O grande desafio da Epidemiologia Genética, atualmente, é identificar, em um espaço de variáveis preditoras de alta dimensão e esparso, fatores de risco genéticos para doenças complexas. Um delineamento amostral útil nestes estudos é coletar dados de trios, que são pequenos núcleos familiares (pai e mãe, livres da doença, e filho afetado) e, em cada indivíduo, obter dados do genótipo de marcadores moleculares, sendo a plataforma de marcadores do tipo SNPs (do inglês, Single Nucleotide Polymorphism), com cerca de 1 milhão de variáveis preditoras genéticas, a mais adotada. Neste trabalho é proposto um procedimento em múltiplos estágios para identificar SNPs associados com a doença em dados de trios. A primeira etapa do procedimento é baseada em uma série de análises unilocos (para cada variável preditora), usando um teste de simetria em tabelas de contingência 2 x 2 (conhecido, em Genética, como teste TDT, do inglês, Transmission Disequilibrium Test). Em um segundo estágio da análise, os resultados destes testes são usados para construir uma estatística de somas acumuladas padronizadas (CUSUM) que permite a seleção de conjuntos de SNPs (isto é, conjuntos de variáveis preditoras), possivelmente associados com a doença. Como um terceiro passo da análise, nas regiões selecionadas no passo dois, são realizadas análises de simetria via testes exatos considerando tabelas 2 x 2 e 4 x 4 (pares de SNPs). A formulação do TDT em termos de testes de simetria é uma inovação na área de Genética e facilita a extensão do caso uniloco para o multilocos. A contribuição deste trabalho reside ainda na formulação exata do teste que é útil em situações de amostras pequenas que ocorrem com frequência em dados de trios. Neste caso inferências parciais foram realizadas a partir de decomposições apropriadas da função de verossimilhança. A modelagem do problema em termos do modelo logístico permitiu concluir que não é necessário corrigir a associação para o efeito de covariáveis avaliadas nos pais. O procedimento é implementado usando recursos dos aplicativos PLINK e R. A aplicação é realizada utilizando dados de 71 trios da população brasileira, em que os indivíduos caso (filhos) foram definidos em termos da ocorrência de uma cardiopatia e, em cada um dos 213 indivíduos, estão disponíveis dados genéticos de uma plataforma de SNPs. / Currently, the great challenge of Genetic Epidemiology is to identify, in a high dimensional and sparse space of predictor variables, genetic risk factors for complex diseases. A useful sampling design in these studies is to collect data from trios, which are small nuclear families (father and mother, free from disease, and affected child), and obtain genotypic information from each individual. The molecular markers platform most commonly used for this purpose is of SNPs (Single Nucleotide Polymorphisms), with about 1 million genetic predictor variables. This work proposes a multi-stage procedure to identify SNPs associated with disease using data from trios. The first step of the procedure is based on a series of single locus analysis (for each predictor variable) using a test for symmetry in 2 x 2 contingency tables (known in genetics as TDT (Transmission Disequilibrium Test). In a second stage of the analysis, the results of these tests are used to construct a standard statistic of the cumulative sums (CUSUM), which allows the selection of sets of adjacent SNPs (ie, sets of predictor variables), possibly associated with the disease. As a third step of the analysis, in the regions selected in step two, are performed an extended analysis of symmetry considering 4 x 4 contingency tables. The TDT formulation in terms of symmetry tests is an innovation in the genetics area and facilitates the extension of the single locus analysis to the multiloci case. The contribution of this work lies in the exact formulation of the symmetry test for square contingency tables that is useful in situations of small sample sizes that often occur in data from trios. In this case, partial inferences were performed from appropriate decompositions of the likelihood function. The structural modeling of the problem in terms of logistic model allowed us to conclude that there is no need to adjust the association for data from parents, but only for the effect of covariates evaluated in each parental haplotype. The procedure is implemented using resources of the R statistical environment and Plink. The application is performed using real data from 71 trios of the Southeast Brazilian population, in which affected child was defined in terms of the occurrence of one congenital heart disease, and in each of the 213 individuals, genomic data were collected using Affymetrix SNP 6.0 platform.

