Maize (Zea mays L.) is an important agronomic crop with the maize industry forming an important component of the South African economy. Considerable effort has been directed towards the genetic improvement of maize through both conventional breeding and biotechnology. Genotype identification by DNA fingerprinting is becoming an important activity in plant breeding. A widely used molecular based and relatively inexpensive method for DNA fingerprinting is the randomly amplified polymorphic DNA (RAPD) technique. The RAPD technique was tested in this study for its potential use in maize breeding programmes. Initial results using the technique showed a low degree of reproducibility, therefore both the DNA isolation and RAPD protocols were extensively optimised. DNA quality and quantity, and choice of Taq polymerase buffer were three of the variables found to be influential in ensuring reproducibility. The ability of the RAPD technique to characterise seven maize genotypes was evaluated. Sixty random oligonucleotide primers were screened. Forty two primers scored a total of 233 fragments (an average of 5.5 per primer), but not all primers gave reproducible profiles. Eighteen primers scored a total of 110 loci for the presence (1) and absence (0) of DNA fragments. RAPD markers were able to distinguish between all seven genotypes with five primers producing specific fragments for four genotypes. Genetic similarity matrices were calculated using two software programmes i.e. Genstat 5™ release 4.1 (1993) and PAUP (Phylogenetic Analysis Using Parsimony) 4.0 beta version (Swafford, 1998). Cluster analysis was used to generate dendrograms to visualise the genetic relationships of the seven maize genotypes (only minor differences were observed between the Genstat or PAUP method of analysis). Genetic diversity ranged from 0.62 to 0.96. The estimation of genetic relationship was in accordance with the presumed pedigree of the genotypes showing that the RAPD technique demonstrates potential for genome analysis of maize. The applicability of the technique for marker assisted selection was also evaluated. Near-isogenic lines (NILs) for leaf blight (Helminthosporium spp.) were screened for polymorphisms using a total of 120 primers. Ten primers identified polymorphisms between the NILs. Four primers produced five polymorphic fragments present in the resistant inbred K0315Y and absent in the susceptible inbred D0940Y. A small F2 population of 14 individuals was produced by selfing the F1 of a cross between K0315Y and D0940Y. To speed up the generation time, the F1 and F2 plants were cultured by embryo rescue from 18d old harvested seed. One fragment of 627 base pairs produced by primer OPB-01 (5' GTTTCGCTCC 3') showed a 3: 1 segregation in the small F2 population and was considered putatively linked to the HtN gene for leaf blight resistance. This study shows that the RAPD technique does have application in maize breeding programmes. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 2000.

The objective of this thesis was to test for associations between genetic polymorphisms of genes related to immune response (growth hormone (GH), growth hormone receptor (GHR), ornithine decarboxylase (ODC), insuline-like growth factor-1 (IGF-1), adrenocorticotropin hormone (ACTH), corticotrophin releasing hormone (CRH), and prolactin (PRL)) and mastitis resistance traits (incidence of clinical mastitis (ICM), occurrence of clinical mastitis (OCM), culling due to mastitis (CDM), and somatic cell scores (SCS)) in Canadian Holsteins. / Using lactation records of cows enrolled in milking recording in Quebec (Programme d'Analyse des Troupeaux Laitiers du Quebec, PATLQ from 1980 to 1994 (411,291 first, 238,432 second, and 130,983 third lactations, respectively) Estimated Transmitting Abilities of traits were generated with a model that included the random effect of sire, and fixed effects of herd-year-season-of calving, age at calving, and genetic group. 721 bulls which had daughters in the phenotypic data sets were genotyped for twenty polymorphisms of the above genes located on autosomes (BTA) 5, 11, 14, 19, 20, and 23. / Two types of analysis of associations were performed: analysis across-population with a model that included the fixed effect of marker and random effect of the son of grandsire, and within-family analysis with a model that included the fixed effects of the grandsire, marker nested within grandsire, and the random effect of son nested within marker and grandsire. Permutation tests were performed to reduce Type I error probability. / Significant associations were found within families for markers of IGF-1 (BTA5), ODC (BTA11), GH (BTA 19), GHR (BTA 20), and PRL (BTA 23) for ICM, OCM, CDM, and SCS in different lactations. Some of these putative quantitative trait loci (QTL) are located on BTA where other authors have reported QTL affecting SCS and udder conformation. The results from this study may contribute to efforts to dissect the genetic basis of mastitis resistance in dairy cattle.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2007. / Härtill 5 uppsatser.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2007. / Härtill 4 uppsatser.

