Thesis (Ph. D.)--University of Missouri-Columbia, 1996. / Typescript. Vita. Includes bibliographical references (leaves 116-131). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 1996. / Typescript. Vita. Includes bibliographical references (leaves 116-131). Also available on the Internet.

Thesis (M.A.)--University of North Carolina at Wilmington, 2006. / Includes bibliographical references (leaf: 24)

Thesis (MSc)--Stellenbosch University, 2008. / ENGLISH ABSTRACT: Haliotis midae, is the only commercially important species of the six abalone species found in South African coastal waters and has become a lucrative commercial commodity. Wild stocks of H. midae are, however, no longer commercially sustainable due to a combination of environmental factors and poaching. The solution to the crisis is artificial production systems in the form of abalone farms. An abalone enhancement programme was initiated in South Africa in 2006, funded by industry and government. This programme focuses on the elucidation of the abalone genome and genetic factors contributing to increased productivity, thereby aiding the commercial production of abalone. The aims of this study, the first of its kind concerning H. midae, were to develop AFLPbased markers (specifically fluorescent AFLP analysis); to monitor the segregation of these markers in a single full-sib family and to use the markers and additional microsatellite markers to generate the first preliminary linkage map for H. midae. Genomic DNA of sufficient quality and purity for fluorescent AFLP analysis was obtained from 3.5-month-old H. midae juveniles. Preliminary linkage maps were constructed using AFLP and microsatellite markers segregating in an F1 family following a pseudo-testcross mapping strategy. Twelve AFLP primer combinations, producing 573 segregating peaks, and 10 microsatellite markers were genotyped in the parents and 108 progeny of the mapping family. Of the 573 segregating AFLP peaks genotyped, 241 segregated in a 1:1 ratio and 332 in a 3:1 ratio. Of these AFLP markers, 90 segregated according to the expected 1:1 Mendelian ratio and 164 segregated according to the expected 3:1 Mendelian ratio at the P = 0.05 level and were used for linkage analysis. Of the 10 microsatellite markers genotyped, nine were informative for linkage mapping analysis. Preliminary male and female genetic linkage maps were developed using markers segregating in the female or male parent. A total of 12 and 10 linkage groups were detected for the female and male maps respectively. The female map covered 1473.5cM and consisted of 56 markers, and the male map covered 738.9cM consisting of 30 markers. Markers with segregation distortion were observed as previously reported in other abalone species and potential homology between one of the linkage groups of the male map and two of the linkage groups of the female map were identified using the 3:1 segregating AFLP markers. In conclusion, the genetic linkage map presented here, despite the fact that it has relatively low genome coverage and low marker density, forms an ideal starting point for more detailed study of the H. midae genome and will provide a scaffold for basic and applied studies in abalone. A high-density linkage map of H. midae should in future be developed with additional co-dominant molecular markers, such as microsatellites, to improve the transferability of the linkage map between different laboratories and among populations. A high-density linkage map will facilitate the mapping of QTL of commercially important traits (i.e. growth) and future MAS breeding