Thesis (Ph. D.)--University of Canterbury, 2008. / Typescript (photocopy). Includes bibliographical references. Also available via the World Wide Web.

Thesis (Ph.D.)--University of Wollongong, 2004. / Typescript. Includes bibliographical references: p. 241-260.

Thesis (MSc)--University of Stellenbosch, 2008. / ENGLISH ABSTRACT: The five leading abalone producers in South Africa have initiated a genetic enhancement program for Haliotis midae in a collaborative effort to improve economically valuable traits. Several independent objective-specific studies were initiated, including the establishment of a Performance Recording Scheme (PRS), utilised in this study, and necessary to monitor the ongoing performance of individuals as the move from mass-selection to marker assisted selection (MAS) is implemented. The primary objective of this study was parentage assignment of F1 offspring mass-selected for size at approximately one year and allocated to either a “faster” or a “slower” growth group. Nine microsatellite markers were used to genotype juveniles and potential parents, with assignment completed using CERVUS 2.0. Average growth results for Abagold and HIK were comparable for both growth groups. Slight environmental effects, although not statistically significant, were evident as growth advantages for juveniles within the faster growth group at two of the five locations and for juveniles within the slower growth group at one of the five rearing locations. Despite measures to standardise environmental influences, variables are difficult to control within the reality of a production environment; and potential genotype x environment interactions may require further investigation and factoring into future breeding programs. The additional costs associated with MAS often make the technology prohibitive to most aquaculture operations, despite the significant genetic gains to be realised from its implementation. Cost-optimising routine processes such as DNA extractions may be one approach to reduce these additional costs. Chelex®100 appears to be a suitable alternative to the CTAB method – being quick and cost-effective to perform. Applying this method in combination with the high throughput of a robotic platform warrants further evaluation. For the microsatellite development, 50% of positive recombinant clones contained inserts. Sequencing of these clones produced 16% perfect repeats and 47% imperfect repeats for which 52 primer sets were designed and tested. In total, 31 polymorphic microsatellite loci of different motifs and composition were developed. Sixty-one percent of sequenced clones were deemed redundant and pre-screening for both uniqueness and the presence of microsatellites would reduce unnecessary sequencing thus improving the efficiency of the FIASCO method and reducing costs. Nine loci were selected for parentage assignments. Null alleles were present for all the selected markers; however, frequencies were below the critical level of 5%. Parentage yielded 91% and 90% successful assignment for Abagold and HIK respectively; however, observations indicate that a measure of relatedness may exist between breeders. Recommendations with regards to future family breeding include, for both Abagold and HIK, retaining selected breeders based on their respective contributions to the F1 progeny while reassessing the potential of remaining breeding stock under more controlled breeding conditions. No obvious trends were observed for growth with most individuals producing both faster and slower growing offspring. Juveniles will be reassessed at two years to determine whether the size advantage or disadvantages were maintained and to ascertain whether growth advantages/disadvantages may be gender specific. / AFRIKAANSE OPSOMMING: Die vyf mees toonaangewende perlemoen produseerders in Suid Afrika het „n genetiese verbeteringsprogram vir Haliotis midae geinisieer in „n gesamentlike poging om ekonomiese belangrike eienskappe te verbeter. Verskeie onafhanklike fokus-spesifieke studies is geinisieer, insluitend die totstandkoming van „n groeiprestasie aantekenstelsel, soos gebruik in hierdie studie, en wat noodsaaklik is om die aaneenlopende prestasie van individue te moniteer soos daar beweeg word van massa seleksie tot merker bemiddelde seleksie. Die primêre fokus van hierdie studie was die ouerskapsbepaling van F1 nageslag wat massa geselekteer is op ouderdom 1 jaar vir grootte en as of “vinniger” of “stadiger” groeiers geklassifiseer is. Nege mikrosatelliet merkers is gebruik om jong perlemoen individue en moontlike ouers te genotipeer, met die ouerskapstoekenning bereken deur CERVUS 2.0. Groei resultate vir Abagold en HIK was