Submitted by (ana.araujo@ufrpe.br) on 2017-02-21T16:20:25Z No. of bitstreams: 1 Romero de Lima Sousa.pdf: 670144 bytes, checksum: d35f2bc03e9baddbb24bad3b4dfd477e (MD5) / Made available in DSpace on 2017-02-21T16:20:25Z (GMT). No. of bitstreams: 1 Romero de Lima Sousa.pdf: 670144 bytes, checksum: d35f2bc03e9baddbb24bad3b4dfd477e (MD5) Previous issue date: 2010-02-22 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / The Brazilian Northeast is the center of origin of cotton Gossypium mustelinum (Miers) Watt. This cotton has not been improved or exploited commercially, but there is evidence of their introgression into the genome of varieties of upland cotton G. hirsutum L. variety marie galante Hutch. When considering the loss of variability can be said that G. mustelinum, G. barbadense L. and G. hirsutum L. var. marie galante Hutch of extinction are very high, high and medium, respectively, requiring immediate efforts for their preservation. This study aims to determine whether there is competition between pollen G. mustelinum and herbaceous in relation to fertilization of wild species, as well as whether there are differences of competition in different proportions of pollen of these species. For both crossings were performed between the two species used the G. mustelinum mother as having been fertilized by pollen from: i) mixture of 50% G. mustelinum and 50% herbaceous ii) a mixture of 75% herbaceous and 25% G. mustelinum iii) a mixture of 25% herbaceous and 75% G. mustelinum iv) herbaceous v) G. mustelinum. The latter two were used as controls to determine the expression pattern of alleles in polyacrylamide gels and validate the crosses with mixed pollen. We obtained seeds from each cross. The molecular analysis determined the proportion of seeds from crosses inter-and intra-specific by genotyping with SSR markers of the type. The frequency of offspring in each proportion of pollen used in crosses were compared using statistical test, chi-square (x²), with expected frequencies of 50% of hybrid seeds and 50% of seeds derived from selfing, 75% of seeds hybrid and 25% of the seeds of self-fertilization, 25% seed and 75% hybrid seed selfing. Were pollinated between 10:42 Flowers in the crosses with mixed pollen. The average number of seeds obtained ranged between nine and 11. Comparing these values with the average number of seeds from the intersection with 100% of pollen of the respective species, it was found that there was little variation. There were no differences in fertility or crossability between the genotypes of G. mustelinum. The only male parent in crosses that did not get the seeds was C27, and this was possibly caused by physiological conditions unfavorable. Through the data can be seen that the higher the percentage of pollen from G. hirsutum, the greater tendency of hybrids between two species. Therefore the higher the percentage of pollen from G. mustelinum, the lower the amount of hybrids. After analyzing the results, the chi-square (x²), a 1% probability it was established that there was competition between pollen from wild species and cultivated at all levels studied. / O Nordeste brasileiro é o centro de origem do algodão Gossypium mustelinum (Miers) Watt. Esta espécie ainda não foi melhorado ou explorado comercialmente, entretanto há evidências de sua introgressão no genoma das variedades de algodoeiro herbáceo G. hirsutum L. variedade marie galante Hutch. Ao considerar a perda de variabilidade pode-se afirmar que G. mustelinum, G. barbadense L. e G. hirsutum L. variedade marie galante Hutch estão com risco de extinção muito alto, alto e médio, respectivamente, necessitando de esforços imediatos para sua preservação. Este trabalho tem por finalidade verificar se há competição de pólen entre G. mustelinum e herbáceo em relação à fertilização da espécie silvestre, bem como se há diferença de competição em diferentes proporções de polens das referidas espécies. Para tanto, foram realizados cruzamentos entre as duas espécies, utilizado o G. mustelinum como genitor feminino tendo sido fecundado por pólen de: i) mistura de 50% herbáceo e 50% de G. mustelinum; ii) mistura de 75% herbáceo e 25% de G. mustelinum; iii) mistura de 25% herbáceo e 75% de G. mustelinum; iv) herbáceo e v) G. mustelinum. Estes dois últimos foram utilizados como controle para saber o padrão da expressão dos alelos nos géis de poliacrilamida e validar os cruzamentos com misturas de pólen. Foram obtidas sementes provenientes de cada cruzamento. Na análise molecular foi determinada a proporção de sementes provenientes de