programmes. / AFRIKAANSE OPSOMMING: Perlemoenspesie, Haliotis midae, is die enigste spesie van kommersiële belang van die ses wat in die kuswater van Suid-Afrika aangetref word en het ‘n winsgewende handelskommoditeit in Suid-Afrika geword. Die ontginning van natuurlike H. midae populasies is egter, as gevolg van ‘n kombinasie van omgewingsfaktore en stropery nie meer kommersieel volhoubaar nie. Die perlemoenkrisis kan die hoof gebied word deur kunsmatige produksiesisteme op perlemoenplase tot stand te bring. ‘n Perlemoen verbeteringsprogram is in 2006 in Suid-Afrika geïnisieer en word deur die industrie en regering befonds. Die program focus op die ontrafeling van die perlemoen genoom en die genetiese faktore wat bydrae tot verhoogde produksie. Sodanige inligting kan gebruik word om kommersiële perlemoenproduksie te bevorder. Die doel van hierdie studie, die eerste met H. midae, is om AFLP-gebaseerde merkers (spesifiek fluoresserende AFLP analise) te ontwikkel; die segregasie van hierdie merkers te monitor in ‘n enkel volledige verwante familie en die merkers en addisionele mikrosatelliet merkers te gebruik om die eerste voorlopige koppelingskaart vir H. midae te genereer. Genomiese DNS van genoegsame kwaliteit en suiwerheid vir fluoresserende AFLP analise is ge-ekstraeer uit 3.5-maand-oue H. midae individue. Voorlopige koppelingskaart is gekonstrueer deur van segregerende AFLP en mikrosatelliet merkers in ‘n F1 familie gebruik te maak deur ‘n pseudo-kruistoets karteringstrategie te volg. Twaalf AFLP inleier kombinasies, wat 573 segregerende fragmente geproduseer het, en 10 mikrosatelliet merkers is gegenotipeer in die ouers en 108 individue van die nageslag van die karteringsfamilie. Van die 573 segregerende AFLP merkers wat gegenotipeer is, het 241 in ‘n 1:1 verhouding en 332 in ‘n 3:1 verhouding gesegregeer. Van hierdie AFLP merkers, het 90 volgens die verwagte 1:1 Mendeliese verhouding en 164 volgens die 3:1 Mendeliese verhouding by die P = 0.05 gesegregeer vlak en is vir die koppelingsanalise gebruik. Van die 10 mikrosatelliet merkers gegenotipeer, was 9 informatief vir koppeling karteringsanalise. Voorlopige manlike en vroulike genetiese koppelingskaarte is ontwikkel met gebruik te maak van merkers wat in die manlike of vroulike ouer segregeer het. ‘n Totaal van 12 en 10 koppelingsgroepe is onderskeidelik in die vroulike en manlike karate gegenereer. Die vroulike kaart dek 1473.5cM and bestaan uit 56 merkers, terwyl die manlike kaart 738.9cM beslaan het met 30 merkers. Merkers wat segregasie distorsie toon is waargeneem soos voorheen in ander perlemoenspesies gerapporteer. Potensiële ooreenstemming tussen een van die koppelingsgroepe van die manlike kaart en twee van die koppelingsgroepe van die vroulike kaart is aangetoon deur van die 3:1 segregerende AFLP merkers gebruik te maak. Die genetiese koppelingskaarte verskaf wel ‘n relatiewe lae genoomdekking en ‘n lae merkerdigtheid, maar is ‘n ideale vertrekpunt vir meer gedetailleerde studie van die H. midae genoom en dien as ‘n raamwerk vir toekomstige basiese en toegepaste studies in perlemoennavorsing. ‘n Hoëdigtheid koppelingskaart van H. midae moet in die toekoms ontwikkel word met gebruik van bykomstige ko-dominante molekulêre merkers, soos mikrosatelliete. Dit sal die oordraagbaarheid van die koppelingskaart tussen verskillende laboratoria asook tussen populasies verbeter. ‘n Hoëdigtheid koppelingskaart sal die kartering van kwantitatiewe kenmerk loki (KKL) vir kommersieel belangrike kenmerke (onder andere groeikrag) en toekomstige merker bemiddelde seleksie (MBS) teelprogramme moontlik maak.

