mppR: An R Package for QTL Analysis in Multi-parent Populations using Linear Mixed Models

mppR is an add-on package for the statistical software R for QTL analyses in multiparent populations composed of genotypes from more than one cross like NAM populations, diallels or factorial designs. mppR contains functions to assist the user in a range of activities of QTL analysis such as: data processing, QTL detection, visualisation of results, and estimation of QTL effects. mppR workflow is structured along main functions allowing to: 1) perform preliminary data quality control; 2) organize data into a single data object; 3) cluster parental lines based on ancestry; 4) perform QTL detection; 5) evaluate QTL discoveries by cross-validation; and 6) determine multi-QTL effect models. The search of QTLs can be done by 4 different models that vary with respect to the way the QTL effects are modelled (cross-specific, parental, ancestral or bi-allelic).