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. 2022 Oct 18:9:1034211.
doi: 10.3389/fvets.2022.1034211. eCollection 2022.

Whole genome re-sequencing reveals artificial and natural selection for milk traits in East Friesian sheep

Xiaolong Li  1 , Lvfeng Yuan  2 , Weimin Wang  3 , Deyin Zhang  3 , Yuan Zhao  3 , Jiangbo Chen  1 , Dan Xu  1 , Liming Zhao  1 , Fadi Li  3 , Xiaoxue Zhang  1
Affiliations

Whole genome re-sequencing reveals artificial and natural selection for milk traits in East Friesian sheep

Xiaolong Li et al. Front Vet Sci. .

Abstract

The East Friesian sheep is one of the important high-yielding dairy sheep breeds, but still little is known about their genetic and genomic variation during domestication. Therefore, we analyzed the genomic data of 46 sheep with the aim of identifying candidate genes that are closely related to milk production traits. Our genomic data consisted of 20 East Friesian sheep and 26 Asian Mouflon wild sheep. Finally, a total of 32590241 SNPs were identified, of which 0.61% (198277) SNPs were located in exonic regions. After further screening, 122 shared genomic regions in the top 1% of F ST and top 1% of Nucleotide diversity ratio were obtained. After genome annotation, these 122 candidate genomic regions were found to contain a total of 184 candidate genes. Finally, the results of KEGG enrichment analysis showed four significantly enriched pathways (P < 0.05): beta-Alanine metabolism (SMOX, HIBCH), Pathways in cancer (GLI2, AR, TXNRD3, TRAF3, FGF16), Non-homologous end-joining (MRE11), Epstein-Barr virus infection (TRAF3, PSMD13, SIN3A). Finally, we identified four important KEGG enrichment pathways and 10 candidate genes that are closely related to milk production in East Friesian sheep. These results provide valuable candidate genes for the study of milk production traits in East Friesian sheep and lay an important foundation for the study of milk production traits.

Keywords: FST; PI; sheep; sheep milk; whole-genome resequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Genome-wide distribution of SNP density and PI in 150 kb size window. (A) Genome-wide distribution of SNP density within 150 kb window. (B) Genome-wide distribution of PI for WS population in 150 kb size window. (C) Genome-wide distribution of PI for EFS population in 150 kb size window.
Figure 2
Figure 2
Phylogenetic and nucleotide diversity analysis. (A) PCA plots of EFS with the first two components of WS. (B) Phylogenetic tree of EFS and WS. (C) Box plot of nucleotide diversity of EFS and WS. (D,E) Nucleotide diversity density plot of EFS and WS.
Figure 3
Figure 3
Genome-wide distribution of FST and θπ ratio. (A) Genome-wide distribution of FST. (B) Genome-wide density distribution of FST. (C) Genome-wide distribution of PI [log2(PI(WS/EFS))]. (D) Genome-wide density distribution of PI. The horizontal red dashed line in the figure shows the window for the top 1% of FST and PI.
Figure 4
Figure 4
Shared genomic region of FST and θπ ratio. (A) Window shared between FST and top 1% of PI. (B) Density distribution of PI in all Windows. (C) Density distribution of FST in all Windows. The red dashed line in the figure is the top 1% threshold line.
Figure 5
Figure 5
Candidate genes previously reported to be highly associated with domestication and its traits.
Figure 6
Figure 6
The top 20 KEGG enrichment pathways.
See this image and copyright information in PMC

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