Thesis (MSc (Genetics))--University of Stellenbosch, 2010. / Includes bibliography. / Title page: Dept. of Genetics, Faculty of Science. / ENGLISH ABSTRACT: Haliotis midae, or Perlemoen, is the only cultured species of abalone in South Africa and is under great international demand. This species is considered endangered, making sustainable farming practises and law enforcement against poaching essential for maintaining wild stocks. A limited amount of broodstock animals are provided to each farm from which thousands of offspring are grown and exported. The prevention of inbreeding and preservation of genetic diversity within farmed stocks is necessary for future sustainable farming and production of genetically stable offspring. Further research into the genetic dynamics of Perlemoen will provide the knowledge for advanced management programs for optimal farming practises and essentially sustainable production. This study focuses on genetic linkage map development with the intention of future identification of markers associated with genes of economic importance, such as growth rate. Identification of markers linked to genes responsible for such phenotypic traits will ultimately allow farming practises to select naturally genetically superior animals for breeding, thereby enhancing production. For the construction of a genetic linkage map of H. midae, microsatellite markers were developed using two strategies: FIASCO and screening of next generation sequence-bysynthesis contig data. The FIASCO-derived markers were characterised by genotype screening in 32 individuals from a full-sib family and analysed using Mendelian segregation expectations. The Illumina-derived markers were characterised by genotype screening in 32 individuals from wild populations and analysed against Hardy-Weinberg expectations. Forty four microsatellite-family combinations were obtained from FIASCO of which 28 provided informative genotype results (32% success). Twenty two markers were developed from sequence-by-synthesis screening. Fourteen provided reliable genotypes (37%) and six conformed to Hardy-Weinberg expectations. These markers were used, in addition to 156 previously developed markers, to develop sex-specific and sex-average linkage maps in two full-sib families consisting of approximately 100 offspring each. One hundred and six polymorphic loci were used for linkage analysis (LOD>3) in both families. The number of linkage groups obtained from sex-specific maps ranged from 13-16. The average genome length ranged from 500 cM to 800 cM with an average marker spacing of 10 cM. The sex-average linkage map provided 18 linkage groups with an average genome length calculation of 1800 cM and average marker spacing of approximately 13 cM. The linkage maps created in this study are preliminary but provide a stepping stone towards a high density map incorporating high throughput markers. This also provides a base for QTL mapping studies, in which phenotypic traits of interest can be identified and associated to specific locations in the H. midae genome for marker-assisted selection. / AFRIKAANSE OPSOMMING: Haliotis midae, ook bekend as Perlemoen, is in groot internasionale aanvraag en is ook die enigste klipkous spesie waarmee in Suid Afrika geboer word. Hierdie spesie word as bedreig beskou en daarom is volhoubare boerdery bedrywe en wetstoepassing teen stroping noodsaaklik om wilde populasies te beskerm. Elke perlemoenplaas word met ‘n beperkte aantal broeidiere verskaf, waarvan die nageslag dan gekweek en uitgevoer word. Voorkoming van inteling en handhawing van genetiese diversiteit binne gekweekte populasies is noodsaakllik vir toekomstige volhoubare kweking en produksie van ń geneties stabiele nageslag. Verdere ondersoeke na die genetiese dinamika van Perlemoen sal die nodige kennis verskaf om sodoende gevorderde bestuursprogramme te ontwikkel, wat tot optimale kweek praktyke en effektiewe volhoubare produksie sal lei. Hierdie studie fokus op die ontwikkeling van ‘n genetiese koppelingskaart met die voorneme om toekomstige merkers te identifiseer wat met gene van ekonomiese belang, soos byvoorbeeld groei tempo geassosieerd is. Identifisering van merkers wat vir sulke fenotipiese eienskappe verantwoordelik is sal sodoende toelaat dat boerdery praktyke kan selekteer vir diere vir verbeterde teling en produksie. Mikrosatelliet merkers is ontwikkel om die genetiese koppelingskaart saam te stel. Die volgende twee strategieë is benut: FIASCO en sifting van volgende generasie volgordebepaling-deur-sintese “contig” data. Die FIASCO-afgeleide merkers is gekarakteriseer deur genotipiese sifting in 32 individue van ‘n volsib familie en is deur Mendeliese segregasie verwagtinge ge-analiseer. Die Illumina-afgeleide merkers is gekarakteriseer deur genotipiese sifting in 32 individue van wilde populasies en is met Hardy-Weinberg ewewig ge-analiseer. Vier en veertig mikrosatelliet-familie kombinasies is deur FIASCO verky, waarvan 28 informatiewe genotipiese resultate gelewer het (32% sukses). Twee en twintig merkers is vanaf volgordebepaling-deur-sintese sifting ontwikkel. Veertien van hierdie merkers het betroubare genotipes (37%) verskaf en ses het aan Hardy-Weinberg verwagtinge voldoen. Hierbenewens is 156 voorheen ontwikkelde merkers gebruik om geslagspesifieke en geslagsgemiddelde koppelingskaarte in twee volsib families saam te stel. Hierdie volsib families het uit ń naslag van 100 elk bestaan. Een honderd en ses polimorfiese lokusse is vir koppelingsanalise gebruik, waar ‘n LOD waarde groter as drie statisties betekenisvol geag was. Die aantal koppelingsgroepe verkry van geslagspesifieke kaarte het tussen 13 en 16 gewissel. Die gemiddelde genoom lengte het van 500 cM tot 800 cM met ‘n gemiddelde merker spasiëring van 10 cM. Die geslagsgemiddelde koppelingskaart het 18 koppelingsgroepe gehad met ‘n gemiddelde genoom lengte berekening van 1800 cM en ‘n gemiddelde merker spasiëring van ongeveer 13 cM. Die koppelingskaarte wat in hierdie studie geskep is, is voorlopig en verskaf ‘n grondslag vir die ontwikkeling van ‘n hoër digtheidskaart, wat hoë deurset merkers inkorporeer. Dit verskaf ook ‘n basis vir kwantitatiewe kenmerk lokus karteringstudies. Hierdie karteringstudies kan fenotipiese eienskappe van belang identifiseer en assosieer met spesifieke posisies binne die H. midae genoom vir merker bemiddelde seleksie.

