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. 2023 Nov 13;12(11):1427.
doi: 10.3390/biology12111427.

Genetic Diversity and Signatures of Selection in the Roughskin Sculpin (Trachidermus fasciatus) Revealed by Whole Genome Sequencing

Lize San  1   2 , Zhongwei He  1   2 , Yufeng Liu  1   2 , Yitong Zhang  1   2 , Wei Cao  1   2 , Jiangong Ren  1   2 , Tian Han  1   2   3 , Bingbu Li  1   2 , Guixing Wang  1   2 , Yufen Wang  1   2 , Jilun Hou  1   2
Affiliations

Genetic Diversity and Signatures of Selection in the Roughskin Sculpin (Trachidermus fasciatus) Revealed by Whole Genome Sequencing

Lize San et al. Biology (Basel). .

Abstract

The roughskin sculpin (Trachidermus fasciatus) is an endangered fish species in China. In recent years, artificial breeding technology has made significant progress, and the population of roughskin sculpin has recovered in the natural environment through enhancement programs and the release of juveniles. However, the effects of released roughskin sculpin on the genetic structure and diversity of wild populations remain unclear. Studies on genetic diversity analysis based on different types and numbers of molecular markers have yielded inconsistent results. In this study, we obtained 2,610,157 high-quality SNPs and 494,698 InDels through whole-genome resequencing of two farmed populations and one wild population. Both farmed populations showed consistent levels of genomic polymorphism and a slight increase in linkage compared with wild populations. The population structure of the two farmed populations was distinct from that of the wild population, but the degree of genetic differentiation was low (overall average Fst = 0.015). Selective sweep analysis showed that 523,529 genes were selected in the two farmed populations, and KEGG enrichment analysis showed that the selected genes were related to amino acid metabolism, which might be caused by artificial feeding. The findings of this study provide valuable additions to the existing genomic resources to help conserve roughskin sculpin populations.

Keywords: Trachidermus fasciatus; genetic diversity; population structure; selective sweeps.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Map of sampling sites for roughskin sculpin.
Figure 2
Figure 2
Box plot of morphometric statistics for growth indices of different populations of roughskin sculpin. The number of samples measured in each population was 64. (A) Weight; (B) body height; (C) body length; (D) total length.
Figure 3
Figure 3
Manhattan plots of Fst values. The X axis represents different chromosome names, and the Y axis represents the Fst values within the corresponding chromosome window. The different colors of point represent different chromosomes.
Figure 4
Figure 4
Genome-wide linkage disequilibrium (LD) decay plots. The x axis represents the distance of LD, and the y axis represents the linkage disequilibrium correlation coefficient.
Figure 5
Figure 5
Sample structure indicated by principal component analysis (PCA) with the first three principal components.
Figure 6
Figure 6
Admixture structure plot. Each column represents an individual, where the length of the different colored segments indicates the proportion of the individual that belongs to different groups.
Figure 7
Figure 7
Identification of the domestication-selective sweeps and the KEGG enrichment analysis. (A) The θπ ratio and Fst values of QHD and SD (green points indicate selection; black points represent not selection.). Line represents the selection threshold of 0.05. (B) The KEGG enrichment analysis of selected genes of SD.
Figure 8
Figure 8
Identification of the domestication-selective sweeps and the KEGG enrichment analysis. (A) The θπ ratio and Fst values of QHD and TJ (green points indicate selection; black points represent not selection.). Line represents the selection threshold of 0.05. (B) The KEGG enrichment analysis of selected genes of TJ.
Figure 9
Figure 9
Identification of the domestication-selective sweeps and the KEGG enrichment analysis. (A) The θπ ratio and Fst values of SD and TJ (green points indicate selection; black points represent not selection.). Line represents the selection threshold of 0.05. (B) The KEGG enrichment analysis of selected genes of TJ.
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References

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