Assessment of genetic variation in Bapedi sheep using microsatellite markers

Abstract

<jats:p>This study was conducted to assess genetic variation in Bapedi sheep using 14 microsatellite markers. Blood samples were collected from 174 unrelated Bapedi sheep on six farms in various districts of Limpopo and from the Agricultural Research Council Animal Production Institute (ARC-API) in Gauteng. Genotypes from other South African indigenous sheep, namely Zulu (N = 14), Damara (N = 11), Dorper (N = 8), and Namaqua (N = 11), were included to represent reference populations. The effective number of alleles averaged 5.6 for across the Bapedi flocks and was 4.9 for the reference breeds. Among the Bapedi flocks, the observed heterozygosity (Ho) ranged from 0.56 ± 0.05 to 0.69 ± 0.03 and expected heterozygosity (He) values were between 0.75 ± 0.04 and 0.88 ± 0.01. Thus, there is considerable genetic diversity within the Bapedi sheep populations. However, the fixation index was high, indicating the possibility of inbreeding becoming a problem for these flocks. A neighbour-joining tree was constructed from the estimates of Nei’s genetic distances among flocks. The presence of Bapedi sheep flocks on all of the main branches of the tree along with one of the reference breeds suggests the present-day Bapedi is not an entirely distinct breed and that there are genetic differences between flocks of these South African indigenous sheep. Sustainable breeding and conservation programmes are needed to control inbreeding and to foreclose possible genetic dilution of Bapedi sheep.&#x0D; Keywords: genetic diversity, germplasm conservation, inbreeding, indigenous sheep</jats:p>

The Use of Hormonal Assay, Phenotypic Morphometry, and CASA Semen Analysis to Estimate Attainment of Puberty in Indigenous Ram Lambs

“…South Africa houses 46 of the 109 different sheep breeds in sub-Saharan Africa [5]; it also houses 19.9 million of the 39 million sheep in the SADC region [6]. Three of South Africa's oldest sheep breeds are the Bapedi, Namaqua-Afrikaner and Zulu sheep: The Bapedi sheep have small frames, they are polled, and have fat-tails along with long legs and a shallow body; they are hardy and disease tolerant [7]. Similar in general phenotype but multicoloured, the Namaqua-Afrikaner is South Africa's oldest indigenous sheep breed [8,9], and is used primarily in smallholder farming systems [10] and has a fat tail.…”

A Comparative Study on the Reproductive Performance of South African Indigenous Sheep Breeds Following Oestrus Synchronization

“…Namaqua Afrikaner sheep and Damara sheep found in drier areas, characterised by having fat-tails and rumps (Molotsi et al, 2020). Zulu sheep along with Bapedi sheep are Nguni type found in wet areas of eastern coast and characterised as fat-tailed and small body framed size (Kunene and Fossey, 2006;Molotsi et al, 2020;Maqhashu et al, 2020). Various authors such as Kunene et al (2009); Mavule et al (2013); Hasani et al (2018) documented a clear role of rearing these breeds in rural farmers where veterinary service and other inputs are lacking (Mavule et al, 2013).…”

“…Various authors such as Kunene et al (2009); Mavule et al (2013); Hasani et al (2018) documented a clear role of rearing these breeds in rural farmers where veterinary service and other inputs are lacking (Mavule et al, 2013). Despite the adaptive traits they built, they are however endangered (FAO-DAD-IS, 2020; Maqhashu et al, 2020) due to indiscriminate crossbreeding to improve growth rate and body weight size (Kunene et al, 2011). Furthermore, uncontrolled mating in rural areas is another factor found to ground genetic erosion of these breeds (Mavule et al, 2016;Selepe et al, 2018) that inhibits adaptive responses to harsh environmental conditions (Bijlsma and Loeschcke, 2012).…”

“…This will thus reduce the number of replacement ewes and rams, sink the selection intensity and complement inbreeding (Selepe et al, 2018). Previous studies in these breeds focused merely on the genetic makeup (Selepe et al, 2018), genetic diversity and population structure (Qwabe et al, 2013;Maqhashu et al, 2020), utilization (Kunene et al, 2011), morphological differentiation (Mavule et al, 2016) and implications for conservations (Soma et al, 2012). However, very little has been done on their reproductive performance.…”

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“…A series of SNP-based methodologies, including those related to genetic diversity (Makina et al, 2014;Makina et al, 2016), have also been applied to Afrikaner, Drakensberger and Nguni breeds, however, including ≤50 samples genotyped for sparser marker densities. Genetic diversity has also been studied in local sheep populations (Soma et al, 2012;Nedambale et al, 2020). SA beef breeds in general have been included in a 3-year national beef genomic program (BGP) (Walsh and Spazzoli, 2018) for building training populations for genomic selection.…”