Training school fish breeding and genomics (with special focus on eel)

Course schedule

Dates Start time End time Location Coordinator registrations
app/max		    
5-8 October 2026 09:00 18:00 Wageningen University Campus WIAS 17 / 25 Apply

Course description

This training school will be organized to train (future) researchers in selective breeding and genomics of fishes, which should already be considered in the selection of broodstock candidates, when considering domestication as tool to facilitate commercial production, and in the design of breeding programmes. The Animal Breeding and Genomics department of Wageningen University and Research is a leading player in this field, educating staff and students in animal breeding and genomics, here focused on fish in aquaculture.

A special focus will be on how to apply the existing knowledge and methodologies on eels. Although fully controlled glass eel production has not been realized yet, it is never early enough to start integrating the principles in current artificial reproduction efforts.

List course objectives

  • Learn the principles of genomics and how to apply them on fish
  • Learn the principles of selective breeding and how to apply them on fish
  • And how can we apply this knowledge and these tools for eels

List learning goals

  • To learn about genomic variation and populations structure; from sequencing to variants; and genomics for breeding population design and management.
  • To learn about why we need breeding programs and design questions; principles of selective breeding and response to selection; breeding values; dissemination and managing genetic variation.
  • To learn about the selective breeding perspectives for eel.

General Information

Target Group

 PhDs, postdocs and other interested researchers

Group size

 A minimum of 15 and a maximum of 25 participants

Course duration

 4 days given once
Credits 1.2 ECTS

Prior knowledge

 Fish biology and aquaculture (at least at MSc level)

Homework/ self- study

 n.a.

Language

 English

Name lecturers/ facilitators  

WUR: Arjan Palstra, John Bastiaansen, Manu Gundappa

2-3 other invited trainers
Course content coordinator  Arjan Palstra (WUR)
Teaching method  Lectures, workshops, practicals and excursion
Venue  Wageningen University campus, the Netherlands

 

Tentative programme

Day 1

Session 1: Genomic variation and populations structure

Lecture

  • Types of variation: SNPs, indels, structural variants
  • Genome architecture in fish: Whole genome duplication (salmonids, carps and eel relevance)
  • Genomic diversity concepts: Heterozygosity, Allele frequencies, Population structure, PCA, Admixture, Linkage disequilibrium, effective population size.

Practical

Discussion

Session 2: From sequencing to variants

Lecture

  • Briefly mention sequencing technologies: how to decide, what coverage to sequence, how many to sequence etc.
  • Illumina sequencing (accuracy, SNPs)
  • Oxford Nanopore sequencing (long reads, SVs)
  • Basic pipeline: Reads → alignment → variant calling → VCF
  • VCF file - Quality control, coverage, missing data, genotype quality
  • SNP filtering for downstream analysis

Practical

Discussion

Day 2

Session 3: Genomics for breeding population design and management

Lecture

  • What makes a good founder population?
  • Maximize genetic diversity, Capture rare alleles, Avoid hidden relatedness
  • Genomic tools for founder selection: Genomic relatedness matrices, clustering (PCA / distance-based), kinship estimation
  • Observed vs expected heterozygosity: Inbreeding coefficient, Predicting and monitoring inbreeding, Runs of Homozygosity (ROH), Detecting recent vs ancient inbreeding. Applications in breeding.

Practical

Discussion

Session 4: Why breeding programs and design questions

Lecture

  • Why breeding programs (genetic diversity, genetic improvement)
  • What is needed, complexity, cost, biological constraints (“why not breeding programs”)

Practical 

Discussion

Lecture

  • Genetic principles of important traits and phenotypes
  • Examples of breeding program designs in aquaculture (integrated, nucleus)

Discussion

Day 3

Session 5: Principles of selective breeding and response to selection

Lectures

  • Breeders equation
  • Heritability and quantitative genetics, sources of variance
  • Selection intensity and expected responses
  • Genetic correlations and their effect on genetic improvement

Practical

Session 6: Selective breeding perspectives for eel

Lectures

  • Selective breeding perspectives for European eel
  • Selective breeding perspectives for Japanese eel

Field trip

Day 4

Session 7: Breeding values

Lecture

  • The concept of a breeding value (predicting progeny performance)
  • Estimating the breeding value of individuals using relatives
  • Effects of different data sources (own phenotype, family information)
  • The advantages of genomic information: accuracy of prediction

Practical 

Session8: Dissemination and managing genetic variation

Lecture

  • Multiplication and dissemination
  • Protection of genetic improvement and economics of breeding programs
  • Economics of breeding programs

Practical

Fee

COST participants free

1) Reduced fee: All Wageningen University PhDs with a TSP

 € 400

2) University fee: All other PhDs, Wageningen University postdocs and staff

 € 850

3) External fee: All other participants

 €1650

Cancellation condition

You may cancel free of charge up to 1 month before the start of the course. After this date you will be charged with the University fee, unless: 

  • You can find someone to replace you in the course and supply the course coordinator with the name and contact information of your replacement. In this case you will be charged a €50,- cancellation fee.
  • You are a PhD of Wageningen University with a valid reason to cancel (illness or death in the family 1st or 2nd degree). In this case you will be charged the reduced fee and your supervisor/PI must send a mail indication the reason for cancellation.

Information

For more information please contact:

paddy.haripersaud@wur.nl or arjan.palstra@wur.nl.