Embora já existam estudos anteriores a respeito da estrutura de população em cana-deaçúcar, até o momento nenhum estudo foi feito usando marcadores SNPs gerados a partir de plataformas de genotipagem de larga escala, como por exemplo, Sequenom iPLEX MassARRAY. No presente trabalho, foi investigada a estrutura populacional no painel brasileiro de variedades de cana-de-açúcar. Esse painel é formado por materiais elites, ancestrais importantes e cultivares utilizados em programa de melhoramento. Um total de 1033 marcadores SNPs foram utilizados para genotipar os acessos do painel. A classificação dos dados feita usando o software SuperMASSA. A estrutura de população foi analisada por meio de análise de componentes principais (ACP), análise de agrupamentos e usando o software STRUCTURE. Devido ao fato que no software STRUCTURE não é possível dados de marcadores moleculares provenientes de espécies poliploides com aneuplodia frequente, o conjunto de dados foi separado e analisado de acordo com nível de ploidias dos SNPs. Com a finalidade de comparar os resultados, foi feita uma análise de coordenadas principais na matriz de distância, com os elementos definidos por 1 - coeficiente de parentesco. A análise de componentes principais revelou presença de estrutura de população. O primeiro componente separou o acesso IN84-58 (S. spontaneum) dos outros acessos que por sua vez estão separados em três grupos: o primeiro grupo formado pelos acessos que são S. sinense, o segundo grupo formado pelos cultivares modernos de cana-de-açúcar e o terceiro grupo formado por acessos que são espécies S. officinarum. Resultados da análise de agrupamento usando distância de alelos compartilhados são condizentes com resultados da ACP. Por outro lado, análise de coordenadas principais e método de agrupamento UPGMA usando o coeficiente de parentesco mostraram uma maior dissimilaridade genética entre os acessos separando as progênies do cultivar RB72454 do grupo formado pelos genitores e ou progenies do cultivar NA56-79. A diferença entre os resultados da análise de componentes principais e de coordenadas principais é devido principalmente a pressuposições nas estimativas do coeficiente de parentesco que são irrealísticas. Com relação a análise feita com o software STRUCTURE, o número de subpopulações e a matriz Q estimada variou de acordo com nível de ploidia dos marcadores. De um modo geral, as análises de estrutura de população mostrou que há evidências de estreitamento da base genética dos acessos devido a cruzamentos recorrentes de indivíduos aparentados. Espera-se que estas informações sejam importantes para o mapeamento associativo e melhoramento genético da espécie. / Although there are several studies inferring population structure in sugarcane, none of them have yet used SNP markers generated from high-throughput platforms, such as, Sequenom iPLEX MassARRAY platform. In this study, it was investigated the population structure in a Brazilian panel of sugarcane varieties. This panel is comprised by elite breeding materials, important ancestors, and cultivars mostly used by breeding programs. 1,033 SNP markers were scored. SNP genotype calling was made using software SuperMASSA. The population structure was analyzed via principal components analysis (PCA), cluster analysis and using the software STRUCTURE. Due to the fact that STRUCTURE is not possible to analyze molecular markers data scored on species withmixed ploidy level, the dataset was separated and analyzed according to SNPs level ploidy estimates. With purpose of comparing the results, it was made a principal coordinate analysis (PCO) of distance matrix, with elements defined by 1 - kinship coefficient. The principal components analysis revealed some structure. The first component separated out IN84-58 (Saccharum spontaneum) from the others acessions, whereby these others acessions were allocated in three groups, comprised by S. sinense species, sugarcane modern cultivars and S. officinarum species. Results from cluster analysis using allele shared distance are in agreement with PCA results. On the other hand, principal coordinates analysis and UPGMA hierarchical clustering method based on kinship coefficient showed a broader genetic dissimilarity between acessions, allocating RB72454 progenies apart from its parents and/or progenies of NA56-79. The difference of results between PCA and PCO are mainly due to irrealistics assumptions in the calculation of kinship. Regarding analysis from the STRUCTURE, the number of subpopulations and Q matrix estimated varied with level ploidy. In general, the study of population structure showed some evidence of narrow genetic distances between accessions, due to recurrent crosses between related individuals. The information presented hereby could be important for association mapping and sugarcane breeding program.