cruzamentos inter e intraespecíficos por meio da genotipagem com marcadores do tipo SSR. A frequência de descendentes em cada proporção de pólen usada no cruzamento foi comparada por meio de teste estatístico do qui-quadrado (x²), com frequência esperada de: 50% de sementes híbridas e 50% de sementes oriundas de autofecundação; 75% de sementes hibridas e 25% de sementes de autofecundação; 25% de sementes hibridas e 75% de sementes de autofecundação. Foram polinizadas entre dez e 42 flores nos cruzamentos com mistura de pólen. O número médio de sementes obtidas variou entre nove e 11. Comparando-se tais valores com o número médio de sementes provenientes do cruzamento com 100% de pólen das respectivas espécies, verificou-se que houve pouca variação. Não foi verificada diferenças de fertilidade ou de cruzabilidade entre os genótipos de G. mustelinum. Os únicos genitores masculinos nos cruzamentos que não obtiveram sementes foram o C27 e Mac 01, fato este ocasionado possivelmente por condições fisiológicas desfavoráveis. Por intermédio dos dados pode-se constatar que quanto maior a porcentagem de pólen de G. hirsutum, maior tendência de híbridos entre as duas espécies. Consequentemente, quanto maior a porcentagem de pólen de G. mustelinum, menor a quantidade de híbridos. Após análise dos resultados obtidos pelo teste de qui-quadrado (x²), a 1% de probabilidade, foi possível constatar que houve competição entre pólen da espécie silvestre e cultivada em todos os níveis estudados.

<p>Poznavanje genetičke divergentnosti predstavlja osnovni preduslov uspe&scaron;nog oplemenjivačkog programa. Pored poznavanja genetičke divergentnosti, u proizvodnji hibrida &scaron;ećerne repe je od izuzetne važnosti i poznavanje kombinacionih sposobnosti oplemenjivačkog materijala. Svako ukr&scaron;tanje inbred linija nema uvek za posledicu pojavu heterozisa, pa je stoga neophodno ispitati op&scaron;te i posebne kombinacione sposobnosti onih linija koje se planiraju koristiti kao roditeljske komponente hibrida. U ovom istraživanju ispitivane su kombinacione sposobnosti multigermnih opra&scaron;ivača, razvijenih u okviru četiri različita oplemenjivačka programa: programa oplemenjivanja &scaron;ećerne repe Instituta za ratarstvo i povrtarstvo, Novi Sad, i tri programa oplemenjivanja &scaron;ećerne repe istraživačkih stanica Ministarstva poljoprivrede SAD (Michigan, Salinas i Fort Collins). Opra&scaron;ivači su se razlikovali u stepenu homozigotnosti u zavisnosti od prisustva gena autofertilnosti, odnosno autosterilnosti. Kao testeri kori&scaron;ćene su dve citoplazmatski sterilne linije Instituta za ratarstvo i povrtarstvo, Novi Sad. Pored određivanja genetičke divergentnosti i kombinacionih sposobnosti cilj ovog istraživanja je bio utvrđivanje vrednosti kvantitativnih svojstava za najvažnija svojstva korena: masu korena, sadržaj &scaron;ećera, sadržaj suve materije, masu glave korena, obim korena, procenat iskori&scaron;ćenja, prinos kristalnog &scaron;ećera i na osnovu njih određivanje genetičke divergentnosti ispitivanih opra&scaron;ivača. Takođe na osnovu dobijenih vrednosti određen je efekat gena i način nasleđivanja za ispitivana kvantitativna svojstva.Opra&scaron;ivač FC220 se izdvojio kao potencijalno stabilan kombinator u<br />iii<br />obe godine istraživanja, beležeći pozitivne vrednosti op&scaron;tih kombinacionih sposobnosti za sva ispitivana svojstva. Sa druge strane opra&scaron;ivač EL53 je u obe godine istraživanja beležio negativne vrednosti op&scaron;tih kombinacionih sposobnosti za sva ispitivana svojstva. U pogledu načina nasleđivanja mase korena, obima korena i prinosa kristalnog &scaron;ećera superiornost su pokazali autofertilni polinatori u odnosu na populacije slobodne oplodnje. Veći stepen homozigotnosti i uniformnost F1 generacije doveli su do ispoljavanja efekta heterozisa kod hibridnih kombinacija gde su roditelji bili autofertilni polinatori. Na osnovu načina grupisanja multigermnih opra&scaron;ivača u zbirnom klasteru, potvrđena je negativna korelacija između mase korena i sadržaja &scaron;ećera. U okviru jedne grupe su se na&scaron;li opra&scaron;ivači sa velikom masom korena i nižim sadržajem &scaron;ećera, a u drugoj grupi sa malom masom korena i vi&scaron;im sadržajem &scaron;ećera. Analizom međusobnih odnosa multigermnih opra&scaron;ivača &scaron;ećerne repe pomoću SSR markera konstruisan je dendrogram u kome su opra&scaron;ivači podeljeni u četiri grupe, shodno centrima porekla iz kojih su dobijeni. Između genetičke udaljenosti određene pomoću podataka dobijenih SSR markerima i posebnih kombinacionih sposobnosti nisu ustanovljene korelacije.