vergelykbaar vir beide groei groepe op drie van die lokaliteite. Geringe omgewingseffekte, alhoewel nie statisties betekenisvol nie, was sigbaar as „n groei voordeel vir jong individue op twee van die vyf lokaliteite. Ongeag maatstawe om omgewingsinvloede te standardiseer, is varieerbares moeilik om te beheer in die produksie omgewing en genotipe x omgewings interaksies mag verdere navorsing vereis en behoort in ag geneem te word in toekomstige telingsprogramme. Die onkoste wat met merker bemiddelde seleksie geassosieer word, maak die tegniek soms onaantreklik vir die meeste akwakultuur operasies; nie teen staande die genetiese voordele wat die gebruik daarvan veroorsaak. Die koste-optimiseering van roetine prosesse, soos byvoorbeeld, DNA ekstraksies, is dalk een aanslag om die addisionele koste te verminder. Chelex®100 blyk „n geskikte alternatief tot die CTAB metode te wees – die tegniek is vinnig en koste-effektief om uit te voer. Die gebruik van hierdie metode in kombinasie met die hoë deurvloei van ‟n robotiese sisteem behoort verder ondersoek te word. Vir die mikrosatelliet ontwikkeling het slegs 50% van die positiewe rekombinante klone invoegings bevat. Nukleotiedvolgorde bepaling van hierdie klone het 16% perfekte herhalings en 47% onderbroke herhalings bevat waaruit 52 inleierstelle ontwikkel en getoets is. In totaal is 31 polimorfiese mikrosatelliet loki van verskillende motiewe en samestelling ontwikkel. Een-en-sestig persent van die volgorde bepaalde klone is oortollig geag en vooraf sifting vir beide uniekheid en die teenwoordigheid van mikrosatelliete sal onnodige volgorde bepaling verhoed, die effektiwiteit van die FIASCO tegniek verhoog sowel as addisionele koste verminder. Nege loki is geselekteer vir ouerskapsbepaling. Nul allele was teenwoordig vir al die geselekteerde merkers, maar die frekwensies was egter laer as die 5% kritieke waarde. Ouerskap is 91% en 90% suksesvol bepaal vir Abagold en HIK onderskeidelik. Waarnemings dui egter daarop dat daar verwantskappe mag wees tussen van die broeidiere. Voorstelle in terme van toekomstige familie teling sluit is, vir beide Abagold en HIK, om geselekteerde broei diere te behou gebaseer op hulle onderskeie bydraes tot die F1 nageslag asook die herevaluaring van die potensiaal van die oorblywende broei diere onder meer beheerde teling toestande. Geen voor-die-handliggende tendense is waargeneem vir groei nie met die meeste individue wat beide vinniger en stadiger groeiende nageslag geproduseer het. Jong individue moet geherevalueer word op tweejarige ouderdom om te bepaal of die groei voordeel of nadele behou is en om te bepaal om groei voordele/nadele geslagspesifiek is.

Thesis (MScAgric)--Stellenbosch University, 2002. / ENGLISH ABSTRACT: Grapevine supports one of the oldest industries in South Africa today, and is also of significant international importance. With increasing international trade and the transport of fruit and other grapevine-derived products between borders, it has become increasingly important for South African farmers and viticulturalists to ensure their products conform to strict international market requirements if they are to remain competitive. Such requirements include the correct and accurate identification of berries and wines according to cultivar. In light of this, 26 different wine, table grape and rootstock cultivars, as well as a number of clones from KWV's core germplasm collection were characterised at 16 microsatellite marker loci. Microsatellite markers are known for their high level of informativeness, reliability and reproducibility, and are widely used in the identification and characterisation of plant varieties, population analyses and forensic applications. Unique allelic profiles were obtained for all but two plants, which proved to be identical at all loci considered, and thus 'clones'. These profiles were collated to form a database, containing the DNA fingerprints of each sample at each locus. The relative levels of informativeness of each marker used were also determined, and compared with those found in the literature. Six markers proved to be highly informative, and are promising in the potential application of this technology to other cultivars. The applicability of microsatellite markers to such studies is confirmed; this approach could easily be extended to include any number of cultivars of national and international interest. The results of such an investigation would have important implications for both the farming and commercial industries alike. / AFRIKAANSE OPSOMMING: Wingerd ondersteun een van die oudste industriee in Suid-Afrika vandag, en is ook van groat intemasionale belang. Met die toenemende