Genome-wide genetic diversity and differentially selected regions among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep

Abstract

Sheep are among the major economically important livestock species worldwide because the animals produce milk, wool, skin, and meat. In the present study, the Illumina OvineSNP50 BeadChip was used to investigate genetic diversity and genome selection among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds from the United States. After quality-control filtering of SNPs (single nucleotide polymorphisms), we used 48,026 SNPs, including 46,850 SNPs on autosomes that were in Hardy-Weinberg equilibrium and 1,176 SNPs on chromosome × for analysis. Phylogenetic analysis based on all 46,850 SNPs clearly separated Suffolk from Rambouillet, Columbia, Polypay, and Targhee, which was not surprising as Rambouillet contributed to the synthesis of the later three breeds. Based on pair-wise estimates of F(ST), significant genetic differentiation appeared between Suffolk and Rambouillet (F(ST) = 0.1621), while Rambouillet and Targhee had the closest relationship (F(ST) = 0.0681). A scan of the genome revealed 45 and 41 differentially selected regions (DSRs) between Suffolk and Rambouillet and among Rambouillet-related breed populations, respectively. Our data indicated that regions 13 and 24 between Suffolk and Rambouillet might be good candidates for evaluating breed differences. Furthermore, ovine genome v3.1 assembly was used as reference to link functionally known homologous genes to economically important traits covered by these differentially selected regions. In brief, our present study provides a comprehensive genome-wide view on within- and between-breed genetic differentiation, biodiversity, and evolution among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds. These results may provide new guidance for the synthesis of new breeds with different breeding objectives.

Figure 1. Neighbor-Joining tree relating the 94 individuals.

The tree was constructed using allele sharing distances averaged over 46,850 SNPs. Different colors in labels represent the origin of breed individuals. S, R, C, P, and T represent Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds, respectively. The meanings of S, R, C, P, and T are same in the following figures.

Figure 2. Multidimensional scaling plots for the genetic differentiations between Suffolk and Rambouillet (left) and among four Rambouillet-related breeds (right).

F _ST represent the pair-wise F _ST between any two sheep breeds.

Figure 3. Genome-wide distribution of F _ST between Suffolk and Rambouillet.

Based on OvineSNP50 BeadChip position, smoothed F _ST show that strong selection signals are observed in regions 13 and 24. S-R represents Suffolk-Rambouillet, while R-C-P-T means Rambouillet-Columbia-Polypay-Targhee.

Figure 4. Genome-wide distribution of F _ST among Rambouillet, Columbia, Polypay and Targhee.

R-C-P-T means Rambouillet-Columbia-Polypay-Targhee.