Genome Wide Association (GWAS) Analysis and genomic heritability for parasite resistance and growth in European seabass

Abstract

There is an increasing demand for the breeding programs to focus on resistance against diseases since the treatments or vaccinations increase production costs and, in some cases, they are not available at all. Most of the studies focus on virus and bacterial diseases, but limited information is available for parasitic diseases in European seabass. A sample of infected fish (985) with Lernanthropus kroyeri and their parents were genotyped using the recently developed MedFISH SNP array. The sample was selected (selective genotyping) in order to capture the genetic variation of the resistance against the Lernanthropus kroyeri. Body weight was recorded at different growth stages in the population. The genetic parameters were estimated for body weight and parasite count, using Restricted Estimation Maximum Likelihood (REML) methods utilizing a Genomic Relationship Matrix (GRM). Additionally, univariate GWAS, multitrait GWAS and Regional Heritability Mapping (RHM) were performed in order to identify genomic areas related to host resistance and growth. A moderate genomic heritability was detected for growth at sea cage (0.39) and for weight at 2, 4, 6 months after the fish were transferred to the sea cage (0.46–0.41). A moderate to low genomic correlation between growth (body weight/growth at the sea cage) and parasites was observed (0.36–0.21). GWAS results indicated two putative QTL affecting host resistance to Lernanthropus kroyeri count, each one of them explaining approximately 2% of the phenotypic variation.