<br />Datum prihvatanja</p> / <p>Information about genetic diversity is basic requirement of every successful breeding program. Beside information about genetic diversity for development of sugar beet hybrids it is very important to know combining abilities of breeding material. Since not all crosses result with appearance of heterosis, it is necessary to test general and specific combining abilities of potential parental lines. In this research were used multigerm pollinators from four different breeding programs: sugar beet breeding program of Institute of Field and Vegetable Crops, Novi Sad, and three programs from different breeding station of the US Department of Agriculture (Michigan, Salinas and Fort Collins). Pollinators differed in the degree of homozygosity, depending on the presence of genes for autofertility or sterility. Testers used in this work were two cytoplasmic sterile lines of the Institute of Field and Vegetable Crops, Novi Sad. In addition to determining the genetic diversity and combining ability, objective of this study was to determine values of quantitative traits for sugar beet root traits: root weight, sugar content, dry matter content, root head weight, root circumference, extractable sugar content, crystal sugar yield and from them a genetic diversity of pollinators. Also on the basis of the obtained values it was determined gene effect and mode of inheritance of studied<br />vi<br />quantitative traits. Pollinator FC220 segregated as a potentially stable combiner, in both years, having positive values of general combining abilities for all traits. On the other hand pollinator EL53 in both years had negative values of general combining abilities for all traits. In terms of the mode of inheritance for root weight, root circumference and crystal sugar yield self-fertile pollinators showed superiority comparing to the population of open pollination. A higher level of homozygosity and uniformity of the F1 generation resulted in the expression of heterosis in hybrid combinations where the parents were self-fertile pollinators. Multigerm pollinators in aggregate cluster confirmed the negative correlation between root weight and sugar content. In one group were found pollinators with a large root mass and lower sugar content, while in the second group were pollinators with a small root mass and higher sugar content. Cluster analysis of multigerm sugar beet pollinators using SSR markers resulted in construction of dendrogram in which pollinators were divided into four groups, according to the centers of origin from which they were obtained. There was no correlation between genetic distance calculated from the data obtained by SSR markers and specific combining ability.</p>

Apesar do destaque do setor citrícola paulista e brasileiro, existe uma séria vulnerabilidade para o cultivo da laranja, que está pautada no uso de poucas variedades comerciais. A instalação de programas de melhoramento de laranjeiras com uso de cruzamentos controlados é dificultada principalmente pelos problemas de poliembrionia nas sementes e pela presença de ciclo juvenil longo nas plantas, o que ocasiona a dificuldade em obter plantas híbridas via cruzamentos controlados e o tempo muito longo para a conclusão de um ciclo de recombinação e seleção. O objetivo deste estudo foi a construção de um mapa de ligação utilizando uma população de 144 híbridos oriunda do cruzamento entre a laranjeira Tobias (CN 1392 e CN 1393), que apresenta ciclo juvenil curto, e laranjeira Pêra-de-Abril, variedade com sementes monoembriônicas. O mapa de ligação foi construído com base em marcadores moleculares SSR e TRAP através de dois softwares (JoinMap e Onemap). O mapa genético construído pelo JoinMap conteve 85 (61%) marcas dispostas em 13 grupos de ligação, totalizando 634 cM, com distância entre os marcadores adjacentes variando de 0 a 29 cM. Os tamanhos individuais dos grupos de ligação variaram de 8 a 85 cM e um total de 55 (39%) marcadores não se ligou ao mapa. Com o software OneMap 87 (62%) marcadores se ligaram em 16 grupos de ligação, totalizando 1.100 cM, com distância entre marcadores adjacentes variando de 0 a 36 cM. Os tamanhos individuais dos grupos de ligação variaram de 8 a 205 cM. Um total de 53 (38%) marcadores não se ligaram no mapa. A marca que constitui o caráter fenotípico de interesse florescimento precoce foi incluída no mapa quando utilizado o software OneMap. Houve similaridade entre os mapas de ligação de híbridos intraespecíficos de laranja doce construídos com