The world population is growing and becoming more connected whereby disease transmission is becoming an increasingly important issue. To learn more about disease spread, honey bees (Apis mellifera) could provide an animal-model system for network transmission. The honey bees have both an individual and a social defense against pathogens, their diseases are well studied and they enable studies on hundreds of individuals. The genetic relatedness is believed to be one of many important factors for disease transmission. A hypothesis is that the more closely related the honey bees are the more interactions will occur. In this study, the genetic relatedness in honey bees was analyzed by the use of microsatellite-DNA primers, in a multiplex PCR. Of the 18 microsatellite-DNA primers that were evaluated, the loci HB-C16-05, A007, AC006, HB-C16-02, AP043 and UN351 showed the highest variation. However, when applied on a larger material, the PCR-products did not yield any chromatograms that were possible to score. Many factors possibly affecting the result are discussed and further efforts will be made to improve the method and thereby determine genetic relatedness.

Parathyroid hormone is a vital mediator of bone metabolism and studies have shown that exogenous treatment can enhance the fracture repair process in murine models. Bone remodeling is a complex process that necessitates multiple molecular and cellular interactions that are affected by genetic variations. These differences contribute to both histological and whole organ level differences of fracture healing. This study was performed to determine the effect of genetic variability of fracture healing in mice treated with parathyroid hormone during two time windows. The first window was the first 14-day period post fracture associated with chondrogensis and the second was the day 15 to day 28 post fracture, which is associated with osteogenesis. Three inbred strains of mice A/J (AJ), C57BL/6J (B6), and C3H/HeJ (C3) that have material and structural differences in bone quality were given Femoral shaft fractures and healing was evaluated at different time points post fracture using quantitative real-time polymerase chain reaction (qRT-PCR) and qualitative radiographic analysis. Chondrogenic genes Sox9, ColIIa, aggrecan, and ColXa and osteogenic genes ostrix, osteocalcin, BSP, and DMP1 were examined. The temporal analysis of mRNA expression revealed that PTH treatment given in the first 14 days post fracture enhanced osteogenic and chondrogenic expression in B6 mice, but hindered expression in AJ mice. Treatment with PTH from post fracture day 14 to day 28 greatly affected the osteogenic expression of B6 mice, but had little affect on other animals. Radiographic analysis showed that each strain presents callus formation at approximately day 7 and reaches maximum size at day 21 post fracture. Additionally B6 mice appear with the largest callus and AJ the smallest. Taken together, these results are consistent with past studies in showing that different strains of mice express a unique temporal and mRNA expression pattern of chondrogenic and osteogenic differentiation. Furthermore, these variations affect the biomechanical properties of the fracture callus during bone remodeling.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A região da Bacia de Campos está exposta a diversas atividades antrópicas, que interferem diretamente no funcionamento do ecossistêmico marinho. O estudo da fauna marinha na costa centro-norte fluminense mostra grande relevância, diversas aves marinhas residem ou passam grande parte de seu período migratório ao longo da Bacia de Campos, entre elas está Sula leucogaster (Boddaert, 1783). Embora essas aves sejam altamente móveis, suas populações apresentam uma estrutura populacional genética robusta. Com o intuito de verificar a estruturação e as relações evolutivas da população de Sula leucogaster na Bacia de Campos foram recolhidas 91 amostras de encalhe e os dados gerados para esta região foram comparados com dados já publicados de outras bacias oceânicas. A partir da região controle do DNA mitocondrial foram gerados 26 haplótipos, todos exclusivos da Bacia de Campos, muitos raros e apenas oito possuíram frequência comum. As análises mostraram que a população da Bacia de Campos é um estoque genético de Sula leucogaster. Tal fato pode ser atribuído ao comportamento filopátrico e ao hábito costeiro dessa espécie que impede o fluxo gênico entre populações. Além disso, a população da Bacia de Campos detém baixa variabilidade genética e possivelmente está sofrendo efeito gargalo ou seleção purificadora, corroborados por valores do teste Fu, o que é comum para