intemasionale ruilhandel en die vervoer van vrugte en ander wingerd produkte tussen grense, het dit toenemend belangrik geword vir SuidAfrikaanse wingerdboere om te. verseker dat hulle produkte voldoen aan die streng vereistes van die intemasional mark, indien hulle kompeterend wil bly. Hierdie vereistes sluit in die korrekte en akkurate identifisering van druiwe en wyn volgens kultivar. Met hierdie vereistes in ag geneem, is 26 verskillende wyn, tafeldruif en wortelstok kultivars, asook 'n aantal klone van die KWV se kern kiemplasma versameling, gekarakteriseer by 16 mikrosatelliet merker loki. Mikrosatelliet merkers word gekenmerk deur 'n hoe vlak van informatiwiteit, betroubaarheid en herhaalbaarheid en word wydverspreid gebruik in die identifisering en karakterisering van plant varieteite, populasie analises en forensiese toepassings. Unieke alleliese profiele is vir a1 die plante verkry, behalwe vir twee plante wat identiese resultate by alle loki opgelewer het en dus as "klone" beskou kan word. Hierdie profiele is bymekaar gevoeg om 'n databasis te vorm wat die DNA vingerafdrukke van elke monster by elke lokus bevat. Die relatiewe vlak van informatiwiteit van al die merkers is ook bepaal en vergelyk met merkers in die literatuur. Ses van die merkers blyk om hoogs informatief te wees en lyk belowend in die potensiele toepassing van hierdie tegnologie op ander kultivars. Die toepaslikheid van mikrosatelliet merkers op sulke studies is bevestig; hierdie benadering kan maklik aangepas word om enige aantal kultivars van nasionale en intemasionale belang in te sluit. Die resultate van s6 'n ondersoek sal belangrike implikasies inhou vir beide die boerdery en kommersiele industriee.

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.

Orientador: Vitor Fernandes Oliveira de Miranda / Resumo: O gênero Genlisea forma parte da maior família de plantas carnívoras, as Lentibulariaceae. Das aproximadamente 30 espécies conhecidas do gênero, 17 encontram-se no Brasil e delas 10 são endêmicas. O gênero tem sido pouco estudado, sendo ainda escassos os estudos sobre aspectos genéticos e praticamente se desconhecem seu estado de conservação ou a fragilidade das populações naturais. Genlisea violacea A.St.-Hil. e G. aurea A.St.-Hil. são endêmicas e estão distribuídas nas formações de Cerrado e de Mata Atlântica, que são biomas muito frágeis. Neste trabalho foram estudadas a biologia reprodutiva e a polinização de G. violacea em duas populações naturais. Além disso, foram analisadas a estrutura genética e a dinâmica de populações de G. violacea e G. aurea. Para isso se desenvolveram microssatélites a partir de dados genômicos de G. aurea, transferíveis nas espécies congenéricas, incluindo G. violacea. Adicionalmente foi estudada a estrutura genética de algumas populações de G. violacea e G. aurea. Segundo as observações e análises realizadas, G. violacea é espécie alógama e autocompatível que oferece néctar aos visitantes, facilitando a autopolinização durante a antese e polinização cruzada durante todo o tempo de vida da flor, por meio de pelo menos duas espécies de abelhas. Mesmo assim, existem diferencias fenotípicas entre populações e incluso apresenta vario morfotipos dentro da mesma população. Ademais, foram desenvolvidos 12 marcadores microssatélites em G. aurea, que sã... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The Genlisea genus is part of the larger family of carnivorous plants, Lentibulariaceae. They are approximately 30 known species of the genus, 17 in Brazil and 10 of them are endemic. The genus has been understudied, yet there are few studies on genetic aspects and practically its conservation status and the fragility of the natural populations are unknown. Genlisea violacea A.St.Hil. and G. aurea A.St.Hil. are endemic and are distributed in the formations of the Cerrado and Atlantic Forest, which are very fragile biomes. In this study we analyzed the reproductive biology and pollination of G. violacea in two natural populations. In addition, we also analyzed the genetic structure and dynamics of G. violacea and G. aurea populations. For this we developed microsatellite from genomic data of G. aurea, and did cross-amplification in congeneric species including G. violacea. According to the observations and analyses, G. violacea is self-compatible and allogamous that offers nectar to visitors, facilitating self-pollination during anthesis and cross-pollination throughout the flower lifetime through at least two species of bees. Also, there are differences between populations and phenotypic features included morphotypes within the same population. In addition, 12 microsatellite markers were developed in G. aurea, which are transferable to congeneric species. The populations of both species have low variability and average, respectively for G. violacea and G. aurea, with high var... (Complete abstract click electronic access below) / Doutor

