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Identification of Single-Nucleotide Polymorphism Markers Associated with Cortisol Response to Crowding in Rainbow Trout

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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.

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Acknowledgments

We would like to thank Roseanna Long and Kristy Shewbridge for making the RAD libraries. The mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture (USDA). USDA is an equal opportunity provider and employer.

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Authors and Affiliations

  1. USDA/ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Rd, Kearneysville, WV, 25430, USA

    Sixin Liu, Roger L. Vallejo, Guangtu Gao, Yniv Palti, Gregory M. Weber & Caird E. Rexroad III

  2. Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA

    Alvaro Hernandez

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  1. Sixin Liu
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  2. Roger L. Vallejo
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  3. Guangtu Gao
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  4. Yniv Palti
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  5. Gregory M. Weber
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  6. Alvaro Hernandez
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  7. Caird E. Rexroad III
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Corresponding author

Correspondence to Sixin Liu.

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Additional file 1

Minimal tilling path of BAC physical contigs based on DNA fingerprinting. The BACs included in each DNA fingerprinting contigs are named using the nomenclature of Dr. Michael Miller (http://www.animalgenome.org). (TXT 547 kb)

Additional file 2

Summary and detailed information of genetic maps of mapping family 2008052. Sheet 1, summary of 29 genetic maps; sheet 2, SNP sequences and mapping results onto the recently published draft sequences of rainbow trout; sheet 3, microsatellite and SNP markers assigned to each chromosome of rainbow trout; and genetic maps of 29 chromosomes are presented in one chromosome per sheet. (XLSX 520 kb)

Additional file 3

Annotation of putative genes in the QTL region on chromosome Omy8 for cortisol response to crowding. (XLSX 9 kb)

Additional file 4

Rainbow trout proteins homologous to the human corticosteroid binding globulin. (XLSX 9 kb)

Additional file 5

Annotation of putative genes in the QTL region on chromosome Omy12 for cortisol response to crowding. (XLSX 10 kb)

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Liu, S., Vallejo, R.L., Gao, G. et al. Identification of Single-Nucleotide Polymorphism Markers Associated with Cortisol Response to Crowding in Rainbow Trout. Mar Biotechnol 17, 328–337 (2015). https://doi.org/10.1007/s10126-015-9621-4

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