breeding-notes

Simple repository of links to tools for plant breeding and genetics, with some annotation. This is for information purposes only.

Mixed-models

A section on mixed-models. See my other repository on examples of mixed-model applications for plant breeding experiments.

R packages

• CRAN task view for mixed-models
• lme4
  • Can be forced to fit compound symmetry, unstructured, and diagonal covariance structures
• glmmTMB
  • Allows for some cool covariance structures, including Toeplitz, AR1, spatial exponential; see here
• blme
  • Extends lme4 and allows for prior distributions; it also allows for the residual variance to be fixed (useful for two-stage analysis)
• rrBLUP
  • Very nice for a single random effect; the go-to for genomewide selection
• sommer
  • Great for mixed models with multiple random effects and with kinship
• lme4GS
  • lme4 language with flexibility for kinship; in theory the more complex covariance structures of lme4 (us, cs, diag) could be deployed
• asreml
  • The gold standard for quickly fitting models with complex covariance sturctures, but you need a license
• mmrm
  • Mixed-models for repeated measures; allows for time-dependent covariance structures like AR1, ante, toep, and exp

Tutorials

QTL mapping / GWAS

R packages

• The Biometris group has several useful R packages:
  • statgenGWAS
    • single-trait GWAS
  • statgenQTLxT
    • multi-trait, multi-environment GWAS
  • statgenIBD
    • Calculate identity-by-decent probabilities in two-, three-, and four-way crosses

Tutorials

GxE

R packages

• statgenGxE
  • Mega-environment analysis, stability, FW-regression, AMMI and GGE, etc. all the fun stuff
• statgenSTA
  • Mixed-model analysis of field trials with or without spatial trends

Tutorials

Phenomics