Field pea (Pisum sativum L.) as a cool season legume crop is sensitive to high day time temperature, especially during flowering. A population of 107 recombinant inbred lines (RILs) known as PR-11 was made from the cross of CDC Centennial (heat tolerant cultivar) X CDC Sage (heat sensitive cultivar) with the objectives of screening heat tolerant traits during flowering and subsequent seed development, and to map the quantitative trait loci (QTLs) responsible for these traits. Experiments were carried out in 2012-2014. PR-11 was seeded at normal seeding dates in 2012 and 2013 at Saskatoon (52º12’N, 106º63’W) and Rosthern (52º66’N, 106º33’W) in Canada, and in 2014 PR-11 was seeded at both normal and late seeding (three weeks later than normal) dates at one location, Saskatoon. Correlation analyses demonstrated that the duration of flowering (DOF) was positively associated with final seed yield under both normal and late seeding date conditions. Yield component traits on the main-stem [reproductive node number (Rnode), pod number (Pod), seed number per pod (Seed), single seed weight (SSW)] were significantly associated with main-stem seed yield, among which pod number appeared to be the component most positively associated with seed yield. However, yield on the main-stem was not significantly associated with seed yield at the plot level, which inferred that the contribution of seed yield on side branches was important. A genetic map consisting of 369 SNPs markers with a total coverage of 746 cM was developed using JoinMap 4.0. A total of 14 QTLs were detected under environments with normal seeding date, six for flowering traits, and eight for yield component traits. Eight QTLs were identified at late seeding, four for flowering traits and four for yield component traits. The total variation in days to flowering (DTF), DOF, Pod, Seed, SSW and grain yield that were each explained by the QTLs under normal seeding environments was 24 %, 43%, 15%, 32%, 34% and 21%, respectively. The QTLs together accounted for 43% of DTF variation, 14% of DOF variation, 17% of Pod variation, 12% of SSW variation and 12% of grain yield variation at the late seeding date. Lines PR-11-2, PR-11-88 and PR-11-91 performed as the top yielding lines under both normal and late seeding environments, and could be considered as heat tolerant lines.

Submitted by Marco Antônio de Ramos Chagas (mchagas@ufv.br) on 2017-06-05T14:33:16Z No. of bitstreams: 1 texto completo.pdf: 756581 bytes, checksum: 1fd2b04358832c05c8ee23d442db0c7c (MD5) / Made available in DSpace on 2017-06-05T14:33:16Z (GMT). No. of bitstreams: 1 texto completo.pdf: 756581 bytes, checksum: 1fd2b04358832c05c8ee23d442db0c7c (MD5) Previous issue date: 2005-02-03 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Na construção de mapas genéticos são usados vários tamanhos de população e número de marcas. Contudo, não se sabe a priori qual é o número mínimo de indivíduos e marcas a ser utilizado para a obtenção de mapas confiáveis. Desta forma, este trabalho, por meio da simulação de dados em computador, teve como objetivos o estudo de população RIL (Recombinant Inbred Line), buscando determinar: 1) a influência do número de indivíduos na população segregante sobre o mapeamento; 2) o efeito da saturação do genoma por marcas sobre o mapeamento e; 3) o número adequado de indivíduos a ser utilizado no mapeamento. Foram gerados três genomas com níveis de saturação de 5, 10 e 20 cM, com 231, 121 e 66 marcas, respectivamente. Cada genoma foi composto por 11 grupos de ligação, 100 cM cada. Para cada saturação do genoma foram geradas populações com 50, 100, 154, 200, 300, 500 e 800 indivíduos, com 100 repetições cada. Portanto, foram geradas um total de 2.100 populações. Estas populações foram mapeadas utilizando um LOD mín de 3 e freqüência máxima de recombinação de 30%. Dos mapas obtidos foram extraídas as informações: número de grupos de ligação e de marcas por grupo, tamanho de grupo de ligação, distância entre marcas adjacentes, variância das distâncias entre marcas adjacentes, inversão de marcas (dada pela correlação de Spearman) e grau de concordância das distâncias nos mapas com o genoma original (dada pelo estresse). População com tamanho igual ou superior a 100, 154 e 500 indivíduos, saturação de 5, 10 e 20 cM, respectivamente, levaram a formação de 11 grupos de ligação, em todas as repetições. Inversão na ordem de marcas e presença de marcas não ligadas foi maior tanto quanto menores foram os tamanhos de populações estudadas. A precisão na estimativa de distância entre marcas adjacentes foi maior tanto quanto maiores foram os tamanhos de população, independente do nível de saturação do genoma. Valores de estresse e variância reduziram significativamente com o aumento do tamanho de população. Concluindo, obtenção de mapas confiáveis a partir de população RIL deve, necessariamente, levar em conta o tamanho da população e