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Gregor Gorjanc @gregorgorjanc.bsky.social · 03/02/2025

I presented the work of Letícia Lara on Evaluation of selective breeding programme designs for black soldier fly larvae body weight (with María Martínez Castillero, Thiago Oliveira, Ivan Pocrnić, Jana Obšteter)

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Gregor Gorjanc @gregorgorjanc.bsky.social · 03/02/2025

Jana Obšteter presented the work of Laura Strachan on Optimizing pedigree reconstruction and patriline determination in honeybees (with Jernej Bubnič and Janez Presern)

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Gregor Gorjanc @gregorgorjanc.bsky.social · 03/02/2025

Irene de Carlos Fernández presented her work on Modelling the Impact of Non-Native Honey Bee Importation on Native Apis mellifera mellifera Populations (with Laura Strachan, Grace McCormack, Jana Obšteter)

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Gregor Gorjanc @gregorgorjanc.bsky.social · 03/02/2025

Last week some of us attended the 1st EAAP - European Federation of Animal Science Insect Genetics Workshop, which was organised with InsectIMP CA22140 COST Action action by Gertje Petersen and Jana Obšteter. We presented

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

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

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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

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

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

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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

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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

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

Gabriela Mafra Fortuna talked abou “Experience with Inferring Ancestral Recombination Graph of the Global Cattle Population” - joint work with Jana Obsteter

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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.

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Gregor Gorjanc @gregorgorjanc.bsky.social · 10/12/2024

A new pre-print “Robust Optimal Contribution Selection” led by Josh Fogg. We show how to account for the uncertainty and correlation of estimated breeding values in the optimal contribution selection problem: arxiv.org/abs/2412.02888

arxiv.org

Robust Optimal Contribution Selection

Optimal contribution selection (OCS) is a selective breeding method that manages the conversion of genetic variation into genetic gain to facilitate short-term competitiveness and long-term sustainabi...

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Gregor Gorjanc @gregorgorjanc.bsky.social · 16/12/2024

AlphaSimR course edin.ac/3wfGSEj Week 2: It’s time for trait simulation - one of the key reasons we developed AlphaSimR - to study the principles of quantitative genetics and selective breeding. Here, we show the outline of such a simulation, ...

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CGDG_Roslin @cgdg.bsky.social · 02/12/2024

📺 In our seminar last week Dr Hannes Becher from @highlanderlab.bsky.social spoke about "Assembly-free estimation of population parameters using single-individual k-mer spectra". 🧬💻 If you missed the seminar, the recording is now available on our YouTube channel 👇 youtu.be/-wHqNbdpEog?... 🧪

youtu.be

Hannes Becher: Assembly-free estimation of population parameters using k-mer spectra

YouTube video by CGDG - Computational Genetics Discussion Group

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Gregor Gorjanc @gregorgorjanc.bsky.social · 10/04/2024

Please share: Exciting post for a Quantitative Genetics and Breeding scientist to to develop and implement a breeding programme for artemia - a Knowledge Transfer Partnership between Aquanzo and Roslin Institute supported by KTN/KTP InnovateUK elxw.fa.em3.oraclecloud.com/hcmUI/Candid...

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Gregor Gorjanc @gregorgorjanc.bsky.social · 11/03/2024

AlphaSimR course edin.ac/3wfGSEj Week 2: Continuing work with genomes and genotype variation, focusing on loci. We extract genotypes from a population, calculate and plot allele frequencies, and calculate and plot linkage-disequilibrium.

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

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

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

Day 5 returned to topics of Day 1 by diving into Ancestral Recombination Graphs (ARGs), coalescent simulations, and fitting linear mixed models on tree structures, including our current experiences in working with ARGs in agricultural datasets.

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

This part used FieldSimR available at cran.r-project.org/package=Fiel... and GxE simulations desribed in doi.org/10.21203/rs....

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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.

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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.

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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!

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

Showcase of plant breeding simulations is available at www.biorxiv.org/content/10.1.... Animal breeding showcase is in development.

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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...

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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.

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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

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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.

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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.

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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.

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

3) Obtain environmental covariates as the eigenvectors and simulate genotype slopes based on the eigenvalues 4) Construct GxE effects by multiplying covariates and slopes

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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

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

The pre-print aims to: * Develop a scalable and reproducible framework for simulating GxE * Demonstrate its use for simulating realistic MET datasets to compare statistical models and improve breeding simulations * Encourage researchers to consider GxE framework in their work

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

Genotype by environment interaction adds complexity to plant breeding and existing simulations rarely consider it.

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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...

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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:)

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Gregor Gorjanc @gregorgorjanc.bsky.social · 02/01/2024

If you are looking for a PhD involving topics mentioned in this thread here is an opportunity to join us findaphd.com/phds/project...

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

This is a wrap. Head over to the pre-print and R scripts to simulate your plant breeding programs!

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

import external haplotypes, specify demography, genomic models, set heritability, use miscellaneous slot. All scripts are available at github.com/HighlanderLa....

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

We also provide a collection of R scripts showing how to incorporate some common breeding and genetic techniques in breeding program simulations: trait introgression, speed breeding, genome editing, mating plans, GWAS, tbc.

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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...

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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...

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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.

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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...

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

7) Replication and statistical comparison

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