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

Nel, Cornelius Loftus (2022-04)

Thesis (PhDAgric)--Stellenbosch University, 2022.

Thesis

ENGLISH ABSTRACT: 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.

AFRIKAANSE OPSOMMING: Die huidige omvang van kleinveeteling is beperk in Suid-Afrika (SA). In teenstelling met Australië (AUS) en Nieu-Seeland, word geen eienskappe aanduidend van die fiksheid of veerkragtigheid van tans in SA aangeteken nie. Genomiese seleksie (GS) kan waardevol wees om die omvang van teeltdoelwitte uit te brei, maar dit is nog nie voldoende in plaaslike populasies skaappopulasies ondersoek nie. SA beskik oor etlike Merino hulpbronkuddes wat omvattend aangeteken word vir ‘n reeks moeilik-meetbare eienskappe. Hierdie hulpbron kan teoreties benut word om soortgelyke eienskappe in kommersiële Merinos te ondersoek. Die Elsenburg Merinokudde is so ‘n hulpbronkudde wat uiteenlopend vir reproduksiesukses in terme van getal lammers gespeen (NLW) geselekteer is, om twee lyne, naamlik die H-Lyn (positiewe seleksie) en die L-Lyn (negatiewe seleksie) te vorm. Die eerste oogmerk van die studie was om opgedateerde genetiese parameters en verhaalde genetiese tendense in dié kudde te vermeld om vordering in ‘n laag-oorerflike, geslagsgekoppelde eienskap wat laat in die dier se lewe gemeet word, te demonstreer. Benewens aandag aan produksie- en reproduksie-eienskappe word daar spesifiek op die genetika van lamoorlewing gefokus. ‘n Tweede oogmerk was om genetiese merkers te gebruik om die populasiestruktuur van belangrike SA en AUS skaaprasse te ontrafel, met fokus op die oor-land verenigbaarheid tussen SA en AUS genetiese hulpbronne. ‘n Derde oogmerk was om die voordele van genetiese inligting vir voorspellings in SA Merinokuddes te ondersoek. Genetiese tendense in die Elsenburglyne het daarop gedui dat langtermynseleksie vir NLW nie genetiese verandering in ander produksie-eienskappe benadeel het nie, met die moontlike uitsondering van skoonvaggewig en stapelsterkte. ‘n Gunstige genetiese tendens (~1% van die algehele gemiddelde) per jaar (pj) is vir NLW in die H-Lyn gevind, ten spyte van ‘n lae oorerflikheid. Genetiese verandering was stadiger (maar steeds noemenswaardig) vir besetting en meerlinggeboortes as komponenteienskappe van NLW. Lamoorlewing tot speen het ook aanvanklik ‘n genetiese toename van na aan 1% pj getoon, in teenstelling met die uitgangspunt dat lamoorlewing nie deur genetiese seleksie verbeter kan word nie. Soos aangedui deur rektale temperatuur, het H-Lynlammers beter tydens koue-strestydperke gevaar. Die beter fiksheid van H- Lynlammers het grootliks met verbeterde aanpassing by koue-stres verband gehou. Populasie-genetika parameters soos skakelingskoppeling en effektiewe populasiegrootte het bevestig dat genetiese diversiteit van skape binne en oor rasse hoog kan wees, veral in Merinos. Imputasie oor lande het daarop gedui dat die SA en AUS Merino databasisse kombineerbaar is. Hierdie resultaat is ondersteun deur die maatstaf van uiteenlopendheid (FST), hoofkomponentanalise en verwantskappe, wat getoon het dat ‘n nouspektrumbenadering van die uiteenlopende populasies moontlik die beste resultate sal lewer. Die uitkomste van GS was belowend in gevalle waar ‘n eenstap GBLUP gebruik is om genetiese meriete in ongevallideerde kandidate vir ‘n reeks produksie- en reproduksie-eienskappe te evalueer. Resultate het egter oor kuddes en eienskappe verskil, tot so ‘n mate dat meer navorsing benodig word om resultate te optimeer. Die studie het ‘n basis vir verdere navorsing op hierdie en aanverwante onderwerpe verskaf.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/124898
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