espécies que se dividem em subpopulações. Os dados filogenéticos demonstram um contato recente entre as populações da Bacia de Campos e da ilha de Ascensão. As condições oceanográficas também têm influência na estruturação de populações de Sula leucogaster, visto que a ausência de barreiras e a proximidade geográfica poderiam favorecer contato secundário com o Mar do Caribe, fato não evidenciado nas análises. Sendo assim, a divergência de populações nessa espécie e a baixa variabilidade genética são fatores preocupantes para a manutenção da população de atobás marrons em uma área de grande impacto ambiental / The region of Campos Basin is exposed to various anthropogenic activities that affect directly the behavior of marine ecosystem. The study of marine fauna in North-Central coast of Rio de Janeiro is of great importance, several marine and coastal birds live or spend most of their migratory period along the Campos Basin, between them is Sula leucogaster (Boddaert, 1783). Although these birds are highly mobile, their populations have a robust genetic population structure. In order to check the structure and evolutionary relationships of the population of Sula leucogaster in the Campos Basin, 91 stranding samples were collected, and the data of this region were compared with the published data. From the control region of mitochondrial DNA, 26 haplotypes were identified, all of them being unique to the Campos Basin. Most of these haplotypes were rare, only eight have common frequencies. The analyses show that the population of the Campos Basin is a genetic stock of Sula leucogaster. This fact can be attributed to the filopatric behavior and coastal habit of this species that prevents the gene flow between populations. Moreover, the population of the Campos Basin has low genetic variability and is possibly suffering a bottleneck effect or purifying selection, supported by Fu test values, which is common for species divided into subpopulations. The phylogenetic data demonstrates a recent contact between the populations of the Campos Basin and Ascensão island. The oceanographic conditions also influence the structuring of populations of Sula leucogaster populations, as the absence of barriers and geographical proximity could favor secondary contact with the Caribbean Sea, which was not evident in the analyzes. Thus, the low amount of gene flow and the low genetic variability are worrying factors for the maintenance of the population of brown boobies in this area of high environmental impact

Made available in DSpace on 2014-06-11T19:26:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-08-05Bitstream added on 2014-06-13T19:33:18Z : No. of bitstreams: 1 meirelles_jad_me_jabo.pdf: 1044355 bytes, checksum: 0bc33764beb92268741c437b1c688dd8 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Os búfalos possuem importância econômica como animais de produção no cenário agropecuário brasileiro e mundial. O conhecimento de polimorfismos em marcadores microssatélites mapeados em búfalos é imprescindível para auxiliar em questões evolutivas da espécie, variabilidade genética intra e inter-populacional, além de serem potencialmente úteis para os programas de melhoramento animal. Foram utilizadas três raças comerciais bubalinas, Mediterrâneo, Jafarabadi e Murrah de rebanhos brasileiros para análise de polimorfismos visando avaliar a diversidade genética existente dentro e entre as raças. Foram analisados 30 animais de cada raça pela amplificação do DNA genômico extraído do bulbo de pelos utilizando quatro locos microssatélites localizados em um cromossomo de interesse econômico. Os produtos de PCR foram separados por eletroforese vertical em gel de poliacrilamida desnaturante. O loco IDVGA-53 não obteve sucesso na amplificação e foi descartado das análises de polimorfismo. Os locos MB099 e BL41 foram monomórficos. Os parâmetros de diversidade foram gerados para o loco CSSM054, o único polimórfico, com média de 3,33 alelos por loco. A heterozigosidade observada com média de 0,503 foi maior que a esperada, indicando excesso de heterozigotos. As raças Mediterrâneo e Jafarabadi apresentaram desvio de equilíbrio de Hardy-Weinberg. O parâmetro Theta indicou evidências de que as três raças diferem entre si, e quando analisadas duas a duas foi possível verificar alta estruturação populacional entre elas. A maior distância genética foi verificada entre as raças Mediterrâneo e Murrah. O conteúdo de informação polimórfica revelou que o loco CSSM054 foi altamente informativo para a raça Mediterrâneo, portanto, considerando todos os resultados, essa raça apresentou maior variabilidade genética / The buffalo water are economically important livestock