HighlanderLab

GitHub - HighlanderLab/RandPedPCA: Principal Component Analysis of Pedigree Relationship Matrix via Randomized SVD Principal Component Analysis of Pedigree Relationship Matrix via Randomized SVD - HighlanderLab/RandPedPCA

This is a joint work with @highlanderlab.bsky.social @gregorgorjanc.bsky.social

The software is available in github and will also be on CRAN as soon as the screening is cleared.

github.com/HighlanderLa...

EdinburghX: Breeding Programme Modelling with AlphaSimR | edX 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 eva...

Lastly I gave a short course on Stochastic simulations of breeding programmes with AlphaSimR - a teaser for our free on-line course www.edx.org/learn/animal...

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)

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

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)

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

@h-a-n.bsky.social

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

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

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

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

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.

EASTBIO: MegaPhase: Pedigree phasing and imputation for mega-scale whole genome sequence data at University of Edinburgh on FindAPhD.com PhD Project - EASTBIO: MegaPhase: Pedigree phasing and imputation for mega-scale whole genome sequence data at University of Edinburgh, listed on FindAPhD.com

Exciting PhD opportunity to join us at Roslin/Edinburgh and work with the largest whole-genome sequencing dataset in selective breeding. www.findaphd.com/phds/project...

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...

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

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, ...

YouTube video by CGDG - Computational Genetics Discussion Group Hannes Becher: Assembly-free estimation of population parameters using k-mer spectra

📺 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?...
🧪

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...

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.

We thank the support from @roslininstitute @TheDickVet @EdinburghUni @BBSRC @TRAINatEd_MSCA @EdinInnovations @Bayer4Crops @UniNewEngland. Fin.

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

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.

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

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.

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!

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

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...

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