Araucaria cunninghamii is an ancient tropical conifer with substantial value as a forestry species in Australia and Papua New Guinea, and has been subject to a genetic improvement program for more than 50 years. This study was undertaken to demonstrate the utility of quantitative genetic analysis in describing the genetic architecture of commercial traits in A. cunninghamii. Linkage maps were prepared using the pseudotestcross strategy in what was believed to be a wide interprovenance cross using microsatellites and AFLP. A very low rate of marker polymorphism and limited differentiation between the parental provenances was identified, resulting in low mapping efficiency. The population genetic structure of A. cunninghamii was assessed to establish the underlying causes for the limited differentiation and low marker heterozygosity and assess the implications for future analysis of quantitative traits. Despite the limited mapping efficiency, genetic maps were generated for both parents. The maternal map for individual H15 contained 14 linkage groups comprising of 51 AFLP and one microsatellite. The map covered 1290 cM, representing 89% of the estimated genome size. The paternal map for individual Gil24 was 633 cM, consisting of eight linkage groups. Genetic architecture of quantitative traits was examined with putative QTL identified for height, DBH and stem straightness; one was highly significant (p<0.01), three significant (0.01<p<0.05) and 13 suggestive (p<0.10). Significant QTL each accounted for 7-11% of the phenotypic variance with a high allele substitution effect (0.63-0.81). These QTL were likely to be associated with genes of moderate effect. The suggestive QTL each accounted for 3-6% of the phenotypic variance with an allele substitution effect of 0.40-0.63. Three genomic regions contributed to the expression of multiple traits at multiple ages. Stable QTL had decreasing phenotypic effects with increasing age. The population genetic survey characterised low levels of allelic diversity across the geographic range. Three broad regions were characterised; Papua New Guinea, Cape York and northern Queensland to NSW. There was limited differentiation between provenances within these regions, and high diversity within provenances. Limited genetic differentiation between provenances seems to be the result of genetic stability due to long overlapping generations, limited founder effects and a very low mutation rate. The latter may also contribute the low heterozygosity. Limited marker polymorphism and limited differentiation between provenances within broad regions are common features in A. cunninghamii. Therefore careful parental selection and alternative experimental approaches will be required before undertaking further analysis of quantitative traits.

[Truncated abstract] Narrow-leaf lupin (Lupinus angustifolius L.) was first recorded as having been introduced into Germany during the mid-19th century for use as green manuring and as fodder crops. However, it was not until post World-War I that there was any serious attempt to domesticate the species. Since that time several key domestication genes have been incorporated to enable the species to be grown as a crop over a range of climates, harvested as a bulk commodity and, the seed used for both animal and human consumption. However, the recent domestication of this species has seen a rather limited use of wild germplasm largely as a result of the difficulty in retaining these key domestication genes. To make the task of retaining these genes manageable, it was decided to resort to molecular technology. A mapping population of F8 derived recombinant inbred lines (RILs) has previously been established by the Department of Agriculture and Food, Western Australia, from a cross between a domesticated breeding line 83A:476 and a wild type P27255 in narrow-leaf lupin. The parents together with 89 RILs (of a population of 115) were subjected to DNA fingerprinting using microsatelliteanchored fragment length polymorphism (MFLP) to rapidly generate DNA markers for construction of a linkage map. Five hundred and twenty two unique markers of which 21% were co-dominant, were generated and mapped. Phenotypic data for the domestication traits: mollis (soft seeds), leucospermus (white flower and seed colour); Lentus (reduced pod-shattering), iucundis (low alkaloid), Ku (early flowering) and moustache pattern on seed coats; were included. Three to 7 molecular markers were identified within 5 cM of each of these domestication genes. The anthracnose resistance gene Lanr1 was also mapped. Linkage groups were constructed using MapManager version QTXb20, resulting in 21 linkage groups consisting of 8 or more markers. ... Five pairs of QTLs were found to be involved in epistasis, 2 of these having an effect on early vigour and another 3 influencing the time to opening of the first florets. Variation explained for each trait ranged from 28% for seed size, to 88% for days to flowering. We showed that it was possible to use this data to predict genotypes of superior progeny for these traits under Mediterranean conditions. QTL regions were compared on a second published linkage map and regions of conserved synteny with the model legume Medicago truncatula high-lighted. The work presented in this thesis demonstrates the importance of tight linkage between markers and genes of interest. It is especially important when dealing with genetically diverse material as found in the wild. One of the main problems faced by molecular scientists is the phenomenon known as linkage disequilibrium in marker populations caused by either small population size or 4 insufficient opportunity for recombination. This frequently results in the development of markers with little or no application outside of the population in which it was developed. Although the relatively small size of the population used in this study exposes it to such constraints, in this case excellent and valuable results were achieved in developing useful markers to at least 3 of the domestication traits within a relatively short time period of less then 4 years.