Thesis (Ph.D. in Human Medical Genetics) -- University of Colorado Denver, 2008. / Typescript. Includes bibliographical references (leaves 112-128). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;

Thesis (Ph. D.)--University of Oklahoma. / Bibliography: leaves 106-134.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2010. / Härtill 4 uppsatser.

Thesis (MScAgric)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: Research into markers for the detection of genetic diversity and cultivar identification has become an important component of the genetic improvement of crops. However, the incorporation of marker assisted selection (MAS) as a tool for the identification and characterization of breeding material has not been fully implemented in the breeding of spring triticale at Stellenbosch University’s Plant Breeding laboratory (SU-PBL). The present study served as a case study in order to achieve this. The first part of the study concerned the detection of genetic diversity in 101 newly sourced triticale cultivars, from a USDA germplasm bank, together with five local control cultivars, in order to identify possible crossing parents. Eight SSR markers, including five derived from rye and three from wheat, and five agronomic characteristics were used to assess diversity. In seedling screening the foreign cultivars showed resistance towards the stem rust isolate used, but were mostly susceptible to the leaf rust isolate. Out of the 8 SSR markers tested, 7 markers were polymorphic and revealed 140 alleles varying from 12 to 26 with an average of 17.5 alleles per locus. The observed polymorphic information content (PIC) value ranged from 0.39 to 0.88 with an average of 0.70, indicative of the good discriminatory ability of the SSR markers. The data revealed that the South African cultivars were genetically closely related to cultivars from the USA and Canada. The second part of the study focused on the introgression of a blue aleurone layer gene (Ba), carried by a wheat cultivar, ‘Cltr1202STR’, and purple pericarp genes (Pp1; Pp3) also carried by a wheat cultivar, ‘Amethyst’, into a triticale background. Unfortunately the introgression of the purple pericarp genes failed. Two lines containing the blue aleurone layer, 11T023 and 11T028, were however successfully created. Molecular typing of these lines with SSR markers were able to show that BC4F1 line 11T023 (Ba) B was genetically similar to the recurrent parent ‘Agbeacon’; and that the BC4F1 11T028 line (Ba) A was closest to the ‘US2007’ recurrent parent. The study illustrated that MAS was a reliable tool for detecting genetic diversity in newly sourced germplasm, and assisted in making a backcross breeding effort more effective. The data generated from MAS could therefore clearly assist in making the SU-PBL breeding program more effective by moving, better informed, decision making toward data based partly on the genotype, thereby minimizing the risks associated with purely phenotypic based decisions. / AFRIKAANSE OPSOMMING: Navorsing rondom die gebruik van merkers vir die bepaling van genetiese-diversiteit en kultivar identifikasie is ‘n toenemend belangriker komponent vir die genetiese verbetering van gewasse. Die inkorporering van merker-bemiddelde-seleksie (MBS) as gereedskap vir die identifikasie en karaktarisering van telingsmateriaal is nog nie ten volle geïmplimenteer in die lente korogtelingsprogram van die Stellenbosch Universiteit Planteteeltlaboratorium (SU-PTL). Die studie het gedien as gevallestudie ten einde dit te bereik. Die eerste gedeelte van die studie het gehandel oor die tipering van die genetiese diversiteit van ‘n 101 kultivars verkry vanaf ‘n USDA kiemplasmabank saam met 5 plaaslike kontroles. Dit was gedien ten einde moontlike kruisings-ouers te kon identifiseer. Agt SSR merkers, insluitend vyf afkomstig van rog en drie vanaf koring, asook vyf agronomiese kenmerke is aangewend om die materiaal se diversiteit te tipeer. Saailingtoetsing is ook gedoen en het aangetoon dat die meeste kultivars weerstandig was vir die stamroes-isolaat, maar nie die blaarroes-isolaat nie. Van die agt SSR merkers getoets het