Em pesquisa Genômica é de grande interesse o mapeamento de genes que controlam traços ou fenótipos quantitativos. Metodologias estatsticas para identicar genes que tenham efeitos sobre um unico traço são bem conhecidas na literatura e têm sido exaustivamente aplicadas no mapeamento genético de muitas doenças. Porem, na pratica, diferentes traços são correlacionados, como é o caso de hipertensão e obesidade, possivelmente, devido a aço de genes comuns envolvidos na sua regulação. Nestes casos, por meio de tecnicas estatísticas multivariadas, que exploram a estrutura de covariância entre os traços, é possvel identificar genes não detectados por analises univariadas, ganhar precisão nas estimativas dos efeitos e conhecer a posicão desses genes, alem de testar efeitos de pleiotropia (um mesmo gene controlando varios traços) e interacções gene-ambiente (os genes que controlam a pressão antes e depois de dieta com sal). Neste trabalho diferentes alternativas de analise estatstica são consideradas para explorar a informacão de vários tracos conjuntamente: modelo de regressão intervalar multivariado (Jiang & Zeng, 1995), mapeamento multivariado via a teoria espectral (Mangin et al.,1998), via medidas resumo relevantes (como a diferenca entre respostas antes e depois de uma exposição) e via ajustes por covariaveis. Também são introduzidas algumas abordagens graficas para o estudo do efeito de pleiotropia e interação geneambiente. As metodologias supracitadas são aplicadas a dados reais fornecidos pelo Laboratorio de Cardiologia e Genética Molecular do InCor/USP, que consideram várias medidas de pressão arterial em ratos provenientes de uma população F2. / In Genomic research, the mapping of genes which control quantitative traits has been of great interest. Statistical methods for detection of genes, in uencing a single trait, are well known in the literature and they have been exhaustive used in the genetic mapping of many diseases. However, in real situations, dierent kind of traits are correlated, such as hypertention and obesity, that would be due to the action of a set of commom genes involved in the regulation of these traits. In these cases, through of multivariate statistical techniques, which explore the covariance structure between the traits, it is possible to identify genes that are not detected by univariated analysis. In addition multivariate analysis are useful to obtain accurate estimates and to know the position of these genes, besides testing eects of pleiotropic (a gene controlling several traits) and geneenvironmental interations (genes that control the pressure before and after salt diet). In this work dierent alternatives from statistical analysis are considered to explore information of several traits jointly: Interval multivariate regression models (Jiang and Zeng, 1995); multivariate mapping through the espectral theory (Mangin et al. 1998), summary measures (for example, models formulated in terms of the dierence between two traits) and adjustments including covariates. Also, graphics procedures are introduced in order to study eects of pleiotropy and geneenvironmental interactions . The methodologies mentioned above are applied to real data set, supplied by the Cardiology and Molecular Genetic Laboratory of Heart institute (InCor-USP), that consider several measurements of blood pressure in rats that come from a F2 population.

Embora não exista uma variedade comercial de maracujazeiro-doce (Passiflora alata Curtis), a fruta vem ganhando espaço no mercado brasileiro, justificando o uso de técnicas convencionais e moleculares no melhoramento da cultura. Nas espécies em que ocorre autoincompatibilidade e o cruzamento entre indivíduos é obrigatório, como nos maracujazeiros, não é possível a obtenção de populações convencionais de mapeamento. Por isso, utiliza-se a técnica two-way pseudo-testcross para a geração de mapas genéticos, usando uma população F1 segregante e marcas dominantes, o que resulta na geração de mapas individuais, sendo um por genitor. A inconveniência desta estratégia tem sido superada pelo uso de marcadores codominantes e estatísticas mais robustas. Marcadores baseados em SSRs (ou microssatélites) e em SNPs são úteis para promover a integração dos mapas, pois são codominantes e abundantes no genoma de plantas. O presente trabalho objetivou gerar um mapa integrado de P. alata, usando novos marcadores SSR, além de M-AFLP e SNP. Os locos SSR foram desenvolvidos a partir de uma biblioteca genômica enriquecida, previamente construída. Dentre os motivos, prevaleceram os dinucleotídicos perfeitos de (AC)n e (AG)n. Neste trabalho, mais 175 primers de SSR foram desenhados e avaliados juntamente com 111 previamente obtidos, observando-se uma taxa de polimorfismo entre os genitores de 31,9%. Ainda com esse conjunto de primers, foi possível recuperar polimorfismos de conformação de fita simples (SSR-SSCP) em 23 locos. A genotipagem de 26 SSRs na população segregante resultou em 40 locos, os quais, associados a um SSR-SSCP, resultaram em seis locos com segregações mais informativas do tipo 1:1:1:1 e 1:2:1. M-AFLPs apresentaram 34,0% de polimorfismo, acrescendo mais seis locos