número de marcas, uma vez que mapas com sérias distorções foram obtidos com utilização de populações de tamanhos insuficientes, mesmo com grande quantidade de marcas. Também, mapas com sérias distorções foram obtidos com o uso de pequena quantidade de marcas, mesmo com populações com grande número de indivíduos. Tamanhos mínimos de 100, 154 e 500 indivíduos foram necessários para a obtenção de mapas com o mesmo número de marcas por grupo de ligação do genoma original, nos casos de saturação de 5, 10 e 20 cM, respectivamente. / During the construction of genetic maps different population sizes and number of markers have been used by different authors. However, the minimum numbers of individuals and markers to be used in order to obtain reliable maps are not known. This work used data simulation aiming to determine: 1) the influence of population size; 2) the effect of genome saturation degree by markers and; 3) the adequate number of individuals to be used in the mapping of recombinant inbred line populations. Three genomes were generated with saturation levels of 5, 10 and 20 cM, each with 231, 121 and 66 markers, respectively. The genomes consisted of 11 linkage groups, each with 100 cM in length. For each saturation level, populations containing 50, 100, 154, 200, 300, 500 and 800 individuals were generated and for each population size 100 replications were analyzed. Thus, a total of 2,100 populations were generated. These populations were mapped using a LOD minimum of 3 and a maximum recombination frequency of 30%. From these maps the following variables were determined: number of linkage groups and number of markers in each group, length of the linkage group, distance between adjacent markers, variance of the distance between adjacent markers, inversion of markers (given by the Spearman correlation) and level of agreement between map distances and original genome distances (given by the stress). Population sizes equal to or greater than 100, 154 and 500 individuals in the saturation levels of 5, 10 and 20 cM, respectively, led the formation of 11 linkage groups, in all replications. As the population size increased, the inversion of markers and the presence of non-linked markers decreased, and the precision of the distance estimates between markers increased, independently of the genome saturation level. Values of stress and variance decreased significantly with the increase on the population size. In conclusion, the construction of reliable maps from RIL populations necessarily needs to consider the population size and the number of markers used, as maps with serious distortions were obtained from small sized populations, even using a large number of markers. On the other hand, maps with xserious distortions were obtained with a small number of markers, even using populations with a large number of individuals. The minimum sizes of 100, 154 and 500 individuals were necessary for obtaining maps with the same number of markers per linkage group of the original genome, in the cases of saturation level of 5, 10 and 20 cM, respectively.

Parmi les contraintes abiotiques la salinité est considérée comme un problème majeur, qui affecte le fonctionnement des plantes, en particulier leur croissance et leur rendement. Afin d’étudier le contrôle génétique de la tolérance à la salinité chez Medicago truncatula, plante modèle de la famille des légumineuses, deux expérimentations ont été réalisées. La première expérimentation visait à étudier l’effet de la contrainte saline sur différents paramètres morpho-physiologiques pour un panel de génotypes de M. truncatula afin de déterminer les traits de phénotypage pour la tolérance à la salinité. Les génotypes A17, TN1.11, DZA315.16, A20, TN1.12 et F83005.5 ont été sélectionnés parmi des lignées originaires de différents pays méditerranéens, qui ont été déjà séquencées (http://www1.montpellierinra.fr/BRC-MTR/mauguio/mauguio.php). Les génotypes ont été étudiés sous 6 traitements salins (0, 30, 60, 90,120 et 150 mM NaCl) dans un essai factoriel sous forme de blocs complets aléatoires en trois répétitions. L’analyse de la variance montre des différences significatives entre les niveaux de salinité et une interaction entre les génotypes et les traitements salins concernant la plupart des caractères étudiés. Le génotype « DZA315.16 » présente les valeurs les plus importantes concernant les effets principaux pour les caractères morphologiques alors que « TN1.11 » présente les valeurs les plus faibles. La projection verticale de la surface foliaire de la plante (Leaf Area=LA), significativement corrélée à la biomasse des plantes, apparaît comme un trait d’intérêt pour le phénotypage de la tolérance à la salinité. La concentration saline la mieux adaptée pour démontrer les différences parmi les lignes étudiées se situe entre 90 et 120 mM NaCl. Le génotype « TN1.11 » contrairement à « DZA315.16 » et à « Jemalong-A17 » présente