Browsing by Author "Venter, Gabriella"
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- ItemGenetic characterization of smallholder sheep flocks in the Western Cape, South Africa(Stellenbosch : Stellenbosch University, 2020-03) Venter, Gabriella; Molotsi, Annelin H.; Stellenbosch University. Faculty of AgriSciences. Dept. of Animal Sciences.ENGLISH ABSTRACT: The arid environment found in South Africa, coupled with the changing climate could present new obstacles that need to be accounted for in farming activities and practises. Smallholder farmers experience a number of limiting factors which emphasised the need to develop an easy and cost-effective approach that should be implemented for the improvement of breeding strategies and selection decisions that will improve the production outputs as well as the overall genetic gain for smallholder farmers. Extensive molecular genetic studies have been done on a number of South African sheep breeds, including genetic diversity and population structure studies. There are, however, very few studies that identify CNVs in sheep breeds and then determine possible correlation between identified CNVs and desirous traits. The aim of this study was to conduct a pedigree analysis to facilitate better breeding management decisions for smallholder farmers, and to identify preliminary CNVs that could assist with the selection of superior animals that may be more adaptable or have superior production outputs, such as superior fertility, desirous body conformation, higher growth rates or even superior feed conversion ratio (FCR). These production outputs depend on the goals set by each individual farmer with regards to his flock. A pedigree was constructed of a smallholder flock from Beaufort-West that consisted of 48 Dorper individuals. Quality control and pruning was carried out on the individuals in Plink. One individual was removed due to missing genotype, and a second individual was removed by the SEQUOIA package in RStudio. Eleven dams were assigned, and four sires were assigned as parents to individuals. Ten dams were assigned as possible relatives with likely parent-offspring (PO) relationships, and nine sires were assigned as possible relatives with likely parent-offspring (PO) relationships. Diversity statistics which were calculated are the inbreeding coefficient, LD and the runs of homozygosity for the sample populations. These sample populations include two smallholder Dorper populations and a Dorper and Namaqua Afrikaner (Namafr) population. The one smallholder population was from a farm outside of Beaufort-West (Dorpersm 2) and the other smallholder flock was from the Ebenheaser community (Dorpersm 1). The Dorper and Namafr populations were from the Nortier research farm. The diversity statistics were calculated in Plink and a PCA was constructed in Rstudio using the pcadapt package. The Namafr population had the highest LD according to the r2 statistic (0,4805 ± 0,2476) followed by Dorper population (0,4156 ± 0,2000), then the two smallholder Dorper populations, Dorpersm 1 (0,3673 ± 0,1714) and Dorpersm 2 (0,3898 ± 0,1774). The smallholder Dorper population from the Ebenheaser community had the highest inbreeding coefficient (-0,0029 ± 0,0409), followed by the smallholder Dorper population from the Beaufort-West community (-0,0265 ± 0,0768) then the Dorper population (0,0535 ± 0,0000) and lastly the Namafr with the lowest inbreeding coefficient (-0,0652 ± 0,0399). Two runs of homozygosity (ROH) were discovered in the Dorper population, 105 ROH were discovered in the Dorpersm 1 population, 22 ROH were discovered in the Dorpersm 2 population and no ROH were discovered in the Namafr population. The constructed PCA identified two distinct clusters, one Namafr cluster and one Dorper cluster. The Dorper cluster showed sub-clusters between the Dorper population from the Nortier farm and the smallholder Dorpers. Preliminary CNVs were identified in a smallholder Dorper population from the Beaufort-West community. CNVs were determined using the PennCNV program. Gene annotation and classification studies were carried out in DAVID on candidate genes that overlapped the identified genes. A total of 206 CNVs were identified in 36 individuals. Candidate genes that were found to overlap with identified CNVs included interferon genes, which are responsible for immune defence mechanisms as well as a number of other genes responsible for biological functions including transport, metabolic precursors, neurogenesis, signalling as well as bone and cartilage matric composition. CNVs are genetic changes/mutations on the DNA level that could result in phenotypic variation between individuals. Copy number detection could thus be an important aspect in understanding the underlying genetic control of phenotypes observed in sheep flocks. Using CNVs that could be advantageous for certain desired traits for selection purposes could be economically beneficial to farmers. Genetic diversity statistics of a population as well as the possible mutations, such as copy number variations, are important genetic information that could be incorporated into breeding strategies to ensure optimal production and genetic gain.