informativos ao mapa de ligação. Os SNPs revelados pelo alinhamento das sequências de AFLP e de genes putativos revelaram uma mutação a cada 110 pb, em média. Foi possível a genotipagem de SNP para um dos genes, e conjuntos de primers para outros locos são propostos. Mapas individuais para ambos os genitores foram obtidos com 175 e 229 marcadores de segregação 1:1, respectivamente, ao passo que o mapa integrado incluiu, além desses, 12, 7 e 40 marcas de segregação 1:1:1:1, 1:2:1 e 3:1, respectivamente. Foi possível estabelecer a correspondência para a maioria dos grupos de ligação individuais e integrados. Observou-se a ampla distribuição de marcadores baseados em microssatélites, com a eventual formação de clusters. Este mapa, embora preliminar, pode ser útil no mapeamento de caracteres agronômicos e em estudos comparativos com o mapa integrado de P. edulis f. flavicarpa. / Although there is no a commercial variety of sweet passion fruit (Passiflora alata Curtis) the crop has gained importance in the Brazilian market. This justifies the use of conventional and molecular techniques for breeding the crop. In species where self-incompatibility occurs and crossing between plants is necessarily required, as in passion fruits, conventional mapping populations are not possible to be produced. Therefore, the two-way pseudo-testcross approach is used for the generation of genetic maps, employing an F1 segregating population and dominant markers, resulting in individual maps, one for each parent. The drawback of this strategy has been overcome by the use of codominant markers and more robust statistics. Markers based on SSRs (or microsatellites) and SNPs are useful for integrating the maps, because of their codominant inheritance and abundance in plant genomes. This study aimed to generate an integrated map of P. alata using new SSR, M-AFLP and SNP markers. The SSR loci were developed from an enriched genomic library previously constructed. Among the motifs, the most frequent were perfect di-nucleotides, (AC)n and (AG)n rich. In this study, 175 SSR primers were designed and evaluated along with 111 previously obtained. A polymorphism rate of 31.9% was observed between the parents. Using these primer sets, it was possible to recover single-stranded conformation polymorphisms (SSR-SSCP) at 23 loci. The genotyping of the segregating population using the 26 SSRs resulted in 40 loci; adding a SSR-SSCP, the result was six informative loci showing segregation rations of 1:1:1:1 and 1:2:1. M-AFLPs showed 34.0% of polymorphism, providing six informative loci to the map. The alignment of parental AFLP and putative gene sequences revealed one SNP per 110 bp on average. It was possible to genotype one gene-derived SNP, and primer sets for other loci are proposed. Individual maps of both parents were obtained with 175 and 229 markers segregating in 1:1 ratio, respectively, while in the integrated map were included 12, 7 and 40 markers segregating in 1:1:1:1, 1:2:1 and 3:1 rations, respectively. It was possible to establish the correspondence for most of the individual linkage groups and the integrated groups. Microsatellite-based markers showed a wide genome distribution, with eventual cluster formation. Although preliminary, this map may be useful for mapping agronomic traits and in comparison studies with the integrated map of P. edulis f. flavicarpa.

Um dos principais desafios do melhoramento de milho doce é aumentar a eficiência da seleção para produtividade e qualidade dos grãos. Uma das formas de aumentar essa eficiência é a utilização de marcadores moleculares para auxiliar a seleção nos programas de melhoramento. Para isso, o estudo da herança por meio do mapeamento de QTL é uma ferramenta importante para o conhecimento da base genética dos caracteres e para gerar informações que possam ser utilizadas na seleção assistida por marcadores moleculares. O presente estudo teve como objetivo mapear QTL em testecrosses de milho doce para produção de grãos, seus componentes e caracteres de qualidade, e avaliar o efeito de diferentes testadores e ambientes no mapeamento de QTL. Para tanto, foi utilizada uma população obtida do cruzamento entre as linhagens B532 e B605 do mesmo grupo heterótico e contrastantes para diversos caracteres. Duzentas e cinqüenta e seis progênies F4:5 foram genotipadas com marcadores moleculares SNP para a construção do mapa genético. Posteriormente, essas progênies foram cruzadas com os testadores A36 e A17 de um grupo heterótico distinto do grupo da população. Os testecrosses obtidos foram avaliados em dois ambientes, Uberlândia, MG, e Itatiba, SP, em látices simples 16 x 16. Os caracteres avaliados foram produção de grãos (PG), número de fileiras de grãos (NF), comprimento de espiga (CE), diâmetro de espiga (DE), comprimento de grãos (CG), coloração de grãos (CL), maciez de grãos (MC) e doçura de grãos (DÇ). O método de mapeamento por intervalo composto expandido para múltiplos ambientes (mCIM) foi utilizado para mapear QTL e detectar a interação QTL x ambiente. Foram mapeados 116 QTL, sendo 21 para PG, 17 para NF, 22 para CE, 14 para DE, 12 para CG, 11 para CL, 11 para MC e 8 para DÇ. Com exceção de 