Genomic characterization of autozygosity in South African Merino sheep

Abstract

The South African (SA) Merino is a medium-framed, white wool breed, and is one of the most prominent breeds in the SA sheep industry. Because of its local importance, the SA Merino is the only SA sheep breed with sufficient single nucleotide polymorphism (SNP) genotypes to implement genomic selection (GS), and this provides comprehensive sample size (i.e. number) and composition (i.e. representation) of genotypic data to study the breed’s diversity and inbreeding. These estimates play a vital role as tools for breeders to maintain genetic progress whilst conserving diversity within flocks. This study aimed to perform a homozygosity-focused SNP investigation of the past and present inbreeding and autozygosity levels in the SA Merino sheep breed. A total of 1 738 animals (1 567 females and 171 males), genotyped using different versions of the Illumina® Ovine 50K SNP panel, were used to estimate various proxy-indicator parameters of genomic variability, runs of homozygosity (ROH) and heterozygosity-rich region (HRR) profiles, and conserved ROH-based selection signatures for the SA Merino breed. The reported observed (HO=0.351± 0.018) and expected (HE=0.365± 0.0001) heterozygosity, and their relationship to one another (i.e. HO<HE), as well as SNP-based inbreeding coefficient (FSNP=0.037±0.05) and effective population size (most recent Ne=305) indicated a slight loss in within-population genetic diversity, and low inbreeding levels. Additionally, high MAF values (0.2750.14) and LD (0.365±0.180) were observed within the SA Merino population. The autozygosity analysis identified a total of 43 147 ROH with a mean chromosome-wide ROH length per chromosome of 6.53Mb, and a corresponding mean FROH of 0.074±0.04 that further supported low inbreeding. Conserved ROH revealed selection signatures harbouring a total of 275 protein-coding genes (within a threshold of 16.4%) associated with various functions in sheep involving reproduction, fibre formation, and inflammatory responses. Overall, the results from this study conveyed that mating programs and intense selection are well managed within the breeding objectives of SA Merino sheep, and that sufficient levels of genetic diversity exists to facilitate sustainable production and genetic improvement in the future.