Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers

Abstract

The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study molecular characterization was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69% (UFH) to 72% PED with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8% of the total genetic variation was due to the genetic differentiation between the populations and 92.2% accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on 2 limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.

Genetic diversity in Zimbabwean Sanga cattle breeds using microsatellite markers

“…Tuli had the highest number (17) of PAs, showing that the breed has been developed as a distinctive genotype without significant admixture from the other two breeds. Breed PAs have been observed in diversity studies on indigenous cattle in Ethiopia (Edea et al, 2013;Ngono-Ema et al, 2014), South Africa (Pienaar et al, 2015;Sanarana et al, 2016), and Mozambique (Bessa et al, 2009). The Na and Ne alleles revealed no appreciable differences in the level of genetic variability among these breeds.…”

“…The level of variation depicted by number and size of alleles at each microsatellite locus is a useful measure of genetic variability and differentiation among breeds within a species (Sharma et al, 2013). All markers except RM067 exceeded FAO's recommended minimum threshold of five alleles per locus, which is required for estimation of genetic differences among animal breeds (FAO, 2011;Sanarana et al, 2016). These microsatellite loci were thus informative enough for exploring within-breed genetic variability and breed differentiation in Zimbabwean Sanga cattle.…”

“…These microsatellite loci were thus informative enough for exploring within-breed genetic variability and breed differentiation in Zimbabwean Sanga cattle. Private alleles are useful for the identification and measurement of the genetic distinctiveness of a population or breed (Ngono-Ema et al, 2014;Sanarana et al, 2016). A total of 119 alleles were observed, with 34 being unique to specific breeds.…”

“…The No of 7.4 alleles per locus was comparable with those for several other indigenous cattle breeds of Africa. For instance, Sanarana et al (2016) reported 6.5 alleles per locus in South African Nguni cattle ecotypes. In Mozambique, Bessa et al (2009) found allelic diversity of 5.9-6.4 alleles per locus.…”

“…Advantages of microsatellites include wide distribution in the genome, low quantities of template DNA required (10-100 ng), multi-allelic attributes, a neutral co-dominant inheritance pattern that allow ease of distinction between homozygous and heterozygous alleles, the option of simultaneous sequencing using multiplex polymerase chain reaction (PCR), and a wide range of immediate applications (Yang et al, 2013;Singh et al, 2014). In southern Africa, microsatellite markers have been used in population genetic studies of some Sanga cattle genotypes such as the Mozambican Landim (Bessa et al, 2009) and the South African Nguni (Sanarana et al, 2016). The genetic diversity of cattle has also recently been studied using SNP markers in Ethiopia (Edea et al, 2013) and South Africa (Makina et al, 2016).…”