Abstract

BackgroundSouth Africa and Australia shares multiple important sheep breeds. For some of these breeds, genomic breeding values are provided to breeders in Australia, but not yet in South Africa. Combining genomic resources could facilitate development for across country selection, but the influence of population structures could be important to the compatability of genomic data from varying origins. The genetic structure within and across breeds, countries and strains was evaluated in this study by population genomic parameters derived from SNP-marker data. Populations were first analysed by breed and country of origin and then by subpopulations of South African and Australian Merinos.ResultsMean estimated relatedness according to the genomic relationship matrix varied by breed (-0.11 to 0.16) and bloodline (-0.08 to 0.06) groups and depended on co-ancestry as well as recent genetic links. Measures of divergence across bloodlines (FST: 0.04–0.12) were sometimes more distant than across some breeds (FST: 0.05–0.24), but the divergence of common breeds from their across-country equivalents was weak (FST: 0.01–0.04). According to mean relatedness, FST, PCA and Admixture, the Australian Ultrafine line was better connected to the SA Cradock Fine Wool flock than with other AUS bloodlines. Levels of linkage disequilibrium (LD) between adjacent markers was generally low, but also varied across breeds (r2: 0.14–0.22) as well as bloodlines (r2: 0.15–0.19). Patterns of LD decay was also unique to breeds, but bloodlines differed only at the absolute level. Estimates of effective population size (Ne) showed genetic diversity to be high for the majority of breeds (Ne: 128–418) but also for bloodlines (Ne: 137–369).ConclusionsThis study reinforced the genetic complexity and diversity of important sheep breeds, especially the Merino breed. The results also showed that implications of isolation can be highly variable and extended beyond breed structures. However, knowledge of useful links across these population substructures allows for a fine-tuned approach in the combination of genomic resources. Isolation across country rarely proved restricting compared to other structures considered. Consequently, research into the accuracy of across-country genomic prediction is recommended.

Highlights

  • South Africa and Australia shares multiple important sheep breeds

  • From ADMIXTURE analysis, the distinct genetic structures of Merino, Border Leicester and Poll Dorset agreed with those three breeds occupying the most distant branches of PC1 and PC2

  • Following the advent of artificial insemination (AI), across bloodline links are considered to have become more common in AUS [18], but these results strongly suggested that the subpopulation, i.e., bloodline of origin, is an important determinant of the genetic composition of Merinos

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Summary

Introduction

South Africa and Australia shares multiple important sheep breeds. For some of these breeds, genomic breeding values are provided to breeders in Australia, but not yet in South Africa. The AUS and SA Merino share a distant relationship from the original Merino thought to have originated from Spain around the 1700s [3] and the AUS Merino was originally a composite of European, Asian and African strains [4]. Besides this ancestral relationship, a SA Merino resource flock has had intermittent genetic links to the AUS Merino by using sires originating from AUS [5], but this is the only known genetic exchange in recent years. Additional breeds in common include the South African Meat Merino (SAMM) pure breed and composites like the Dohne Merino and the Dorper meat breeds [5] which originated in South Africa and were exported to Australia

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