2 QTL para NF que explicaram 12,19% e 10,03% e de 1 QTL para CE que explicou 10,48%, todos os outros explicaram menos de 10% da variância fenotípica. Considerando todos os caracteres, 91% dos QTL mapeados foram específicos para cada testador, evidenciando uma elevada interação QTL x testador. Dos 116 QTL mapeados apenas 22 apresentaram interação QTL x ambiente, indicando que houve baixa interação QTL x ambiente. Dessa forma, a maioria dos caracteres de importância econômica em milho doce foi controlada por muitos QTL de baixos efeitos na variação fenotípica, os quais apresentaram uma elevada interação QTL x testador e uma reduzida interação QTL x ambiente. O elevado número de QTL controlando os caracteres e a elevada interação QTL x testador mostram a complexidade da aplicação da seleção assistida no melhoramento de milho doce. / One of the main challenges in sweet corn breeding is to improve the efficiency of selection for grain yield and quality traits. The use of molecular markers would be a way to increase the selection efficiency in breeding programs. QTL mapping is an important tool for understanding the genetic basis of the traits and to generate information that can be used in marker assisted selection. This study aimed to map QTL in sweet corn testecrosses for grain yield, its components and quality traits, and evaluate the effect of different testers and environments in QTL mapping. For this study a population was obtained by crossing lines B532 and B605, from the same heterotic group and contrasting for different traits. Two hundred and fifty-six F4:5 progenies were genotyped with SNP markers for the construction of the genetic map. Subsequently, these progenies were crossed with the testers A36 and A17 from a different heterotic group than the population. The obtained testecrosses were evaluated in two environments, Uberlândia, MG, e Itatiba, SP, in a simple lattice design 16 x 16. The traits evaluated were: grain yield (PG); number of rows (NF); ear length (CE); ear diameter (DE); kernel depth (CG), kernel color (CL); kernel tenderness (MC) and kernel sweetness (DÇ). The composite interval mapping extended to multiple environments (mCIM) was used to map QTL and to detect the QTL x environment interaction. One hundred and sixteen QTL were mapped; with 21 for PG, 17 for NF, 22 for CE, 14 for DE, 12 for CG, 11 for CL, 11 for MC and 8 for DÇ. With the exception of 2 QTL for NF which explained 12%,19% and 10,03% and by 1 QTL for CE which explained 10,48%, all the others explained less than 10% of the phenotypic variance. Considering all of the traits, 91% of the mapped QTL were specific to each tester, indicating a high QTL x tester interaction. Out of the 116 QTL mapped, only 22 showed significant QTL x environment interaction, indicating that there was a small QTL x environment interaction. Thus, most traits of economic importance in sweet corn seem to be controlled by many QTL with small effects, which showed a large QTL x tester interaction and a small QTL x environment interaction. The large number of QTL controlling the traits and the large QTL x tester interactions demonstrate the complexity of the implementation of marker assisted selection in sweet corn breeding.

O maracujazeiro-doce (Passiflora alata Curtis) é uma espécie de cruzamento e diploide (2n = 18) que vem se destacando no Brasil por alcançar melhores cotações no mercado de frutas. Apesar disso, é sensível às adversidades em monocultura, sendo extremamente afetada por variações climáticas, pragas e doenças, dentre elas, a bacteriose causada por Xanthomonas axonopodis pv. passiflorae. O patógeno é endêmico no país, apresentando considerável variabilidade genética nas populações naturais. O presente trabalho teve como objetivo contribuir para o melhoramento genético do maracujazeiro-doce por meio do mapeamento de QTL (Quantitative Trait Loci) relacionados à resistência à bacteriose de uma população F1 segregante, composta de 100 indivíduos e oriunda do cruzamento simples entre dois acessos não endogâmicos. A população foi mantida em casa de vegetação, em delineamento em blocos ao acaso, e foi inoculada com três isolados bacterianos, M129, PA8-2 e AP302, durante 2010, 2012 e 2013, respectivamente. Aos 14 dias após a inoculação, as folhas foram fotografadas e a partir das imagens digitalizadas foram mensuradas as áreas: sadia, de clorose, necrose e lesão (soma das áreas de clorose e necrose), além da área total da folha. Inicialmente, foi realizada uma análise exploratória dos dados e subsequentemente foram selecionados os caracteres área de necrose e de lesão foliar para fins de mapeamento de QTL. Para tanto foi usada uma estratégia desenvolvida para a detecção de QTL em F1 segregantes, com base em modelos mistos, considerando diferentes estruturas de variância e covariância, visando explicar os padrões de variação existentes. A herdabilidade variou de 14% a 64% para o carater necrose, e se manteve estável (28%) para o carater área de lesão, nos três anos de avaliação. Com base em um mapa de ligação integrado previamente construído, foi realizado o mapeamento de QTL por intervalo composto. Foram identificados 20 QTL, sendo 9 