HighlanderLab
@highlanderlab.bsky.social
Research on managing and improving populations at
@RoslinInstitute & @TheDickVet. Led by the chief Highlander @GregorGorjanc.
@RoslinInstitute & @TheDickVet. Led by the chief Highlander @GregorGorjanc.
Xinger (Evie) Tang presented a poster “A Pedigree-Based Method for Localization of Recombination Events”
January 17, 2025 at 6:15 AM
Xinger (Evie) Tang presented a poster “A Pedigree-Based Method for Localization of Recombination Events”
Jaime Ortiz Cuadros presented a poster “Accounting for uncertainty in Optimal Contribution Selection” - joint work with Josh Fogg, Julian Hall, and Ivan Pocrnic
January 17, 2025 at 6:15 AM
Jaime Ortiz Cuadros presented a poster “Accounting for uncertainty in Optimal Contribution Selection” - joint work with Josh Fogg, Julian Hall, and Ivan Pocrnic
Yu (Uni) Zhang presented a poster “How well must we characterise empirical populations for breeding simulations?”
January 17, 2025 at 6:15 AM
Yu (Uni) Zhang presented a poster “How well must we characterise empirical populations for breeding simulations?”
Hannes Becher presented a poster “Fast pedigree PCA with the randPedPCA R package”- joint work with @epigenci.bsky.social
January 17, 2025 at 6:15 AM
Hannes Becher presented a poster “Fast pedigree PCA with the randPedPCA R package”- joint work with @epigenci.bsky.social
Ros Craddock talked about “General Pedigree Tracking of Disease-causing Alleles for Recessive Monogenic Diseases in Dogs” - joint work with Joanna ilska, Cathryn Mellersh, Pam Wiener, and Audrey Martin
January 17, 2025 at 6:15 AM
Ros Craddock talked about “General Pedigree Tracking of Disease-causing Alleles for Recessive Monogenic Diseases in Dogs” - joint work with Joanna ilska, Cathryn Mellersh, Pam Wiener, and Audrey Martin
HighlanderLab at PopGroup58 in Sheffield! It’s always interesting to attend the highly diverse set of talks and posters on population genetics and associated fields at the PopGroup conference. This year it was hosted by the University of Sheffield. We contributed with two talks and four posters.
January 17, 2025 at 6:15 AM
HighlanderLab at PopGroup58 in Sheffield! It’s always interesting to attend the highly diverse set of talks and posters on population genetics and associated fields at the PopGroup conference. This year it was hosted by the University of Sheffield. We contributed with two talks and four posters.
All course material is available at: jvanderw.une.edu.au/aabc2024.htm - enjoy your independent study;)
February 12, 2024 at 4:37 AM
All course material is available at: jvanderw.une.edu.au/aabc2024.htm - enjoy your independent study;)
Day 4 dived into plant breeding trials, experimental design, spatial variation, genotype by environment (GxE) interactions, and how to simulate and model these sources of variation.
February 12, 2024 at 4:37 AM
Day 4 dived into plant breeding trials, experimental design, spatial variation, genotype by environment (GxE) interactions, and how to simulate and model these sources of variation.
Day 3 reversed the flow from forward data simulations to inverse probability statements about unknown parameters from the observed data - all based on linear mixed models with pedigree and genomic data.
February 12, 2024 at 4:36 AM
Day 3 reversed the flow from forward data simulations to inverse probability statements about unknown parameters from the observed data - all based on linear mixed models with pedigree and genomic data.
Day 2 delved into quantitative genetics, how it is implemented in AlphaSimR, and demonstrating fundamental results from the theory. With AlphaSimR we can now easily inspect where and how these fundamental results come about!
February 12, 2024 at 4:36 AM
Day 2 delved into quantitative genetics, how it is implemented in AlphaSimR, and demonstrating fundamental results from the theory. With AlphaSimR we can now easily inspect where and how these fundamental results come about!
AlphaSimR is available from cran.r-project.org/package=Alph...
Free intro on-line course on AlphaSimR is available from www.edx.org/course/breed...
Free intro on-line course on AlphaSimR is available from www.edx.org/course/breed...
February 12, 2024 at 4:35 AM
AlphaSimR is available from cran.r-project.org/package=Alph...
Free intro on-line course on AlphaSimR is available from www.edx.org/course/breed...
Free intro on-line course on AlphaSimR is available from www.edx.org/course/breed...
Day 1 started with an overview of simulating breeding programmes, the essential components of such simulations, and AlphaSimR implementation with simple and advanced examples.
