Whole-genome resequencing reveals domestication and signatures of selection in Ujimqin, Sunit, and Wu Ranke Mongolian sheep breeds

Abstract

Objective: The current study aimed to perform whole-genome resequencing of Chinese indigenous Mongolian sheep breeds including Ujimqin, Sunit, and Wu Ranke sheep breeds (UJMQ, SNT, WRK) and deeply analyze genetic variation, population structure, domestication, and selection for domestication traits among these Mongolian sheep breeds.

Methods: Blood samples were collected from a total of 60 individuals comprising 20 WRK, 20 UJMQ, and 20 SNT. For genome sequencing, about 1.5 μg of genomic DNA was used for library construction with an insert size of about 350 bp. Pair-end sequencing were performed on Illumina NovaSeq platform, with the read length of 150 bp at each end. We then investigated the domestication and signatures of selection in these sheep breeds.

Results: According to the population and demographic analyses, WRK and SNT populations were very similar, which were different from UJMQ populations. Genome wide association study identified 468 and 779 significant loci from SNT vs UJMQ, and UJMQ vs WRK, respectively. However, only 3 loci were identified from SNT vs WRK. Genomic comparison and selective sweep analysis among these sheep breeds suggested that genes associated with regulation of secretion, metabolic pathways including estrogen metabolism and amino acid metabolism, and neuron development have undergone strong selection during domestication.

Conclusion: Our findings will facilitate the understanding of Chinese indigenous Mongolian sheep breeds domestication and selection for complex traits and provide a valuable genomic resource for future studies of sheep and other domestic animal breeding.

Keywords: Domestication; Metabolism; Selection; Sheep; Whole-genome Resequencing.

Figure 1

Experimental design and genetic variation. (A) Geographic distribution of three sheep breeds in this study. (B) The SNPs among three sheep breeds. (C) The homozygosity, and heterozygosity numbers. (D) The INDELs among WRK, SNT, and UJMQ. SNP, single nucleotide polymorphism; UJMQ, Ujimqin sheep; SNT, Sunit sheep; WRK, Wu Ranke sheep.

Figure 2

GWAS among three sheep breeds. (A) Manhattan plot of analysis results. (B) The number of SNPs between UJMQ and WRK. (C) The number of SNPs between SNT and UJMQ. GWAS, genome-wide association study; SNP, single nucleotide polymorphism; UJMQ, Ujimqin sheep; SNT, Sunit sheep; WRK, Wu Ranke sheep.

Figure 3

Population genetic structure and demographic history of three sheep populations. (A) Neighbor-joining phylogenetic tree of three sheep populations. (B) PCA plot of sheep populations. (C) Population genetic structure of 60 sheep, where number of ancestral clusters were set from K = 2 to 5. (D) Demographic history of sheep populations. PCA, principal component analysis.

Figure 4

Genomic regions with strong selective sweep signals between SNT and UJMQ. (A) Distribution of –Log₂(θ_π ratios) and Fst values calculated with a sliding window approach (100 kb windows with 10 kb increments). (B) Genome-wide distribution of global Fst. (C) –Log₂(θ_π ratios) and Fst values around the RPH3AL locus. Tajima’s D values around the RPH3AL locus. The red line and blue line indicate Fst and θ_π ratios, respectively. (D) –Log₂(θ_π ratios) and Fst values around the CPS1 locus. Tajima’s D values around the CPS1 locus. The green line and purple line indicate UJMQ and WRK, respectively. UJMQ, Ujimqin sheep; SNT, Sunit sheep; WRK, Wu Ranke sheep.

Figure 5

Genomic regions with strong selective sweep signals between UJMQ and WRK. (A) Distribution of –Log₂(θ_π ratios) and Fst values calculated with a sliding window approach (100 kb windows with 10 kb increments). (B) Genome-wide distribution of global Fst. (C) –Log₂(θ_π ratios) and Fst values around the FANCC locus. Tajima’s D values around the FANCC locus. The red line and blue line indicate Fst and θ_π ratios, respectively. (D) –Log₂(θ_π ratios) and Fst values around the STK10 locus. Tajima’s D values around the STK10 locus. The green line and purple line indicate UJMQ and WRK, respectively. UJMQ, Ujimqin sheep; WRK, Wu Ranke sheep.