deles referentes à necrose e 11 referentes à lesão. Os efeitos individuais variaram de 0,2% a 15,7%, sendo que dois QTL de maior efeito (R² = 15,7%) foram identificados em resposta ao isolado PA8-2, um localizado no grupo de ligação III e o outro no IV do mapa genético integrado do maracujazeiro-doce. Essas informações, aliadas a outros estudos relacionados à produção de frutos, devem contribuir para o melhoramento do maracujazeiro-doce. / The sweet passion fruit (Passiflora alata Curtis) is an outcrossing and diploid (2n = 18) species that is achieving a competitive advantage in the fruit markets in Brazil. Nevertheless, the crop is sensitive to monoculture, being greatly affected by weather changes, pests and diseases, among them the bacterial disease caused by Xanthomonas axonopodis pv. passiflorae. The pathogen is endemic in the country, with considerable genetic variability in natural populations. The present study aimed to contribute to genetic improvement of sweet passion fruit through QTL (Quantitative Trait Loci) mapping associated with bacterial resistance using a F1 segregating population containing 100 individuals, which resulted from a single cross between two outbred accessions. The population was kept in a greenhouse, arranged in a randomized block design, and innoculated with three bacterial isolates, M129, PA8-2 and AP302, during 2010, 2012 and 2013, respectively. At 14 days after inoculation, the inoculated leaves were photographed, and the following areas from the scanned images were measured: healthy, with chlorosis, necrosis and leaf lesion (sum of the areas with chlorosis and necrosis), in addition to the total area of the leaf. Initially all data were investigated trough an exploratory analysis and those relative to necrotic and leaf lesion areas were subsequently used for QTLmapping. For that we used a strategy developed for QTL detection in F1 segregating populations based on composite interval mapping and mixed models considering different variance and covariance structures in order to explain the existing patterns of variation. Heritabilities ranged from 14% to 64% for the trait necrosis, and remained stable (28%) for the trait leaf lesion for the three years of evaluation. Based on an integrated linkage map previously constructed, we performed a composite interval mapping of QTL. Twenty QTL were identified, 9 of them related to necrosis and 11 related to the leaf lesion. The individual effects ranged from 0,2% to 15,7%, and two large-effect QTL (R² = 15,7%) were identified in response to isolate PA8-2, one assigned to linkage group III and other to linkage group IV of the integrated genetic map of sweet passion fruit. This information combined with other studies related to fruit production may contribute to sweet passion fruit breeding.

Evaluer l'effet du climat sur la croissance des arbres forestiers, et notamment leur capacité de production de biomasse en situation de contrainte hydrique, passe par la quantification du niveau de plasticité phénotypique des individus et de la diversité génétique des populations au sein de l'espèce étudiée. Le pin maritime, plante pérenne d'intérêt économique majeur en Aquitaine, largement étudiée au niveau génétique et écophysiologique, est un excellent modèle biologique pour mener à bien ce type d'étude. Dans le cadre de cette thèse, nous avons étudié la variabilité phénotypique de nombreux caractères liés à la croissance du pin maritime au jeune âge, en fonction de contraintes abiotiques essentiellement liées à la disponibilité en eau. Nous avons par ailleurs documenté l'architecture génétique de ces traits en termes de nombre, position sur une carte génétique et effet des gènes majeurs (QTL) qui contrôlent une partie de cette variabilité phénotypique.Dans le cadre de travaux de cette thèse, nous avons utilisé deux dispositifs expérimentaux: l'un composé de trois familles F1 issues de croisements contrôlés de parents d'origines géographiques contrastées (Corse, Landes et Maroc), l'autre d'une famille F2 issue de l'autofécondation d'un hybride Corse x Landes. Le premier essai comprenait 1500 individus semés en 2007 sur lesquels la hauteur et le diamètre ont été mesurés annuellement de 2010 à 2014. Nous avons également noté l'évolution de la phénologie du débourrement apical pendant deux années consécutives (2012 et 2013). Enfin, la dynamique de la croissance radiale de 239 génotypes (répartis sur deux des trois familles) a été suivie en continu pendant trois années (2011-2013) grâce à un dispositif unique de capteurs de déplacement continu (microdendromètres). Le second essai comprenait 500 arbres semés en 1998 et dont le carottage au niveau du tronc début 2011 a permis d’établir le profil microdensitométrique sur 7 années consécutives (2004-2010). En parallèle, le génotypage des descendants des 4 croisements a été réalisé grâce à l'aide de biopuces à ADN, ce qui a permis de construire des cartes génétiques. L'analyse conjointe de l'information phénotypique et génotypique a permis d'identifier des QTL pour l'ensemble des caractères et d'étudier leur stabilité en fonction des conditions environnementales et du fond génétique.Cette étude a