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dc.contributor.advisorMacNeil, M. D.
dc.contributor.advisorNeser, F. W. C.
dc.contributor.advisorScholtz, M. M.
dc.contributor.authorVan der Westhuizen, Lene
dc.date.accessioned2018-08-08T09:39:02Z
dc.date.available2018-08-08T09:39:02Z
dc.date.issued2018-03
dc.identifier.urihttp://hdl.handle.net/11660/9073
dc.description.abstractEnglish: Wet carcass syndrome (WCS) is a condition predominantly found in sheep, which negatively affects the quality of their carcasses. The Northern Cape Province in South Africa and the southern part of Namibia have been identified as geographic regions with a high occurrence rate of WCS. During the pre-slaughter period, the animal appears to be clinically normal, showing no symptoms of an abnormality. However, after the removal of the skin during the slaughter process the carcass appears to be “wet”. The condition is phenotypically described as a subcutaneous accumulation of watery fluid. The areas on the carcass most affected are the brisket, flanks, hindquarters, sides, and back. The watery fluid is also found in the intramuscular connective tissue layers of both the flank and subscapular area. Unfortunately, WCS results in sheep carcasses that are deemed to be unacceptable by the end consumer from both an appearance point of view and an apparent reduced shelf life. When the description and results of previous research are considered, no physiological-, environmental- or management system was conclusively identified as a causative agent of WCS. However, stress experienced by the animals during the pre-slaughter period was identified as a possible cause and is continuously discussed throughout the current research to date. The tentative breed-specificity, i.e. Dorper sheep breed, of the condition lends some credence to a potential genetic basis for it. However, previous research has not considered a genetic variant as a causal agent of WCS. The current study employed the Ovine Infinium® HD SNP BeadChip and a genome-wide association analysis (GWAS) approach to scan the genomes of both afflicted- and unafflicted sheep in search of putative quantitative trait loci associated with the WCS phenotype. This study was not only one of the first in Southern Africa to make use of this specific BeadChip but also the first to investigate the role of genetics as a causative factor of WCS. Muscle samples from sheep carcasses (33 afflicted and 36 unafflicted) were collected from three different abattoirs in the Northern Cape Province of South Africa and Southern Namibia. By using a candidate gene approach it was possible to map genetic loci, RYR1 and PRKAG3 (RN¯) causative of phenotypically similar conditions such as porcine stress syndrome and red, soft and exudative meat to the ovine genome. The positions of these loci (RYR1 on Chromosome 14 and PRKAG3 on Chromosome 2) mapped to the ovine genome were not in accordance with the loci showing significant association with the WCS phenotype; and no relationship was found between single nucleotide polymorphisms located within these genes and WCS. Furthermore, along with the latter approach the test of runs of homozygosity presented similar results as well as providing plausible evidence that WCS is not a recessive inherited condition. To test for an association between the phenotype (WCS) and an autosomal genetic marker(s) i.e. SNPs, a case-control study design was implemented. Given the relatively small sample size of the current study, the results obtained from the GWAS attested strong evidence of at least two loci, oar3_OARX_29903534 and oar3_OARX_113973214 positioned within the non-homologous region of the X chromosome for WCS carcasses. All afflicted animals, both males and females, carried at least one G2 allele for marker oar3_OARX_113973214, which was shown to be related to the WCS phenotype. Given the apparent influence of stress on WCS, these unafflicted males and females in all likelihood did not experience adequate levels of stress to manifest the WCS condition post-slaughter. The results of the current study also indicated that WCS may possibly be a rare X-linked inherited condition, provided only female individuals are considered. Finally, two possible major loci involving two major genes, HTR2C and DMD, positioned on the non-homologous region of the X chromosome have been identified as novel positional and functional candidate genes for WCS in sheep.en_ZA
