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

Abstract

Summary 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.

Clustering patterns mirror the geographical distribution and genetic history of Lemnos and Lesvos sheep populations

“…Both sheep populations studied herein maintained sufficient genetic variation as inferred by H O with values in the range of 0.36 to 0.39. These estimates are comparable or higher to other southern and western European (0.22-0.38) [16] sheep breeds, are higher than the Oxford sheep breed (0.35) in the United States [17] and comparable (Lemnos) or higher (Lesvos) than other Greek breeds such as Chios, Kymi and Lesvos [5].…”

Placental Characteristics Classification of Various Native Turkish Sheep Breeds

“…Overall similarity was found to be 98.8% on the Mahalanobis distance of the Barbados Black Belly Cross, Garut Local, Garut Composite, Sumatra Composite, and St. Croix Cross sheep breeds based on body measurements [ 20 ]. Classifying of 16 terminal sheep breeds of USA was separated into six clusters according to SNP, and overall similarity was found to be 99% [ 28 ]. The close clustering of East African sheep populations and distinct separation from their northern counterparts was well demonstrated by phylogenetic, principal component, and cluster analyses.…”

“…DNA markers were used to describe the goat genetic distance and diversity [22,23], and the sheep breeds' [24,25] mitochondrial DNA sequence was reported to calculate the genetic distance in sheep [26], sheep breeds were also classified according to wool profiles [27]. Hierarchical clustering was also successfully used to classify 16 terminal breeds such as Hampshire, Suffolk, Dorset and Rambouillet by SNP data [28].…”

Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty‐first century

“… 2013 ; Davenport et al . 2020 ). Some example breeds and their classifications are Lincoln, Leicester Longwool, Cotswold and Romney as longwool; Hampshire and Suffolk as meat; St Croix and Barbados Blackbelly as hair; and Rambouillet, Targhee and Columbia as fine wool.…”