montré que le débourrement est variable en années en fonction des contraintes de températures et du fond génétique. Tout comme la croissance primaire et secondaire, le débourrement est contrôlé par de nombreux QTL à effets modérés qui varient en fonction de l’environnement climatique et du fond génétique. Le suivi de la dynamique saisonnière de la formation du bois a également montré une interaction QTL x environnement révélant que la densité du bois est régulée par différents gènes ou le même jeu de gènes régulé de façon différentielle en fonction du climat. Enfin, La dernière partie de cette étude a permis de mettre en évidence, pour la première fois, la variabilité intra-spécifique des fluctuations journalières du tronc et son interaction avec des variables environnementales. [...] / Evaluating the impact of climate change on current plantations supposes the evaluation of their phenotypic plasticity and their genotypic diversity within the species, under abiotic pressure. Maritime pine is a perennial species of major economical interest in the french Aquitaine region. Wildly studied genetically and ecophysiologically, maritime pine is a very good biological model to see that type of study to the end. In this thesis, we intend to study various traits related to maritime pine growth under a biotic constraints, according to the following approaches: (1) evalutation of the phenotypic variability and (2)dissection of the genetic architecture of the traits (number, location and effects of QTLs). The comparisonbetween envrionmental and phenotypic data will allow us to appreciate the phenotypic pasticity of individuals. Afterwards, studying the genetic architecture of these traits and its variability according to the genetic background of individuals and environmental conditions will allow us to assess the stability ofdetected QTLs.We used 4 progenies of maritime pines: 3 controlled crosses of parents originated from contrasted ecotypes (Corsica, Landes and Morocco) and 1 controlled cross from a second generation of self-pollination (F2). Micro-cores were extracted from the individuals of the F2 population andmicrodensity profiles were established trough 7 consecutive years. Total height and diameter of eachindividual were measured once a year on the 3 others crosses, from 2010 to 2014. Dynamics of apical budburst was also followed on the same individuals in 2012 and 2013. Finally, dynamics of radial growth were monitored on a sub-sample of 239 individuals (spread in 2 of the 3 controlled crosses) during 3 yearsthanks to a unique device of microdendrometers.At the same time, all individuals (form the 4 crosses) were genotyped with several DNA bioarraysof molecular markers, allowing the building of genetic maps. The confrontation of phenotypic and genotypic data enabled to identify genome are as involved in the genetic architecture behind the traitsand to study their stability according to environmental conditions and the genetic background of individuals.This study showed that bud burst varies from year to year, depending on the conditions oftemperature and of the genetic background of individuals. Same way as growth, bud burst is controlled bymany QTLs of moderate effect, varying according to climatic conditions and the genetic background of individuals. The monitoring of seasonal dynamics of wood formation also showed a QTL x environment interaction revealing that wood density is regulated by different genes or the same set of genes,differentially regulated in response to the climate. The last part of the study puts forwards, for the firsttime, the variability of radius daily fluctuations within a full-sib family and its interaction with environmental variables. [...]

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This thesis involves the important crop plant soybean (Glycine max), and provides a rich information resource for breeders and geneticists working towards improving traits for pathogen resistance.Results reported here provide a systemic view at both the genetic and biochemical level, and were generated by data-mining gene expression data from soybean cultivars inoculated with plant pathogens and also recombinant inbred line (RIL) populations.The genome variability based on Single Feature Polymorphisms (SFPs) was measured for the first time in soybean, using a genetically diverse set of cultivated G. max lines and also a G. soja line. Additionally, a genetic map spanning all 20 soybean chromosomes groups were assembled in a large RIL population.The well studied metabolic pathways from the model plant Arabidopsis thaliana, were reconstructed in G. max based on sequence similarity comparison between the genomes of the two species. We performed algorithmic analysis of pathways in our set of soybean lines and RILs using the gene expression data, and acquired a systemic view of the metabolic response to pathogen infection in different genetic backgrounds.Significant differences in the patterns of pathway perturbation was observed in the different lines, and also between four different chromosomal regions that have been known to contain genetic elements contributing to pathogen resistance. / Ph. D.

