Skip to main content
Research article - Peer-reviewed, 2021

Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss)

Cadiz, Maria I.; Lopez, Maria E.; Diaz-Dominguez, Diego; Caceres, Giovanna; Marin-Nahuelpi, Rodrigo; Gomez-Uchida, Daniel; Canales-Aguirre, Cristian B.; Orozco-terWengel, Pablo; Yanez, Jose M.


Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest.


Selection signatures; Fish domestication; Salmonids; Genetic diversity

Published in

2021, volume: 113, number: 5, pages: 3395-3404

Authors' information

Cadiz, Maria I.
Universidad de Chile
López, Maria-Eugenia (López, María-Eugenia)
Swedish University of Agricultural Sciences, Department of Aquatic Resources
Diaz-Dominguez, Diego
Universidad de Chile
Caceres, Giovanna
Universidad de Chile
Marin-Nahuelpi, Rodrigo
Universidad de Chile
Gomez-Uchida, Daniel
Universidad de Concepcion
Canales-Aguirre, Cristian B.
Universidad de Los Lagos
Orozco-terWengel, Pablo
Cardiff University
Yanez, Jose M.
Universidad de Chile

UKÄ Subject classification

Fish and Aquacultural Science

Publication Identifiers


URI (permanent link to this page)