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. 2020 Mar;51(2):284-291.
doi: 10.1111/age.12905. Epub 2020 Jan 23.

Genetic structure and admixture in sheep from terminal breeds in the United States

K M Davenport  1 , C Hiemke  2 , S D McKay  3 , J W Thorne  1   4 , R M Lewis  5 , T Taylor  6 , B M Murdoch  1
Affiliations

Genetic structure and admixture in sheep from terminal breeds in the United States

K M Davenport et al. Anim Genet. 2020 Mar.

Abstract

Selection for performance in diverse production settings has resulted in variation across sheep breeds worldwide. Although sheep are an important species to the United States, the current genetic relationship among many terminal sire breeds is not well characterized. Suffolk, Hampshire, Shropshire and Oxford (terminal) and Rambouillet (dual purpose) sheep (n = 248) sampled from different flocks were genotyped using the Applied Biosystems Axiom Ovine Genotyping Array (50K), and additional Shropshire sheep (n = 26) using the Illumina Ovine SNP50 BeadChip. Relationships were investigated by calculating observed heterozygosity, inbreeding coefficients, eigenvalues, pairwise Wright's FST estimates and an identity by state matrix. The mean observed heterozygosity for each breed ranged from 0.30 to 0.35 and was consistent with data reported in other US and Australian sheep. Suffolk from two different regions of the United States (Midwest and West) clustered separately in eigenvalue plots and the rectangular cladogram. Further, divergence was detected between Suffolk from different regions with Wright's FST estimate. Shropshire animals showed the greatest divergence from other terminal breeds in this study. Admixture between breeds was examined using admixture, and based on cross-validation estimates, the best fit number of populations (clusters) was K = 6. The greatest admixture was observed within Hampshire, Suffolk, and Shropshire breeds. When plotting eigenvalues, US terminal breeds clustered separately in comparison with sheep from other locations of the world. Understanding the genetic relationships between terminal sire breeds in sheep will inform us about the potential applicability of markers derived in one breed to other breeds based on relatedness.

Keywords: genetic admixture; genetic relationships; sheep; terminal sheep breeds.

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Figures

Figure 1
Figure 1
Plot of calculated eigenvalues for breeds of US sheep. (a) Eigenvalues plotted for US terminal breeds of sheep. (b) Eigenvalues plotted for US terminal breeds and Rambouillet sheep. Each point represents an individual animal and points are colored by reported breed.
Figure 2
Figure 2
Rectangular cladogram of individuals clustered based on identity by state and colored by reported breed.
Figure 3
Figure 3
admixture model clustering output with K = 6 populations. Each bar represents an individual animal for each terminal breed and Rambouillet, and the six colors represent each K population cluster.
Figure 4
Figure 4
Eigenvalue plots of US sheep in this study compared with other breeds across the world as part of the Sheep HapMap study. (a) Eigenvalue plot of US terminal breeds and Dorset and Suffolk HapMap breeds. (b) Eigenvalue plot of all US sheep in this study compared with HapMap terminal and wool sheep. (c) Eigenvalue plot of US sheep in this study compared with all breeds present in the Sheep HapMap study.
See this image and copyright information in PMC

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