Whole-Genome Scanning for Selection Signatures Reveals Candidate Genes Associated with Growth and Tail Length in Sheep

Abstract

Compared to Chinese indigenous sheep, Western sheep have rapid growth rate, larger physique, and higher meat yield. These excellent Western sheep were introduced into China for crossbreeding to expedite the enhancement of production performance and mutton quality in local breeds. Here, we investigated population genetic structure and genome-wide selection signatures among the Chinese indigenous sheep and the introduced sheep based on whole-genome resequencing data. The PCA, N-J tree and ADMIXTURE results showed significant genetic difference between Chinese indigenous sheep and introduced sheep. The nucleotide diversity (π) and linkage disequilibrium (LD) decay results indicated that the genomic diversity of introduced breeds were lower. Then, F_st & π ratio, XP-EHH, and de-correlated composite of multiple signals (DCMS) methods were used to detect the selection signals. The results showed that we identified important candidate genes related to growth rate and body size in the introduced breeds. Selected genes with stronger selection signatures are associated with growth rate (CRADD), embryonic development (BVES, LIN28B, and WNT11), body size (HMGA2, MSRB3, and PTCH1), muscle development and fat metabolism (MSTN, PDE3A, LGALS12, GGPS1, and SAR1B), wool color (ASIP), and hair development (KRT71, KRT74, and IRF2BP2). Thus, these genes have the potential to serve as candidate genes for enhancing the growth traits of Chinese indigenous sheep. We also identified tail-length trait-related candidate genes (HOXB13, LIN28A, PAX3, and VEGFA) in Chinese long-tailed breeds. Among these genes, HOXB13 is the main candidate gene for sheep tail length phenotype. LIN28A, PAX3, and VEGFA are related to embryonic development and angiogenesis, so these genes may be candidate genes for sheep tail type traits. This study will serve as a foundation for further genetic improvement of Chinese indigenous sheep and as a reference for studies related to growth and development of sheep.

Keywords: DCMS; body size; candidate genes; growth rate; sheep; tail length.

Figure 1

Population genetic structure of introduced breeds and Chinese native breeds: (a,b) principal component analysis (PCA) of all sheep individuals, and Chinese indigenous breeds, respectively. (c) neighbor-joining tree of 54 sheep. Introduced breeds are indicated in blue, and Chinese native breeds are indicated in red. (d) model-based clustering of sheep breeds using ADMIXTURE with K = 2 to K = 4.

Figure 2

The nucleotide diversity of 15 sheep breeds (a) and the whole-genome average LD between the introduced population and native population (b).

Figure 3

The results of selection signatures in the introduced sheep population. (a) The results of the combined analysis of F_st and π ratio. The selected regions for the introduced breeds are indicated by red dots. (b,c) Manhattan plots showing the selection regions in F_st and XP-EHH methods between introduced breeds and native breeds. (d) Venn diagram showing the overlapped genes from the F_st, π ratio, and XP-EHH analyses.

Figure 4

Manhattan plot showing the selected regions of the introduced breeds according to the DCMS method. The dotted line indicates the q-value = 0.05, and the data points above the dotted line are the selected regions.

Figure 5

The results of selection signatures in long-fat tail sheep population. (a) The results of the combined analysis of F_st and π ratio. The selected regions for long-tailed breeds are denoted by red dots. (b,c) Manhattan plot showing the selected regions based on F_st and XP-EHH methods between the long-fat-tailed breeds and short-fat-tailed breeds. (d) Venn diagram showing the overlapped genes from the F_st, π ratio, and XP-EHH analyses.

Figure 5

The results of selection signatures in long-fat tail sheep population. (a) The results of the combined analysis of F_st and π ratio. The selected regions for long-tailed breeds are denoted by red dots. (b,c) Manhattan plot showing the selected regions based on F_st and XP-EHH methods between the long-fat-tailed breeds and short-fat-tailed breeds. (d) Venn diagram showing the overlapped genes from the F_st, π ratio, and XP-EHH analyses.

Figure 6

Manhattan plot showing the selected regions of long-tailed breeds according to the DCMS method. The dotted line indicates the q-value = 0.05, and data points above the dotted line are the selected regions.