Genome-wide association analysis reveals loci associated with resistance against Piscirickettsia salmonis in two Atlantic salmon (Salmo salar L.) chromosomes.
BACKGROUND
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 purpose of the study was to dissect the genetic variation in the resistance to this pathogen in Atlantic salmon.


METHODS
2,601 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.


RESULTS
Genome 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.


CONCLUSIONS
Due 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.
Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av Santa Rosa 11735, Santiago, Chile. katharinacorrea@gmail.com.
Katharina
K
Correa
Aquainnovo, Talca 60, Puerto Montt, Chile. jean.lhorente@aquainnovo.com.
Jean P
JP
Lhorente
Facultad de Ciencias Agronómicas, Universidad de Chile, Av Santa Rosa 11315, Santiago, Chile. me.lopez.dinamarca@gmail.com.
María E
ME
López
Facultad de Ciencias Agronómicas, Universidad de Chile, Av Santa Rosa 11315, Santiago, Chile. lianebassini@gmail.com.
Liane
L
Bassini
Genus plc, 100 Bluegrass Commons Blvd. Suite 2200, Hendersonville, TN, 37075, USA. Sudhir.Naswa@genusplc.com.
Sudhir
S
Naswa
Genus plc, 100 Bluegrass Commons Blvd. Suite 2200, Hendersonville, TN, 37075, USA. Joseph.Deeb@genusplc.com.
Nader
N
Deeb
Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation, Universidad de Chile, Beauchef 851, Santiago, Chile. digenova@gmail.com.
Alex
A
Di Genova
Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation, Universidad de Chile, Beauchef 851, Santiago, Chile. amaass@dim.uchile.cl.
Alejandro
A
Maass
Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada. wdaviso@sfu.ca.
William S
WS
Davidson
Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av Santa Rosa 11735, Santiago, Chile. jmayanez@uchile.cl.
José M
JM
Yáñez
D000483:Alleles; D000818:Animals; D002875:Chromosomes; D060467:Disease Resistance / Q000235:genetics*; D005393:Fish Diseases / Q000235:genetics* / Q000382:microbiology* / Q000401:mortality; D005787:Gene Frequency; D056726:Genetic Association Studies; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium; D010641:Phenotype; D053522:Piscirickettsia; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D020317:Salmo salar / Q000235:genetics* / Q000382:microbiology*