in Brazilian global and agricultural scenario. The knowledge of polymorphisms in microsatellites markers mapped in buffaloes is essential to assist in evolutionary studies of species, genetic variability within and between populations, as well as being potentially useful for animal breeding programs. Three commercial breeds of buffalos (Mediterranean, Jaffarabadi and Murrah) of Brazilian herds were used for polymorphisms analysis to evaluate the genetic diversity within and among them. In each breed 30 animals were analysed by amplification of genomic DND extracted from the hair bulbs using four microsatellite loci located on a chromosome of economic interest. PCR products were separated by vertical electrophoresis in denaturing polyacrylamide gel. The IDVGA-53 locus was not successful in amplifying and was discarded from the analysis of polymorphism. The loci MB099 and CSSM054 were monomorphic. The parameters of diversity were generated for the locus CSSM054, the only polymorphic, with an average of 3.33 alleles per locus. With a mean value of 0.503, the observed heterozygosity was higher than the expected, indicating excess of heterozygotes. Mediterranean and Jaffarabadi breeds had deviation of Hardy-Weinberg equilibrium. The parameter Theta indicated evidence that the three breeds differ and when they were analyzed in pairs, it was observed high population differentiation among them. The largest genetic distance was found between the Mediterranean and Murrah breeds. The polymorphic information content revealed that the locus CSSM054 was highly informative to the Mediterranean breed, therefore considering all the results that race had a high genetic variability

Made available in DSpace on 2014-06-11T19:26:09Z (GMT). No. of bitstreams: 0 Previous issue date: 2003-11-28Bitstream added on 2014-06-13T18:29:33Z : No. of bitstreams: 1 ganga_rmd_me_jabo.pdf: 819507 bytes, checksum: 5ba45956cafb05a742d55332f642a8b2 (MD5) / Os maracujazeiros pertencem à família Passifloraceae e ao gênero Passiflora, reunindo mais de 500 espécies distribuídas pelos trópicos, principalmente no Brasil, centro de origem de pelo menos um terço das espécies, o que determina uma grande variabilidade genética. Como maior produtor mundial da fruta, o Brasil tem cerca de 35 mil hectares de área colhida e produção superior a 317 mil toneladas por ano, no qual Bahia, São Paulo e Sergipe respondem por mais de 50% da produção no País. A avaliação da variabilidade presente é indispensável aos trabalhos de melhoramento genético, cuja caracterização molecular pode fornecer a base para estudos de diversidade, pautando-se na composição genética sem influência do ambiente. Marcadores moleculares fAFLP foram utilizados para estimar a diversidade genética entre 36 acessos de maracujá amarelo (Passiflora edulis f. flavicarpa Deg.) coletados em 18 estados do Brasil. Os resultados obtidos permitiram concluir que os marcadores fAFLP se mostraram consistentes na verificação da variabilidade genética, detectando e quantificando a ampla divergência genética entre os 36 acessos de Passiflora edulis f. flavicarpa Deg. analisados, bem como a não formação de estruturação geográfica. Tais resultados podem auxiliar na definição de estratégias mais eficientes a serem utilizadas em programas de melhoramento genético de maracujazeiro amarelo. / Passion fruit trees belong to the Passionfloraceae family and to the Passiflora genus, gathering more than 500 species distributed over the tropics, mainly in Brazil, source of at least one third of the species, what determines a great genetic variability. As the world's biggest producing country, Brazil has around 35 thousand hectares of harvest area, and a production superior to 317 thousand tons per year from which Bahia, São Paulo and Sergipe are responsible for more than 50%. The assessment of the variability is essential to genetic breeding works, whose molecular characterization can provide us with the basis for studies on diversity, taking into account the genetic composition without environmental influence. fAFLP molecular markers were utilized to estimate genetic diversity among 36 yellow passion fruit accessions (Passiflora edulis f. flavicarpa Deg.) colleted in 18 Brazilian states. The obtained results led to the conclusion that the fAFLP markers were consistent regarding to the evaluation of genetic variability, detecting and quantifying the ample genetic divergence among the 36 analyzed accessions, as well as to the no geographic structural formation. Such results can be useful to the definition of more efficient strategies to be applied in genetic breeding programs of yellow passion fruit tree.