os aplicativos JoinMap e OneMap. A distinção encontrada ocorreu, principalmente, devido aos marcadores com segregação distorcida / Despite the prominence of the citrus sector in São Paulo and Brazil, there is a serious vulnerability for the cultivation of orange, which is guided by the use of a few commercial varieties. Orange breeding programs that make use of controlled breeding are hampered mainly by the problems of polyembryony and the presence of long juvenile cycle, which impair the obtainment of hybrid plants through controlled crossings as well as taking a long time for the conclusion of a cycle of recombination and selection. The goal of this study was the construction of a linkage map using a population of 144 hybrids from crosses between Tobias sweet orange (CN 1392 and CN 1393), which present short juvenile cycle, and Pêra-de-Abril sweet orange, variety with monoembryonic seeds. The linkage map was constructed based on molecular markers SSR and TRAP using two softwares (JoinMap and Onemap). The genetic map obtained by JoinMap showed 85 (61%) markers arranged in 13 linkage groups totalizing 634cM, with the distance between adjacent markers ranging from 0 to 29 cM. The sizes of individual linkage groups ranged from 8-85 cM and a total of 55 (39%) markers could not be linked to the map. With the software OneMap 87 (62%) markers were linked in 16 linkage groups, totalizing 1.100 cM, with the distances between adjacent markers ranging from 0 to 36 cM. The sizes of individual linkage groups ranged from 8-205 cM. A total of 53 (38%) markers could not be linked on the map. The mark related to flowering, which is the phenotypic character of interest, was found using the software OneMap. There was similarity between the linkage maps of intraspecific hybrids of sweet orange built with JoinMap and OneMap softwares. The distinction found was mainly due to the markers with segregation distortion

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2016-01-07T10:43:43Z No. of bitstreams: 2 Dissertação - Vanessa Bernardes - 2014.pdf: 2035312 bytes, checksum: 8b960a119417d6138d7c9fbbdf6c6ad0 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-01-07T10:46:22Z (GMT) No. of bitstreams: 2 Dissertação - Vanessa Bernardes - 2014.pdf: 2035312 bytes, checksum: 8b960a119417d6138d7c9fbbdf6c6ad0 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2016-01-07T10:46:22Z (GMT). No. of bitstreams: 2 Dissertação - Vanessa Bernardes - 2014.pdf: 2035312 bytes, checksum: 8b960a119417d6138d7c9fbbdf6c6ad0 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-03-13 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Molecular markers are identifiable DNA sequences found at specific sites in the genome and transmitted by the standard laws of inheritance from one generation to the next. Markers known as microsatellite are indicated for genetic population analysis; due they are widely distributed in the genome and their high polymorphic information content per locus. To support different management practices, genebanks, conservation studies is important to perform the analysis of genetic variability in natural populations of the species of interest. In the biome Cerrado there are inumerous medicinal and fruit trees that are used in a extractive way, among them are those of the gender Byrsonima sp. popularly known as murici, belonging to the family Malpighiaceae. In Brazil presents about 70 species with wide distribution in the Cerrado. The murici is a multi- potential plant and although not be domesticated, its economic exploitation can be viable. In this context, the objective was to develop a set of microsatellite markers for species Byrsonima cydoniifolia A. JUSS. and test the potential transferability of this set of markers for species Byrsonima crassifolia L. Kunth. The microsatellite regions were isolated using genomic libraries enriched for repetitive regions and then they were used for primer design. Using the primers designed temociclagem conditions were tested and the products were characterized using the DNA of 90 individuals of B. cydoniifolia and 24 indivuduals of B. crassifolia. Of these, 14 loci were polymorphic and 3 monomorphic in three populations of B. cydoniifolia. The number of alleles ranged from 3 to 17, with an average of 10.45 alleles per locus. The observed heterozygosity was similar to the expected heterozygosity, the values ranged from 0.20 to 0.92 and 0.43 to 0.92; respectively. 