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R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations.

Karl W Broman1, Daniel M Gatti2, Petr Simecek2

  • 1Departments of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Wisconsin 53706 broman@wisc.edu.

Genetics
|December 29, 2018
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Summary

R/qtl2 is a new software for quantitative trait loci (QTL) mapping in diverse experimental populations. It handles complex genetic data and enables advanced analyses like genome scans and association mapping.

Keywords:
Collaborative CrossDiversity Outbred miceMAGICMPPMultiparent Advanced Generation Inter-Cross (MAGIC)QTLheterogeneous stockmultiparent populationssoftware

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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Quantitative trait loci (QTL) mapping is crucial for understanding genetic contributions to complex traits.
  • Existing software like R/qtl has limitations with multiparental populations and high-dimensional data.
  • There is a need for advanced tools to analyze complex genetic architectures in diverse experimental populations.

Purpose of the Study:

  • Introduce R/qtl2, an enhanced software environment for QTL analysis.
  • Expand QTL mapping capabilities to multiparent populations and high-density genotype data.
  • Facilitate the analysis of high-dimensional molecular phenotypes in genetic studies.

Main Methods:

  • Developed R/qtl2 using R and C++ programming languages.
  • Implemented genome scans using linear mixed models to control for population structure.
  • Integrated SNP imputation from founder strain genomes and association mapping functionalities.

Main Results:

  • R/qtl2 supports multiparent populations (e.g., Collaborative Cross, Diversity Outbred, MAGIC).
  • The software efficiently processes high-density genotyping data and high-dimensional molecular phenotypes.
  • R/qtl2 provides essential QTL mapping features, including graphical displays and summary reports.

Conclusions:

  • R/qtl2 significantly advances QTL mapping capabilities for complex experimental populations.
  • The software is a versatile and extensible tool for genetic research.
  • R/qtl2 is free, open-source, and includes a test framework for reliability.