dc.description.abstractAfrikaans: Natkarkassindroom (NKS) is ‘n toestand wat hoofsaaklik onder skape voorkom en wat die gehalte van hul karkasse negatief beïnvloed. Die Noord-Kaap-provinsie in Suid-Afrika asook die suidelike deel van Namibië is geïdentifiseer as geografiese gebiede met ’n hoë voorkoms van NKS. Gedurende die tydperk voor die skape geslag word, kom die dier klinies normaal voor en toon geen simptome van abnormaliteit nie. Nadat die vel egter gedurende die slagproses verwyder word, kom die karkas as “nat” voor. Die toestand word fenotipies beskryf as die onderhuidse aansameling van ‘n waterige vloeistof. Die dele van die karkas wat die meeste geaffekteer word is die borsstuk, lies, agterkwart, sye en rug. Die waterige vloeistof word ook aangetref in die binnespierse bindweefsel-lae van beide die lies- en die bladbeen-area. Ongelukkig is NKS skaapkarkasse nie aanvaarbaar vir die eindverbruiker, nie slegs omdat dit ’n onaanvaarbare voorkoms het nie, maar ook omdat dit ’n korter rakleeftyd het. Wanneer die beskrywings en resultate van vorige navorsing in ag geneem word, kon geen fisiologiese-, omgewings-, of bestuurstelsel oortuigend geïdentifiseer wat NKS veroorsaak nie. Die stres wat die diere gedurende die tydperk voor die slagproses ervaar, is egter geïdentifiseer as ’n moontlike oorsaak en word deurlopend in die navorsing tot nou toe bespreek. Die tentatiewe ras-spesifieke geneigdheid dat die toestand meer onder Dorperskape voorkom dui daarop dat daar ’n moontlike genetiese basis daarvoor is. Vorige navorsing het egter nie ’n genetiese variant as ’n veroorsakende faktor van NKS ondersoek nie. Die huidige studie het gebruik gemaak van die ‘Ovine Infinium® HD SNP’ skyfie en ’n genoomwye assossiasie-analise (GWA) om die genome van beide aangetaste- en onaangetaste skape te skandeer in die soeke na vermeende kwantitatiewe-eienskap-loki (KEL) wat geassosieer kan word met die NKS-fenotipe. Hierdie studie is nie net slegs een van die enigste studies in Suider-Afrika om hierdie spesifieke skyfie te gebruik nie, maar ook die eerste studie wat die rol van genetika as ’n veroorsakende faktor van NKS ondersoek. Spiermonsters van 33 aangetaste- en 36 onaangetaste skaapkarkasse is versamel vanaf drie verskillende abattoirs in die Noord-Kaap-provinsie van Suid-Afrika, asook die suidelike dele van Namibië. Deur ’n kandidaatgeenbenadering te gebruik, was dit moontlik om genetiese loki, RYR1 en PRKAG3 (RN¯), wat fenotipies-soortgelyke toestande soos varkstressindroom, en rooi, sagte en afskeidingsvleis veroorsaak, in die skaapgenoom te beskryf. Liggings van hierdie loki (RYR1 op Chromosoom 14 (OAR14) en PRKAG3 op Chromosoom 2 (OAR2)) wat op die skaapgenoom afgebeeld is, was nie in ooreenstemming met die loki wat ’n beduidende assosiasie met die NKS-fenotipe getoon het nie; en geen verhouding kon gevind word tussen enkel-nukleotied-polimorfismes (ENPs) binne hierdie gene en NKS nie. Voorts, tesame met die laasgenoemde benadering, het die genomiese soektog vir gebiede van homosigositeit (GVH) soortgelyke resultate gelewer, asook aanvaarbare bewyse dat NKS nie ’n resessiewe oorerflike toestand is nie. Om te toets vir ’n assosiasie tussen die fenotipe (NKS) en ’n outosomale genetiese merker(s), m.a.w. ENP, is daar van ’n geval-kontrolestudie gebruik gemaak. Gegewe die relatiewe klein steekproef van die huidige studie, het die resultate van die GWA-analise sterk bewyse getoon van ten minste twee loki, oar3_OARX_29903534 en oar3_OARX_113973214, in die nie-homogene area van die X-chromosoom vir NKS-karkasse. Alle aangetaste diere, beide ramme en ooie, het ten minste een G2-alleel vir merker oar3_OARX_113973214 gedra, wat duidelik ’n beduidende invloed op die NKS-fenotipe gehad het. Gegewe die oënskynlike invloed van stres op NKS, het onaangetaste ramme en ooie wat ook hierdie G2 allele dra, in alle waarskynlikheid nie genoegsame vlakke van stres ervaar om die NKS-toestand ná die slagproses te toon nie. Die resultate van die huidige studie het ook daarop gedui dat NKS moontlik ’n skaars, X-gekoppelde oorerflike toestand kan wees, gegewe slegs vroulike diere word in ag geneem. Laastens, twee moontlike KEL-areas wat twee hoofgene, HTR2C en DMD, betrek, wat geleë is op die nie-homogene area van die X-chromosoom, is geïdentifiseer as moontlike posisionele en funksionele kandidaatgene vir NKS in skape.en_ZA
dc.description.sponsorshipRed Meat Research and Development SA (RMRD SA)en_ZA
dc.description.sponsorshipTechnology Human Resources for Industry Programme (THRIP)en_ZA
dc.language.isoenen_ZA
dc.publisherUniversity of the Free Stateen_ZA
dc.subjectWet carcass syndrome (WCS)en_ZA
dc.subjectBeef carcassesen_ZA
dc.subjectOvinesen_ZA
dc.subjectBovinesen_ZA
dc.subjectQuantitative geneticsen_ZA
dc.subjectThesis (Ph.D. (Animal, Wildlife and Grassland Sciences))--University of the Free State, 2018en_ZA
dc.titleIdentification of quantitative trait loci affecting wet carcass syndrome in sheep using high density snp genotypesen_ZA
dc.typeThesisen_ZA
dc.rights.holderUniversity of the Free Stateen_ZA


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