39 private alleles were identified. This set of markers showed high combined probability of paternity exclusion (Q) equal to 0.999 and combined probability of identity (I) equal to I=7.84x10-1. The global values for the fixation index (FIS) were not significant (P<0.05), whereas the values of FST=0,082 and FIT=0,143 were significant. For Byrsonima crassifolia species, nine pairs of primers produced good patterns of cross amplification in the study population, with a mean of 7.56 alleles per locus. The observed heterozygosity ranged from 0.250 to 0.958, which was higher than the expected heterozygosity ranging from 0.223 to 0.905. The combined probability of paternity exclusion (Q) was equal to 0.99847 and high combined probability of identity equal to 6.42x10-9. The strategy of development of microsatellite markers from the genomic library enriched methodology was efficient to generate a panel with eleven polymorphic microsatellite markers for B. cydoniifolia and nine polymorphic microsatellite markers successfully transferred to B. crassifolia, providing a useful tool for population genetic studies not only for the species B. cydoniifolia and B. crassifolia, but possibly for other related species evolutionarily. / Marcadores moleculares são sequências de DNA identificáveis, encontrados em locais específicos do genoma e transmitidos pelas leis padrão de herança de uma geração para a seguinte. Os marcadores moleculares conhecidos como microssatélites são indicados para análises genético-populacionais, por serem amplamente distribuídos no genoma e apresentarem alto conteúdo de informação polimórfica por loco. Para subsidiar diferentes práticas de manejo, bancos de germoplasma e estudos de conservação é importante realizar a análise da variabilidade genética nas populações naturais das espécies de interesse. No bioma Cerrado encontram-se inúmeras espécies medicinais e frutíferas que são utilizadas de forma extrativista, dentre elas estão as do gênero Byrsonima sp., conhecidas popularmente como murici, que são pertencentes à família Malpighiaceae. No Brasil, existem cerca de 70 espécies com ampla distribuição no Cerrado. O murici é uma planta de múltiplas potencialidades e apesar de não ser domesticada, a sua exploração econômica apresenta potencial. Nesse contexto, o objetivo do trabalho foi desenvolver um conjunto de marcadores microssatélites para a espécie Byrsonima cydoniifolia A. JUSS. e testar o potencial de transferibilidade deste conjunto de marcadores para a espécie Byrsonima crassifolia L. Kunth. As regiões microssatélites foram isoladas utilizando bibliotecas genômicas enriquecida para regiões repetitivas e, posteriormente, as mesmas foram utilizadas para o desenho de primers. A partir dos primers desenvolvidos foram testadas condições de temociclagem e seus produtos foram caracterizados utilizando o DNA de 90 indivíduos de B. cydoniifolia e 24 indivíduos de B. crassifolia. Das 60 sequências obtidas, foi possível identificar 22 regiões microssatélites e desenhar pares de primers para 17. Destes, 14 locos apresentaram polimorfismo e três foram monomórficos em três populações de B. cydoniifolia. O número de alelos variou de 3 a 17, com uma média de 10,45 alelos por loco. A heterozigosidade observada foi semelhante à heterozigosidade esperada, com os valores variando de 0,20 a 0,92 e 0,43 a 0,92, respectivamente. Foram identificados 39 alelos privados. Este conjunto de marcadores apresentou alta probabilidade combinada de exclusão de paternidade (Q) igual a 0,999 e probabilidade de identidade combinada (I) igual a I=7,84x10-1. Os valores globais obtidos para o índice de fixação (FIS) não foram significativos (P<0,05), enquanto que os valores de FST=0,082 e FIT=0,143 foram significativos. Para a espécie Byrsonima crassifolia, nove pares de primers produziram bons padrões de amplificação cruzada na população avaliada, apresentando uma média de 7,56 alelos por loco. A heterozigosidade observada variou de 0,250 a 0,958, maior do que a heterozigosidade esperada, que variou de 0,223 a 0,905. A probabilidade combinada de exclusão de paternidade (Q) foi alta igual a 0,998 e a probabilidade combinada de identidade igual a 6,42x10-9. A estratégia de desenvolvimento de marcadores microssatélites a partir da metodologia de biblioteca genômica enriquecida foi eficiente para gerar um painel com onze marcadores microssatélites polimórficos para B. cydoniifolia e nove marcadores microssatélites polimórficos transferidos com sucesso para B. crassifolia, disponibilizando uma ferramenta útil para estudos genético-populacionais não só para as espécies B. cydoniifolia e B. crassifolia, mas possivelmente para outras espécies próximas evolutivamente.