<p>&nbsp / </p> <p align="left">The domesticated apple (<i><font face="TimesNewRomanPS-ItalicMT">Malus </font><font face="TimesNewRomanPSMT">x </font><i><font face="TimesNewRomanPS-ItalicMT">domestica </font><font face="TimesNewRomanPSMT">Borkh.), belonging to the </font><i><font face="TimesNewRomanPS-ItalicMT">Malus </font><font face="TimesNewRomanPSMT">genus of the Rosaceae family, is one of the edible pomaceous fruits. Since it is one of the important commercial fruit crops worldwide, the quality of the fruit is crucial to breeders and farmers as it ultimately determines acceptance of a cultivar for consumption. Fruit quality is also a critical determinant factor that is used to estimate the potential of apples to have a long shelf life. The introduction of marker-assisted selection (MAS) has allowed hastening of traditional breeding and selection of high-quality apple cultivars. The availability of genetic linkage maps, constructed by positioning molecular markers throughout the apple genome, enables the detection and analysis of major genes and quantitative trait loci (QTLs) contributing to the quality traits of a given genotype.&nbsp / herefore, the primary aim of this study was to construct a genetic linkage map of the &lsquo / Golden Delicious&rsquo / x &lsquo / Dietrich&rsquo / population for the identification of QTLs associated with fruit quality traits and then to examine the apple fruit pulp proteome with a specific focus on fruit firmness. In this regard, genomic DNA was extracted from leaves of the &lsquo / Golden Delicious&rsquo / x Dietrich&rsquo / population and used in megaplex PCR reactions. The PCR products were analysed prior to scoring of alleles. Polymorphic markers were then used to construct genetic linkage maps. The genetic linkage maps constructed in this study comprise of 167 simple sequence repeats (SSR) markers, 33 of these were newly developed markers. The 17 linkage groups of apple were constructed and aligned to existing apple genetic maps. The maps span 1,437.8 cM and 1,491.5 cM for &lsquo / Golden Delicious&rsquo / and &lsquo / Dietrich&rsquo / , respectively.</font></i></i></i></p>

Domestic animals have rich phenotypic diversity that can be explored to advance our understanding of the relationship between molecular genetics and phenotypic variation. Since the advent of second generation sequencing, it has become easier to identify structural variants and associate them with phenotypic outcomes. This thesis details studies on three such variants associated with monogenic traits. The first studies on Rose-comb in the chicken were published over a century ago, seminally describing Mendelian inheritance and epistatic interaction in animals. Homozygosity for the otherwise dominant Rose-comb allele was later associated with reduced rooster fertility. We show that a 7.38 Mb inversion is causal for Rose-comb, and that two alleles exist for Rose-comb, R1 and R2. A novel genomic context for the gene MNR2 is causative for the comb phenotype, and the bisection of the gene CCDC108 is associated with fertility issues. The recombined R2 allele has intact CCDC108, and normal fertility. The dominant phenotype Greying with Age in horses was previously associated with an intronic duplication in STX17. By utilising second generation sequencing we have examined the genomic region surrounding the duplication in detail, and excluded all other discovered variants as causative for Grey. Dun is the ancestral coat colour of equids, where the individual is mostly pale in colour, but carries intensely pigmented primitive markings, most notably a dorsal stripe. Dun is a dominant trait, and yet most domestic horses are non-dun in colour and intensely pigmented. We show that Dun colour is established by radially asymmetric expression of the transcription factor TBX3 in hair follicles. This results in a microscopic spotting phenotype on the level of the individual hair, giving the impression of pigment dilution. Non-dun colour is caused by two different alleles, non-dun1 and non-dun2, both of which disrupt the TBX3-mediated regulation of pigmentation. Non-dun1 is associated with a SNP variant 5 kb downstream of TBX3, and non-dun2 with a 1.6 kb deletion that overlaps the non-dun1 SNP. Homozygotes for non-dun2 show a more intensely pigmented appearance than horses with one or two non-dun1 alleles. We have also shown by genotyping of ancient DNA that non-dun1 predates domestication.

