Breeding Programme Modelling with AlphaSimR
Breeding Programme Modelling with AlphaSimR
From the University of Edinburgh Roslin Institute.
Breeding programmes are key to the genetic improvement of plant varieties and animal breeds used in agriculture. This unique course shows how to model an existing or new breeding programme and the evaluation of alternative breeding scenarios.
This online course will equip participants with an understanding of computer modelling of breeding programmes to enhance genetic improvements in agriculture. The modelling is done through the AlphaSimR package.
The package provides a set of functions that represent breeding activities. The combination of these functions in an R script allows the modelling of simple and arbitrarily complex breeding programmes. It also allows evaluation of the effects of alternative breeding scenarios on the rate of genetic improvement and other key performance indicators.
The course is taught by experts in the field and is applicable to a range of breeding programmes as demonstrated through local and global case studies.
These videos are free, open resources originally created for the short online course Breeding Programme Modelling with AlphaSimR. If the course is not currently running, you can still work through the media resources in your own time.
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This vignette shows how to simulate a bit more realistic animal breeding programme with overlapping generations and different selection intensities in males and females.…
Animal Breeding Programme with AlphaSimR - Part 2
From Geoff Fortescue
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This vignette will show how to simulate the wheat breeding programme described in Gaynor et al. (2017). In this breeding programme, there are several stages in a…
Plant Breeding
From Geoff Fortescue
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This vignette shows how to simulate a bit more realistic animal breeding programme with overlapping generations and different selection intensities in males and females.…
Animal Breeding Programme with AlphaSimR - Part 1
From Geoff Fortescue
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The following audio recording is delivered by Chris Gaynor, a senior data scientist at Bayer Crop Science. While working at The Roslin Institute in Edinburgh, he…
Genomic selection in plant breeding
From Geoff Fortescue
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Now we explore the multi-trait selection in AlphaSimR so that we can design a sustainable and holistic approach to breeding productive and resilient individuals. This…
Selection on multiple traits in AlphaSimR - Part 3
From Geoff Fortescue
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Now we explore the multi-trait selection in AlphaSimR so that we can design a sustainable and holistic approach to breeding productive and resilient individuals. This…
Selection on multiple traits in AlphaSimR - Part 2
From Geoff Fortescue
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Now we explore the multi-trait selection in AlphaSimR so that we can design a sustainable and holistic approach to breeding productive and resilient individuals. This…
Selection on multiple traits in AlphaSimR - Part 1
From Geoff Fortescue
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We will now look at the randomness of DNA inheritance (the DNA lottery) between parents and progeny, and how this process drives variation and resemblance between…
DNA lottery in AlphaSimR Genome - Part 2
From Geoff Fortescue
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We will now look at the randomness of DNA inheritance (the DNA lottery) between parents and progeny, and how this process drives variation and resemblance between…
DNA lottery in AlphaSimR Genome - Part 1
From Geoff Fortescue
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In this vignette, we will learn about simulating selection to improve a single trait and explore some of the intricacies of the breeder’s equation. (Part 2)
Selection on a single trait in AlphaSimR - Part 2
From Geoff Fortescue
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AlphaSimR simulates traits by defining the type of trait genetic effects, number of DNA sites controlling the trait, mean, genetic variance, and environmental variance.…
Simulating traits in AlphaSimR - Part 2
From Geoff Fortescue
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In this vignette, we will learn about simulating selection to improve a single trait and explore some of the intricacies of the breeder’s equation. (Part 1)
Selection on a single trait in AlphaSimR - Part 1
From Gregor Gorjanc
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We will now look at the randomness of DNA inheritance (the DNA lottery) between parents and progeny, and how this process drives variation in genetic and phenotype…
DNA lottery in AlphaSimR Traits
From Gregor Gorjanc
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AlphaSimR simulates traits by defining the type of trait genetic effects, number of DNA sites controlling the trait, mean, genetic variance, and environmental variance.…
Simulating traits in AlphaSimR - Part 1
From Gregor Gorjanc
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AlphaSimR simulates DNA for a founding pool of genomes based on species' genome parameters and demography. We use this founding pool of genomes to initiate a…
Simulating DNA in AlphaSimR
From Gregor Gorjanc
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