Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information

Abstract

Animal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection, known as selection signatures or selective sweeps, have been traced in the genomes of many animal livestock species by exploiting variation in linkage disequilibrium patterns and/or reduction of genetic diversity. Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subjected to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes such anapc2, alad, chp2 and myn, which have been previously associated with body weight in Atlantic salmon, or sec24d and robo1, which have been associated with resistance to Piscirickettsia salmonis in coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon.

Figure 1

Decay of average linkage disequilibrium (r²) over distance across the two farmed populations. Different color lines represent populations: Pop-A = green, Pop-B = magenta.

Figure 2

Principal components analysis (PCA) of genetic differentiation among individuals. Three first components are shown. Each point represents one individual, and different colors represent populations: Pop-A = green, Pop-B = magenta.

Figure 3

Individual assignment probabilities generated with ADMIXTURE (K = 10). Each color represents a cluster, and the ratio of vertical lines is proportional to assignment probability of an individual to each cluster.

Figure 4

Circos plot of the global distribution of selection signatures across the genome in Pop-A. The circles from inside to outside illustrate: (A) -log₁₀(p-value) of iHS (Blue); (B) −log₁₀(p value) of XP-EHH (Purple) and (C) CLR values (Green). Values for each test surpassing the threshold (iHS and XP-EHH ≥ 3, and CLR ≥ 4.81) are highlighted in red.

Figure 5

Circos plot of the global distribution of selection signatures across the genome in Pop-B. The circles from inside to outside illustrate: (A) −log₁₀(p value) of iHS (Blue); (B) −log₁₀(p value) of XP-EHH (Purple) and (C) CLR values (Green). Values for each test surpassing the threshold (iHS and XP-EHH ≥ 3, and CLR ≥ 4.64) are highlighted in red.

Figure 6

Functional annotation of candidate selective sweeps genes. Gene ontology (GO) analysis performed for Biological process. Color intensity of circle shows the significance of GO term and the size of the circle represents the number of genes associated with the GO term.

Figure 7

Genomic distribution of selection signatures detected by iHS, XP-EHH, CLR and per populations on all chromosomes.