February 12, 2024 at 4:34 AM
Day 1 started with an overview of simulating breeding programmes, the essential components of such simulations, and AlphaSimR implementation with simple and advanced examples.
We just completed Armidale Genetics Summer Course on “Theory and Tools for Designing Breeding Programs of Animals and Plants”.
jvanderw.une.edu.au/aabc2024.htm
jvanderw.une.edu.au/aabc2024.htm
February 12, 2024 at 4:33 AM
We just completed Armidale Genetics Summer Course on “Theory and Tools for Designing Breeding Programs of Animals and Plants”.
jvanderw.une.edu.au/aabc2024.htm
jvanderw.une.edu.au/aabc2024.htm
To obtain more realistic long-term projections, we integrated our framework in a phenotypic and genomic selection line breeding program simulation using AlphaSimR and compared outcomes in TPE and MET under different levels of GxE.
February 2, 2024 at 6:45 AM
To obtain more realistic long-term projections, we integrated our framework in a phenotypic and genomic selection line breeding program simulation using AlphaSimR and compared outcomes in TPE and MET under different levels of GxE.
To highlight how our framework can aid decision-making for statistical methods, we sampled 1000 MET datasets from large simulated TPEs with different levels of GxE and compared models.
February 2, 2024 at 6:44 AM
To highlight how our framework can aid decision-making for statistical methods, we sampled 1000 MET datasets from large simulated TPEs with different levels of GxE and compared models.
Embed GxE effects including spatial effects and other terms in the linear mixed model to generate phenotypes for constructing realistic MET datasets.
February 2, 2024 at 6:44 AM
Embed GxE effects including spatial effects and other terms in the linear mixed model to generate phenotypes for constructing realistic MET datasets.
The framework has four key steps:
1) Provide real or simulated between-environment genetic variance matrix
2) Decompose it to obtain k eigenvectors/values
1) Provide real or simulated between-environment genetic variance matrix
2) Decompose it to obtain k eigenvectors/values
February 2, 2024 at 6:44 AM
The framework has four key steps:
1) Provide real or simulated between-environment genetic variance matrix
2) Decompose it to obtain k eigenvectors/values
1) Provide real or simulated between-environment genetic variance matrix
2) Decompose it to obtain k eigenvectors/values
New pre-print: "A framework for simulating GxE interaction using multiplicative models" by Jon Bancic, @gregorgorjanc.bsky.social and Daniel Tolhurst
. researchsquare.com/article/rs-3...
. researchsquare.com/article/rs-3...
February 2, 2024 at 2:31 AM
New pre-print: "A framework for simulating GxE interaction using multiplicative models" by Jon Bancic, @gregorgorjanc.bsky.social and Daniel Tolhurst
. researchsquare.com/article/rs-3...
. researchsquare.com/article/rs-3...
We welcome Alex Lipka for a sabbatical at our lab at Roslin Institute. He took an obligatory photo with the founder of our vet school:)
January 11, 2024 at 2:01 PM
We welcome Alex Lipka for a sabbatical at our lab at Roslin Institute. He took an obligatory photo with the founder of our vet school:)
Here is an example of a hybrid breeding program in maize following closely Powell et al. (2020) doi.org/10.1101/2020... with R script available at github.com/HighlanderLa...
December 31, 2023 at 3:08 PM
Here is an example of a hybrid breeding program in maize following closely Powell et al. (2020) doi.org/10.1101/2020... with R script available at github.com/HighlanderLa...
Here is an example of a clonal breeding program in tea following closely Lubanga et al. (2023) doi.org/10.1002/tpg2... with R script available at github.com/HighlanderLa...
December 31, 2023 at 3:08 PM
Here is an example of a clonal breeding program in tea following closely Lubanga et al. (2023) doi.org/10.1002/tpg2... with R script available at github.com/HighlanderLa...
Here is an example of results from simulating such a breeding program with phenotypic selection and genomic selection.
December 31, 2023 at 3:07 PM
Here is an example of results from simulating such a breeding program with phenotypic selection and genomic selection.
Here is an example of a line breeding program in wheat following closely Gaynor et al. (2017) doi.org/10.2135/crop... with R script available at github.com/HighlanderLa...
December 31, 2023 at 3:06 PM
Here is an example of a line breeding program in wheat following closely Gaynor et al. (2017) doi.org/10.2135/crop... with R script available at github.com/HighlanderLa...
Before starting with a plant breeding simulation, it’s essential to be aware of the key areas of a plant breeding program.
December 31, 2023 at 3:05 PM
Before starting with a plant breeding simulation, it’s essential to be aware of the key areas of a plant breeding program.