Have a look at the paper for more details, and if you have any feedback I would be keen to hear about it! 👩‍🔬

This work was done within the AquaImpact project (Horizon 2020) and in collaboration with Mowi Genetics using datasets from there breeding programme. 🐟🧬

What to take home? If you're want to reduce the cost of your genotyping to save money or to increase the number of fish you genotype (with a fixed budget, thus increasing the selection intensity) you can decide to only genotype selection candidates on a HD SNP array, and not the parents.

But we saw very little effect on the accuracy (and bias) of genomic predictions! Even for the scenario with the lowest accuracy of imputation (~80%) the accuracy of prediction was really close to the one obtained with the HD panel! and significantly better than pedigree based one which we expected

We showed a small impact of the make-up of the reference population on imputation accuracy: it was lower when no parents were included and, higher when parents and colarerals where included (that scenario increased the accuracy especially for individuals with missings parents in the dataset)

Our scenarios where:
Only the parents (all traits together or one trait at a time ie: increasing the target population size)
Only the selection candidates (validation dataset)
Parents and selection candidates
Parents and some collaterals (100-1000)
in 3 traits: Growth, resistance to PD and to CMS

We know that having the parents genotyped at high-density in the reference panel for imputation is enough to get really high (>90%) imputation accuracies from very low density (500 SNPs or less) panels in fish species. But what is the impact of changing this reference panel?

It was a great collaboration with Eirikur who visited our lab in summer 2022 during his PhD in the University of Copenhagen to learn how to perform GWAS and other quantitative genetics approaches. It's always great to collaborate with other groups and to see promissing outputs like this paper!

We (Eirikur) used 16SRNA profiling of gill microbiota from A. salmon after a AGD challenge 🐟 🧬 * 🦠 and detected differences in the microbiota traits based on AGD scoring methods, showcasing the potential of using traits of the microbiota to study AGD disease resistance mechanisms.
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Varsha won the second 🥈 prize for beat oral communication! Well done Varsha well deserved !

It's not a difference in cell types but how the fish use their cells (encapsulation of the parasite for coho for example) or how the parasite immunomodulatea the fish (as in Atlantic salmons)
Sarah is leaving the Roslin and starting her group in @exeter.ac.uk, she will be missed !

José's group has been instrumental in developing genomic selection and investigating generic architecture of complex disease resistance traits in salmonids in Chile with also a worldwide impact. The present resolve around high density, wgs data, will the future be gene editing? 🧬✂️
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There will be more, including a talk by @lucavegu.bsky.social later today on host génome and skin microbiome information for sea lice burden in A. salmon!
There are a few posters as well to look at during the breaks and poster session 👀

The Chilean delegation came in number, we had a couple of talks already on rainbow trout: on IPNv resistance and impact of l vaccination of Genomic predictions, characterisation of impact of transposable elements in response to SRS 🌈🐟

@romainmorvezen.bsky.social is now looking for a postdoc to analyse new dataset of phenotypes and genotypes for field mortality resistance so if you want to join the SYSAAF team in Rennes reach out to him (I've collaborated with them during my PhD and it's a great group!)
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In France, mass selection is combined with parentage assignment to maintain genetic diversity since 2012 and since 2019 genomic selection is also used to improve oyster resistance to diseases, with great success so far !

In France oysters are pretty important, and hatchery spat (baby 🦪) represent 30/40% of total spat but more than 50% of final produce because selected oysters perform better than wild one, especially when facing pathogens

Using cohabitation Batya tried to answer if those fishes can be infected by the virus (not really) if they can transmit the disease and infect common carp (no) and with injection she looked at resistance (do they die? No)
A super clever approach! I can't wait to read the publication! 🧬🐟

Omics can also be used to detect early pathogen outbreaks in pounds for barramundi, as shown by Varsha Balu (James Cook Uni, Australia). Using eDNA from water sampling (non invasive) she was able to detect the presence of two pathogens in pounds, that could be associated with changes in salinity.