Orientadores: Claudio Lopes de Souza Junior, Anete Pereira de Souza / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-06T11:28:57Z (GMT). No. of bitstreams: 1 Lima_MilenadeLunaAlves_D.pdf: 1291219 bytes, checksum: a3a078e58517d0d64e9051437ce18432 (MD5) Previous issue date: 2006 / Resumo: A maior parte dos caracteres de importância agronômica e econômica do milho estão sob o controle de diversos locos gênicos, denominados locos de caracteres quantitativos (QTL). A possibilidade do uso de marcadores moleculares e o aperfeiçoamento dos modelos estatístico-genéticos possibilitaram o mapeamento desses locos gênicos que afetam tais caracteres. Pouco enfoque no estudo de mapeamento de QTL foi dado em populações derivadas do germoplasma do milho tropical, o qual possui uma base genética ampla com maior diversidade do que o germoplasma temperado. Da mesma forma, pouco se conhece sobre as interações dos QTL nos diferentes ambientes (QTL X E). Duzentos e cinqüenta e seis progênies F2:3, derivadas do cruzamento de duas linhagens de milho tropical, foram avaliadas em cinco ambientes. O mapa genético foi desenvolvido com 139 marcadores microssatélites, utilizando o programa MAPMAKER/EXP versão 3.0b. As análises de mapeamento de QTL e a detecção da interação QTL X E foram realizadas utilizando o procedimento JZmapQTL do programa Windows QTL-Cartographer versão 2.5, que se baseia na análise de mapeamento em ambientes múltiplos (mCIM). A extensão total do mapa genético foi de 1.858,61 cM com intervalo médio entre marcadores de 13,47 cM. Dezesseis QTL foram mapeados para produção de grãos, oito para espiga por planta, seis para acamamento, seis para altura de planta, nove para altura de espiga e dois para número de folhas. Os efeitos genéticos dos QTL mapeados apresentaram variação em sinal e magnitude, demonstrando que cada QTL contribui de forma particular para a expressão dos caracteres. A maioria destes QTL apresentou ação gênica sobredominante, e muitos deles também apresentaram significante interação QTL X E. Esses resultados forneceram dados para uma melhor compreensão da arquitetura genética do genoma do milho tropical. Estas informações podem ser utilizadas em programas de seleção assistida dessa espécie, utilizando marcadores moleculares, gerando mais eficiência nos programas brasileiros de melhoramento / Abstract: Most of important agricultural and economical traits in maize are under the control of several gene loci, named quantitative trait loci (QTL). The possibility of using molecular markers and the statistic-genetic models made possible the mapping of these gene loci that affect such traits. Little focus has been given to QTL mapping study in populations derived from tropical maize germplasm, which has a broad genetic base with greater variability than temperate maize germplasm. Also, not much is known about the interaction of QTL in various environments (QTL X E). Two-hundred and fifty-six F2:3 progenies, derived from a crossing between two tropical maize inbred lines, were evaluated in five environments. The genetic map was developed with 139 microsatellite markers, using the software MAPMAKER/EXP version 3.0b. The analyses of QTL mapping and the detection of QTL X E interaction were performed using the Windows QTL-Cartographer version 2.5, JZmapQTL procedure, which is based on multiple-environment joint analysis (mCIM). The genetic map spanned 1,858.61 cM in length with an internal average of 13.47 cM between markers. Sixteen QTL were mapped for grain yield, eight for ears per plant, six for plant lodging, six for plant height, nine for ear height and two for number of leaves. The genetic effects of the mapped QTL presented varied signal and magnitude, displaying that each QTL contributes in a particular way for trait expression. Most of these QTL displayed gene action overdominance, many of them with significant QTL X E interaction detected. These results provide data for a better comprehension of genetic architecture on tropical maize genome. This information can be used in the marker-breeding selection of this species, leading more efficiency to Brazilian breeding programs / Doutorado / Genetica Vegetal e Melhoramento / Doutor em Genetica e Biologia Molecular