un maintien de la surface foliaire de la plante en réponse à la salinité. Pour la deuxième expérimentation, une population de cent lignées recombinantes (Recombinant Inbred Lines=RILs) produite par le croisement entre « TN1.11 » et « Jemalong-A17 » a été retenue pour l’analyse du contrôle génétique de la tolérance à la salinité. Les RILs ont été développés par la méthode de descendant mono graines (Single Seed descent= SSD) jusqu’ à la génération F6 à l’INP-ENSAT, France. Le plan d’experimentation est « Spli plots » , sous forme de blocs randomisés avec trois répétitions et deux conditions : traitement salin (100 mM NaCl) et témoin (eau). L’expérience a été menée pour déterminer la variabilité génétique et pour identifier les QTLs contrôlant les caractères morphologiques et physiologiques chez la population des lignées recombinantes (RILs). L’analyse de la variance a montré une large variation génétique et une ségrégation transgressive pour les caractères étudiés. La différence entre la moyenne des RILs et la moyenne de leurs parents n’est pas significative concernant tous les caractères étudiés dans les deux conditions, ce qui montre que les RILs utilisées dans notre expérimentation sont représentatives de toutes les lignées recombinantes possibles du croisement « TN1.11 x Jemalong-A17 ». 21 QTLs ont été détectés dans la condition témoin et 19 QTLs ont été identifiés sous contrainte saline (100 mM NaCl). Le pourcentage de la variance phénotypique expliqué par les QTLs varie entre 4.60% et 23.01%. Certains de ces QTLs sont spécifiques à la condition saline, ce qui démontre l’existence du contrôle génétique de la tolérance à la salinité chez M. truncatula ; tandis que les autres ne sont pas spécifiques et contrôlent un même caractère dans les deux conditions. Des QTLs superposés concernant différents caractères ont été aussi observés. Les résultats fournissent des informations importantes en vue de futures analyses fonctionnelles de la tolérance à la salinité chez M.truncatula et pour d’autres espèces voisines. / Among abiotic stresses salinity is considered as a serious problem affecting plant functions especially growth and yield. In order to study the genetic control of salt stress in the model legume Medicago truncatula, two experiments were performed. The first experiment was conducted to study the effect of salt stress on some morpho-physiological parameters in M. truncatula genotypes and to determine the eventual use of some traits as tolerance criteria. Genotypes including A17, TN1.11, DZA315.16, A20, TN1.12 and F83005.5 are selected through a sequenced lines collection (http://www1.montpellierinra.fr/BRC-MTR/mauguio/mauguio.php) which are originated from different Mediterranean countries. Genotypes were studied under 6 salinity treatments (0, 30, 60, 90,120 and 150 mM NaCl) in a factorial design based on randomized complete blocks with three replications. Analysis of variance show significant differences among genotypes, salinity levels and interaction between genotypes and salt treatments for most of studied traits. “DZA315.16” genotype presents the highest main effect values for morphological traits whereas”TN1.11” has low values. Vertically projected leaf area (LA); show the highest variability through all studied salt concentrations. The best concentration to find differences between parental lines is 90 to 120 mM Nacl. A segregating population of recombinant inbred lines (100 RILs) of M.truncatula derived from a cross between TN1.11 and Jemalong-A17 was used for the second experiment. RILs were developed by single-seed descent until F6 generation at the INP-ENSAT, France. The experiment was undertaken to determine the genetic variability and to identify QTLs controlling several traits related to plant growth and physiology, in the population of recombinant inbred lines (RILs). Analyses of variance showed a large genetic variation and transgressive segregation for the traits studied. The difference between the mean of RILs and the mean of their parents was not significant for all of the traits in both conditions, showing that the RILs used in our experiment are representative of the possible recombinant lines from the cross TN1.11 x A17. A total of 21 QTLs were detected under control and 19 QTLs were identified under 100mM salt stress conditions. The percentage of total phenotypic variance explained by the QTLs ranged from 4.60% to 23.01%. Some of the QTLs were specific for one condition, demonstrating that the genetic control of a traits differed under control and salt stress conditions. Some others are non-specific and control a trait in both conditions. Overlapping QTLs for different traits were also observed. The results provide important information for further functional analysis of salt tolerance in M. truncatula

