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Long Unsupervised

Implementing Genomic Selection: From Theory to Practice (GS_ASReml)

(Course expiry: 90 days after purchase. Trial license expiry 90 days)

In this asynchronous course we will focus on the fundamentals of Genomic Prediction by fitting several linear mixed models (LMM) using different methodologies. An array of R libraries will be used in this course including ASReml-R version 4.2, BGLR, and rrBLUP, among others.

The genomic models considered include some of the Bayesian alphabet (e.g., Bayes A, Bayes B), genomic-BLUP and SNP-BLUP. In this course, we will walk through a workflow that includes: 1) preparing the phenotypic and genotypic data, 2) obtaining relevant filtered marker and/or genomic relationship matrices, and 3) fitting and evaluating genomic prediction models. In addition, some extensions of the GBLUP model are considered, with the illustration of multi-trait and multi-environment models, calculation and incorporation of a dominance relationship matrix, and the use of single-step GBLUP (ssGBLUP) by combining pedigree-based and genomic-based relationship matrices.

This course focuses on appropriate definitions of LMMs, with required random or fixed effects, heterogeneous error structures, and modelling of correlated observations (as implemented in ASReml-R). In addition, all datasets used are real-life examples, and here we will interpret results and discuss implications of the use of genomic prediction models in the context of operational breeding programs. For this course we recommend that you have some basic understanding of linear models and be familiar with the statistical package R.

Do you have a licence for ASReml-R version 4.2? As a participant of this training, you have access to a free trial licence of ASReml-R for 90 days. Once purchased you will be sent a licence and link to download the software within 24 hours. Please note this will ONLY be sent to the email from which you signed up.
  • VIDEO: Lecture Session 1
  • SESSION 2: Preparing Phenotypic and Genotypic Data
  • VIDEO: Lecture Session 2
  • VIDEO: Practical Session 2
  • SESSION 3: Obtaining a Relationship / Kinship Matrix
  • VIDEO: Lecture Session 3
  • VIDEO: Practical Session 3 - APPLE
  • VIDEO: Practical Session 3 - SALMON
  • SESSION 4: Animal Model
  • VIDEO: Lecture Session 4
  • SESSION 5: Introduction to Genomic Selection
  • VIDEO: Lecture Session 5
  • SESSION 6: Overview of Genomic Selection Methods
  • VIDEO: Lecture Session 6
  • SESSION 7: Evaluation of a Genomic Selection Model
  • VIDEO: Lecture Session 7
  • SESSION 8: Bayesian Genomic Selection Methods with BGLR
  • VIDEO: Lecture Session 8
  • VIDEO: Practical Session 8 - APPLE
  • VIDEO: Practical Session 8 - SALMON
  • VIDEO: Lecture Session 9
  • VIDEO: Practical Session 9 - APPLE
  • VIDEO: Practical Session 9 - SALMON
  • SESSION 10: Genomic-BLUP (GBLUP) with ASReml-R
  • VIDEO: Lecture Session 10
  • VIDEO: Practical Session 10 - APPLE
  • VIDEO: Practical Session 10 - SALMON
  • SESSION 11: Single-Step GBLUP (ssGBLUP) Analyses with ASReml-R
  • VIDEO: Lecture Session 11
  • VIDEO: Practical Session 11
  • SESSION 12: Complex GBLUP Analyses with ASReml-R
  • VIDEO: Lecture Session 12
  • VIDEO: Practical Session 12 - APPLE
  • VIDEO: Practical Session 12 - SALMON
  • SESSION 13: Incorporating Genomic Selection in a Breeding Strategy
  • VIDEO: Lecture Session 13
Completion rules
  • All units must be completed
  • Leads to a certificate with a duration: Forever