Orientador: Maria do Carmo Estanislau do Amaral / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-13T10:16:12Z (GMT). No. of bitstreams: 1 Caddah_MayaraKrasinski_M.pdf: 2640500 bytes, checksum: be32f5cbfeac9f9405106ac2f8ab3f90 (MD5) Previous issue date: 2009 / Resumo: Kielmeyera Mart. & Zucc. (Clusiaceae) inclui 47 espécies e sua revisão mais recente foi baseada em caracteres morfológicos. A série Coriaceae (Wawra) Saddi distingue-se das demais principalmente pelas folhas coriáceas e pelo hábito arbóreo/arbustivo. Em sua nova circunscrição, a série apresenta apenas duas espécies, K. coriacea, com duas subespécies e sete variedades, e K. grandiflora, que antes estava incluída na primeira espécie como variedade. Apesar da recente revisão, a circunscrição taxonômica das espécies ainda é muito problemática. Kielmeyera coriacea é amplamente conhecida como um dos principais componentes do Cerrado, enquanto K. grandiflora é pouquíssimo conhecida. Dessa forma, os dois táxons específicos envolvidos na série Coriaceae (Wawra) Saddi foram investigados para esclarecer o relacionamento dentro do grupo e para propor, se fosse o caso, uma classificação mais clara. Para tanto foram procedidos estudos morfológicos, anatômicos, fenológicos e moleculares. A morfologia e a anatomia foliar não foram satisfatoriamente informativas, e apenas revelaram caracteres sem consistência taxonômica. Apenas o padrão de nervação secundária, a tonalidade das folhas e a quantidade e distribuição dos compostos fenólicos se mostraram disgnósticos para as duas espécies. Adicionalmente, análises da superfície foliar em Microscopia Eletrônica de Varredura mostraram um padrão de estruturas epicuticulares distinto nas duas espécies. Para o estudo da biologia molecular das espécies, foram utilizados marcadores microssatélites, capazes de detectar polimorfismo ao nível específico. Foram desenvolvidos 22 pares de primers a partir de uma biblioteca enriquecida para K. coriacea. Onze pares de primers amplificaram locos polimórficos e com bom padrão de amplificação para leitura. Nesta espécie, o padrão de bandas apresentou de 12 a 32 bandas por loco, e de duas a oito bandas por indivíduo. Kielmeyera grandiflora apresentou padrão de bandas semelhante. Foram amostradas duas populações de cada espécie (uma alopátrica e uma simpátrica, todas do estado de São Paulo). Trinta plantas de cada população foram genotipadas com oito pares de primers e 213 alelos foram encontrados ao total, quase metade deles sendo compartilhado pelas duas espécies. Diversas abordagens utilizando softwares de genética de populações indicaram dois grupos distintos dentro das populações amostradas, suportando a manutenção das duas espécies propostas por Saddi. A presença de vários alelos específicos de K. grandiflora em plantas de K. coriacea na área onde as espécies são simpátricas sugerem a ocorrência de hibridação introgressiva. Com os resultados obtidos neste trabalho, a proposta de Saddi de separação de K. grandiflora de K. coriacea foi corroborada, e o esclarecimento das relações entre os táxons infraespecíficos de K. coriacea tornou-se iminente à luz das novas ferramentas desenvolvidas. / Abstract: Kielmeyera Mart. & Zucc. (Clusiaceae) has 47 species and its more recent revision was based on morphological characters. The Coriaceae (Wawra) Saddi series is distinguished from the other series mainly by its coriaceous leaves and shrub/tree habit. In its latest circumscription, the series has two species, K. coriacea, with two subspecies and seven varieties, and K. grandiflora, which in the past was considered a variety of the later. However, the circumscription of the two species is problematic and they form the "K. coriacea complex". Kielmeyera coriacea is considered one of the main components of the Cerrado, while K. grandiflora is poorly known. Therefore, both specific taxa of the Coriaceae were investigated to clarify their relationship and to set out a more accurate classification, if necessary. Thus, we carried out morphological, anatomical, phenological, and molecular studies with the two species of the complex. Morphological and leaf anatomy studies were not satisfactory informative and revealed inconsistent differences between the species. Only the secondary veins pattern, the leaf shade and quantity and distribution of phenolic compounds in leaves tissues could be considered diagnostic characters. In addition, the analysis of the leaf surface in Scanning Electron Microscope showed a distinct pattern of epicuticular structure in both species. Microsatellite markers were used in the molecular studies, due to their capacity to detect polymorphism at specific level. Twenty-two primers pairs were developed from an enriched library of K. coriacea and eleven of them amplified polymorphic and readable loci. In this species, the band pattern presented 12 to 32 bands per locus and two to eight bands per individual. Kielmeyera