WP5 - Exploiting genome functional annotation to enhance fish breeding (UEDIN)
The overarching aim of WP5 is to understand functional mechanisms underpinning host resistance to infectious disease, and to enhance accuracy of genomic prediction of disease resistance by harnessing functional annotation data. A fuller understanding of the genotype-to-phenotype relationship for complex traits is essential to move towards identification of causative genomic variants, and enabling precision breeding to deliver genetic improvement in key economic traits for aquaculture. Further, improved knowledge of the functional mechanisms underlying these traits facilitates improvements in accuracy and affordability of genomic selection, thereby facilitating improved industry uptake of this technology. Therefore, in WP5, we will focus on two major interrelated sets of experiments: the first is a large-scale exemplar genotype-to-phenotype study to understand and improve resistance to Viral Nervous Necrosis (VNN) in sea bass, which is arguably the biggest disease problem for Mediterranean aquaculture. The second is functional annotation of disease resistance QTL to develop functionally-enriched low-density marker panels to improve genomic selection and its affordability across several target species.
Define genetic architecture of VNN resistance in European seabass.
Establish functional-genomic basis of VNN resistance in European seabass.
Functionally annotate disease resistance QTL regions in four AQUA-FAANG species.
Develop functionally-enriched marker panels to improve genomic prediction of disease resistance.
Links with other WPs
As the hub of industry-facing research activities, WP5 will feed extensively into WP7 dissemination and communication activities targeting industrial stakeholders in aquaculture. All functional annotation assays performed in WP5 will be done using standardized WP1 and WP2 approaches. The ImmunoMaps produced in WP3 and their biological interpretations in WP3/WP6 will provide WP5 with key data for prioritizing functional variants in disease resistance QTL regions.
WP1 - Functional annotation assays
WP2- Bioinformatics and data analysis
WP3 - Genomic basis of immune phenotypes
WP4 - Novel approaches to reveal disease resistance
WP5 - Exploiting genome functional annotation to enhance fish breeding
WP6 - Comparative analyses
WP7 - Dissemination, exploitation and communication
WP8 - Management and coordination
WP9 - Ethics Requirements