|Weber, Gregory - Greg|
|HERNANDEZ, ALVARO - University Of Illinois|
Submitted to: Marine Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/8/2015
Publication Date: 2/5/2015
Citation: Liu, S., Vallejo, R.L., Gao, G., Palti, Y., Weber, G.M., Hernandez, A., Rexroad III, C.E. 2015. Identification of single nucleotide polymorphism markers associated with cortisol response to crowding in Rainbow Trout. Marine Biotechnology. DOI: 10.1007\s10126-015-9621-4.
Interpretive Summary: Understanding stress responses is essential for improving animal welfare and increasing agriculture production efficiency. Fish in aquaculture production environments experience various stressful conditions such as handling, crowding, sub-optimal water quality and temperature fluctuations. Chronic stress has negative impacts on fish performance including decreased growth rates, compromised feed conversion efficiencies, increased disease incidence and mortality. We employed next-generation DNA sequencing technology to enhance previous analysis of genetic variation of stress in rainbow trout. As a result, genetic mapping, gene expression, and genome sequence information were combined to identify genes that may affect stress response in this species.
Technical 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. Our main objectives were to identify SNP markers associated with cortisol response to crowding in rainbow trout using both GWAS and QTL mapping methods; and to employ rapidly expanding genomic resources for rainbow trout towards 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 4,874 informative SNPs. GWAS identified 26 SNPs associated with cortisol response to crowding whereas QTL mapping revealed two significant QTL on chromosomes Omy8 and Omy12. Positional candidate genes were identified using marker sequences to search the draft genome assembly of rainbow trout. Three previously reported liver differentially expressed transcripts (DETs) in response to handling and confinement stress were mapped to a putative serine/threonine protein kinase gene in the QTL interval on Omy12. This gene is homologous to a differentially expressed gene in zebrafish embryos exposed to diclofenac, a non-steroidal 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.