Made available in DSpace on 2014-06-11T19:26:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-07-20Bitstream added on 2014-06-13T18:54:02Z : No. of bitstreams: 1 valente_ts_me_jabo.pdf: 897721 bytes, checksum: 4458844f82fdd959839e922f15297ae3 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Este trabalho foi desenvolvido com o objetivo de estudar a associação genética entre características indicadoras de temperamento e de precocidade sexual de fêmeas bovinas da raça Nelore. Foram utilizados dados de temperamento de 7.500 bovinos machos e fêmeas com 18 meses de idade (sobreano) das safras de 2008 e 2009 da Agropecuária Jacarezinho Ltda. (AJ). As características indicadoras de precocidade sexual das fêmeas foram obtidas a partir do arquivo zootécnico da fazenda, para animais nascidos entre os anos de 1984 e 2009. O temperamento foi avaliado durante o manejo de pesagem ao sobreano por meio do teste de movimentação na balança (MOV), atribuindo-se escores de 1 (nenhum movimento) a 5 (animal salta, elevando os membros superiores pelo menos 2,5 centímetros do solo), teste de velocidade de fuga (VF), com uso de um dispositivo de células fotoelétricas que registra o tempo (em segundos) para percorrer uma distância determinada ao sair do tronco de contenção após o manejo de pesagem e o escore de temperamento (ET) realizado pela AJ, atribuindo-se escores 1 (animal calmo) a 5 (animal muito reativo – comportamento agressivo ao observador). Como características indicadoras de precocidade sexual foram utilizadas: a idade ao primeiro parto, em dias (IPP) e a ocorrência de prenhez precoce (PRECO), característica binária, com escore 2 para as novilhas que pariram até 30 meses de idade e escore 1 para as que falharam. Para a estimação dos componentes de (co)variância e parâmetros genéticos para as características estudadas foi utilizada a Inferência Bayesiana. Para VF e IPP foi utilizado um modelo linear e para MOV, ET e PRECO um modelo não-linear (threshold). As estimativas de herdabilidade a posteriori para VF, MOV, ET, IPP e PRECO foram 0,27, 0,11, 0,16, 0,09 e 0,44, respectivamente. As correlações... / The aim of this study was to estimate genetic associations between temperament and female sexual precocity traits in Nellore beef cattle. The temperament was assessed for 7,500 male and female cattle, at 18 months of age (yearling) and born in 2008 and 2009, from the herd of Agropecuária Jacarezinho Ltda. (AJ). The female sexual precocity traits were obtained from the files of the farm for animals born between 1990 and 2009. Temperament was evaluated during the handling for weight determination using a movement score (MOV), assigning scores from 1 (no movement) to 5 (animal jumps, raising the forelegs at least 2.5 cm of the soil); the flight speed (VF), using an electronic device that records the speed at which the animals exit the crush (in m/s) and; temperament score (ET), already in use by AJ, assigning a score from 1 (animal calm) to 5 (animal very reactive - aggressive behavior toward the observer). The female sexual precocity traits used were: age at first calving, in days (IPP) and; occurrence of precocious pregnancy (PRECO), a binary trait in scores of 2 for heifers that calved until 30 months of age and, 1 for the heifers that failed. Bayesian Inference was used for estimation of (co)variance components and genetic parameters. For VF and IPP, a linear model was applied and for MOV, PRECO and ET, a threshold model. The heritability estimates for VF, MOV, ET, IPP and PRECO were 0.27, 0.11, 0.16, 0.09 and 0.44, respectively. The genetic correlations of IPP with VF (0.14), MOV (0.13) and ET (0.09) were all low, as well as for PRECO with VF (-0.19), MOV (-0.03) and ET (-0.03). Although low, all correlations were in a favorable direction, indicating that the temperament is positively associated with sexual precocity. These results suggest that to improve the beef cattle temperament and the sexual precocity, these traits... (Complete abstract click electronic access below)