Thesis (PhD)--Stellenbosch University, 2015 / ENGLISH ABSTRACT : Diuraphis noxia Kurdjumov (Russian Wheat Aphid; RWA) is a pest of wheat and barley that has spread from its home range in the fertile crescent to most wheat producing countries except Australia. Since its first introduction to South Africa and the USA in the late 20th century, breeding programs for wheat phenotypes resistant to the aphid were put in place. Conventional breeding practices rely on phenotypic screening to verify traits carried by offspring and genetic tools such as marker assisted selection (MAS) have greatly aided this process in speed and accuracy. The size and complexity of the wheat genome, its allopolyploid nature and repetitive elements have, however, posed a challenge to studies on the genetics of this cereal crop. Many studies have focused on chromosome 3B which is the largest of the wheat chromosomes and easily separated from the redundant genomic background by techniques such as flow cytometry. The similarity in size of the remaining chromosomes however, limits the application of flow cytometry to their isolation. Databases such as Grain-Genes (http://wheat.pw.usda.gov/GG2/index.shtml) house marker data from various mapping studies for all wheat chromosomes and in 2014 the International Wheat Genome Sequencing Consortium (IWGSC) completed the draft genome sequence of wheat categorized by chromosome. Sources of resistance (Dn resistance genes) against RWA are located on chromosome 7D. but despite the marker and sequence data available currently, mapping studies specific for the Dn resistance genes are few. Additionally, sequence data available is derived from cultivars susceptible to RWA and is not comprehensively annotated and assembled in many cases. In this study, we demonstrate a novel, combined approach to isolate and characterize the Dn resistance genes through the use of a genetic map constructed from Amplified Fragment Length Polymorphism (AFLP), Expressed Sequence Tag (EST) and microsatellite markers and a physical map constructed from Next Generation Sequencing (NGS) data of ditelosomic chromosomes (7DS and 7DL) isolated by microdissection on the PALM microbeam system. A 122.8 cM genetic map was produced from 38 polymorphic AFLP markers and two ESTs with the microsatellite Xgwm111 as anchor to related genetic maps. Through comparison to maps available on GrainGenes the location of the Dn1 resistance gene was narrowed down to a deletion bin (7DS5-0.36-0.62) on the short arm of chromosome 7D with an AFLP marker (E-ACT/M-CTG_0270.84) mapping closely at 3.5 cM and two ESTs mapping at 15.3 cM and 15.9 cM from Dn1. Isolation of individual chromosome arms 7DS and 7DL using the PALM Microbeam system allowed sequencing of the chromosome without the redundancy of the remainder of the hexaploid genome. Through isolating the chromosome arms in this way, a >80-fold reduction in genome size was achieved as well as a major reduction in repetitive elements. Analysis of the sequencing data confirmed that 7DL is the physically shorter arm of the chromosome though it contains the majority of protein coding sequences. / AFRIKAANSE OPSOMMING : Diuraphis noxia Kurdjumov (Russiese koring-luis; RWA) is « pes wat op koring en gars voorkom. Die pes het vanaf sy tuiste in die midde Ooste na meeste koringproduserende lande behalwe Australië versprei. Sedert die eerste bekendstelling van RWA in Suid Afrika en die VSA in die vroeë 20ste eeu is teelprogramme ten gunste van koring lyne met weerstand teen RWA begin. Tradisionele teelprogramme maak op fisieise observasie van die fenotipe staat om te verifieer of plante in die nageslag die gewenste eienskap dra. Genetiese metodes soos merkerondersteunde seleksie (MAS) versnel hierdie selekteringsproses grootliks. Die grootte en kompleksiteit van die koring genoom asook die polyploïde en herhalende natuur daarvan is « groot hindernis vir genetiese studies van hierdie graangewas. Baie studies het op chromosoom 3B gefokus wat die grootste van die koring chromosome is en dus maklik vanaf die res van die oorbodige genomiese agtergond deur tegnieke soos vloeisitometrie geskei word. Die ooreenkoms in grootte tussen die res van die chromosome bemoeilik die toepassing van vloeisitometrie om hulle te isoleer. Databasisse soos GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml) bevat merker data vanaf verskeie karterings-studies vir al die chromosome en in 2014 het die "International Wheat Genome Sequencing Consortium"(IWGSC) die voorlopige basispaarvolgorde van die koring genoom bekendgestel, gekategoriseer volgens chromosoom. Weerstandsbronne (Dn weerstandsgene) teen RWA kom meestal op chromosoom 7D voor. Ten spyte van merker en basispaarvolgorde data tans beskikbaar is karterings-studies spesifiek tot die Dn gene skaars en basispaarvolgorde data is vanaf kultivars afkomstig wat nie weerstandbiedend teen RWA is nie en waarvan die annotasie en samestelling baie keer nie goed is nie. In hierdie studie demonstreer ons « nuwe, gekombineerde aanslag om die Dn weerstandsgene te isoleer en karakteriseer deur van « genetiese kaart opgestel met "Amplified Fragment Length Polymorphism"(AFLP), "Expressed Sequence Tag"(EST) en mikrosatelliet merkers asook « fisiese kaart saamgestel deur die volgende-generasiebasispaarvolgordebepaling van ditelosomiese chromosome (7DS en 7DL) geïsoleer deur mikrodisseksie met die "PALM Microbeam"sisteem gebruik te maak. « Genetiese kaart van 122.8 cM was met 38 polimorfiese AFLP merkers en twee EST merkers geskep. Die mikrosatelliet, Xgwm111, is ook ingesluit en het as anker vir verwante genetiese-kaarte gedien. Deur vergelyking met genetiese-kaarte op GrainGenes is die posisie van die Dn1 weerstandsgeen vernou na « delesie bin (7DS5-0.36-0.62) op die kort arm van chromosoom 7D met « AFLP merker (EACT/ M-CTG_0270.84) wat ongeveer 3.5 cM vanaf die geen karteer. Die twee EST merkers is 15.3 cM en 15.9 cM vanaf die geen gekarteer. Isolering van die individuele chromosoom arms, 7DS en 7DL, deur van die "PALM Microbeam"sisteem gebruik te maak het basispaarvolgordebepaling van die chromosoom toegelaat sonder die oortolligheid van die res van die hexaploïde genoom. Deur die chromosoom so te isoleer is « >80-maal verkleining in genoom grootte bereik insluitend « groot reduksie in herhalende elemente. Analise van die data vanaf basispaarvolgordebepaling het bevestig dat chromosoom 7D die fisiese kleiner chromosoom is maar dat dit die meerderheid van proteïn koderende basispaarvolgordes bevat.

