Multiparental populations | MPP-ME QTL detection | Model description | $$V\begin | QTL detection procedure | Approximate Wald statistic computation | QTL effects estimation | QTL by environment effect determination | QTL by environmental covariate (EC) effect estimation | QTL analysis example | Data | Simple interval mapping (SIM) | Cofactors selection | Composite interval mapping (CIM) | QTLs selection | QTLs effect and significance estimations | QTLs R2 calculation | QTL profile plot | Whole-genome genetic effect significance plot | mppGE_proc: wrapper function | QTLxEC effect estimation | Plot QTL x EC sensitivity slopes | Computation time | References

Abstract | Introduction | Statistical methodology | Connectivity | General model | QTL effects | Cross-specific model | Parental model | Ancestral model | Parental and ancestral model constraints | Bi-allelic model | Variance covariance structure | Homogeneous residual term | Cross-specific residual terms | Pedigree and HRT | Pedigree and CSRT | Test statistics | QTL detection procedure | Significance threshold determination | Multi-QTL model determination | Multi-QTL effect (MQE) model | QTL effect estimation | Genetic effect estimation and interpretation | Global $R^{2}$ | Partial $R^{2}$ | Cross-validation | Illustration: US-NAM population QTL analysis | Overview | US-NAM data and raw data format | Genotypic data | Map data | Phenotypic data | Cross parents information | Data processing | create a mppData object | Marker quality control - QC | IBS processing | IBD processing | Parent clustering | mppData manipulation | mppData subset | Modify mppData phenotypes or add new phenotype | QTL analysis | Multi QTL Effect (MQE) model | QTL effects estimation | Results visualisation | Parallelization | Limitations | Summary | Funding | References