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Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms - PubMed

  • ️Tue Jan 01 2019

Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms

Bo-Hye Nam et al. Sci Rep. 2019.

Erratum in

Abstract

Red sea bream, a popular fish resource in Korea and Japan, is being bred in fish farms of the two countries. It is hypothesized that the genomes of red sea bream are influenced by decades of artificial selection. This study investigates the impact of artificial selection on genomes of red sea bream. Whole genome sequencing was conducted for 40 samples of red sea bream either from Ehime, Nagasaki and Tongyeong fish farms or from the wild. Population stratification based on whole genome data was investigated and the genomic regions of fish farm populations under selection were identified using XP-EHH and relative nucleotide diversity. Gene ontology analysis revealed that different functions were enriched in different fish farms. In conclusion, this study highlights the difference between independently cultured red sea bream populations by showing that influence of artificial selection acted upon completely different genes related to different functions including metabolic and developmental processes.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1

Red sea bream of Korea and Japan. The representative samples of red sea bream collected from Tongyeong, Ehime and Nagasaki fish farms and wild-type samples collected from two distinct locations of Jeju island, Korea are presented. (The map of Korea and Japan shown in Fig. 1 was drawn using R package “maps”),.

Figure 2
Figure 2

Population stratification analysis of red sea bream. The population stratification was visualized using (a) principal component analysis (PCA) based on genome-wide SNP data, (b) genome-wide nucleotide diversity distribution, (c) admixture analysis and (d) maximum likelihood tree.

Figure 3
Figure 3

Selective sweep region of fish farm populations. The genome-wide distribution and the number of significant bins of (a) XP-EHH and (b) relative nucleotide diversity are presented.

Figure 4
Figure 4

Functional annotation of candidate selective sweep genes. The summary of gene ontology (GO) analysis performed for (A) biological process, (B) cellular component and (C) molecular function in three fish farm populations are shown. Individual circle shows the significance of GO term and the size of the circle represents the number of genes associated with the GO term. The red dotted line represents p-value cut-off of 0.05.

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