sewe getoon om polimorfies te wees en het ‘n 140 allele gegee wat gewissel het vanaf 12 tot 26 per lokus met ‘n gemiddeld van 17.5. Die waargenome polimorfiese inligtings inhoud (PII) waarde het gewissel vanaf 0.39 tot 0.88 met ‘n gemiddeld van 0.70. Die merkers kon dus suksesvol diskrimineer. Die data het aangetoon dat die Suid-Afrikaanse kultivars genetiese die naaste verwant was aan die kultivars afkomstig vanaf die VSA en Kanada. Die tweede gedeelte van die studie het gefokus op die introgressie van ‘n blou aleuron-laag geen (Ba), afkomstig vanaf die koringkultivar ‘Cltr1202STR’, en twee pers-perikarp gene (Pp1; Pp3), afkomstig vanaf die koringkultivar ‘Amethyst’, na ‘n korog agtergrond. Ongelukkig het die oordrag van die pers-perikarp gene gefaal. Twee lyne wat die blou aleuron- laag bevat, 11T023 en 11T028, is egter suksesvol geskep. Tipering van die lyne met die SSR merkers het aangetoon dat die BC4F1 lyn 11T023 (Ba) B genetiese baie na aan die herhalende ouers ‘Agbeacon’ is en dat die BC4F1 11T028 lyn (Ba) A nader is aan die herhalende ouer ‘US2007’. Die studie het dus geïllustreer dat MBS gebruik kan word as ‘n betroubare manier om genetiese diversiteit te bepaal en by te dra tot die sukses van ‘n terugkruisingsprogram. Die data wat dus voortspruit uit MBS kan dus help om die SU-PTL se telingsprogram te assisteer in die besluitnemingsproses tydens teling deur beter genotipe gebaseerde besluite te neem wat die riskio van fenotipe gebaseerde besluite kan help verminder.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Haliotis midae (commonly referred to as perlemoen) is the only one of five endemic species in South Africa that is commercially valued both locally and internationally. Unfortunately, natural perlemoen populations have become a dwindling resource due to commercial exploitation, poaching and the influx of natural threats, such as the West Coast rock lobster, Jasus lalandii. To preserve the natural diversity and sustainability of natural populations as well as commercial stocks, genetic management and improvement of perlemoen is critical. Genetic management requires the utilisation of molecular markers, which aid in the construction of linkage maps and the identification of quantitative trait loci (QTL) associated with economically significant traits. This will allow improvement of commercial stock management in terms of broodstock selection as well as provide valuable insight into natural population dynamics. Single Nucleotide Polymorphisms (SNPs) were selected as the marker of choice due to their successful employment as molecular markers and their wide distribution and abundance within the genomes of various marine species. This study focuses on the characterisation of novel SNPs from transcript sequences generated by Next Generation Sequencing technology. Approximately 40% of the transcripts facilitated the isolation of 105 putative markers, indicating a SNP frequency of ~1% within the H. midae genome. A subset of 24 markers, in addition to 24 previously developed markers, was characterised using the Illumina GoldenGate genotyping assay with the VeraCode technology, a medium to high-throughput genotyping technology. This is the first reported medium- to highthroughput characterisation of SNPs in H. midae. The selected markers were used to determine the efficiency and overall success rate of the GoldenGate platform. Marker characterisation was completed in both natural and commercial populations to determine the utility of these markers for genetic diversity and population structure inference. An 85% genotyping success rate was achieved with the platform. Statistical analysis indicated that the markers developed in this study are suitable for applications including population genetic structure inference, genetic diversity estimation and possibly other downstream applications such as linkage mapping. These markers are considered to be invaluable for future work regarding the genetic management and conservation of H. midae. / AFRIKAANSE OPSOMMING: Haliotis midae (ook bekend as perlemoen) is die enigste van vyf inheemse spesies in Suid-Afrika wat noemenswaardige