Single-step genome-wide association study for resistance toPiscirickettsia salmonisin rainbow trout (Oncorhynchus mykiss)

Abstract

44One of the main pathogens affecting rainbow trout (Oncorhynchus mykiss) farming is the 45 facultative intracellular bacteria Piscirickettsia salmonis. Current treatments, such as 46 antibiotics and vaccines, have not had the expected effectiveness in field conditions. Genetic 47 improvement by means of selection for resistance is proposed as a viable alternative for 48 control. Genomic information can be used to identify the genomic regions associated with 49 resistance and enhance the genetic evaluation methods to speed up the genetic improvement 50 for the trait. The objectives of this study were to i) identify the genomic regions associated 51 with resistance to P. salmonis; and ii) identify candidate genes associated with the trait. We 52 experimentally challenged 2,130 rainbow trout with P. salmonis and genotyped them with a 53 57 K SNP array. Resistance to P. salmonis was defined as time to death (TD) and as binary 54 survival (BS). Significant heritabilities were estimated for TD and BS (0.48 ± 0.04 and 0.34 55 ± 0.04, respectively). A total of 2,047 fish and 26,068 SNPs passed quality control for 56 samples and genotypes. Using a single-step genome wide association analysis (ssGWAS) we 57 identified four genomic regions explaining over 1% of the genetic variance for TD and three 58 for BS. Interestingly, the same genomic region located on Omy27 was found to explain the 59 highest proportion of genetic variance for both traits (2.4 and 1.5% for TD and BS, 60 respectively). The identified SNP in this region is located within an exon of a gene related 61 with actin cytoskeletal organization, a protein exploited by P. salmonis during infection. 62Other important candidate genes identified are related with innate immune response and 63 oxidative stress. The moderate heritability values estimated in the present study show it is 64 possible to improve resistance to P. salmonis through artificial selection in the current 65 rainbow trout population. Furthermore, our results suggest a polygenic genetic architecture 66 4 and provide novel insights into the candidate genes underpinning resistance to P. salmonis 67 in O. mykiss. 68 69 70 71 72 As in any intensive animal production system, infectious diseases are one of the main 73 threats affecting the success and sustainability of aquaculture (Yáñez et al. 2014a). In the 74 case of salmonid production, one of the major pathogens affecting productivity is the 75 facultative intracellular bacteria Pisciricketssia salmonis, etiological agent of salmonid 76 rickettsial syndrome (SRS). This bacterium was first identified in 1989 in Chile, in a farmed 77 coho salmon (Oncorhynchus kisutch) population (Cvitanich et al. 1991). Since then, 78 mortalities resulting from SRS have been also identified in Atlantic salmon (Salmo salar) 79 and rainbow trout (Oncorhynchus mykiss) in several countries, such as Scotland, Ireland, 80 Norway and Chile (Fryer and Hedrick 2003). In Chile, SRS was responsible for 20.7, 67.9 81 and 92.6% of the mortalities associated with infectious disea...