Proceedings of the World Congress on Genetics Applied to Livestock Production, 11. 482. Development and applications of new genomic tools for turbot selection programmes M. Saura 1 , A. Fernández 1 , F. Maroso 2 , M. Hermida 3 , P. Martínez 2,3 , S. Cabaleiro 5 , A.B. Doeschl-Wilson 6 , O. Anacleto 6 , R.D. Houston 6 , A. Millán 2 , J. Fernández 1 , M.A. Toro 4 , M. J. Carabaño 1 , C. Bouza 3 & B. Villanueva 1 1 INIA, Departamento de Mejora Genética Animal, Crta. La Coruña Km 7.5, 28040 Madrid, Spain saura.maria@inia.es (Corresponding Author) 2 Geneaqua SL, 27002 Lugo, Spain 3 Universidade de Santiago de Compostela, Departamento de Xenética, Lugo 27002, Spain 4 Universidad Politécnica de Madrid, Departamento de Producción Agraria, 28040 Madrid, Spain 5 CETGA, Cluster de Acuicultura de Galicia, 15695 Aguiño-Ribeira, Spain 6 The Roslin Institute and Royal (Dick) School of Veterinary Studies, Division of Genetics and Genomics, Midlothian EH25 9RG, UK Summary Several genetic improvement programmes are underway for turbot (Scophthalmus maximus), a flatfish of great commercial value. Although the main objective in these programmes has been to increase growth rate, the interest in improving other economically important traits such as disease resistance is currently increasing. The development of genomic tools for this species is central not only for improving these complex traits but also for controlling inbreeding and the loss of genetic variability. In this study, a genotyping by sequencing approach (2bRAD-seq) was used to identify 18,125 SNPs in a sample of 1,439 turbot fish (from 36 families) coming from an innovative disease transmission experiment specifically designed for disentangling the different components of the host response to infection by Philaterides dicentrarchi. This parasite causes scuticulociliatosis, a disease that results in severe economic losses in the aquaculture industry. The genomic information obtained allowed a better integration of the genetic and physical maps and a more refined version of the current turbot genome, improving the anchoring of the genome assembly from 80 to 97%. The new maps were then used to address several issues in turbot for the first time. These included to (i) obtain within-family and population-wide linkage disequilibrium (LD) patterns; (ii) estimate effective population size from LD measures; (iii) estimate genomic inbreeding; and (iv) investigate the genetic basis of different components (susceptibility, tolerance, resilience) of the host response to P. dicentrarchi, through a genome-wide association study. Effective population size declined from 221 fish 30 generations ago to 50 fish three generations ago although selection breeding programmes are unlikely to be the responsible of this decrease. Recent inbreeding, estimated as the proportion of the genome in runs of homozygosity, was low suggesting also that at least to some extent, inbreeding has been controlled. Genomic information allowed the identification of a candidate QTL region for resilience to scuticulociliatosis that explained 33% of the total genetic variance, and had an effect of about five days of increased survival. This region may be a target for marker-