kommersiële waarde toon plaaslik sowel as internasionaal. Ongelukkig het kommersiële uitbuiting, wildstropery en natuurlike bedreiging (bv. die Weskus kreef Jasus lalandii), wilde perlemoen populasies noemenswaardig verminder. Dus, om natuurlike diversiteit en die voortbestaan van beide wilde en kommersiële populasies te beskerm, is genetiese bestuur en verbetering absoluut noodsaaklik. Genetiese bestuur vereis die gebruik van molekulêre merkers as ’n hulpmiddel in die opstellingvan koppelingskaarte, en die identifisering van die relevante kwantitatiewe eienskap loki (QTL) tipies geassosieer met ekonomies belangrike eienskappe. Die laasgenoemde beoog om kommersiële voorraad bestuur te verbeter, kragtens deur broeidier seleksie sowel as om insig te verskaf m.b.t. wilde bevolking dinamika. Enkel Nukleotied Polimorfismes (SNPs) is gekies as die toepaslike merker vanweë die omvattende toepaslikheid van hierdie merkers binne die genome van verskeie mariene spesies. Hierdie studie fokus op die karakterisering van nuwe SNPs vanuit transkript volgordes ontwikkel deur middel van Volgende Generasie Volgordebepaling (“Next Generation Sequencing”). ’n Beraamde 40% van transkripte het gelei tot die ontwikkeling van 105 potensiëlemerkers, aanduidend van ’n SNP frekwensie van ~1% binne die H. midae genoom. ’n Sub-versameling van 24 merkers, tesame met 24 bestaande merkers, is gekarakteriseer deur die Illumina GoldenGate genotiperings toets met die VeraCode tegnologie, ’n medium tot hoë deurvloei genotiperingstegnologie. Hierdie is die eerste berig van medium tot hoë deurvloei karakterisering van SNPs in H. midae. Die geselekteerde merkers is gebruik om die doeltreffendheid van die GoldenGate platform te bepaal. Merker karakterisering is uitgevoer in beide wilde en kommersiële bevolkings om die effektiewe bruikbaarheid van hierdie merkers m.b.t. genetiese diversiteit, en bevolking struktuur bepaling, te ondersoek. Die platform het ’n 85% genotiperingsukses syfer getoon. Statistiese analise dui daarop dat merkers ontwikkel tydens hierdie studie toepaslik is vir bevolking genetiese struktuur bepaling, genetiese diversiteitberaming en moontlik ook genetiese koppelingskartering. Hierdie merkers word bestempel as onmisbaar vir toekomstige navorsing in genetiese bestuur en bewaring van H. midae.

Thesis (MSc)--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: The indigenous abalone Haliotis midae is one of the most remarkable and highly exploited species of marine molluscs in South Africa. It is the only species of southern African Haliotidae to be commercially reared and has been successfully cultured for almost two decades. Its short history of domestication along with market demands and the need to develop efficiency in the production process has resulted in an increased interest in the possible genetic improvement of this species. The unhurried growth rate associated with H. midae is a cause of particular concern to the industry, predominantly with regards to profitability and competitiveness in the market place. A modest amount of work has so far been directed at establishing a means of enhancement for selective breeding on the commercial level. Genetics plays a key role in the establishment of successful improvement programmes in various aquaculture species. The aim of this study was to develop species-specific microsatellite markers for the abalone and subsequently perform parentage assignment on farm produced animals entered into a growth performance recording scheme. Animals were obtained from the hatcheries of three commercial abalone farms situated in the Walker Bay region in the Western Cape. Microsatellites were isolated using the enrichment-based FIASCO method, and characterised into perfect, imperfect and compound repeats according to the structural nature of their repetitive units. From the partial gDNA libraries obtained and 365 screened colonies, a total of 54 loci were located. PCR primers were designed for 36 markers and the 15 primer pairs that displayed loci with the highest level of polymorphism were subsequently chosen for fluorescent labelling. The markers were tested on a subset