title: Association mapping of disease resistance traits in rainbow trout using restriction site associated DNA sequencing.
abstract: Recent advances in genotyping-by-sequencing have enabled genome-wide association studies in nonmodel species including those in aquaculture programs. As with other aquaculture species, rainbow trout and steelhead (Oncorhynchus mykiss) are susceptible to disease and outbreaks can lead to significant losses. Fish culturists have therefore been pursuing strategies to prevent losses to common pathogens such as Flavobacterium psychrophilum (the etiological agent for bacterial cold water disease [CWD]) and infectious hematopoietic necrosis virus (IHNV) by adjusting feed formulations, vaccine development, and selective breeding. However, discovery of genetic markers linked to disease resistance offers the potential to use marker-assisted selection to increase resistance and reduce outbreaks. For this study we sampled juvenile fish from 40 families from 2-yr classes that either survived or died after controlled exposure to either CWD or IHNV. Restriction site-associated DNA sequencing produced 4661 polymorphic single-nucleotide polymorphism loci after strict filtering. Genotypes from individual survivors and mortalities were then used to test for association between disease resistance and genotype at each locus using the program TASSEL. After we accounted for kinship and stratification of the samples, tests revealed 12 single-nucleotide polymorphism 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 selection for various aquaculture programs.
authors.affiliation: Columbia River Inter-Tribal Fish Commission, Hagerman, Idaho 83332 camn@critfc.org.
authors.forename: Nathan R
authors.initials: NR
authors.lastname: Campbell
authors.affiliation: Clear Springs Foods Inc., Research Division, Buhl, Idaho 83316.
authors.forename: Scott E
authors.initials: SE
authors.lastname: LaPatra
authors.affiliation: USDA-ARS, Hagerman, Idaho 83332.
authors.forename: Ken
authors.initials: K
authors.lastname: Overturf
authors.affiliation: GeneTec Consulting, Payette, Idaho 83661.
authors.forename: Richard
authors.initials: R
authors.lastname: Towner
authors.affiliation: Columbia River Inter-Tribal Fish Commission, Hagerman, Idaho 83332.
authors.forename: Shawn R
authors.initials: SR
authors.lastname: Narum
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D004262:DNA Restriction Enzymes / Q000378:metabolism; D060467:Disease Resistance / Q000235:genetics*; D005393:Fish Diseases / Q000382:microbiology; D045826:Flavobacteriaceae Infections / Q000382:microbiology / Q000662:veterinary; D005417:Flavobacterium / Q000502:physiology; D056426:Genetic Loci; D005819:Genetic Markers / Q000235:genetics; D055106:Genome-Wide Association Study; D005838:Genotype; D029142:Infectious hematopoietic necrosis virus / Q000502:physiology; D015810:Linkage Disequilibrium; D017686:Oncorhynchus mykiss / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D018353:Rhabdoviridae Infections / Q000662:veterinary / Q000821:virology; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers; D004262:DNA Restriction Enzymes
keywords: Flavobacterium psychrophilum; cold water disease; genetics of immunity; genotyping by sequencing; infectious hematopoietic necrosis virus