Deliverable 1.1 - SNP-chip tool validation

This deliverable describes a major task in WP1 “Selective Breeding for Robust Fish” to design, implement and validate a SNP-array that will serve as a basic tool for selective breeding in both species. SNP-chips have already been developed and applied to improve livestock in traditionally domesticated terrestrial animals such as cow (see Nikolazzi et al. 2014 for an overview), chicken (Groenen et al. 2011; Kranis et al. 2013), pig (Ramos et al. 2009) and goat (Tosser-Klopp et al.2014). Regarding fish, previous experience on SNP-chip development comes among others from the Atlantic salmon (Houston et al. 2014; Yanez et al. 2014), common carp (Xu et al. 2014) and rainbow trout (Palti et al. 2015). Especially for the Atlantic salmon, the chip application has led to GWAS analysis (Correa et al. 2015; Tsai et al. 2015) illustrating the advantages of such a tool.

Till now, the chosen strategies from different studies include either sequencing a part of the genome (e.g. RNASeq, GBS) of many individuals or whole genome re-sequencing of fewer individuals. The former provides higher coverage of the sequenced moiety of the genome, while the latter identifies many more markers evenly distributed across the genome with lower coverage.
In this deliverable, farmed as well as wild populations’ samples of both European sea bass (BSS) and gilthead sea bream (SBG) were collected under the responsibility of HCMR and UNIPD, respectively. Samples covered the full range from the Atlantic Ocean to the Eastern Mediterranean; some additional domesticated populations were provided through the MedAID consortium.

The samples were deeply sequenced using the technique PoolSeq (Hivert et al. 2018) which resulted in the discovery of SNPs genome-wide. Following multiple bioinformatic filters, a total of 29,888 and 29,807 SNP markers for BSS and SBG, respectively, have been included in the Med_Fish SNP chip. Both sequencing and bioinformatic analysis effort in means of costs and human resources were jointly undertaken by the PerformFISH and MedAID consortia towards having a common SNP-arrays for both species. Furthermore, a number of SNPs was shared by the French-funded project GèneSEA to allow for comparable results between the two platforms. A first validation of the designed SNP revealed a highly successful tool with 90% high resolution markers for BSS and 85% for SBG.