<p>&nbsp / </p> <p align="left">The domesticated apple (<i><font face="TimesNewRomanPS-ItalicMT">Malus </font><font face="TimesNewRomanPSMT">x </font><i><font face="TimesNewRomanPS-ItalicMT">domestica </font><font face="TimesNewRomanPSMT">Borkh.), belonging to the </font><i><font face="TimesNewRomanPS-ItalicMT">Malus </font><font face="TimesNewRomanPSMT">genus of the Rosaceae family, is one of the edible pomaceous fruits. Since it is one of the important commercial fruit crops worldwide, the quality of the fruit is crucial to breeders and farmers as it ultimately determines acceptance of a cultivar for consumption. Fruit quality is also a critical determinant factor that is used to estimate the potential of apples to have a long shelf life. The introduction of marker-assisted selection (MAS) has allowed hastening of traditional breeding and selection of high-quality apple cultivars. The availability of genetic linkage maps, constructed by positioning molecular markers throughout the apple genome, enables the detection and analysis of major genes and quantitative trait loci (QTLs) contributing to the quality traits of a given genotype.&nbsp / herefore, the primary aim of this study was to construct a genetic linkage map of the &lsquo / Golden Delicious&rsquo / x &lsquo / Dietrich&rsquo / population for the identification of QTLs associated with fruit quality traits and then to examine the apple fruit pulp proteome with a specific focus on fruit firmness. In this regard, genomic DNA was extracted from leaves of the &lsquo / Golden Delicious&rsquo / x Dietrich&rsquo / population and used in megaplex PCR reactions. The PCR products were analysed prior to scoring of alleles. Polymorphic markers were then used to construct genetic linkage maps. The genetic linkage maps constructed in this study comprise of 167 simple sequence repeats (SSR) markers, 33 of these were newly developed markers. The 17 linkage groups of apple were constructed and aligned to existing apple genetic maps. The maps span 1,437.8 cM and 1,491.5 cM for &lsquo / Golden Delicious&rsquo / and &lsquo / Dietrich&rsquo / , respectively.</font></i></i></i></p>

Araucaria cunninghamii is an ancient tropical conifer with substantial value as a forestry species in Australia and Papua New Guinea, and has been subject to a genetic improvement program for more than 50 years. This study was undertaken to demonstrate the utility of quantitative genetic analysis in describing the genetic architecture of commercial traits in A. cunninghamii. Linkage maps were prepared using the pseudotestcross strategy in what was believed to be a wide interprovenance cross using microsatellites and AFLP. A very low rate of marker polymorphism and limited differentiation between the parental provenances was identified, resulting in low mapping efficiency. The population genetic structure of A. cunninghamii was assessed to establish the underlying causes for the limited differentiation and low marker heterozygosity and assess the implications for future analysis of quantitative traits. Despite the limited mapping efficiency, genetic maps were generated for both parents. The maternal map for individual H15 contained 14 linkage groups comprising of 51 AFLP and one microsatellite. The map covered 1290 cM, representing 89% of the estimated genome size. The paternal map for individual Gil24 was 633 cM, consisting of eight linkage groups. Genetic architecture of quantitative traits was examined with putative QTL identified for height, DBH and stem straightness; one was highly significant (p<0.01), three significant (0.01<p<0.05) and 13 suggestive (p<0.10). Significant QTL each accounted for 7-11% of the phenotypic variance with a high allele substitution effect (0.63-0.81). These QTL were likely to be associated with genes of moderate effect. The suggestive QTL each accounted for 3-6% of the phenotypic variance with an allele substitution effect of 0.40-0.63. Three genomic regions contributed to the expression of multiple traits at multiple ages. Stable QTL had decreasing phenotypic effects with increasing age. The population genetic survey characterised low levels of allelic diversity across the geographic range. Three broad regions were characterised; Papua New Guinea, Cape York and northern Queensland to NSW. There was limited differentiation between provenances within these regions, and high diversity within provenances. Limited genetic differentiation between provenances seems to be the result of genetic stability due to long overlapping generations, limited founder effects and a very low mutation rate. The latter may also contribute the low heterozygosity. Limited marker polymorphism and limited differentiation between provenances within broad regions are common features in A. cunninghamii. Therefore careful parental selection and alternative experimental approaches will be required before undertaking further analysis of quantitative traits.

