add-on packages.
• Testing framework: Includes a test framework to support validation and verification.

Scientific Applications:

• QTL discovery in multiparent populations: Mapping genetic loci that influence quantitative traits in Collaborative Cross, Diversity Outbred, heterogeneous stocks, and MAGIC populations.
• Genotype–phenotype integration: Associating high-density genotype data with high-dimensional molecular phenotypes such as gene expression and proteomics.
• Association mapping: Conducting association mapping using imputed SNPs derived from founder strain genomes.
• Accounting for population structure: Reducing confounding in genome scans by modeling relatedness and population structure with linear mixed models.
• SNP imputation using founder genomes: Inferring unobserved SNP genotypes based on founder strain reference genomes to increase marker density for analyses.

Methodology:

Genome scans use linear mixed models to account for population structure; SNPs are imputed from founder strain genomes and association mapping is performed using the imputed genotypes.