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Stellenbosch University (2020)

GENETIC CHARACTERIZATION OF SMALLHOLDER SHEEP FLOCKS IN THE WESTERN CAPE, SOUTH AFRICA

Venter, Gabriella

Titre : GENETIC CHARACTERIZATION OF SMALLHOLDER SHEEP FLOCKS IN THE WESTERN CAPE, SOUTH AFRICA

Auteur : Venter, Gabriella

Université de soutenance : Stellenbosch University

Grade : Master of Science (Agriculture) 2020

Résumé partiel
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.

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