grandiflora showed a similar band pattern. For each species we sampled two populations (one allopatric and one sympatric, all from São Paulo state). Thirty plants of each population were genotyped with eight microsatellites and 213 alleles were found; almost half of that were shared by the two species. Different approaches using population genetics softwares indicated two distinct groups inside the four populations, supporting the maintenance of the two species proposed by Saddi. The presence of many alleles specific to K. grandiflora in K. coriacea plants of the sympatric area suggests an introgressive hybridization. Our results corroborated Saddis's proposal of recognize both K. grandiflora and K. coriacea, and the clarification of the infraspecific taxa of K. coriacea becomes imminent in the light of these new developed tools. / Mestrado / Mestre em Biologia Vegetal

Orientador: Hildete Prisco Pinheiro / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Matematica, Estatistica e Computação Cientifica / Made available in DSpace on 2018-08-08T04:40:31Z (GMT). No. of bitstreams: 1 Taglianetti_TatianaBurattoBordin_M.pdf: 5877530 bytes, checksum: 8766580b60704d96ff1ae1a0288803fb (MD5) Previous issue date: 2007 / Resumo: Neste trabalho, o principal interesse é estudar as medidas de distância genética para loci de microsatélites baseadas nos desvios absolutos e quadráticos sob o modelo de mutação ¿stepwise¿. Os estudos em microsatélites têm sido cada vez mais freqüentes devido a sua importância na aplicação em mapeamento genético. Desta forma, surgeriu-se um modelo para explicar a mutação nas seqüências de repetições nos loci de microsatélites, que é conhecido por modelo de mutação ¿stepwise¿. Nesse modelo supõe-se que a cada geração,cada alelo pode sofrer mutação para outra classe alélica. Na sua forma mais simples,que é o modelo mutacional de um passo o alelo pode sofrer mutação, aumentando ou diminuindo em um estado com probabilidade B. Vamos assumir o modelo de mutação¿stepwise¿ de um passo para desenvolver as medidas de distância baseadas nos desvios absolutos e quadráticos. Propõe-se dois testes de homogeneidade, um baseado na medida de distância dos desvios quadráticos e outro na dos devios absolutos. Suas distribuições assintóticas são estudadas utilizando-se a teoria de Estatística U. Para verificar os resultados analíticos com respeito a distribuição assintótica, um modelo de simulação foi aplicado baseado no modelo de mutação ¿stepwise¿ de um passo e na teoria de coalescência. Os testes de homogeneidade são aplicados a dados reais com o interesse de verificar se existe ou não diferença na variação do número de repetições para os grupos definidos pela etnia e o índice de alcolismo (ALDX1) em um determinado locus / Abstract: In this work, the main interest is to study the measures of genetic distance for microsatelliteloci based on the absolute and the quadratic diferences under the it stepwise mutation model. The study in microsatellite has become the mainstay due to its importance to developgenetic map. Therefore, one suggests a model to explain the mutation that occurs inthe repeated sequence (microsatellite loci), called ¿stepwise¿ mutation model. The modelassumes that in each generation, each allele can mutate to another allelic class. In thesimplest case, which we call the ¿one-step model¿, ones assumes that the allele can increaseor decrease by one unit with probability B. We assume the one-step model to develop themeasures of genetic distance based on absolute and quadratic differences. We suggest two types of homogeneity tests, one based in the measure of quadraticdistance and the other based in the absolute distance. Its asymptotic distributions aregoing to be study using U-statistics theory. In order to certify the analytical results about the asymptotic distribution, a simulation study based on one-step mutation model and coalescence theory was employed. An application using real microsatellite data was performed in order to verify if there are differences in the distribution in the repeat sequence among groups de_ned by ethnicity and alcoholism index (ALDX1) in a determined locus using the homogeneity tests / Mestrado / Bioestatistica / Mestre em Estatística