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A região da Bacia de Campos está exposta a diversas atividades antrópicas, que interferem diretamente no funcionamento do ecossistêmico marinho. O estudo da fauna marinha na costa centro-norte fluminense mostra grande relevância, diversas aves marinhas residem ou passam grande parte de seu período migratório ao longo da Bacia de Campos, entre elas está Sula leucogaster (Boddaert, 1783). Embora essas aves sejam altamente móveis, suas populações apresentam uma estrutura populacional genética robusta. Com o intuito de verificar a estruturação e as relações evolutivas da população de Sula leucogaster na Bacia de Campos foram recolhidas 91 amostras de encalhe e os dados gerados para esta região foram comparados com dados já publicados de outras bacias oceânicas. A partir da região controle do DNA mitocondrial foram gerados 26 haplótipos, todos exclusivos da Bacia de Campos, muitos raros e apenas oito possuíram frequência comum. As análises mostraram que a população da Bacia de Campos é um estoque genético de Sula leucogaster. Tal fato pode ser atribuído ao comportamento filopátrico e ao hábito costeiro dessa espécie que impede o fluxo gênico entre populações. Além disso, a população da Bacia de Campos detém baixa variabilidade genética e possivelmente está sofrendo efeito gargalo ou seleção purificadora, corroborados por valores do teste Fu, o que é comum para espécies que se dividem em subpopulações. Os dados filogenéticos demonstram um contato recente entre as populações da Bacia de Campos e da ilha de Ascensão. As condições oceanográficas também têm influência na estruturação de populações de Sula leucogaster, visto que a ausência de barreiras e a proximidade geográfica poderiam favorecer contato secundário com o Mar do Caribe, fato não evidenciado nas análises. Sendo assim, a divergência de populações nessa espécie e a baixa variabilidade genética são fatores preocupantes para a manutenção da população de atobás marrons em uma área de grande impacto ambiental / The region of Campos Basin is exposed to various anthropogenic activities that affect directly the behavior of marine ecosystem. The study of marine fauna in North-Central coast of Rio de Janeiro is of great importance, several marine and coastal birds live or spend most of their migratory period along the Campos Basin, between them is Sula leucogaster (Boddaert, 1783). Although these birds are highly mobile, their populations have a robust genetic population structure. In order to check the structure and evolutionary relationships of the population of Sula leucogaster in the Campos Basin, 91 stranding samples were collected, and the data of this region were compared with the published data. From the control region of mitochondrial DNA, 26 haplotypes were identified, all of them being unique to the Campos Basin. Most of these haplotypes were rare, only eight have common frequencies. The analyses show that the population of the Campos Basin is a genetic stock of Sula leucogaster. This fact can be attributed to the filopatric behavior and coastal habit of this species that prevents the gene flow between populations. Moreover, the population of the Campos Basin has low genetic variability and is possibly suffering a bottleneck effect or purifying selection, supported by Fu test values, which is common for species divided into subpopulations. The phylogenetic data demonstrates a recent contact between the populations of the Campos Basin and Ascensão island. The oceanographic conditions also influence the structuring of populations of Sula leucogaster populations, as the absence of barriers and geographical proximity could favor secondary contact with the Caribbean Sea, which was not evident in the analyzes. Thus, the low amount of gene flow and the low genetic variability are worrying factors for the maintenance of the population of brown boobies in this area of high environmental impact

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Grapevine fanleaf virus (GFLV) is one of the oldest, most widespread and devastating viruses infecting grapevine, and occurs globally where Vitis vinifera is grown. In South Africa (SA) GFLV is predominant in the Breede River Valley, one of the highest wine producing regions in SA. To date, only three GFLV isolates have been completely sequenced internationally, and limited sequence information is available for SA GFLV isolates. In this study, the first full-length GFLV genome sequence from a South African isolate, GFLV-SAPCS3, was determined. Full-length sequences were used for phylogenetic analysis and revealed that the SA isolates are separate from other sequenced GFLV isolates. Full-length sequences were also