Genetic characterization of smallholder sheep flocks in the Western Cape, South Africa

Venter, Gabriella (2020-03)

Thesis (MScAgric)--Stellenbosch University, 2020.

Thesis

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.

AFRIKAANSE OPSOMMING: Die droë omgewing in Suid-Afrika, tesame met die veranderende klimaat, kan nuwe hindernisse inhou wat in die boerdery-aktiwiteite en -praktyke in ag geneem moet word. Kleinboere ervaar 'n aantal beperkende faktore wat die noodsaaklikheid beklemtoon om ‘n maklike en koste-effektiewe benadering te ontwikkel wat geïmplementeer moet word vir die verbetering van teel strategieë en seleksie besluite wat die produksie uitsette en die algemene genetiese wins vir kleinboere sal verbeter. Uitgebreide genetiese molekulêre studies is al op ‘n aantal Suid-Afrikaanse skaaprasse gedoen, insluitend genetiese diversiteit en populasie struktuur. Daar is egter baie min studies wat genetiese variante in skaaprasse identifiseer en moontlike korrelasie tussen geïdentifiseerde genetiese variante en begerige eienskappe bepaal. Die doel van hierdie studie was om 'n stamboom analise te doen om beter teel bestuur besluite vir kleinboere te fasiliteer, en om voorlopige CNVs te identifiseer wat kan help met die seleksie van verhewe diere wat meer aanpasbaar is of beter produksie-uitsette het, soos superieure vrugbaarheid, gewenste liggaamsbou, hoër groeitempo of selfs 'n beter voeromsetverhouding (FCR). Hierdie produksie-uitsette hang af van die doelwitte wat elke individuele boer ten opsigte van sy kudde stel. Elf ooie en vier ramme is as ouers aan individue toegewys. Tien ooie is as moontlike familielede met waarskynlik ouer-nakomeling verhoudings toegewys, en nege ramme is as moontlike familielede met waarskynlike ouer-nakomeling verhoudings toegewys. ‘n Stamboom was saamgestel van ‘n kleinboer skaap trop uit Beaufort-Wes wat uit 48 Dorper-individue bestaan. Kwaliteitskontrole is op die individue in Plink uitgevoer. Een individu is verwyder weens die ontbrekende genotipe, en 'n tweede individu is deur die SEQUOIA-pakket in RStudio verwyder. Elf ooie en vier ramme is as ouers aan individue toegewys. Tien ooie is as moontlike familielede met waarskynlik ouer-nakomeling verhoudings toegewys, en nege ramme is as moontlike familielede met waarskynlike ouer-nakomeling verhoudings toegewys. Die diversiteit statistieke wat bereken is sluit in die teel koëffisiënt, onewewigtigheid koppeling en die mate van homosigositeit van die kudde. Die populasies sluit in twee kleinboer Dorper kuddes, ‘n Dorper kudde en ‘n Namaqua Afrikaner (Namafr) kudde. Die een Dorper kleinboer kudde kom van 'n plaas buite Beaufort-Wes (Dorpersm 2) en die ander kleinvee-kudde kom van die Ebenheaser-gemeenskap (Dorpersm 1). Die Dorper- en Namafr-kudde kom van die Nortier-navorsing plaas. Die diversiteit statistieke is in Plink bereken en ‘n hoof komponentanalise was in Rstudio opgestel met behulp van die pcadapt-pakket. Die Namafr kudde het die hoogste onewewigtigheid koppeling volgens die r2-statistiek (0,4805 ± 0,2476) gevolg deur die Dorper kudde (0,4156 ± 0,2000), daarna die twee kleinboer Dorper kuddes, Dorpersm 1 (0,3673 ± 0 , 1714) en Dorpersm 2 (0,3898 ± 0,1774). Die Dorper kudde van die kleinboer uit die Ebenheaser-gemeenskap het die hoogste teel koëffisiënt (-0,0029 ± 0,0409), gevolg deur die Dorper kudde uit die Beaufort-Wes-gemeenskap (-0,0265 ± 0,0768) en dan die Dorper kudde (0,0535 ± 0,0000) en laastens die Namafr met die laagste teel koëffisiënt (-0,0652 ± 0,0399). Twee lopies van homosigositeit (ROH) is in die Dorper kudde ontdek, 105 ROH is in die Dorpersm 1-kudde gevind, 22 ROH in die Dorpersm 2-kudde en geen ROH is in die Namafr-kudde gevind nie. Die gekonstrueerde hoof komponentanalise (PCA) het twee afsonderlike groepe geïdentifiseer, een Namafr-groepering en een Dorper-groepering. Die Dorper-groepering het onderlinge tussen die Dorper-kudde van die Nortier-navorsing plaas en die kleinboer Dorpers getoon. Voorlopig aantal kopie variante (CNV) was geïdentifiseer in 'n kleinboer Dorper kudde uit die Beaufort-Wes-gemeenskap. CNVs is met behulp van die PennCNV-program bepaal. Gene aantekening- en klassifikasie studies is in DAVID uitgevoer op kandidaat gene wat die geïdentifiseerde gene oorvleuel. Altesaam was 206 CNVs is in 36 individue geïdentifiseer. Kandidaat gene wat gevind was wat oorvleuel het met geïdentifiseerde CNVs, sluit interferon-gene in, wat verantwoordelik is vir immuun verdedigingsmeganismes, asook 'n aantal ander gene wat verantwoordelik is vir biologiese funksies, insluitend vervoer, metaboliese voorlopers, nekrogeniese, seine, as ook been- en kraakbeen matriek samestelling. CNVs is genetiese veranderinge / mutasies op die DNA-vlak wat kan lei tot fenotipiese variasie tussen individue. Die identifisering van kopie nommers kan dus 'n belangrike aspek wees in die begrip van die onderliggende genetiese beheer van fenotipes wat by skaap kuddes waargeneem kan word. Die gebruik van CNVs wat voordelig kan wees vir sekere eienskappe vir keurings doeleindes, kan ekonomies voordelig wees vir boere. Statistieke oor genetiese diversiteit van 'n kudde, sowel as die moontlike mutasies, soos kopiegetalvariasies, is belangrike genetiese inligting wat in teel strategieë geïnkorporeer kan word om optimale produksie en genetiese wins te verseker.

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