Browsing by Author "Malan, Isaack Nichol"

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    Analysis of genetic diversity and population structure of indigenous (fat-tailed) sheep in South Africa
    (Stellenbosch : Stellenbosch University, 2022-03) Malan, Isaack Nichol; Molotsi, Annelin H.; Cloete, Schalk W. P. ; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Science.
    ENGLISH ABSTRACT: Indigenous fat-tailed sheep breeds are primarily kept by rural peoples, especially in developing countries. These livestock species contribute to household income, is a source of food security, plays a role in social and crop production (fertilizer) systems. The diversity within these indigenous breeds allows them to be productive under harsh environmental conditions, thus genetic and phenotypic characterization is pivotal for future sustainable farming practices. The aim of this study was to elucidate the genetic structure of indigenous fat-tailed sheep in South Africa and to trace selection pressure applied to fat-tailed sheep for adaptation. The first objective was to elucidate the genetic variation and population structure of indigenous fat-tailed sheep in South Africa. The second objective was to determine if selection pressure has been placed on these indigenous sheep breeds for adaptation traits. The first objective was achieved by sampling blood from indigenous sheep breeds (30 Damara, 30 Pedi, 30 Zulu, 20 Meatmaster and 54 Karakul animals). The extracted DNA was genotyped using the OvineSNP50K BeadChip. Genotype data from 48 Namaqua Afrikaners and 98 Merinos were included for comparative purposes. Several genetic parameters were analysed to determine the genetic diversity within and between the sheep populations: observed heterozygosity (Ho), expected heterozygosity (He), inbreeding coefficients (F) and Linkage disequilibrium (LD). The highest and lowest observed heterozygosity was seen in the Pedi and Damara sheep (0.4 and 0.34 respectively). The Merino exhibited the highest expected heterozygosity of 0.38 and the Namaqua Afrikaner the lowest at 0.345. The highest LD was reported in the Namaqua Afrikaner at r²= 0.45 and the lowest LD was observed in the Merino at r²= 0.37. The population structure of the indigenous sheep breeds was studied by conducting a Principal Component Analysis (PCA), where PC1 (6.8%) and PC2 (5.0%) describes the total genetic variation. A Bayesian approach was used to calculate maximum likelihood estimates in the FastSTRUCTURE program, which elucidate the true ancestral populations (K= 8) of the sheep breeds. Lastly, through hapFLK analysis, Reynolds genetic distances between the different sheep populations were calculated and a neighbour-joining population tree was generated. These could be used to determine the relatedness and dissimilarities (dendogram) found between the indigenous fat-tailed sheep. A close relationship could be seen between the Zulu and Damara sheep breeds. Despite the lower diversity, the Namaqua Afrikaner displays the highest genetic distance from the other indigenous fat-tailed breeds. The Pedi and Karakul populations also exhibited distinct clustering and separation. Admixture within the Meatmaster breed with the Merino was observed. This is to be expected as the Merino could have been used as a parental breed in the make-up of this composite (Meatmaster) sheep. To determine selection sweeps in the indigenous sheep breeds, the hapFLK approach was used and 13 regions were found to be under selection, spanning a total of 11 chromosomes. The candidate genes associated with the SNPs of interest was linked to traits involved in metabolic process such as DNA synthesis and transcription (CEP41, TLL1, EIF1B, SCN5A, SCN8A, SCN10A, SCN11A), immune response (BPIFC, CLDN12, CLDN14, TRL4), ultraviolet exposure and thermoregulation (SLX4, ASCL4, KCNJ5, LAMB1, GPR26, CX3CR1), energy metabolism (MYH9) and meat production (PDEZA, UTRN). These candidate genes give an insight into the adaptive traits of indigenous sheep in South Africa and further genotyping is needed to elucidate more of the robust characteristics exhibited by these locally acclimated genetic resources.