Simon Frederick Lashmar
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Carina Visser
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Moses Okpeku
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Farai Catherine Muchadeyi
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Ntanganedzeni Olivia Mapholi
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Abstract
In southern Africa, the Nguni cattle breed is classified as an indigenous and transboundary animal genetic resource that manifests unique adaptation abilities across distinct agroecological zones. The genetic integrity of various ecotypes is under potential threat due to both indiscriminate crossbreeding and uncontrolled inbreeding. The aim of this study was to assess the genetic diversity and autozygosity that exists both across countries (ES: eSwatini; SA: South Africa) and within-country (SA), between purebred stud animals (SA-S) and research herds (SA-R). Subsets of 96 ES, 96 SA-S and 96 SA-R genotyped for 40 930 common SNPs were used to study inbreeding, runs of homozygosity (ROH) and heterozygosity (ROHet) profiles as well as population structure. The highest proportion (0.513) of the 3 595 ROH was <4Mb in length, while the majority (0.560) of the 4 409 ROHet segments fell within the 0.5-1Mb length category. Inbreeding coefficients indicated low inbreeding (FROH range: 0.025 for SA-S to 0.029 for SA-R). Principal component (PCA) and population structure (K=5) analyses illustrated genomic distinctiveness between SA and ES populations, greater admixture for SA-R (mean±standard deviation proportion shared=0.631±0.353) compared to SA-S (mean±standard deviation proportion shared=0.741±0.123), and three subpopulations for ES. Overall, results illustrated that genetic distinctiveness in the Nguni resulted from both geographic isolation and exposure to different production strategies. Although no impending threat to genetic diversity was observed, further loss should be monitored to prevent endangerment of unique and beneficial indigenous resources.
Temporal Variation in Genetic Diversity and Population Structure of Burlina Cattle Breed