used to investigate putative intra- and interspecies recombination events involving GFLV-SAPCS3 RNA1 and RNA2 between GFLV and Arabis mosaic virus (ArMV) isolates. Using two different recombination analysis software packages, the most notable of the putative recombination events involving GFLV-SAPCS3 indicated that the GFLV-SAPCS3 RNA2 5’ UTR might have evolved from an interspecies recombination event between GFLVF13- type and ArMV Ta-type isolates. The presence of satellite RNAs (satRNA) associated with South African GFLV isolates was also investigated. In a collaborative study (see Chapter 4 for details), more than a 100 GFLV- infected grapevine plants were screened for satRNAs. SatRNAs were present in only two plants, containing isolates GFLV-SACH44 and GFLV-SACH47. The full-length nucleotide sequences of the GFLV-SACH44 genomic RNAs 1 and 2, and the associated satRNA were determined. No significant sequence variation could be detected between the GFLV isolates that had the presence of a satRNA and those that had not. The GFLV-SACH44 RNA2 5’ UTR also had the same conserved sequence that was found in GFLVSAPCS3, which suggests that GFLV-SACH44, like GFLV-SAPCS3, may have arisen from a common ancestor, which may have originated from an interspecies recombination event. The GFLV-SACH44 satRNA was found to be more closely related to the ArMV large satRNA than to the satRNA associated with GFLV-F13. A full-length cDNA clone of GFLV-SACH44 satRNA was constructed and its replication and systemic spread in herbaceous hosts, when mechanically co-inoculated with two GFLV isolates as helper viruses, was demonstrated. Replication of the GFLV-SACH44 satRNA cDNA clone was however abolished when co-inoculated with an ArMV helper virus, even though it is phylogenetically more closely related to ArMV satRNAs. The full-length satRNA clones were modified to be used as vectors for expression and/or silencing of foreign genes, by inserting the green fluorescence protein (GFP) full-length or partial sequences downstream of the open reading frame of the satRNA. These constructs were cloned into a binary vector to allow for agro-infiltration into plants. Full-length cDNA clones of GFLV-SAPCS3 RNA1 and RNA2 were constructed to be used in conjunction with modified GFLV-SACH44 satRNA full-length clones. The full length GFLV-SAPCS3 RNA1 and RNA2 clones were however not infectious in Nicotiana benthamiana after agro-infiltration and therefore the evaluation of the modified satRNA expression and silencing constructs had to be aborted. Attempts to understand this failure revealed that, among other point mutations, four frameshifts had occurred in the RNA1 full-length clone, rendering the transcripts untranslatable, and hence noninfectious. Strategies to correct the mutations are discussed. Once these mutations have been corrected this study can continue in evaluating the use of the satRNA component for expression and silencing analysis. / AFRIKAANSE OPSOMMING: Grapevine fanleaf virus (GFLV) is een van die oudste, mees wydverspreide en mees verwoestende virusse wat wingerd affekteer en word wêreldwyd waar Vitis vinifera verbou word, gevind. In Suid Afrika (SA) kom GFLV veral in die Breederivier vallei, een van die mees produktiewe wyn-produserende areas in SA, voor. Tot dusver is daar net drie GFLV isolate waarvan die volledige nukleïensuurvolgorde internasionaal bepaal is. Die nukleïensuurvolgorde informasie vir SA GFLV isolate is redelik beperk. In hierdie studie was die eerste volledige nukleïensuurvolgorde van ‘n SA GFLV isolaat, GFLVSAPCS3, bepaal. Die volledige nukleïensuurvolgordes was vir filogenetiese analise gebruik, en vermeende intra- en interspesie rekombinasie gebeurtenisse, wat GFLVSAPCS3 RNA1 en RNA2 betrek, tussen GFLV en Arabis mosaic virus (ArMV) isolate was ondersoek. Twee verskillende rekombinasie-analise sagteware programme was gebruik en die noemenswaardigste van die vermeende rekombinasie gebeurtenisse, met betrekking tot GFLV-SAPCS3, het aangedui dat die GFLV-SAPCS3 RNA2 5’ ontransleerde streek (UTR) waarskynlik van ‘n interspesie rekombinasie gebeurtenis tussen ‘n GFLV-F13-tipe en ‘n ArMV-Ta-tipe isolaat ontwikkel het. Die teenwoordigheid van satelliet RNAs (satRNAs), wat met SA GFLV isolate geassosieer is, was ook ondersoek. Meer as ‘n 100 GFLV ge-infekteerde wingerd plante was in ‘n samewerkingsprojek (sien Hoofstuk 4 vir besonderhede) getoets vir die teenwoordigheid van satRNAs. SatRNAs was net in twee plante teenwoordig, in isolate GFLV-SACH44 en GFLV-SACH47. Die vollengte nukleïensuurvolgordes van GFLVSACH44 RNA1, RNA2 en geassosieerde satRNA was bepaal. Geen beduidende volgorde variasie tussen die GFLV isolate wat satRNAs