Adequate high-throughput genotyping arrays, i.e. SNP chips, are essential tools for genetic studies. A substantial database of SNP markers now exists for both bass and bream as a result of ongoing research programmes, particularly the EU-funded collaborations AquaTrace and FISHBOOST, which have utilised RAD sequencing techniques.
In WP3, representative farmed populations of European seabass and gilthead seabream will be sequenced to discover and characterise a substantial SNP database. This SNP set will be harnessed to provide a combined-species SNP array for European seabass and gilthead seabream, targeted to commercial farmed populations. The SNP chips will be applied to gene mapping, genomic selection and estimation of effective population sizes and relationships between populations throughout the Mediterranean area.
Genotype-by-environment (GxE) interaction is the phenomenon that different genotypes perform differently in different environments and if it exists, selection strategies need to be adapted or separate environment-specific breeding programs need to be developed. In bass, GxE was observed for growth rate, expressed as thermal growth coefficient, across the Mediterranean basin. Other studies have shown genotype by diet interaction for diets that are composed of vegetal ingredients (reviewed in Sae-Lim et al., 2015. MedAID will explore GxE interactions in gilthead seabream at different temperature profiles in two separate locations.
- To develop a combined SNP array for gilthead seabream and European seabass
- To develop and test genomic selection to improve key production traits in gilthead seabream and European seabass breeding.
- To discover individual genes associated with production traits in European seabass and gilthead seabream.
- To characterize the genetic diversity of representative populations of farmed European seabass and gilthead seabream, and test measures on inbreeding.
- To assess the existence and extent for GxE interaction for temperature and on production efficiency for gilthead seabream.