of 32 wild H. midae individuals to determine their usefulness and efficiency in genotyping. Five markers, along with five others that were previously designed, were chosen for assigning parentage to the animals submitted to the performance recording scheme. Three thousand offspring from each of the three participating farms were equally divided and reared at five different locations. From each location 20 fast growing and 20 slow growing juveniles, as well as the broodstocks, were sampled and genotyped using the ten chosen microsatellite loci. Two farms had 60% of offspring unambiguously assigned to a single parental couple. Assignments showed patterns of dominant male and female brooders, but no trend in brooders specifically contributing to fast or slow growing offspring. Parentage assignment for the third farm was, however, unsuccessful due to lack of broodstock data. In future, screening of all available broodstock will ensure acquisition of relevant pedigree information. The results obtained in this study are an initial step in the development of a genetic improvement programme for commercial Haliotis midae. / AFRIKAANSE OPSOMMING: Die inheemse skulpvis Haliotis midae is een van die mees merkwaardige en hoogs oorbenutte mariene slakspesies in Suid-Afrika. Dit is die enigste suidelike Afrika Haliotidae spesie wat kommersieel benut word en dit word al meer as twee dekades suksesvol geteel. Die spesie se kort domestiseringsgeskiedenis, toenemende mark aanvraag en die behoefte om meer effektiewe produksie daar te stel, het gelei tot toenemende belangstelling in die moontlike genetiese verbetering van die spesie. Die stadige groeitempo geassosieer met H. midae is veral ‘n punt van kommer vir die industrie, veral in terme van winsgewendheid en kompetering in die markplek. Minimale werk is sover gedoen in die daarstelling van verbetering deur selektiewe teling op ‘n kommersiële skaal. Genetika speel ’n sleutelrol in die daarstelling van suksesvolle verbeteringsprogramme van verskeie akwakultuur spesies. Die doel van hierdie studie was om spesie-spesifieke mikrosatelliet merkers vir perlemoen te ontwikkel en vervolgens ouerskapsbepaling van kommersiële diere, wat deelneem aan ‘n groeiprestasie aantekenstelsel, uit te voer. Diere is voorsien deur die teelstasies van drie kommersiële perlemoenplase geleë in die Walker Bay omgewing in die Wes-Kaap. Mikrosatelliete is geïsoleer deur die verrykings-gebaseerde FIASCO metode, en gekarakteriseer as perfekte, onderbroke of saamgestelde herhalings gebaseer op die strukturele aard van die herhalings eenhede. Vanaf die gedeeltelik gDNA biblioteke wat bekom is en 365 gesifte kolonies, is ‘n totaal van 54 loki opgespoor. PKR inleiers is ontwerp vir 36 merkers en die 15 inleierpare, wat loki met die hoogste polimorfisme geamplifiseer het, is vervolgens geselekteer vir fluoreserende merking. Die merkers is getoets op ’n kleiner groep van 32 natuurlike H. midae individue om hulle bruikbaarheid en genotiperingseffektiwiteit te bepaal. Vyf merkers is saam met vyf reeds ontwikkelde merkers gekies vir ouerskapsbepaling van die diere in die prestasie aantekenstelsel. Drieduisend nageslag diere vanaf elkeen van die drie deelnemde plase is gelykop verdeel en grootgemaak op die vyf verskillende lokaliteite. ‘n Monster van 20 vinnig groeiende en 20 stadig groeiende jong perlemoen, sowel as broeidiere, is vanaf elke lokaliteit geneem en gegenotipeer deur middel van die 10 geselekteerde mikrosatelliet loki. Sestig persent van twee van die plase se nageslag is onteenseglik toegesê aan ‘n enkele ouerpaar. Ouerskapstoekenning het patrone van dominante vroulike en manlike broeidiere getoon, maar geen tendens in terme van bydrae tot vinnig en stadig groeiende nageslag kon gevind word nie. Ouerskapstoekenning vir die derde plaas was onsuksesvol as gevolg van ’n gebrek aan data vir die broeidiere. In die toekoms sal genotipering van alle beskikbare broeidiere die daarstelling van relevante stamboominligting verseker. Die resultate verkry in hierdie studie verteenwoordig ‘n eerste stap in die ontwikkeling van ’n genetiese verbeteringsprogram vir kommersiële Haliotis midae.