INTEGRATION OF GENOMIC, RNASEQ AND QTL RESOURCES IDENTIFIES VARIATION IN CANDIDATE GENES FOR GROWTH IN TURBOT (Scophthalmus maximus L.)

ROBLEDO D.; FERNÁNDEZ C.; HERMIDA, M.; ARRANZ, S.E.; SCIARA, A.A.; ÁLVAREZ-DIOS, J.A.; CAAMAÑO, R.; ÁLVAREZ-CASTRO, J.M.; NETTELBLAD, C.; MARTÍNEZ, P.; BOUZA, C.

Santiago de Compostela

Simposio; INTERNATIONAL SYMPOSIUM ON GENETICS IN AQUACULTURE XII; 2015

Turbot is a marine flatfish of commercial importance in Europe and China, the main goal of genetic breeding programs in this species is improving growth traits. Previous genomic stud¬ies have detected several growth-related quantitative trait loci (QTL), of interest for marker assisted selection. In this study, integrative genomics was applied to dissect the genetic ba¬sis of growth traits in turbot. RNAseq was carried out to analyze muscle and liver transcrip¬tomes under nutritional stress to look for genes involved in growth regulation. Muscle and liver cDNA samples from fastened and control turbot were sequenced using Illumina HiSeq. A total of 36,793,041 paired-end reads were generated, accounting for 20,447 genes after align¬ment against the draft turbot genome. Muscle and liver transcriptomes were used to look for SNP variation at growth-related genes, which were anchored to structural QTL-mapping by means of the recently assembled turbot genome as a way to tackle the genetic basis behind phenotytes. Sixty-four genes were found to be close to growth QTL associated markers. Forty-five genes-SNPs were selected based on the availability of feasible SNPs, the proximity of QTL growth markers and functional relevance for growth, including the insulin growth factors 1 and 2, leptin receptor, myostatin1, parvalbumin1 or growth hormone receptor2, which were associated with growth traits in other vertebrates and teleosts. 60% of these SNPs were located within untranslated regions, 31% in coding sequences and the rest in putative splicing regions derived from RNAseq assembly, and thus putative candidates for functional changes underlying growth phenotypes. Technically feasible SNPs (96%) were validated in a wild Atlantic population, 91% of them were polymorphic (mean unbiased gene diversity=0.30, range:0.06-0.51; mean minimum allele frequency=0.22, range:0.03-0.50) and all loci were in Hardy-Weinberg equilibrium. Linkage mapping of informative SNP and association with phe¬notypic variation for growth traits, including a search for epistatic effects, were performed using a large set of farmed families. These markers were also analyzed to look for adaptive diversity in wild and domestic populations of turbot. Integrative genomics has successfully identified SNP markers in growth-related genes suitable for population and family associa¬tion studies, as a basis for marker assisted selection strategies.