Orientador: Luciana Rossini Pinto / Coorientador: Renato Vicentini dos Santos / Banca: Dilermando Perecin / Banca: Gustavo Vitti Môro / Banca: Fernanda Raquel Camilo dos Santos / Banca: Michael dos Santos Brito / Resumo: O genoma do sorgo tem sido utilizado como referência em estudos de genômica funcional e comparativa em cana-de-açúcar. A utilização do genoma do sorgo, em estudos de mapeamento comparativo, tem contribuído para auxiliar a detecção de QTL (locus de caracteres quantitativos) em cana-de-açúcar. Marcadores microssatélites de sorgo podem ser empregados no mapeamento comparativo com a cana-de-açúcar, assim como, o desenvolvimento de marcadores microssatélites a partir de sequências ortólogas conservadas (COS - Conserved Orthologous Sequences) podem servir de "marcadores âncoras" entre estas duas espécies. No presente trabalho, marcadores microssatélites de sorgo foram incorporados em um mapa prévio de ligação derivado do cruzamento entre o clone IACSP95-3018 e a cultivar IACSP93-3046, ambos do Programa de Melhoramento Genético de Cana-de-Açúcar do Instituto Agronômico de Campinas (IAC). Paralelamente, um conjunto de marcadores microssatélites obtidos a partir da identificação de sequências expressas ortólogas conservadas (COS) entre cana-de-açúcar e sorgo foram desenvolvidos e avaliados quanto ao seu potencial de polimorfismo e mapeamento em cana-de-açúcar. Os marcadores obtidos também foram utilizados para identificar associações putativas aos parâmetros de qualidade (Fibra% e Pol%Cana). Um total de 41 pares de microssatélites COS-EST-SSRs foi desenhado, dos quais 34 produziram amplicons em um grupo de 24 genótipos de Saccharum e Sorghum. O número de alelos variou de 2 a 15 com va... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Sorghum genome has been used as a reference in functional and comparative genomics studies of sugarcane. The sorghum genome has aided to colocalize QTL (quantitative trait locus) in sugarcane through comparative mapping approach. Sorghum microsatellite markers, as well as, the development of microsatellite markers derived from orthologous conserved sequences (COS) can serve as "anchors markers" in comparative mapping between these two species. In the present study, sorghum microsatellite markers were included in a previous map derived from a bi-parental cross between a clone (IACSP95-3018) and a sugarcane cultivar (IACSP93-3046) from the Instituto Agronômico de Campinas (IAC) sugarcane breeding program. A set of microsatellite markers derived from conserved orthologous (COS-EST-SSRs) sequences between sugarcane and sorghum was developed and evaluated for their polymorphism and mapping potential in sugarcane. These markers were also used to identify putative associations for sugarcane quality parameters (fiber% and Pol% Cane). A total of 41 COS-EST-SSRs primer pairs was designed, of which 34 produced amplicons in a group of 24 genotypes of Saccharum and Sorghum. The number of alleles ranged from 2 to 15 with an PIC (polymorphism information content) average value of 0.71. The 29 sorghum SSR primer pairs along with the 41 COS-EST-SSR primer pairs was genotyped in the mapping population and produced a total of 120 polymorphic markers, of which 92 were single dose markers. Of the... (Complete abstract click electronic access below) / Doutor

Two plaque-pure phage lambda clones designated as λhtX-l and λhtX-2 that hybridized to unfractionated bovine liver tRNA were isolated from a human X chromosome-specific library. The λDNAs were characterized by restriction mapping and Southern blot hybridization techniques. The human DNA segment in λhtX-l contains five or more presumptive tRNA genes and at least one Alu family member. The 19-kilobase human DNA insert in λhtX-2 contains two or more presumptive tRNA genes and at least three Alu family members. Another human genomic clone designated λhVKV7 hybridized to mammalian valine tRNA IAC. The clone was characterized by physical mapping and Southern blot hybridization techniques. The 18.5-kilobase human DNA fragment in λhVKV7 contains a cluster of three tRNA genes and at least nine Alu family members.