A despeito da importância comercial da cultura do maracujá-amarelo para o Brasil, estudos genéticos e de melhoramento são bastante escassos. Neste trabalho, foi conduzido um experimento visando construir mapas de ligação e mapear QTL para caracteres relacionados à produção e qualidade de frutos. Foi utilizada uma população composta por 160 indivíduos, proveniente do cruzamento de duas plantas dos acessos IAPAR-06 e IAPAR-123. Devido à alogamia da espécie, optou-se pela abordagem de mapeamento conhecida por "pseudocruzamento teste" para a construção de dois mapas de ligação, sendo um para cada genitor, utilizando marcadores moleculares do tipo AFLP, com segregação 1:1 e 3:1. No mapa do acesso IAPAR-06 foram obtidos 10 grupos de ligação, enquanto que no mapa do IAPAR-123, nove grupos foram obtidos. Os locos bi-parentais foram alocados como marcas acessórias nos mapas de ligação e serviram para o estabelecimento da homologia entre os grupos de ligação de cada genitor. Um total de oito grupos de ligação foi alinhado com base nesses locos. Em paralelo, procedeu-se a avaliação fenotípica de 100 indivíduos dessa mesma população, os quais foram avaliados em campo, na primeira safra de produção da cultura, para uma série de caracteres, quais sejam: velocidade de crescimento; produção total; número total de frutos; peso médio de frutos; comprimento e largura média de frutos; porcentagem de polpa; teor de sólidos solúveis totais; e formato médio de frutos. As análises genético-estatísticas dos dados fenotípicos indicaram que a população é amplamente variável para os caracteres avaliados, com exceção da velocidade de crescimento, apresentando coeficientes de herdabilidade entre médias que variaram de 52,6 a 83,0%. O mapeamento de QTL, utilizando o método de mapeamento por intervalo composto, identificou várias regiões associadas ao controle desses caracteres nos mapas individuais. Foram mapeados QTL para todos os caracteres que apresentaram variabilidade genética na população. A proporção da variação fenotípica explicada pelos QTL detectados variou de 4,6 até 21,8%. / Although the yellow passion-fruit plays an important commercial role in Brazil, breeding and genetics studies are insipient. The present study was conducted aiming the construction of linkage maps and mapping of QTL for traits related to yield and fruit quality. It was used a population, composed of 160 individuals, derived from a cross from two plants of the IAPAR-06 and IAPAR-123 accessions. Since this is an allogamous species, the pseudo testcross mapping strategy was used for the construction of two linkage maps, one for each parent, using AFLP markers segregating in 1:1 and 3:1 configuration. The IAPAR-06 map was composed of 10 linkage groups, while in IAPAR-123 map, nine linkage groups were obtained. The bi-parental loci were located as accessory markers and served to establish the homology between the groups of each parent. Eight linkage groups were aligned using these markers. For the phenotypic evaluation, 100 individuals were evaluated in the field, during the first harvest of the culture, for various traits, including: growth increment, total yield, total number of fruits, average fruit weight, average fruit length, average fruit width, percentage of pulp, soluble solids content and fruit shape. The results of the phenotypic data indicated that the population had a wide genetic variance for all the traits, with the exception of growth increment, presenting broad-sense heritability varying from 52.6% to 83.0%. The analysis of QTL, using the composite interval method, has mapped various regions associated with the traits evaluated in both maps. It was mapped QTL for all the traits that exhibited genetic variation. The proportion of the phenotypic variation explained by the QTL identified ranged from 4.6 to 21.8%.

