DNA sequencing and restriction fragment length polymorphism analysis (RFLP) of polymerase chain reaction (PCR) amplified mitochondrial DNA fragments, and random amplified polymorphic DNA sequence (RAPD) analysis were techniques evaluated in this study for applicability in the investigation various aspects of genetic diversity within the ostrich (Struthio camelus). The genetic aspects that were investigated were (i) relationships between ostrich subspecies, (ii) genetic variability between and within domesticated populations of southern African ostriches (Struthio camelus australis), (iii) linking egg production in domesticated ostriches to RAPD profiles, and (iv) determining the zygosity of twin ostriches. In the first part of this study DNA sequencing and the polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) methods were evaluated for resolving genetic differences in the small mtDNA fragments ofthe ostrich. DNA sequencing ofPCR amplified 450 bp 12S rRNA gene fragments of representatives from the southern African population ostrich (S.c. australis) did not reveal any differences between the populatiohs from different geographical areas, representing ostrich lineages with different breeding histories. The PCRRFLP analysis ofmtDNA fragments (450 bp 12S rRNA gene fragment and 550 bp D-loop region) also did not reveal any genetic variability between the domesticated s.,c. australis populations included in this study. PCR-RFLP analysis of a 450 bp 12S rRNA gene fragment, however, showed differences between the subspecies s.c. australis and s.c. molybdophanes. The proportion of shared fragments (F) between these two subspecies was 0.286 and nucleotide sequence divergence estimated at 8.9 %. Divergence time between these two subspecies was estimated at 4.5 million years ago. The data presented from this study are comparable to the data from a previous study in which the entire mitochondrial genome and a larger number of restriction enzymes were used. The PCR-RFLP method thus demonstrated its usefulness for genetic studies of ostriches at thesubspecies level. The sequences used in this study could not reveal any markers that were useful for genetic studies of ostriches at the population level. In the second part of the study the RAPD method was evaluated for application in the genetic studies of ostriches. RAPD profiles, based on three RAPD primers, revealed differences between three subspecies of ostriches and indicated relationships between these subspecies that are consistent with observations from other studies. The numerical analysis of pooled and individual primer data demonstrated that the subspecies s.c. australis is more closely related to s.c. massaicus than to s.c. molybdophanes. RAPD marker differences between s.c. molybdophanes on the one hand, and s.c. massaicus and s.c. australis on the other is also consistent with observations from studies that proposed separate specie~ status for s.c. molybdophanes. RAPD analysis by five primers revealed geographic variation between s.c. australis populations. The clustering patterns observed in the dendrograms and Neighbour Joining Trees generated by computer programs showed trends of separating ostric1;t populations into geographical groups, possibly reflecting their different breeding histories. In the RAPD profiles of the inbred population, band-sharing was generally greater than in the outbreeding group. RAPD analysis thus showed that it may be a useful method in the population studies of domesticated S. c. australis. RAPDs also generated data that grouped ostriches according to trends in egg production capabilities. Analysis ofRAPD profiles by computer software showed a Neighbour Joining Tree and a dendrogram that predominantly grouped ostriches into clusters associated with either good or poor egg production. Evidence supporting the suitability of RAPDs as a tool in breeding programmes of ostriches was thus provided by this study. RAPDs also provided data, demonstrating that two sets of ostrich twins were non-identical twins. It was demonstrated by this study that RAPDs analysis may be a useful technique for applying to (1) systematic (2) population (3) breeding and (4) twin studies of ostriches (Struthio camelus).

