title: Identification of single-nucleotide polymorphism markers associated with cortisol response to crowding in rainbow trout.
abstract: Understanding stress responses is essential for improving animal welfare and increasing agriculture production efficiency. Previously, we reported microsatellite markers associated with quantitative trait loci (QTL) affecting plasma cortisol response to crowding in rainbow trout. In this study, our main objectives were to identify single-nucleotide polymorphism (SNP) markers associated with cortisol response to crowding in rainbow trout using both GWAS (genome-wide association studies) and QTL mapping methods and to employ rapidly expanding genomic resources for rainbow trout toward the identification of candidate genes affecting this trait. A three-generation F2 mapping family (2008052) was genotyped using RAD-seq (restriction-site-associated DNA sequencing) to identify 4874 informative SNPs. GWAS identified 26 SNPs associated with cortisol response to crowding whereas QTL mapping revealed two significant QTL on chromosomes Omy8 and Omy12, respectively. Positional candidate genes were identified using marker sequences to search the draft genome assembly of rainbow trout. One of the genes in the QTL interval on Omy12 is a putative serine/threonine protein kinase gene that was differentially expressed in the liver in response to handling and confinement stress in our previous study. A homologue of this gene was differentially expressed in zebrafish embryos exposed to diclofenac, a nonsteroidal anti-inflammatory drug (NSAID) and an environmental toxicant. NSAIDs have been shown to affect the cortisol response in rainbow trout; therefore, this gene is a good candidate based on its physical position and expression. However, the reference genome resources currently available for rainbow trout require continued improvement as demonstrated by the unmapped SNPs and the putative assembly errors detected in this study.
authors: USDA/ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Rd, Kearneysville, WV, 25430, USA, sixin.liu@ars.usda.gov.
authors: Sixin
authors: S
authors: Liu
authors: Roger L
authors: RL
authors: Vallejo
authors: Guangtu
authors: G
authors: Gao
authors: Yniv
authors: Y
authors: Palti
authors: Gregory M
authors: GM
authors: Weber
authors: Alvaro
authors: A
authors: Hernandez
authors: Caird E
authors: CE
authors: Rexroad
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D002875:Chromosomes / Q000737:chemistry*; D003441:Crowding; D029941:Fish Proteins / Q000235:genetics; D008040:Genetic Linkage; D005819:Genetic Markers; D055106:Genome-Wide Association Study; D005838:Genotype; D006854:Hydrocortisone / Q000096:biosynthesis / Q000235:genetics*; D018895:Microsatellite Repeats; D017686:Oncorhynchus mykiss / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017346:Protein Serine-Threonine Kinases / Q000235:genetics; D040641:Quantitative Trait Loci; D013312:Stress, Physiological / Q000235:genetics*
chemical_list: D029941:Fish Proteins; D005819:Genetic Markers; D017346:Protein Serine-Threonine Kinases; D006854:Hydrocortisone
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