bevat het, en die GFLV isolate sonder satRNA was waargeneem nie. Die GFLV-SACH44 RNA2 5’ UTR het ook die gekonserveerde volgorde, wat in GFLV-SAPCS3 teenwoordig was, gehad en dit dui daarop dat GFLV-SACH44, soos GFLV-SAPCS3, van dieselfde stamvader, wat tydens ‘n vorige rekombinasie gebeurtenis ontstaan het, mag ontwikkel het. Die GFLVSACH44 satRNA was meer naverwant aan die ArMV satRNAs as aan die satRNA, wat met GFLV-F13. ‘n Vollengte cDNA kloon van die GFLV-SACH44 satRNA was ontwikkel en die replisering en sistemiese verspreiding in sagte plante, nadat dit met twee GFLV isolate as helper virusse saam ge-inokuleer was, was gedemonstreer. Replisering van die GFLV-SACH44 satRNA cDNA kloon was egter ontwrig toe dit saam met ‘n ArMV helper virus saam ge-inokuleer was, al is dit filogeneties meer verwant aan ArMV satRNAs. Die vol-lengte satRNA klone was gemodifiseer om as vektore vir uitdrukking en/of uitdowing van transgene te dien, deur om vol-lengte of gedeeltelike groen fluoressensie proteïen (GFP) nukleïensuurvolgordes aan die einde van die satRNA leesraam te koppel. Hierdie konstrukte was in ‘n binêre vektor gekloon om agroinfiltrasie in plante toe te laat. Vol-lengte cDNA klone van GFLV-SAPCS3 RNA1 en RNA2 was ontwikkel om in samewerking met die gemodifiseerde GFLV-SACH44 satRNA konstrukte gebruik te word. Die vol-lengte GFLV-SAPCS3 RNA1 en RNA2 klone het egter nie in Nicotiana benthamiana gerepliseer na agro-infiltrasie nie, daarom was die evaluasie van die gemodifiseerde satRNA konstrukte gestaak. Pogings om die mislukking te verstaan, het daarop gewys dat, behalwe punt mutasies, vier leesraam versteurings in die RNA1 vollengte kloon voorgekom het, wat ontransleerbare transkripte, en dus nie-repliserende konstrukte tot gevolg gehad het. Strategieë om die mutasies te korrigeer is bespreek. Sodra die mutasies gekorrigeer is, kan die studie voortgaan om te evalueer of die satRNA komponent vir uitdrukking en uitdowing analise gebruik kan word.

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A cana-de-açúcar (Saccharum ssp.) é uma cultura valiosa na produção de alimento, fibra e energia para o Brasil e, especialmente, para o estado de São Paulo. Com o advento da biotecnologia, alternativas de melhoramento genético têm despertado a atenção da comunidade científica, sendo etapas cruciais para tais avanços o sequenciamento e a caracterização do genoma das espécies cultivadas. Dada sua natureza poliploide, com frequente aneuploidia, a cana-de-açúcar apresenta dificuldades às práticas convencionais em genômica, de maneira que é vantajoso fazer uso de recursos de sequenciamento de nova geração e de espécies próximas para elucidar de forma mais efetiva o genoma da gramínea. Uma contribuição interessante, nesse sentido, é a caracterização funcional de polimorfismos genéticos existentes entre genótipos do gênero Saccharum, auxiliando investigações relacionadas à genômica de poliploides complexos, desenvolvendo um recurso a ser utilizado futuramente por melhoristas. Esse trabalho realizou a caracterização da variabilidade genômica a partir de dados genotípicos de indivíduos do Painel Brasileiro de Genótipos de Cana-de-Açúcar, obtidos via genotipagem-por-sequenciamento, utilizando como referência o genoma já sequenciado do sorgo. Os sítios variantes (sobretudo polimorfismos de nucleotídeo único) foram detectados com o software FreeBayes e suas possíveis funções e posições foram anotadas com o programa SnpEff. Utilizaram-se estatísticas de genética de populações, como a frequência alélica para várias classes de polimorfimo, o Teste de McDonald & Kreitman (busca de evidêcias de evolução adaptativa) e a heterozigosidade combinada (busca de regiões genômicas com assinatura de seleção), de modo a identificar regiões genômicas potencialmente envolvidas em eventos evolutivos. Os resultados demonstraram a perda de variabilidade entre os genótipos melhorados em relação aos ancestrais, com evidências de assinaturas de seleção, envolvendo questões sensíveis ao funcionamento da maquinaria celular (como respiração e fotossíntese) e a características valoradas para a cultura (destacando-se a resistência a patógenos e a biossíntese da sacarose). Tais indícios fornecem subsídios à compreensão do genoma e ao melhoramento genético desse poliploide. / Sugarcane (Saccharum ssp.) is a valuable crop for food, fiber and energy production in Brazil, especially to the São Paulo State. With the advent of biotechnology, alternatives to breeding have enticed attention of the scientific community, with genome sequencing and characterization being crucial steps to these advances. Because sugarcane is polyploid, with frequent aneuploidy, it presents