Thesis (MScAgric (Animal Sciences))--University of Stellenbosch, 2011. / Includes bibliography. / ENGLISH ABSTRACT: A study was conducted to characterize the three ostrich breeds available as genetic resource in South Africa, namely the South African Black (SAB), Zimbabwean Blue (ZB) and the Kenyan Redneck (KR), and their respective crosses. Growth, slaughter traits and reproduction of these ostriches were recorded at Oudtshoorn Research Farm in the Western Cape of South Africa. Individual non-linear regressions (Gompertz) were fitted to the data of 390 purebred and 41 crossbred ostriches, using the SAS NLIN function. Heterosis was estimated for each parameter of the Gompertz model. The estimated adult weight (Aparameter) of the ZB (147 kg) and the KR breeds (148 kg) were higher than that of the SAB breed (129 kg). The overall growth rate (B-parameter) of the ZB breed (0.0075) and the SAB breed (0.0080) was lower than that of the KR (0.0150). The age at maximum weight gain (C-parameter) was higher for the ZB breed (226 days) compared to the SAB (198 days) and the KR (194 days). Heterosis for the A-parameter was estimated at -6.2% and at -12% for the C-parameter. The slaughter traits studied were slaughter weight (SLW), carcass weight (CW), dressing percentage (DP), fan fillet weight (FFW), pH0, pH24, drip loss % (DL%), cooking loss % (CL%), tenderness and meat colour traits. Differences were observed between the means for SLW of the SAB (86.5 kg) and ZB (93.9 kg). Mean DP of the KR breed (52.5%) was increased relative to the low DP of their SAB contemporaries (48.8%). The sire lines (ZB and KR) and crosses were heavier than the SAB (dam line), whereas the crosses resembled the dam line for meat quality traits. Means for pH24 also differed, with higher values for the sire lines (ZB – 6.36; KR – 6.4) relative to the SAB (5.85). The instrumental b* colour value also differed between the SAB (9.4) and KR (6.9). Records used for assessing the reproduction and body measurements of purebred and crossbred dams were 428 in total. Traits analyzed were, total egg production (TEP), the number of fertile eggs, number dead in shell chicks, hatchability and chick production (CP), the time to lay, live weight, front chest circumferences as well as tail circumference. The ZB and KR were heavier in live weight and of larger body measurements than the SAB, whereas the SAB exhibited superior reproduction performance in comparison with the ZB and KR breeds. Derived heterosis estimates amounted to 2.2% for tail circumference, 12% for TEP, 12% for hatchability and 19% for CP. Genetic variation between and within the breeds were determined utilizing 19 microsatellite markers. Significant molecular genetic differences were observed between the three breeds. The SAB and ZB (Fst = 0.10 and Nei = 0.49) were genetically most similar, whereas the genetic distance between the KR and ZB breeds were furthest (Fst = 0.13 and Nei = 0.61). The SAB breed exhibited the highest heterozygosity within its population and the ZB the lowest heterozygosity. These results contribute to a better understanding of the utilization of the distinct ostrich breeds for commercial production. / AFRIKAANSE OPSOMMING: Die doel van hierdie studie was om die verskille tussen drie volstruisrasse wat tans in Suid Afrika mee geboer word te karakteriseer, naamlik die “South African Black” (SAB), “Zimbabwean Blue” (ZB) en die “Kenyan Redneck” (KR) en hulle onderskeie kruisse. Rekords van die groei-, slag- en reproduksie eienskappe van die volstruise was by Oudtshoorn Navorsingsplaas in die Wes-Kaap aangeteken. Individuele nie-lineêre regressies (Gompertz) is op die data van 390 suiwerras en 42 kruisgeteelde volstruise gepas, met die gebruik van die “NLIN” prosedure van SAS, (2006). Heterose is beraam vir elke parameter van die Gompertz model. Die beraamde volwasse gewig (A-parameter) van die ZB (147 kg) en die KR ras (148 kg) was hoër as die van die SAB ras (129 kg). Die totale groeitempo (B-parameter) van die ZB ras (0.0075) en die SAB ras (0.0080) was laer as die van die KR (0.0150). Die ouderdom by maksimum groei (C-parameter) was hoër vir die ZB ras (226 dae) in vergelyking met die SAB (198 dae) en die KR (194 dae). Heterose vir