The genomic architecture of South African mutton, pelt, dual‐purpose and nondescript sheep breeds relative to global sheep populations

Abstract

South Africa has a diverse array of phenotypically distinct and locally adapted sheep breeds that have been developed for different production systems ranging from mutton to wool and pelt, and some dual-purpose and nondescript breeds kept by smallholder farmers. This study investigated genetic diversity, population genetic structure and divergence between South African sheep breeds in order to gain an insight into breed history and genomic architecture aligned to breeding goals and production systems. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 14 breeds representing mutton, pelt and mutton and wool dual-purpose breeds. Nguni sheep were included as a representative of indigenous nondescript breeds that are reared by smallholder farmers. Seeking a clearer understanding of the genetic diversity of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. These sheep breeds included six African, two Asian and eight European breeds. Across breeds, genetic diversity ranged from observed heterozygosity (H 0) = 0.26 AE 0.02 in Namaqua Afrikaner to H 0 = 0.38 AE 0.01 in Dohne Merino. The overall mean H 0 was 0.35 AE 0.04. The African and Asian populations were the most inbred populations with F IS ranging from 0.17 AE 0.05 in Grey Swakara and Ronderib Afrikaner sheep to 0.34 AE 0.07 in the Namaqua Afrikaner. The South African Dohne Merino (F IS = 0.03 AE 0.01), SA Merino (F IS = 0.05 AE 0.04) and Afrino (F IS = 0.09 AE 0.02) and other global Merino-derived breeds were the least inbred. The first principal component explained 27.7% of the variation and separated the fat-and rump-tailed sheep (i.e. Swakara, Nguni, Blackhead Persian, Ethiopian Menzi, Meatmaster) from the Merino and Merino-derived breeds and the Dorset Horn. The second principal component separated the Merino and Merino-derived breeds from the English breed of Dorset Horn. Overall, South African indigenous breeds clustered together with indigenous breeds from other African and Asian countries. The optimal ADMIXTURE cluster (K = 20) revealed various sources of within-and amongst-breed genomic variation associated with production purpose, adaptation and history of the breeds. The Blackhead Persian, Nguni and Namaqua Afrikaner breeds differed significantly from other breeds, particularly with the South African Mutton Merino and Dorset Horn. Breed-differentiating SNPs were observed within genomic regions associated with growth, adaptation and reproduction. Genes such as RAB44, associated with growth and meat/carcass traits, differentiated the Blackhead Persian from the Dorset Horn and South African Mutton Merino. The MAP2 and HRAS genes, which are associated with immune traits involving Toll-like receptors and Chemokine signalling pathways, differentiated the Nguni from the Dorset Horn. The current results give insight into the current status of the sheep genetic resources of South Africa relative to the global sheep population, highlighting both genetic

Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders

“…This would be regarded as a biased selection objective towards growth and meat production traits, which explains why the AFR clustered with the SAMM. The Ronderib Afrikaner sheep are an improved form of the Namaqua Afrikaner sheep (Epstein, 1960), and together with the Damara and Nguni sheep are fat-tailed sheep (Peters et al, 2010), which could have formed the basis of their clustering (Dzomba et al, 2020) that included more populations and sample sizes from which the investigated data set was subsampled, which validates the results. Similar clustering of Merino-type and non-Merino-type breeds was reported in other studies (Gifford-Gonzalez and Hanotte, 2011;Kijas et al , 2012).…”

“…In this study, the Illumina OvineSNP 50K BeadChip genotypes (as reported by Nxumalo et al (2018); Dzomba et al (2020); and ISGC, http://www.sheephapmap.org) were subjected to quality control using PLINK v1.07 (Purcell et al, 2007) and Golden Helix SVS v8.1 (Golden Helix,Inc.,Bozeman,MT,www.goldenhelix.com) to ensure all SNPs had less than 5% missing genotypes, a call rate more than 95%, a minor allele frequency (MAF) less than 5%, and in Hardy-Weinberg equilibrium (p < 0.0001). Additional quality control measures ensured that individual animals had an IBD <0.025.…”

Genetic Basis of Dorper Sheep (Ovis aries) Revealed by Long-Read De Novo Genome Assembly

“…In a population structure research of African sheep breeds, Dorper sheep were clustered in between the Dorset and Blackhead Persian clusters based on PCA and ADMIXTURE analysis. The research confirmed the relationship between Doper sheep and their ancestors ( Dzomba et al, 2020 ). Given the breeding and genomic background of Doper sheep, we can determine that this breed inherits desirable traits from the Dorset Horn and Blackhead Persian sheep.…”

Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations

“…The Pedi, Namaqua Afrikaner and East African Damara are all considered fat-tailed breeds. The fat rumped Blackhead Persian was introduced from Somalia as a hair breed, but is well-equipped to tolerate the harsh South African environment and is mainly kept as a mutton breed (Dzomba et al, 2020). Both the Damara and Blackhead Persian are regarded as indigenous, transboundary breeds (Molotsi et al, 2020).…”