RNAseq identification of SNP markers for growth-related genes in turbot Scophthalmus maximus L.

ROBLEDO D.; FERNANDEZ M.; HERMIDA, M.; SCIARA A.A.; RIERA P.; MARTINEZ, P.; BOUZA, C.

Donostia

Congreso; Aquaculture Europe 2014; 2014

European Aquaculture Society

Turbot (Scophthalmus maximus, L.) is a flatfish intensively cultured in Europe for over 25 years. Turbot aquaculture accounts for over 10,000 tons/year in Europe, and has recently increased in China, reaching more than 60,000 tons in 2011 (APROMAR 2012; http://www.apromar.es). Growth related traits constitute one of the main goals of the ongoing genetic breeding programs for this species. The construction of a high dense linkage map in turbot (Bouza et al. 2008) has allowed the detection of quantitative trait loci (QTL) associated to growth traits (Sánchez-Molano et al. 2011), to be further investigated for marker assisted selection. The genetic basis of growth traits is still not well understood in fish. Fasting-refeeding experiments have been used to identify novel genes involved in growth regulation in teleosts (Johnston el al. 2011). In addition, next-generation sequencing technologies have enabled whole transcriptomes sequencing (RNAseq) and SNP discovery at candidate genes suitable for growth association studies (Salem et al. 2012). In this study, RNAseq was carried out in turbot under nutritional stress for a better knowledge of growth transcriptome and to identify SNP markers at candidate genes involved in growth traits for this species. Moreover, the growth-related QTL and associated markers have been located on the turbot genome which has been recently sequenced and assembled. This study demonstrated that integrative genomics is an effective strategy for identifying SNPs at candidate genes to dissect the genetic basis of biological traits of productive interest in aquaculture. RNAseq at high sequence coverage based on divergent individuals under nutritional stress provided muscle and liver transcriptomic resources enriched in growth-related genes in turbot. This functional approach was complemented with the co-localization of the candidate genes from previously reported growth QTLs onto the recently assembled genome of this species. Our approach involved to look for SNP markers at growth-related genes responsible for growth QTL effects to be further tested for family-based association studies and marker assisted selecction (MAS) for growth traits in turbot aquaculture.