A Mata Atlântica é considerada mundialmente um dos biomas prioritários para conservação, devido à elevada riqueza de sua biodiversidade. A preservação da vegetação natural deve estar associada à restauração florestal, de modo que se possa assegurar a continuidade desta rica biota. No Brasil, grande parte dos projetos de restauração florestal realizados até agora tem se preocupado apenas em buscar diversidade florística, contemplando uma baixa diversidade genética em sua implantação, o que têm criado muitos problemas relativos à viabilidade biológica de suas comunidades. O presente trabalho se propôs a realizar um estudo comparando a diversidade genética (utilizando marcadores SSR, cpSSR e AFLP) da espécie arbórea Piptadenia gonoacantha (Mart.) J. F. Macbr. em duas áreas em processo de restauração florestal e dois remanescentes naturais de floresta estacional semidecidual da Mata Atlântica do estado de São Paulo, Brasil. A partir da biblioteca genômica construída, foram obtidos 12 locos SSR. A heterozigosidade média esperada no equilíbrio de Hardy Weinberg (HE = 0,494) foi maior do que a heterozigosidade observada (HO = 0,251) em todas as populações, indicando taxa relativamente alta de endogamia (FIS = 0,342). Os resultados obtidos com os locos cpSSR mostraram, ao todo, 16 haplótipos, dos quais 10 foram encontrados nos remanescentes de floresta nativa e oito nas áreas restauradas. As análises realizadas com os marcadores AFLP resultaram em 303 marcas polimórficas. Uma estrutura genética muito forte foi encontrada relativa às quatro populações, valores de FST foram 0,283, 0,83 e 0,177 em SSR, cpSSR e AFLP, respectivamente. Dez locos de AFLP que podem estar sujeitos a seleção foram encontrados. As análises de agrupamento delimitam claramente as amostras das quarto populações, evidenciando que não existe fluxo gênico significativo entre elas. P. gonoacantha apresentou auto correlação espacial nas quatro populações. Os três tipos de marcadores detectaram maior diversidade genética nos remanescentes naturais do que nas áreas restauradas. Apesar da menor diversidade apresentada pelas áreas restauradas em comparação com as áreas de remanescentes florestais, o tamanho efetivo populacional estimado para essas áreas permite a manutenção da variabilidade existente a curto prazo. As informações obtidas poderão servir para o manejo sustentado desta espécie, bem como para o planejamento de sua conservação. / The Atlantic Forest is considered one of the world biomes for conservation priority due to the high richness of its biodiversity. The preservation of natural vegetation should be associated to forest restoration, so that the continuity of this rich biota can be ensured. Recent studies and practices of reforestation in degraded areas have taken population genetics as a great ally. Several of the forest restoration projects carried out in Brazil so far has been concerned just with floristic diversity, contemplating low genetic diversity. This fact has created many problems related to the biological viability of their communities. The present project proposes to carry out a study on the diversity genetic structure of the arboreal species Piptadenia gonoacantha (Mart.) J. F. Macbr. In this study, we used six chloroplast simple-sequence repeats (cpSSRs), AFLP markers and the construction of an enriched SSR DNA library to investigate the genetic diversity of P. gonoacantha. This species was evaluated in two areas that are under forest restoration process and compared then with two natural remnants of semideciduous seasonal Atlantic Forest. 12 SSR markers were obtained and the average HO=0.251 was smaller than the average HE=0.494, evidencing a heterozygote deficit (average FIS= 0.342). The samples shows a strong structure with a significant differentiation. FST values were 0.283, 0.83 and 0.177 for SSR, cpSSR and AFLP respectively. The cluster analyzes clearly demarcating the samples of the four populations. cpSSR markers showed 16 haplotypes, ten of them were found in the remaining native forest and eight in the restored areas. Ten AFLP outliers loci were found. The three types of markers detected a higher genetic diversity in natural remnant than in restored areas. Despite the lower diversity presented by the restored areas compared with areas of forest remaining, the effective population size estimated for these areas allows the maintenance of existing variability. The results of this study prove that there is greater genetic diversity in the remaining natural areas than in the areas undergoing a reforestation process. The information obtained may be used for the sustainable management of this species, as well as for conservation planning.

