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Quantitative Trait Loci Affecting Response to Crowding Stress in an F2 Generation of Rainbow Trout Produced Through Phenotypic Selection

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Abstract

Selective breeding programs for salmonids typically aim to improve traits associated with growth and disease resistance. It has been established that stressors common to production environments can adversely affect these and other traits which are important to producers and consumers. Previously, we employed phenotypic selection to create families that exhibit high or low plasma cortisol concentrations in response to crowding stress. Subsequent crosses of high × low phenotypes founded a multigenerational breeding scheme with the aim of dissecting the genetic basis for variation underlying stress response through the identification of quantitative trait loci (QTL). Multiple methods of QTL analyses differing in their assumptions of homozygosity of the causal alleles in the grandparental generation yielded similar results in the F1 generation, and the analysis of two stress response phenotype measurement indexes were highly correlated. In the current study, we conducted a genome scan with microsatellites to detect QTL in the F2 generation of two families created through phenotypic selection and having larger numbers of offspring than families screened in the previous generation. Seven suggestive and three significant QTL were detected, seven of which were not previously detected in the National Center for Cool and Cold Water Aquaculture germplasm, bringing the total number of chromosomes containing significant and suggestive stress response QTL to 4 and 15, respectively. One significant QTL which peaks at 7 cM on chromosome Omy12 spans 12 cM and explains 25 % of the phenotypic variance in family 2008052 particularly warrants further investigation. Five QTL with significant parent-of-origin effects were detected in family 2008052, including two QTL on Omy12. The 95 % confidence intervals for the remaining QTL we detected were broad, requiring validation and fine mapping with other genotyping approaches and mapping strategies. These results will facilitate identification of potential casual alleles that can be employed in strategies aimed at better understanding the genetic and physiological basis of stress responses to crowding in rainbow trout aquaculture production.

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Abbreviations

QTL:

Quantitative trait loci

NCCCWA:

National Center for Cool and Cold Water Aquaculture

BLUP:

Best linear unbiased prediction

EBV:

Estimated breeding value

MSD:

Mendelian segregation distortion

Omy1:

Oncorhynchus mykiss chromosome 1

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Acknowledgments

We would like to acknowledge the following individuals for providing excellent technical assistance including Roseanna Long, Kristy Shewbridge, and Brian Smith for genotyping; Lisa Radler, Jill Birkett, Mark Hostuttler and David Payne for phenotyping fish for stress response; and Josh Kretzer, Jim Everson, Kyle Jenkins, Jenea McGowan, Kevin Melody for animal care. We also thank Guangtu Gao for processing the genotype data files. 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 is an equal opportunity provider and employer.

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

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

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  1. Caird E. Rexroad
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  2. Roger L. Vallejo
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  3. Sixin Liu
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  4. Yniv Palti
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Correspondence to Caird E. Rexroad.

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Caird E. Rexroad and Roger L. Vallejo contributed equally to this work.

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Rexroad, C.E., Vallejo, R.L., Liu, S. et al. Quantitative Trait Loci Affecting Response to Crowding Stress in an F2 Generation of Rainbow Trout Produced Through Phenotypic Selection. Mar Biotechnol 15, 613–627 (2013). https://doi.org/10.1007/s10126-013-9512-5

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