iiinova — where your digital self keeps evolving

HighlanderLab @highlanderlab.bsky.social · 17/01/2025

Xinger (Evie) Tang presented a poster “A Pedigree-Based Method for Localization of Recombination Events”

HighlanderLab @highlanderlab.bsky.social · 17/01/2025

Jaime Ortiz Cuadros presented a poster “Accounting for uncertainty in Optimal Contribution Selection” - joint work with Josh Fogg, Julian Hall, and Ivan Pocrnic

111

HighlanderLab @highlanderlab.bsky.social · 17/01/2025

Yu (Uni) Zhang presented a poster “How well must we characterise empirical populations for breeding simulations?”

111

HighlanderLab @highlanderlab.bsky.social · 17/01/2025

Hannes Becher presented a poster “Fast pedigree PCA with the randPedPCA R package”- joint work with @epigenci.bsky.social

121

HighlanderLab @highlanderlab.bsky.social · 17/01/2025

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

111

HighlanderLab @highlanderlab.bsky.social · 17/01/2025

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.

221

HighlanderLab @highlanderlab.bsky.social · 12/02/2024

All course material is available at: jvanderw.une.edu.au/aabc2024.htm - enjoy your independent study;)

100

HighlanderLab @highlanderlab.bsky.social · 12/02/2024

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.

100

HighlanderLab @highlanderlab.bsky.social · 12/02/2024

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.

100

HighlanderLab @highlanderlab.bsky.social · 12/02/2024

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!

100

HighlanderLab @highlanderlab.bsky.social · 12/02/2024

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...

100

HighlanderLab @highlanderlab.bsky.social · 12/02/2024

Day 1 started with an overview of simulating breeding programmes, the essential components of such simulations, and AlphaSimR implementation with simple and advanced examples.

100

HighlanderLab @highlanderlab.bsky.social · 12/02/2024

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

131

HighlanderLab @highlanderlab.bsky.social · 02/02/2024

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.

000

HighlanderLab @highlanderlab.bsky.social · 02/02/2024

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.

100

HighlanderLab @highlanderlab.bsky.social · 02/02/2024

Embed GxE effects including spatial effects and other terms in the linear mixed model to generate phenotypes for constructing realistic MET datasets.

100

HighlanderLab @highlanderlab.bsky.social · 02/02/2024

The framework has four key steps: 1) Provide real or simulated between-environment genetic variance matrix 2) Decompose it to obtain k eigenvectors/values

100

HighlanderLab @highlanderlab.bsky.social · 02/02/2024

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...

121

HighlanderLab @highlanderlab.bsky.social · 11/01/2024

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:)

011

HighlanderLab @highlanderlab.bsky.social · 31/12/2023

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...

100

HighlanderLab @highlanderlab.bsky.social · 31/12/2023

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...

100

HighlanderLab @highlanderlab.bsky.social · 31/12/2023

Here is an example of results from simulating such a breeding program with phenotypic selection and genomic selection.

100

HighlanderLab @highlanderlab.bsky.social · 31/12/2023

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...

110

HighlanderLab @highlanderlab.bsky.social · 31/12/2023

Before starting with a plant breeding simulation, it’s essential to be aware of the key areas of a plant breeding program.

100

HighlanderLab @highlanderlab.bsky.social · 31/12/2023

New pre-print: “Plant breeding simulations with AlphaSimR” led by Jon Bancic in collaboration with Philip Greenspoon, Chris Gaynor, and @gregorgorjanc.bsky.social www.biorxiv.org/content/10.1... A short thread with highlights.

282