La nouvelle distribution et classification des Coffea (124 espèces Psilanthus incluses, en Afrique, îles de l‟océan Indien (IOI), Inde, Asie du Sud-Est et Australasie) pose la question de leur origine. Des données sont disponibles pour les caféiers africains mais pas pour les Mascarocoffea (caféiers des IOI représentant la moitié des espèces du genre). Les objectifs de cette thèse sont i)- estimer la divergence morphologique, génétique (13 SSR) et génomique des Mascarocoffea, ii)- établir la phylogénie moléculaire du genre (20 COSII) et iii) reconstituer l‟histoire évolutive des caféiers.La diversité morphologique bien que sous forme de continuum, permet la caractérisation de groupements et de stratégies reproductives originales. Les tailles de génome varient de 0,96 à 1,41 pg/2C, avec tendance à l‟augmentation du Nord au Sud-Est de Madagascar.Les nombres moyens d‟allèles par locus et par grande région sont élevés et 20% des allèles totaux sont partagés par ces régions. La phylogénie moléculaire place Psilanthus à la base de l‟arbre et indique une nette divergence entre les Mascarocoffea et les espèces africaines. Il n‟y a pas de structuration hiérarchisée indiquant une divergence indépendante de chaque grand clade.Nos résultats et des données de la littérature nous permettent de proposer un scenario de l‟histoire évolutive des caféiers dont l‟origine est non africaine. Deux centres de diversification primaire sont mis en évidence, situé l‟un en Afrique dans la région Kenya – Ethiopie (à l‟origine de diversifications secondaires vers le Centre, l‟Ouest et l‟Est) et l‟autre dans le Nord Madagascar (à l‟origine des diversifications secondaires à Madagascar et Maurice). / The new classification and repartition of the genus Coffea (124 species including ex-genus Psilanthus native to Africa, Indian Ocean islands (IOIs), India, southeast Asia and Australasia) rises the question on its origin. Genetic and cytogenetic data are available for African species but not for Mascarocoffea (coffees from IOIs including half part of the species). The aims of this thesis were i) to estimate the morphologic, genetic (13 SSRs) and cytogenetic divergence of and among Mascarocoffea; ii) to produce a molecular phylogeny and iii) to reconstruct the coffees evolutionary history.Although the global morphological diversity appears as a continuum, it permits the identification of groupings and obvious specific reproductive strategies. Genomes size varied from 0.96 to 1.41 pg/2C with an increasing global trend from north to southeast Madagascar.Average alleles number per locus is high whatever the region and 20% total alleles are shared by African and IOIs coffees.The molecular phylogeny shows a basal position for Psilanthus, clear divergence between African and IOIs species. Clearly, IOIs clade is not nested within the African. Our results and information from other works permit us to elaborate a new scenario for the evolutionary history of coffees. The centre of origin should be located in India. Then two primary centres of diversification occurred; one in Kenya- Ethiopia, Africa the other in north Madagascar. From these centres, migrations towards centre and west and towards east Africa led to secondary centres of diversification while in Madagascar, migrations towards southeast and towards the other islands led to radiative speciation.

The burgeoning frequency of genome sequencing in recent years is a testament to both the improvements in sequencing technologies and the utility of genomic analyses for biological discovery. The rapid proliferation in technological advancements and availability of complementary data types and techniques has obfuscated the optimal process of genome assembly and raised the barrier to entry to unprecedented levels. In this dissertation, we describe the genome assemblies performed for several marine teleosts and discuss the algorithms and applications required for genome assembly, including some of our specific contributions to the genome assembly and annotation space. In Chapter 1 and Chapter 2, we review the taxonomy, life history, and biogeography of the Roundjaw Bonefish (Albula glossodonta) and describe its genome assembly. The genome assemblies with some analyses are described for the Bluefin (Caranx melampygus) and Giant (Caranx ignobilis) Trevallies in Chapter 3 and Chapter 4, respectively. Chapter 5 and Chapter 6 define and assess algorithms for the annotation of simple sequence repeats in genomic sequences. Publicly available annotations of carbapenem-resistance plasmids were epidemiologically analyzed in Chapter 7. The resiliency of phylogenetic trees to the removal of taxa is explored with a new nodal stability metric and algorithm, TANOS, in Chapter 8. Finally, in Chapter 9, a review of and commentary on vertebrate genome assembly is presented with recommendations for new projects. The aim of this dissertation, and the final chapter in particular, is to explore genome assembly methods and reduce the barrier to entry for new entrants.