Submitted by Tatiany Aparecida Teixeira Soratto (tatiany_soratto@hotmail.com) on 2017-10-31T12:37:37Z No. of bitstreams: 2 DISSERTACAO_Tatiany_final.pdf: 3171924 bytes, checksum: 81e554e8e0137d88785acf8a80455d32 (MD5) Encaminhamento do orientador.pdf: 236358 bytes, checksum: 344f7f279720c6058970c50ae22f4a46 (MD5) / Approved for entry into archive by Alini Demarchi (alini@cca.ufscar.br) on 2017-11-30T14:04:32Z (GMT) No. of bitstreams: 2 DISSERTACAO_Tatiany_final.pdf: 3171924 bytes, checksum: 81e554e8e0137d88785acf8a80455d32 (MD5) Encaminhamento do orientador.pdf: 236358 bytes, checksum: 344f7f279720c6058970c50ae22f4a46 (MD5) / Approved for entry into archive by Alini Demarchi (ri.bar@ufscar.br) on 2018-01-15T17:25:13Z (GMT) No. of bitstreams: 2 DISSERTACAO_Tatiany_final.pdf: 3171924 bytes, checksum: 81e554e8e0137d88785acf8a80455d32 (MD5) Encaminhamento do orientador.pdf: 236358 bytes, checksum: 344f7f279720c6058970c50ae22f4a46 (MD5) / Made available in DSpace on 2018-02-01T13:19:19Z (GMT). No. of bitstreams: 2 DISSERTACAO_Tatiany_final.pdf: 3171924 bytes, checksum: 81e554e8e0137d88785acf8a80455d32 (MD5) Encaminhamento do orientador.pdf: 236358 bytes, checksum: 344f7f279720c6058970c50ae22f4a46 (MD5) Previous issue date: 2017-09-01 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / The Centro APTA Citros Sylvio Moreira/IAC has been conducting an extensive breeding program of citrus via directed crosses. In a previous study with Citrushuanglongbing pathosystem (HLB) held in our group, using a population obtained by hybridization between Citrus sunki and Poncirus trifoliata, differences were found in the multiplication of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent of HLB, in the parents and in the progeny. It was observed that the rate of infection and bacterial concentration was higher in C. sunki than in P. trifoliata. Thus, it is important to deepen the studies with this genus and hybrids to increase knowledge of which mechanisms could be involved in the tolerance to HLB, considered the most important disease of citrus currently. In this sense, the objective of this study was to establish sinteny between the linkage groups of the C. sunki and P. trifoliata maps with the genome of Citrus sinensis and to map genomic regions associated to tolerance CLas bacterium through phenotypic analysis (QTLs) and gene expression (eQTLs). With the comparative analysis between maps and genome, it was observed that all the linkage groups showed synteny with reference genome chromosomes used, with the exception of the linkage group 10 of the C. sunki map. For the phenotypic data, a population of 79 F1 hybrids between C. sunki and P. trifoliata was used. The quantification of the bacterium and accumulation of starch in the leaves were evaluated after two years of inoculation with the pathogen. Through the statistical analysis of the mixed model it was possible to group the hybrids into resistant, tolerant and susceptible, being important the validation of these data in the field. The expression of 14 candidate genes related to HLB was performed in 72 hybrids of the population and used as expression data for the mapping of eQTLs. It was possible to locate nine QTLs and 52 eQTLs on the C. sunki genitor map and 17 QTLs and 40 eQTLs were found on the P. trifoliata genitor map. The overlapping eQTLs of the majority genes of QTL (phenotypic data) indicates that the genes are related to the phenotype and are probably responsive to the pathogen infection. / O Centro APTA Citros Sylvio Moreira/IAC vem realizando um amplo programa de melhoramento genético de citros via cruzamentos dirigidos. Em um estudo prévio com o patossistema Citros-huanglongbing (HLB) realizado pelo nosso grupo, utilizando uma população obtida por hibridação controlada entre Citrus sunki e Poncirus trifoliata, foram verificadas diferenças na multiplicação da bactéria Candidatus Liberibacter asiaticus (CLas), agente causal do HLB, tanto nos genitores quanto na progênie. A taxa de infecção e a concentração de bactéria foi maior em Citrus sunki em relação ao P. trifoliata. Assim, é importante aprofundar os estudos com esses gêneros e seus híbridos para ampliar