Philosophiae Doctor - PhD / With easy access to technology to generate expressed sequence tags (ESTs), several groups have sequenced from thousands to several thousands of ESTs. These ESTs benefit from consolidation and organization to deliver significant biological value. A number of EST projects are underway to extract maximum value from fragmented EST resources by constructing gene indices, where all transcripts are partitioned into index classes such that transcripts are put into the same index class if they represent the same gene. Therefore a gene index should ideally represent a non-redundant set of transcripts. Indeed, most gene indices aim to reconstruct the gene complement of a genome and their technological developments are directed at achieving this goal. The South African National Bioinformatics Institute (SANBI), on the other hand, embarked on the development of the sequence alignment and consensus knowledgebase (STACK) database that focused on the detection and visualisation of transcript variation in the context of developmental and pathological states, using all publicly available ESTs. Preliminary work on the STACK project employed an approach of partitioning the EST data into arbitrarily chosen tissue categories as a means of reducing the EST sequences to manageable sizes for subsequent processing. The tissue partitioning provided the template material for developing error-checking tools to analyse the information embedded in the error-laden EST sequences. However, tissue partitioning increases redundancy in the sequence data because one gene can be expressed in multiple tissues, with the result that multiple tissue partitioned transcripts will correspond to the same gene.Therefore, the sequence data represented by each tissue category had to be merged in order to obtain a comprehensive view of expressed transcript variation across all available tissues. The need to consolidate all EST information provided the impetus for developing a STACK human gene index, also referred to as a whole-body index. In this dissertation, I report on the development of a STACK human gene index represented by consensus transcripts where all constituent ESTs sample single or multiple tissues in order to provide the correct development and pathological context for investigating sequence variation. Furthermore, the availability of a human gene index is assessed as a diseasecandidate gene discovery resource. A feasible approach to construction of a whole-body index required the ability to process error-prone EST data in excess of one million sequences (1,198,607 ESTs as of December 1998). In the absence of new clustering algorithms, at that time, we successfully ported D2_CLUSTER, an EST clustering algorithm, to the high performance shared multiprocessor machine, Origin2000. Improvements to the parallelised version of D2_CLUSTER included: (i) ability to cluster sequences on as many as 126 processors. For example, 462000 ESTs were clustered in 31 hours on 126 R10000 MHz processors, Origin2000. (ii) enhanced memory management that allowed for clustering of mRNA sequences as long as 83000 base pairs. (iii) ability to have the input sequence data accessible to all processors, allowing rapid access to the sequences. (iv) a restart module that allowed a job to be restarted if it was interrupted. The successful enhancements to the parallelised version of D2_CLUSTER, as listed above, allowed for the processing of EST datasets in excess of 1 million sequences. An hierarchical approach was adopted where 1,198,607 million ESTs from GenBank release 110 (October 1998) were partitioned into "tissue bins" and each tissue bin was processed through a pipeline that included masking for contaminants, clustering, assembly, assembly analysis and consensus generation. A total of 478,707 consensus transcripts were generated for all the tissue categories and these sequences served as the input data for the generation of the wholebody index sequences. The clustering of all tissue-derived consensus transcripts was followed by the collapse of each consensus sequence to its individual ESTs prior to assembly and whole-body index consensus sequence generation. The hierarchical approach demonstrated a consolidation of the input EST data from 1,198607 ESTs to 69,158 multi-sequence clusters and 162,439 singletons (or individual ESTs). Chromosomal locations were added to 25,793 whole-body index sequences through assignment of genetic markers such as radiation hybrid markers and généthon markers. The whole-body index sequences were made available to the research community through a sequence-based search engine (http://ziggy.sanbi.ac.za/~alan/researchINDEX.html). / South Africa

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