Orientador: André Olmos Simões / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-26T03:43:07Z (GMT). No. of bitstreams: 1 Scatigna_AndreVito_M.pdf: 3305692 bytes, checksum: 2c9fe2f311dab327995537083164034a (MD5) Previous issue date: 2014 / Resumo: Philcoxia é um gênero recentemente descrito, composto por quatro espécies reconhecidas e uma nova espécie, endêmicas das formações arenosas do Cerrado e Caatinga. Por conta de sua raridade e da vulnerabilidade de seu habitat, o gênero pode ser considerado criticamente ameaçado de extinção. Recentes evidências filogenéticas sustentam a inclusão do gênero na tribo Gratioleae (Plantaginaceae). Entretanto, as relações de Philcoxia dentro da tribo continuam controversas desde sua descrição. Apresentamos, aqui, estudos filogenéticos de Gratioleae, focados no teste do monofiletismo de Philcoxia, suas relações interespecíficas e seu posicionamento. As análises filogenéticas foram feitas pelos métodos de Máxima Parcimônia e inferência Bayesiana. Sequências dos íntrons rpl16, rps16 e trnL e do espaçador trnL-trnF, todas do DNA cloroplastidial, foram analisadas, incluindo 31 amostras, entre as quais quatro espécies de Philcoxia, 23 outras espécies de Gratioleae e mais quatro táxons (grupo externo) de Plantaginaceae. As espécies de Philcoxia formam um clado fortemente sustentado, irmão de Stemodia stellata. Philcoxia minensis é mais próxima de P. rhizomatosa e P. bahiensis é mais próxima de P. tuberosa. O clado que inlcui Philcoxia e S. stellata é relacionado aos clados formados por Achetaria, Scoparia e alguns representantes de Stemodia. Realizamos, também, o desenvolvimento e caracterização de marcadores microssatélites inéditos para estudos em genética de populações voltados para conservação de P. minensis. Pares de iniciadores foram desenhados para 27 locos de microssatélites e testados em 30 indivíduos de uma população de P. minensis e em quatro indivíduos de P. bahiensis. Dezessete locos foram amplificados com sucesso, doze dos quais se mostraram polimórficos. Os 12 marcadores polimórficos serão usados em futuros estudos relacionados ao sistema de reprodução e à diversidade genética de P. minensis e são potenciais ferramentas para esses estudos com P. bahiensis. Além disso, a nova espécie Philcoxia rhizomatosa é descrita e ilustrada. Ela apresenta folhas maiores que outras espécies do gênero e também possui um rizoma bastante conspícuo e ramificado. Esta nova espécie é aparentemente endêmica de um areal em Botumirim, Minas Gerais, em vegetação de transição entre Cerrado e Caatinga. Testes de carnivoria positivos sugerem que P. rhizomatosa é uma planta carnívora / Abstract: Philcoxia is a recently described genus, composed of four currently recognized species and one additional new species, endemic to the Brazilian sandy formations of the Cerrado and Caatinga. Due to its rarity and the vulnerability of the formation where it occurs, this genus could be treated as critically endangered. Recent evidences from molecular phylogenetics support the inclusion of the genus within the tribe Gratioleae (Plantaginaceae). The affinities of Philcoxia within the tribe, however, have been controversial since it was first described. Here, we present a phylogenetic analysis of Gratioleae, focusing on the test of the monophyly of Philcoxia, its interspecific relationships and its placement. Phylogenetic analyses were conducted using Maximum Parsimony and Bayesian approaches. Sequence data from rpl16, rps16 and trnL introns and trnL-trnF intergenic spacer were analysed, including 31 samples representing four species of Philcoxia, 23 additional Gratioleae species and four outgroup taxa from Plantaginaceae. Philcoxia species form a strongly supported clade, sister of Stemodia stellata. Philcoxia minensis is closely related to P. rhizomatosa and P. bahiensis is closer to P. tuberosa. The clade Philcoxia plus S. stellata is related to clades formed by Achetaria, Scoparia and Stemodia representatives. We also developed and characterized new microsatellite markers as tools for further studies in population genetics aiming the conservation of P. minensis. Primer pairs were developed for 27 microsatellite loci and validated in 30 individuals of P. minensis from a natural population and tested in four idivividuals from a natural population of P. bahiensis. Seventeen loci successfully amplified, twelve of which were polymorphic. The 12 polymorphic markers are suitable for studies concerning mating system and genetic diversity of P. minensis and also may be usefull tools to study similar issues regarding its related species, P. bahiensis. In addition, the new species Philcoxia rhizomatosa is described and illustrated. It has bigger leaves than other species in the genus and presents a conspicuous and branched rhizome. This new taxa is possibly endemic to a sand patch in the transition vegetation between the Cerrado and the Caatinga in Botumirim, Minas Gerais, Brazil. Tests for carnivory were performed and showed activity of phosphatase, suggesting that P. rhizomatosa is a carnivorous plant / Mestrado / Biologia Vegetal / Mestre em Biologia Vegetal