o conhecimento de quais mecanismos poderiam estar envolvidos na tolerância ao HLB, considerada a mais importante doença dos citros atualmente. O objetivo do trabalho foi estabelecer sintenia entre os grupos de ligação dos mapas de C. sunki e P. trifoliata com o genoma de Citrus sinensis e mapear regiões genômicas associadas à tolerância a CLas por meio de análise fenotípica (QTLs) e de expressão gênica (eQTLs). Com a análise comparativa entre mapas e genoma, foi observado que todos os grupos de ligação apresentaram sintenia com pseudocromossomos do genoma de referência utilizado, com exceção do grupo de ligação 10 do mapa da C. sunki. Para os dados fenotípicos foi utilizada uma população de 79 híbridos F1 entre C. sunki e P. trifoliata, sendo avaliada a quantificação da bactéria e acúmulo de amido nas folhas após dois anos da inoculação com o patógeno. Com a análise estatística utilizando modelo misto foi possível agrupar os híbridos em resistentes, tolerantes e suscetíveis, sendo importante a validação desses dados em campo. A análise de expressão de 14 genes candidatos relacionados ao HLB foi realizada em 72 híbridos da população e utilizados como dados de expressão para o mapeamento de eQTLs. Foram encontrados nove QTLs e 52 eQTLs no mapa do genitor C. sunki enquanto no mapa do genitor P. trifoliata foram encontrados 17 QTLs e 40 eQTLs. A sobreposição de eQTLs da grande maioria dos genes com QTLs dos dados fenotípicos, indicam que os genes têm relação com o fenótipo e que provavelmente são responsivos à infecção do patógeno.

Made available in DSpace on 2015-03-26T13:42:07Z (GMT). No. of bitstreams: 1 texto completo.pdf: 334704 bytes, checksum: 88b0cef0d0e14e1c75e6e5e034dca776 (MD5) Previous issue date: 2008-02-26 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / The improvement programs have been concerned, more and more, with the development of productive varieties and with high protein content and oil. The use of molecular markers in studies of genetic mapping has been taking the identification of QTLs involved with the genetic control of several characteristics of interest in soybean, above all, productivity and protein content and oil of the grain. In spite of the considerable number of QTLs mapped for such characters available in the literature, it still exist limited and inconsistent information about the confirmation of these QTLs. This work had as objectives the identification of QTLs associated to protein content (PTN) and oil (OIL) and production components in soybean (weight of seeds for plant - WS; weigh of a hundred seeds - WH, number of nodules for plant - NN, number of seeds for plant - NS). The study of QTL mapping was permormed from 206 F2 individuals obtained of the crossing among the soybean line CS3035PTA276-1-5-2 (high protein and low oil content) and the variety UFVS2012 (low protein and high oil content). F3 plants were phenotypic evaluated for 11 characteristics of the soybean in an experiment that consisted of three repetitions or blocks, so that each F3 family was sowed in three repetitions. The results of the variance analyses and of the estimates of the genetic parameters of the characteristics indicated the existence of genetic variability in the population for the eleven characteristics at the level of significance of 1%. Besides, the existence of contrasts among the averages of the genitors was evidenced for most of the characteristics. With base in these results, the genetic potential of the population was confirmed for the study of QTL mapping. Forty eight microsatellite markers had his segregation assessed in the 206 F2 individuals. Were obtained nine linkage groups, formed by the grouping of 25 markers. The analyses of association of simple mark and simple and composed interval mapping were used to detect and to map genomic areas associated to the characteristics in subject. The analyses of QTL were driven by linkage group separately and addressed to the characteristics of the grain and to the production components, main focus of the work. Were identified four QTLs associated to the protein content in the linkage groups A1, D1a, G and I that explained among 6,24% and 18,94% of