Evaluation of the OvineSNP50 chip for use in four South African sheep breeds

Abstract

Relatively rapid and cost-effective genotyping using the OvineSNP50 chip holds great promise for the South African sheep industry and research partners. However, SNP ascertainment bias may influence inferences from the genotyping results of South African sheep breeds. Therefore, samples from Dorper, Namaqua Afrikaner (NA), South African Merino (SA Merino) and South African Mutton Merino (SAMM) were genotyped to determine the utility of the OvineSNP50 chip for these important South African sheep breeds. After quality control measures had been implemented, 85 SA Merino, 20 Dorper, 20 NA and 19 SAMM samples remained, with an average call rate of 99.72%. A total of 49 517 (91.30%) SNPs on the chip met quality control measures and were included in downstream analyses. The NA had the fewest polymorphic loci, 69.20%, while the SAMM, Dorper and SA Merino had between 81.16% and 86.85% polymorphic loci. Most loci of the SA Merino, Dorper and SAMM had a MAF greater than or equal to 0.3. In contrast, the NA exhibited a large number of rare alleles (MAF < 0.1) and a uniform distribution of other loci across the MAF range (0.1 < MAF ≤ 0.5). The NA exhibited the least genetic diversity and had the greatest inbreeding coefficient among the four breeds. The results of the Dorper, SA Merino, and SAMM compare favourably with those of international breeds and thus demonstrate the utility of the OvineSNP50 chip for these breeds. Effects of SNP ascertainment bias, however, could be seen in the number of non-polymorphic loci and MAF distribution of the three commercial breeds in comparison with those of the NA. The implementation of methods to reduce the effect of SNP ascertainment bias and to ensure unbiased interpretation of genotype results should therefore be considered for future studies using OvineSNP50 chip genotype results.

The Current Status of Indigenous Ovine Genetic Resources in Southern Africa and Future Sustainable Utilisation to Improve Livelihoods

“…Fat-tailed breeds also exhibited low levels of genetic diversity (0.480 to 0.637). The low heterozygosity of fat-tailed sheep was confirmed by Sandenbergh et al [16] for the Damara and Namaqua Afrikaner by using single nucleotide polymorphic (SNP) markers. The wool type breeds of European origin exhibited the highest genetic diversity levels (0.527 to 0.711).…”

“…The use of genomics to further characterize indigenous ovine resources is also valuable to ensure sustainable utilization [1]. Various population structure studies using genomics have been done to determine the genetic diversity between and within local breeds [14][15][16]. Genome-wide association studies and functional genomic studies have also been conducted on the Damara breed to identify genes associated with polyceraty [17].…”

“…The wool type breeds of European origin exhibited the highest genetic diversity levels (0.527 to 0.711). The high levels of genetic diversity for Merino breeds have been confirmed by molecular studies using SNP markers [15,16]. Zulu sheep have been characterised both phenotypically [19] and genetically [19,20].…”

Assessment of OvineSNP50 in Nigerian and Kenyan sheep populations

“…The OvineSNP50 which is a microarraybased system was designed to determine the genotype of approximately 54 000 single nucleotide polymorphisms spaced evenly across the ovine genome, yet excluding the Nigerian a n d o t h e r A f r i c a n s h e e p p o p u l a t i o n s (Sandenbergh et al, 2016). Sample-based filtering relates to the call rate, which is the fraction of called SNPs per sample over the total number of SNPs in the dataset and can be influenced by factors such as DNA quality and concentration (Anderson et al, 2010).…”

Genomics for the advancement of livestock production: A South African perspective

“…More recently, research has been performed by applying SNP markers to population genetics. Genetic diversity, inbreeding and effective population size estimates have been reported in South African farm animals, including cattle (Makina et al, 2014;Makina et al, 2015b), goats (Lashmar et al, 2015;Mdladla et al, 2016;Visser et al, 2016) and sheep (Sandenbergh et al, 2016;Molotsi et al, 2017).…”