Genome-wide association analysis reveals loci associated with resistance against Piscirickettsia salmonis in two Atlantic salmon (Salmo salar L.) chromosomes.

Katharina Correa,Jean P Lhorente,María E López,Alex Di Genova,Liane Bassini,Alejandro Maass,José M Yáñez,William S Davidson,Nader Deeb,Sudhir Naswa

doi:10.1186/s12864-015-2038-7

Abstract

BackgroundPisciricketssia salmonis is the causal agent of Salmon Rickettsial Syndrome (SRS), which affects salmon species and causes severe economic losses. Selective breeding for disease resistance represents one approach for controlling SRS in farmed Atlantic salmon. Knowledge concerning the architecture of the resistance trait is needed before deciding on the most appropriate approach to enhance artificial selection for P. salmonis resistance in Atlantic salmon. The purpose of the study was to dissect the genetic variation in the resistance to this pathogen in Atlantic salmon.Methods2,601 Atlantic salmon smolts were experimentally challenged against P. salmonis by means of intra-peritoneal injection. These smolts were the progeny of 40 sires and 118 dams from a Chilean breeding population. Mortalities were recorded daily and the experiment ended at day 40 post-inoculation. Fish were genotyped using a 50K Affymetrix® Axiom® myDesignTM Single Nucleotide Polymorphism (SNP) Genotyping Array. A Genome Wide Association Analysis was performed on data from the challenged fish. Linear regression and logistic regression models were tested.ResultsGenome Wide Association Analysis indicated that resistance to P. salmonis is a moderately polygenic trait. There were five SNPs in chromosomes Ssa01 and Ssa17 significantly associated with the traits analysed. The proportion of the phenotypic variance explained by each marker is small, ranging from 0.007 to 0.045. Candidate genes including interleukin receptors and fucosyltransferase have been found to be physically linked with these genetic markers and may play an important role in the differential immune response against this pathogen.ConclusionsDue to the small amount of variance explained by each significant marker we conclude that genetic resistance to this pathogen can be more efficiently improved with the implementation of genetic evaluations incorporating genotype information from a dense SNP array.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2038-7) contains supplementary material, which is available to authorized users.

Highlights

Pisciricketssia salmonis is the causal agent of Salmon Rickettsial Syndrome (SRS), which affects salmon species and causes severe economic losses
Previous studies have estimated low to moderate heritabilities, ranging between 0.11 and 0.41 for resistance to P. salmonis [15, 16] in the same commercial population of Atlantic salmon used in the present study; indicating a potential for selective breeding for P. salmonis resistance in this population
Taking the relatively small proportion of the genetic variance explained by the significant markers into account, the results presented in this study suggest that a Genomic Selection (GS) approach will be the most appropriate way of incorporating molecular information to assist artificial selection for P. salmonis resistance in Atlantic salmon

Summary

Introduction

Pisciricketssia salmonis is the causal agent of Salmon Rickettsial Syndrome (SRS), which affects salmon species and causes severe economic losses. Selective breeding for disease resistance represents one approach for controlling SRS in farmed Atlantic salmon. Knowledge concerning the architecture of the resistance trait is needed before deciding on the most appropriate approach to enhance artificial selection for P. salmonis resistance in Atlantic salmon. The control of infectious diseases is a prime concern in salmon farming due to severe economic losses, reduced animal welfare and challenges to the sustainability of the industry [1, 2]. Previous studies have estimated low to moderate heritabilities (proportion of the phenotypic variance that is accounted for by the additive genetic variance), ranging between 0.11 and 0.41 for resistance to P. salmonis [15, 16] in the same commercial population of Atlantic salmon used in the present study; indicating a potential for selective breeding for P. salmonis resistance in this population

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