Association Mapping Of Disease Resistance Traits In Rainbow Trout Using RAD Sequencing

As with other aquaculture species, rainbow trout are susceptible to disease when reared at high densities and outbreaks can lead to significant losses.  Commercial rainbow trout producers have therefore been pursuing strategies to prevent such losses such as adjusting feed formulations, vaccine development, and selective breeding.  In some commercial programs, rainbow trout have been selectively bred for resistance to cold water disease (CWD) and Infectious hematopoietic necrosis virus (IHNV).  This is accomplished by testing disease resistance in juvenile fish by either direct injection (CWD) or waterborne exposure (IHNV) with each pathogen and selecting only fish from the most resistant families as broodstock.  For this study we sampled juvenile fish from 40 families from two year classes that either survived or died during disease challenge to either CWD or IHNV.  Restriction-site associated DNA (RAD) sequencing using an Illumina HiSeq instrument produced 4,661 unique SNP loci after strict filtering.  Genotypes from each SNP for individual survivors and mortalities were then used to test for association between disease resistance and genotype at each locus using the program TASSEL.  After accounting for kinship and stratification of the samples, tests revealed 12 SNP markers that were highly associated with resistance to CWD and 19 markers associated with resistance to IHNV.  These markers are candidates for further investigation and are expected to be useful for marker assisted selection in future broodstock programs.