R/qtl: QTL mapping in experimental crosses.

Area of Science:

• Genetics
• Bioinformatics
• Statistical Genetics

Background:

• Quantitative trait loci (QTL) mapping is crucial for understanding the genetic basis of complex traits.
• Experimental populations derived from inbred lines are commonly used for genetic analysis.
• Statistical software environments enhance the capabilities of genetic research.

Purpose of the Study:

• To introduce R/qtl, an extensible and interactive software package for QTL mapping.
• To provide researchers with a versatile tool for analyzing genetic data from experimental populations.

Main Methods:

• R/qtl is implemented as an add-on package for the R statistical software.
• The package includes functions for genetic map estimation and genotyping error identification.
• It supports single-QTL and two-dimensional, two-QTL genome scans using various statistical methods.

Main Results:

• R/qtl provides a comprehensive environment for QTL analysis.
• The software enables the inclusion of covariates in genome scans.
• It facilitates robust identification and analysis of QTL.

Conclusions:

• R/qtl is a powerful and flexible tool for quantitative trait loci mapping.
• Its integration with R makes it accessible to a wide range of researchers.
• The package supports advanced analyses, including multi-locus QTL mapping and covariate incorporation.