Quantitative trait loci affecting response to crowding stress in an F2 generation of rainbow trout produced through phenotypic selection

Authors: Rexroad, Caird; Vallejo, Roger; Liu, Sixin; Palti, Yniv; Weber, Gregory - Greg

Submitted to: Marine Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/9/2013
Publication Date: 9/1/2013
Publication URL: http://handle.nal.usda.gov/10113/57342
Citation: Rexroad III, C.E., Vallejo, R.L., Liu, S., Palti, Y., Weber, G.M. 2013. Quantitative trait loci affecting response to crowding stress in an F2 generation of rainbow trout produced through phenotypic selection. Marine Biotechnology. 15(5): 613-627: DOI 10.1007/s10126-013-9512-5.

Interpretive Summary: 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. Identifying genetic variation in complex traits such as response to stress will enhance our ability to mitigate the negative effects of stressors on aquaculture production efficiency through selective breeding or management practices. We evaluated DNA markers on three generations of two families of rainbow trout selected based on their response to crowding to identify regions of ten chromosomes that are associated with this trait. In total, fifteen chromosomes have now been associated with stress response in NCCCWA broodstock.

Technical 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 x 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 NCCCWA 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.