The genomic structure of isolation across breed, country and strain for important South African and Australian sheep populations

Cornelius Nel; Phillip Gurman; Andrew Swan; Julius van der Werf; Margaretha Snyman; Kennedy Dzama; Klint Gore; Anna Scholtz; Schalk Cloete

doi:10.1186/s12864-021-08020-3

The genomic structure of isolation across breed, country and strain for important South African and Australian sheep populations

BMC Genomics. 2022 Jan 4;23(1):23. doi: 10.1186/s12864-021-08020-3.

Authors

Cornelius Nel^{1

2}, Phillip Gurman³, Andrew Swan³, Julius van der Werf⁴, Margaretha Snyman⁵, Kennedy Dzama⁶, Klint Gore³, Anna Scholtz⁷, Schalk Cloete^{6

7}

Affiliations

¹ Department of Animal Sciences, Stellenbosch University, 7602, Stellenbosch, South Africa. NeliusN@elsenburg.com.
² Animal Sciences, Western Cape Department of Agriculture, 7607, Elsenburg, South Africa. NeliusN@elsenburg.com.
³ Animal Genetics & Breeding Unit, University of New England, NSW, 2351, Armidale, Australia.
⁴ School of Environmental and Rural Science, University of New England, 2351, Armidale, NSW, Australia.
⁵ Department of Agriculture, Land Reform and Rural Development, Grootfontein Agricultural Development Institute, 5900, Middelburg, South Africa.
⁶ Department of Animal Sciences, Stellenbosch University, 7602, Stellenbosch, South Africa.
⁷ Animal Sciences, Western Cape Department of Agriculture, 7607, Elsenburg, South Africa.

Abstract

Background: 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. 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.

Results: Mean 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 (F_ST: 0.04-0.12) were sometimes more distant than across some breeds (F_ST: 0.05-0.24), but the divergence of common breeds from their across-country equivalents was weak (F_ST: 0.01-0.04). According to mean relatedness, F_ST, 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 (N_e) showed genetic diversity to be high for the majority of breeds (N_e: 128-418) but also for bloodlines (N_e: 137-369).

Conclusions: This 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.

Keywords: Across-country; Genetic variation; Merino; Population genetics; SNP markers; Sheep.

MeSH terms

Animals
Australia
Breeding
Genetics, Population*
Genomics*
Genotype
Linkage Disequilibrium
Sheep / genetics
Sheep, Domestic / genetics*
South Africa