O uso de marcadores moleculares tem contribuído para o estudo da domesticação das espécies de Phaseolus, origem e diversidade das cultivares atuais de feijão-comum (P. vulgaris), e do controle genético da resistência a diversas doenças. Mapas de ligação têm sido estabelecidos em feijão-comum com base em marcas de RFLP, RAPD, SCAR, isoenzimas e locos fenotípicos, sendo que alguns deles foram reunidos em um mapa mais denso e completo do genoma do feijão, chamado mapa núcleo. No entanto, para o uso efetivo de mapas de ligação em programas de melhoramento estes devem ser suficientemente saturados. O presente trabalho se insere neste contexto, visando saturar o mapa núcleo de P. vulgaris a partir do mapeamento de novos marcadores moleculares como AFLP e SSR baseados em EST. Assim, buscou-se desenvolver e caracterizar marcadores SSR oriundos de uma biblioteca de EST, testar a transferibilidade destes para outros cultivares e espécies relacionadas, gerar marcadores AFLP e integrá-los ao mapa consenso da espécie. Também, construir um mapa genético para uma população de interesse no Brasil (Carioca x Flor de Mayo), e promover o seu alinhamento com o mapa consenso, complementando desta forma, a caracterização genômica da espécie. Pares de primers foram desenhados para 156 SSR-EST. Destes, 138 SSR-EST amplificaram locos claros e reprodutíveis e foram caracterizados usando um conjunto de 26 genótipos de feijões cultivados. Dos locos analisados, 85 se mostraram polimórficos entre os genótipos estudados e apresentaram em média 2,96 alelos por loco e um PIC médio de 0,38. Entre todos os SSR-EST analisados, 50 locos segregaram na população de mapeamento Bat 93 x Jalo EEP558, 20 locos segregaram na população Carioca x Flor de Mayo e 12 locos foram polimórficos nas duas populações. Marcadores AFLP foram gerados e genotipados nas duas populações. Os 262 locos microssatélites e AFLP genotipados na população Bat 93 x Jalo EEP558 foram integrados ao mapa núcleo da espécie. Foi obtido um mapa de 1353 cM de comprimento total, contendo 357 marcas, incluindo 9 SSR-genômico, 47 SSR-EST e 190 AFLP. Além disso, outro mapa foi gerado a partir da análise de segregação de 252 marcadores na população Carioca x Flor de Mayo. Este mapa teve 807,5 cM de comprimento, com uma distância média de 5,3 cM entre marcas. Os marcadores microssatélites comuns foram usados como ponte para alinhar e comparar os mapas das duas populações estudadas. / The use of molecular markers has contributed to the studies regarding domestication of Phaseolus species, origin and diversity of current common bean cultivars (P. vulgaris), and the genetic control of resistance to several diseases. Linkage maps have been constructed for common bean by using RFLP, RADP, SCAR, isoenzymes and phenotypic markers, some of which were meeting in a more dense and complete map of bean genome, called core map. However, for the effective use of linkage maps in breeding programs they must be sufficiently saturated. This work fits in this context, aiming to saturate the core map of P. vulgaris from the mapping of new molecular markers as AFLP and SSR EST-based. Thus, it was tried to develop and characterize SSR markers from a EST library, to test the transferability of these markers to other cultivars and related species, to generate AFLP markers and integrate them to the consensus map of the species. Also, build a genetic map for a population of interest in Brazil ( \'Carioca\' x \'Flor de Mayo\'), and promoting its alignment with the consensus map, thus complementing the genomic characterization of the species. Pairs of primers were designed for 156 EST-SSR. Of these, 138 EST-SSR amplified clear and reproducible loci and were characterized using a set of 26 genotypes of cultivated beans. Of the loci tested, 85 were polymorphic between the genotypes studied and showed an average 2.96 alleles per locus and a PIC average of 0.38. Among all examined EST-SSR, 50 loci segregated in \'Bat 93\' x \'Jalo EEP558\' mapping population, 20 loci segregated in \'Carioca\' x \'Flor de Mayo\' population and 12 loci were polymorphic in both two populations. AFLP markers were generated and genotyped in the two populations. The 262 microsatellites and AFLP loci genotyped in \'Bat 93\' x \'Jalo EEP558\' population were integrated onto the core map of the species. A map of 1353 cM total length was obtained, containing 357 markers, including 9 genomic-SSR, 47 EST-SSR and 190 AFLP. Moreover, another map was generated from the analysis of segregation of 252 markers in \'Carioca\' x \'Flor de Mayo population. This map was 807.5 cM long, with an average distance of 5.3 cM between markers. The common microsatellites markers were used as a bridge to align and compare the maps of the two studied populations.