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University of KwaZulu-Natal (2016)

Landscape genomic approach to investigate genetic adaptation in South African indigenous goat populations

Mdladla, Khanyisile.

Titre : Landscape genomic approach to investigate genetic adaptation in South African indigenous goat populations

Auteur : Mdladla, Khanyisile.

Université de soutenance : University of KwaZulu-Natal

Grade : Doctor of Philosophy in Genetics 2016

Résumé partiel
Traditional indigenous goat breeds have evolved the crucial ability to adapt and survive in challenging environments and ecological conditions associated with their geographical origins. The environments are heterogeneous and production conditions fluctuate with seasons. Although indications of local adaptation have been reported in most indigenous goats and other livestock species, there are many unknowns regarding the genetic mechanisms that determine the response of indigenous goats to their production and climatic environments. There is potential for these goats to be used for sustainable improvement of productivity in the tropics through combining ecologically adaptive and economically important production traits. Identifying regions that are potentially adaptive in indigenous goats will allow us to explore the adaptive potential for specific environments. This is particularly relevant now when goats and other livestock species are faced with immense production, climatic and other natural selection pressures. South Africa for example is endemic to heartwater and a number of goat populations are frequently exposed and need to adapt. There has been major developments in appropriate genomics technologies such as next-generation sequencing (NGS) and genome wide single nucleotide polymorphism (SNP) BeadChips, and bioinformatics analytical methods, which will facilitate comprehensive characterization of these genetic resources. The study targeted the major goat producing provinces and analysed the diversity in production systems, and the morphological variations of the indigenous goats that they keep, prevalence of heartwater and how genetic diversity has been shaped by the production, climatic and other geographic conditions.
The first objective of this study was to determine the flock composition, the role of goats at household level, and the management practices under which goats are raised in the villages of South Africa. Results obtained from this study were based on the field survey that captured rural community goat raisers’ opinion in the form of a questionnaire, and direct observation and measurement of phenotypic characteristics on randomly selected goats. In total, 130 smallholder communal farmers were interviewed from 26 villages from the Eastern Cape (n = 2), KwaZulu-Natal (n = 6), Limpopo (n = 13) and North West (n = 5) provinces of South Africa. The mean flock size per household ranged from 13.2±12.39 in Limpopo to 34.18±28.36 in Eastern Cape, with majority of goats in a flock being adults and females. Goats play a unique role in supporting some of the poorest people in South Africa, and thestudy observed that home consumption was the major role of keeping goats. Goats were maintained under scavenging regime with no supplemental feeding in Limpopo, while a few farmers in Eastern Cape, KwaZulu-Natal and North West provinces provided supplemental feed to their animals. Parasites and diseases such as heartwater, ORFV (scabs), gall sickness, mange, and diarrhea are major constraints to goat production thus limiting their potential for commercialization in these communities. The studied goats were highly diverse presenting a variety of phenotypic characters and body size measurements within and between populations. White was the most dominant color among the Tswana and Xhosa, while black was dominant in the Venda, Zulu and Tankwa populations. The canonical discriminant analysis showed that most Zulu, Xhosa, Tankwa, Tswana individuals were assigned to their source population (90.41%, 82.93%, 74.07% and 57.50%) whilst 32 (39.51%) Venda individuals were classified as Zulu individuals. Lowest percentage (> 50%) of individuals of commercial breeds (Boer, Kalahari Red and Savanna) and Venda population were correctly classified into their source population. The first principal component (PC1) explained 43.2% of the observed genetic variation and PC2 accounted for 29.3%, showing admixed individuals. Weak population structuring basis of breed or population was observed with the highest numbers of individuals of the commercial breeds admixed and the lowest observed for Tankwa breed. These results support the population overlaps and incorrect assignment of individuals in the discriminatory analysis. The diversity patterns observed may suggest the effect of production system and that these populations share similar genetic identities thus reflect their adaptation to different production systems and local conditions.

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