Work Package 1

Work Package Overview‍

Objectives

O1.1: To create an optimal bioinformatic pipeline for whole-genome imputation from sparse genotyping data using reference panels

O1.2 To develop a cross-population/cross-generation genomic prediction model based on functional prioritisation of genetic variants

O1.3 To develop OA-safe reproductive technologies for controlled mating in the European sea bass

O1.4 To develop breeding technologies for OA-safe all-female rainbow trout populations

Task Descriptions

Task 1.1 Optimal WGS data imputation using species-specific genome sequence panels

Lead: UNIPD; Participants: UEDIN, INRAE

Subtask 1.1.1 Producing novel WGS for the gilthead sea bream [M1-M12]

Subtask 1.1.2 Creating reference genome sequence panels for the four species [M1-M22]

Subtask 1.1.3 Developing an optimised pipeline for WGS data imputation reference genome sequence panels for the four species [M1-M30]

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Task 1.2 Optimising genomic prediction using functional prioritisation of genetic variants [M1-M36]

Lead: UNIPD; Participants: UEDIN, INRAE

Subtask 1.2.1 Optimising and training prediction models [1-M30]

Subtask 1.2.2 Validating prediction models on an independent data set [M30-M36]

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Task 1.3 Developing methods to obtain optimal mating schemes in the European seabass [M1-40]

Lead: IRTA; Participants: UNIPD, VISIFISH

Subtask 1.3.1 Developing behavioural predicting models [M1-M36]

Subtask 1.3.2 Developing behavioural predicting models [M18-M40]

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Task 1.4 Using temperature and QTLs for spontaneous masculinisation to produce hormone-free neomales and all-female rainbow trout populations [M1-M48]

Lead: INRAE; Participants: UEDIN

Subtask 1.4.1 Producing the experimental population and testing thermal profiles [M1-M30]

Subtask 1.4.2 Genomic analysis [M30-M48]

Subtask 1.4.3 DNA methylation analysis [M30-M48]

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