Multi-Parent Population QTL Analysis

Analysis of experimental multi-parent populations to detect regions of the genome (called quantitative trait loci, QTLs) influencing phenotypic traits measured in unique and multiple environments. The population must be composed of crosses between a set of at least three parents (e.g. factorial design, 'diallel', or nested association mapping). The functions cover data processing, QTL detection, and results visualization. The implemented methodology is described in Garin, Wimmer, Mezmouk, Malosetti and van Eeuwijk (2017) , in Garin, Malosetti and van Eeuwijk (2020) , and in Garin, Diallo, Tekete, Thera, ..., and Rami (2024) .

mppR: Multi-Parent Population QTL Analysis

Overview

mppR is an R package to perform QTL analysis of experimental multi-parent populations. The population must be composed of crosses between a set of at least three parents (e.g. factorial design, 'diallel', or nested association mapping). The functions cover data processing, QTL detection, and results visualization.

Installation

mppR has two different branches: "master" and "mppR_CRAN". The "master" branch allows to perform MPP mixed model QTL detection calling the asreml-R package and function parent_cluster.mppData that call the archived R package clusthaplo for parent clustering. The branch "mppR_CRAN" do not contain the mixed models and the call to clusthaplo.

devtools::install_github("vincentgarin/mppR", ref = "master")

Usage

See the two vignettes attached to the package.

Travis