difficulties to the application of standard practices in genomics, such that it is advantageous to make use of next generation sequencing alternatives and resources from related species to more effectively elucidate the genome of this grass. Thus, an interesting contribution is the functional characterization of genetic polymorphisms from the Saccharum genus, aiding investigations related to genomics of complex polyploids, developing a resource to be used in the future by breeders. Our goal was to perform this characterization with genotypic data from individuals of the Brazilian Panel of Sugarcane Genotypes, obtained by genotyping-by-sequencing (GBS), using as reference the previously sequenced sorghum genome. We called the variants (mainly single nucleotide polymorphisms) with FreeBayes and annotated their functions and positions with SnpEff. We used population genetics statistics, such as the allele frequency, the McDonald & Kreitman Test and the pooled heterozygosity, to identify genomic regions potentially involved in evolutionary events. The results showed a loss of variability between bred genotypes in relation to the ancestors, with evidences of selective sweeps, involving regions related to the cellular machinery (such as respiration and photosynthesis) and specific crop traits (especially disease resistance and sucrose biosynthesis). These results support understanding of the genome and breeding efforts in this polyploid grass.

Les deux principaux objectifs de ce travail sont de proposer des outils pour la selection d'animaux résistants aux strongles gastro-intestinaux, parasites du tube digestif, et de faire progresser la compréhension des mécanismes de résistance chez la chèvre créole. La variabilité génétique du caractère de résistance au parasitisme digestif a été étudiée afin de vérifier quels critères décrivant le mieux la résistance, peuvent être utilisés pour la sélection. L'ensemble des résultats obtenus suggèrent que le critère d'excrétion d'oeufs et le critère d'éosinophilie sont les plus adaptés pour un schéma de sélection puisqu'ils possèdent une héritabillté moyenne et représentent le mieux la résistance. De plus, ils ne semblent pas en opposition avec le poids, principal critère de production. Le déterminisme génétique de la résistance aux strongles gastro-intestinaux a été étudié et a permis de mettre en évidence l'existence d'un gène majeur pour la résistance chez la population de chèvre créole. De plus, la primo-détection de qtl a permis d'identifier 13 régions du génome ayant un effet sur les critères de résistance. Les mécanismes responsables de la résistance aux strongles gastro-intestinaux ont également été à l'étude. L'ensemble des résultats met en évidence le rôle des éosinophiles dans la mise en place de la résistance aux strongles gastro-intestinaux. L'activité des immunogobulines e semblent dirigés vers les larves l3 d'haemonchus contortus et suggère la mise en place d'une réaction protectrice. Chez la chèvre créole. Ces deux mécanismes semblent donc jouer un rôle important dans la mise en place de la résistance aux strongles gastro-intestinaux / The two main objectives of this work are to propose tools for the selection of resistant animals to gastrointestinal nematodes and advance knowledge on mechanisms of resistance of creole goats. this work has analysed the genetic variability of resistance to digestive parasitism in order to determine which criteria best describes the resistance and can be use for selection. the overall results suggest that the egg excretion and the eosinophilia are the criteria most suitable for a breeding scheme because they have moderate heritability estimates and best represent the resistance. moreover, they do not seem in conflict with the weight, the main criterion of production. the genetic determinism of resistance to gastrointestinal parasites has been studied and has highlighted the existence of a major gene for resistance in creole goats. in addition, the primodetection of qtl identified 13 genomic regions that affect the resistance. the mechanisms behind the resistance to gastrointestinal parasites were also studied and first hypothesis regarding the involvment of the immune response in resistance have been made in goats. the overall results highlighted the role of eosinophils in the development of resistance to gastrointestinal nematodes. the activity of immunoglobulin e seems directed toward l3 larvae of haemonchus contortus and may be imply in the establishment of a protective response agasint nematode parasites. in creole goats, these two mechanisms seem to play an important role in the development of resistance to gastrointestinal nematode infections