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Stellenbosch University (2022)

Studies on genetic responses and genomic characterisation in South African and Australian sheep

Nel, Cornelius Loftus

Titre : Studies on genetic responses and genomic characterisation in South African and Australian sheep

Auteur : Nel, Cornelius Loftus

Université de soutenance : Stellenbosch University

Grade : Doctor of Philosophy (PhDAgric) 2022

Résumé
The current scope of small stock breeding in South African (SA) Merinos is constrained. In contrast to Australia (AUS) and New Zealand, no traits indicative of animal resilience or fitness are currently being recorded. Furthermore, the use of genomic selection (GS) could be a valuable tool to widen the scope of breeding objectives, but has not been formally explored on local populations. SA hosts multiple Merino resource flocks that are well recorded for a series of difficult to measure fitness traits, which can be exploited to the benefit of evaluating similar traits in commercial Merinos. The Elsenburg Merino flock is a resource flock that has been divergently selected for reproductive success on number of lambs weaned (NLW) that separates the H-Line (positive selection) from the L-Line (negative selection). The first aim of this study was to elaborate genetic parameters and realized genetic trends obtained in the Elsenburg flock as a demonstration of responses to genetic selection on a lowly heritable, sex-limited trait recorded late in an animal’s lifetime. Apart from a focus on production and reproduction traits, the genetics and factors influencing lamb survival received special attention. A second aim of this study was to use marker data to better define the population genetic architecture of important SA and AUS sheep breeds, with a focus on the across country compatibility of SA and AUS ovine genetic resources. A third aim of this study was to assess the benefits of genomic information in genetic prediction of SA Merinos. Genetic trends in the Elsenburg lines showed that long term divergent selection for NLW did not have severely detrimental effects on the genetic change in other production traits, with a possible exception of clean fleece weight and staple strength. Despite the low heritability, favorable genetic trends ( 1% of the overall mean) per year were reported for NLW in the H-Line. Genetic change was more moderate, but also worthwhile for component traits, namely conception rate and litter size. Survival to weaning, as a trait of the lamb, also showed a rate of gain close to 1% in the early years of the experiment, which contradicted the premise that lamb survival is not amenable to genetic selection. As measured by rectal temperature, H-Line lambs also performed better during cold stress conditions, and the fitness of H-Line lambs was strongly linked to increased cold stress adaption. Population genetic parameters such as linkage disequilibrium and effective population size reiterated the fact that the genetic diversity of sheep can be high both across and within breeds, especially for Merinos. According to across country imputation, there is opportunity to combine SA and AUS Merino databases. This was supported by parameters of divergence (FST), principal component analysis and relatedness, but a narrow spectrum approach of specific populations is most likely to deliver the best results. The outcomes of GS were promising when a single-step GBLUP was used to predict genetic merit in unvalidated candidates for a series of production and reproduction traits. However, results varied across flocks and traits, and more research is needed to optimize these results. The study provided a foundation for further research on these and related topics.

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Page publiée le 21 janvier 2023