die A-parameter was beraam teen -6.2% en teen -12% vir die C-parameter. Die slageienskappe wat ondersoek was, was slagmassa (SLW), karkasmassa (CW), uitslag persentasie (DP), “fan fillet” massa (FFW), pH0, pH24, drupverlies % (DL%), kookverlies % (CL%), sagtheid en kleureienskappe. Beduidendende verskille is waargeneem tussen die gemiddeldes vir SLW vir die SAB (86.5 kg) en ZB (93.9 kg). Gemiddelde DP van die KR ras (52.5%) was beter as die van die SAB ras (48.8%). Die mannetjielyne (ZB en KR) en die kruisse was swaarder as die SAB (wyfielyn), en die kruise was vergelykbaar met die wyfielyn vir vleiskwaliteit eienskappe. Gemiddeldes vir die pH24 het verskil, met hoër waardes vir die vaar lyne (ZB – 6.36; KR – 6.4) relatief tot die SAB (5.85). Die instrumentale b* kleurwaarde het ook verskil tussen die SAB (9.4) en KR (6.9). ‘n Totaal van 428 rekords is gebruik om reproduksie en liggaamsmetings van die suiwer en kruisteelwyfies te ondersoek. Reproduksie eienskappe ge-analiseer was: die aantal broeisels, totale eierproduksie (TEP), die aantal vrugbare eiers, die aantal kuikens dood in dop, uitbroeibaarheid, kuiken produksie (CP), tyd tot produksie van die eerste eier, volwasse gewig, voorbors omtrek, sowel as, kruisomtrek. Die ZB en KR rasse was swaarder as die SAB, en het groter liggaamsmetings gehad. Die SAB het beter reproduksie in vergelyking met die ZB- en KR rasse gehad. Heterose beramings was 2.2% vir kruisomtrek, 12% vir TEP, 12% vir uitbroeibaarheid en 19% vir CP. Genetiese variasie tussen en binne die rasse was vasgestel deur die gebruik van 19 mikrosatelliete merkers. Beduidende genetiese verskille op ‘n molekulêre vlak was waargeneem tussen die drie rasse. Die SAB en ZB (Fst = 0.10 en Nei = 0.49) was geneties meer gelyk terwyl die KR en ZB genetiese verder verwyder is (Fst = 0.13 en Nei = 0.61). Die SAB ras het die hoogste heterosigositeit binne populasie getoon, en die ZB die laagste. Hierdie resultate dra by tot ‘n beter begrip van die gebruik van die drie rasse in kommersïele produksie.

Ostrich (Struthio camelus) breeding is a well-developed industry in South Africa. However, successful genetic management has yet to be implemented. Parentage in colony breeding ostriches is unknown, where for a given offspring, a number of possible parents exist. Molecular markers have been extensively used in the livestock industry to resolve parentage issues and are only beginning to be utilized to address the issues of the ostrich industry. The aims of this investigation were to test known microsatellite markers developed for other ostrich subspecies in a South African Black ostrich population, and to further test these markers for their use in individual and parentage identification. DNA was extracted from venous blood obtained from two pair bred families and a colony of 97 individuals. Eleven polymorphic microsatellite markers were tested by PCR amplification of DNA samples followed by multiplexing on polyacrylamide gels to generate DNA fingerprints for each individual. Alleles were sized and quantified and used to create genotypes for each individual. Parentage analysis was performed using exclusion and likelihood methods. Pedigrees were constructed for the families by comparison of genotypes. Breeding statistics were calculated for the colony individuals. Three microsatellite markers did not amplify in this population and one marker was found to be monomorphic in this population. Four of the microsatellite markers that successfully amplified produced anonymous amplification products suggesting a second annealing site in the genome sequence of Blacks. All loci displayed low observed heterozygosities indicative of little genetic variation in this population. For the colony sample, four individuals were not assigned either parent and one female did not contribute any offspring. On average females produced 4.86 ± 2.71 fertile eggs during the sampling period with a coefficient of variation of 55.86%. A total of 79.2% of individuals were assigned paternity and 88.3% were assigned maternity. A greater number of loci are required to improve the power of parentage analysis within breeding flocks incorporating all eggs laid. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2005.