the phenotypic variation of the characteristic. Three QTLs for content oil were detected in the groups A1, I and O what explained among 17,26% and 25,93% of the variation of the characteristic. For production of grains were identified two QTLs in the linkage groups A1 and D1a that explained 12,32% and 9,03% of the phenotypic variation, respectively. In the linkage group A1 were still detected QTLs associated to the number of nodules by plant and number of seeds for plant. These QTLs explained 9,43% and 7,19% of the variation to these phenotypes, respectively. The population used in this work demonstrated great potential for the QTL mapping. And the considerable number of significant associations detected between markers and characteristics presupposes the existence of others QTLs that can be characterized by the analysis of more markers in certain areas. / Os programas de melhoramento têm se preocupado, cada vez mais, com o desenvolvimento de variedades produtivas e com altos conteúdos de proteína e óleo. A utilização de marcadores moleculares em estudos de mapeamento genético tem levado a identificação de QTLs envolvidos com o controle genético de diversas características de interesse em soja, sobretudo, produtividade e conteúdo de proteína e óleo do grão. Apesar do número considerável de QTLs mapeados para tais caracteres disponíveis na literatura, existe ainda informação limitada e inconsistente sobre a confirmação desses QTLs. Este trabalho teve como objetivos a identificação de QTLs associados a conteúdo de proteína (PTN) e óleo (OLEO) e componentes de produção em soja (peso de sementes por planta - PRO ; peso de cem sementes - PCS, número de vagens por planta - NVP, número de sementes por planta - NSP). O estudo de mapeamento de QTL foi realizado a partir de 206 indivíduos F2 obtidos do cruzamento entre a linhagem de soja CS3035PTA276-1-5-2 (alto teor de proteína e baixo teor de óleo) e a variedade UFVS2012 (baixo teor de proteína e alto teor de óleo). Plantas F3 foram avaliadas fenotipicamente para 11 características da soja em um experimento que constou de três repetições ou blocos, de forma que cada família F3 foi semeada em três repetições. Os resultados das análises de variância e das estimativas dos parâmetros genéticos das características indicaram a existência de variabilidade genética na população para as onze características ao nível de significância de 1%. Além disso, foi evidenciada a existência de contrastes entre as médias dos genitores para a maioria das características Com base nesses resultados, foi confirmado o potencial genético da população para o estudo de mapeamento de QTL. Quarenta e oito marcadores microssatélites tiveram sua segregação avaliada nos 206 indivíduos F2. Foram obtidos nove grupos de ligação, formados pelo agrupamento de 25 marcadores. As análises de associação de marca simples e mapeamento por intervalo simples e composto foram utilizadas para detectar e mapear regiões genômicas associadas as características em questão. As análises de QTL foram conduzidas por grupo de ligação separadamente e direcionadas as características do grão e aos componentes de produção, foco principal do trabalho. Foram identificados quatro QTLs associados ao conteúdo de proteína nos grupos de ligação A1, D1a, G e I que explicaram entre 6,24% e 18,94% da variação fenotípica da característica. Três QTLs para conteúdo óleo foram detectados nos grupos A1, I e O que explicaram entre 17,26% e 25,93% da variação da característica. Para produção de grãos foram identificados dois QTLs nos grupos de ligação A1 e D1a que explicaram 12,32% e 9,03% da variação fenotípica, respectivamente. No grupo de ligação A1 foram ainda detectados QTLs associados ao número de vagens por planta e número de sementes por planta. Estes QTLs explicaram 9,43% e 7,19% da variação para estes fenótipos, respectivamente. A população utilizada neste trabalho demonstrou grande potencial para o mapeamento de QTL. E o número considerável de associações significativas detectadas entre marcadores e características pressupõe a existência de outros QTLs que poderão ser caracterizados pela análise de mais marcadores em determinadas regiões.