Chemical Mechanical Polishing, (CMP), pads made of polyurethane material are utilized in the Integrated Circuit, (IC), industry to planarize wafers between successive process steps. The properties of such pads and their behavior must be known in order to determine under what conditions and for how long they can be used efficiently. This research involved the development of a system to study the properties of such pads. The system developed during this research enabled the pads to be tested under varying physical conditions. The setup used a combination of several instruments to provide excitation to the pad and acquire a measure its response. A central computer controlled the instrumentation system employed. In this research the determination of the physical properties of CMP pads was accomplished through the use of Ultra Sound testing. Ultra sound methods offer a non-destructive method of characterizing pads to be used in the production of IC wafers. Ultra sound characterization is currently one of the most widely used techniques utilized for non-destructive inspection. This report provides a detailed account of the hardware instruments involved and the method of integration of those instruments into a system that could easily, rapidly and accurately characterize CMP pads. The pad response was measured in terms of the signal voltage transmitted through the pad to the ultrasound sensor. The software stored these readings for every set of testing conditions. Changing the temperature, humidity and depth from the pad's surface where measurements are made changed the test conditions. These data were analyzed statistically to determine the behavior of the pad. This research was part of a larger research effort that provided the statistical tool required to determine the uniformity of a CMP pad.

Lately the rate of genetic gain in most agronomic crop species has been reduced due to several factors that limit breeding efficiency and genetic gain. New genetic tools and more powerful statistical analyses provide an alternative approach to enhance genetic improvements through the identification of molecular markers linked to genomic regions or QTLs controlling quantitative traits. The main objective of this research was to identify genomic regions associated with enhanced agronomic performance in lines per se and hybrid combination in Sorghum bicolor (L.) Moench. A population composed of 187 F5:6 recombinant inbred lines (RIL) was derived from the cross of restorer lines RTx430 and RTx7000. Also, a testcross hybrid population (TCH) was developed by using each RIL as a pollinator onto ATx2752. A linkage map was constructed using 174 marker loci generated from AFLP and SSR primer combinations. These markers were assigned to 12 different linkage groups. The linkage map covers 1573 cM with marker loci spaced at an averaged 9.04 cM. In this study, 89 QTL that control variation in seven different morphological traits were identified in the recombinant inbred line population, while in the testcross hybrid population, 79 QTL were identified. These traits included grain yield, plant height, days to mid-anthesis, panicle number, panicle length, panicle exsertion and panicle weight. These putative QTL explained from 4 to 42% of the phenotypic variation observed for each trait. Many of the QTL were not consistent across populations and across environments. Nevertheless, a few key QTL were identified and the source of the positive additive genetics isolated. RTx7000 was consistently associated with better agronomic performance in RIL, while in testcrosses, RTx430 was. Some genomic regions from RTx7000 may be utilized to improve RTx430 as a line per se. However, it is very unlikely that such regions will have a positive effect on the combining ability of RTx430 since testcross results did not reveal any transgressive segregants from the RIL population.

Population based association studies in crops that were established by domestication and early breeding can be a valuable basis for the identification of QTLs. A case control design in a population is an ideal way to identify maximum candidate sites contributing to a complex polygenic trait such as drought. In the current study, marker loci associated with drought related QTLs were identified in sugarcane (Saccharum spp), one of the most complex crop genomes, with its polyploid nature (>8), chromosome number (&gt;100) and interspecific origin. The objectives of this investigation were: 1) development of genic markers, which can be used for marker-assisted selection of drought tolerant genotypes of sugarcane. 2) genotypic characterization of sugarcane population at drought related loci using EST-SSR markers. Using 55 microsatellite markers, 56 polymorphisms were scored among 80 modern sugarcane genotypes. Homogeneity of the population was confirmed by determining the distribution of allele frequencies obtained by random genomic microsatellite markers. This analysis was conducted in the STRUCTURE program and the population was divided in 3 subgroups based on the allelic distribution. Phenotypic data to evaluate drought tolerance among the genotypes was collected by measuring chlorophyll content, chlorophyll fluorescence, leaf temperature and leaf relative water content. A generalized linear model in SPSS was used to find association between marker loci and phenotypic data. Markers with significant association (P 0.001 level) with the trait were subjected to linear regression to screen the spurious associations. Based on the results, 21 EST-SSR markers and 11 TRAP markers related to drought-defining physiological parameters were considered as genuine associations in this study. Fifty-six polymorphisms produced by 13 EST-SSR primers were used to produce genetic similarity matrix for 80 genotypes. Dendrogram prepared from this genetic similarity matrix will be useful in selecting parents carrying diversity at drought specific loci.