Le maintien de la croissance foliaire en situation de déficit hydrique résulte du maintien de l´absorption racinaire et de la production de biomasse au niveau foliaire. Pour optimiser les deux processus, la plante ajuste la croissance de ses organes, et la répartition de la biomasse produite, entre les différents organes (root/shoot ratio) ou au sein de chaque organe (surface foliaire spécifique, longueur racinaire spécifique). Les principaux objectifs de ce travail de thèse étaient (i) d´évaluer l´impact des modifications de répartition de biomasse sur le maintien de la croissance foliaire en situation de déficit hydrique, (ii) de relier la réponse de la croissance d´un génotype aux caractéristiques de son habitat d´origine, and (iii) d´identifier les régions du génome responsables de la variation des croissances foliaires et racinaires en situation de déficit hydrique. Différent types de populations d´Arabidopsis thaliana ont été utilisés, une population de lignées recombinantes, ainsi que différents groupes d´accessions collectées dans des environnements naturels contrastés. Une analyse des relations allométriques entre les variables foliaires et racinaires en conditions de culture optimales puis en situation de déficit hydrique a permis de mettre en évidence le rôle clé de la surface foliaire spécifique dans l´amélioration de la tolérance au déficit hydrique. Une caractérisation détaillée du climat des régions dans lesquelles les accessions avaient été collectées a permis de faire le lien entre la tolérance accrue de certains génotypes et la faible balance climatique dans laquelle ils évoluaient. Enfin, en utilisant ces génotypes, une analyse de génétique quantitative (combinant recherche de QTL et génétique d´association) a été menée. Les régions génomiques controllant les croissances foliaires et racinaires étaient très liées, en particulier en situation hydrique optimale, mais le calcul de variables utilisant la croissance de la plante comme cofacteur a permis d´identifier des régions spécifiques de la croissance racinaire, dont une a été confirmée en utilisant des lignées quasi isogéniques. En situation de contrainte hydrique, les déterminants génétiques des croissances foliaires et racinaires étaient moins liés, et plusieurs régions très fortement associées spécifiquement aux variations de croissance racinaire ou foliaire ont été détectées. Des régions associées au maintien de la croissance foliaire en situation de déficit hydrique ont pu être mises en évidence, et la précision des études de génétique d´association a permis de réveler la présence de gènes d´intéret dans ces régions. / Growth maintenance under water deficit mainly results from the maintenance of water uptake at the root level,and assimilates production by leaves. To optimize both processes, plant need to adjust organ growth and biomassallocation patterns between roots and shoots (root/shoot ratio), but also within the organs, through specific leaf areaand specific root length variations. The main objectives of this study were (i) to evaluate the impact of growth andbiomass allocation patterns modifications on growth maintenance under drought conditions, (ii) to rely the genotypicresponses to water deficit conditions and the climatic features of the natural environment in which they evolved, and(iii) to identify the key genetic regions responsible for shoot and root growth variation in response to water deficitconditions. We used different sets of genotypes, a population of recombinant inbred lines, and different sets ofaccessions of Arabidopsis thaliana, collected in a wide range of environments. An analysis of the allometricrelationships between shoot and root growth related variables under both well watered and water deficit conditionsallowed to highlight the importance of specific leaf area plasticity to maintain plant growth under water deficit. Adetailed climatic characterization of the natural habitats of the accessions studied, combined to the evaluation ofgrowth response to water deficit in these accessions allowed connecting low climatic water balance to better toleranceto water deficit conditions in specific regions, suggesting that this climatic feature could have shaped the evolution ofgenotypes in certain regions. Finally, using these two sets of genotypes, joint linkage and linkage disequilibriumanalysis were performed on growth related traits under well watered and water deficit conditions. Some genetic regionsinvolved in the control of root and shoot related traits were strongly coupled, especially in well watered experiments,but we managed to identify root specific regions using calculated variables that takes global plant growth as a cofactor.Under water deficit, the regions controlling root and shoot growth were less associated, and very strong QTL weredetected, specifically associated to one or the other part. Genomic regions associated to growth response to waterdeficit were also detected, and the accuracy of association mapping enabled to identify target genes that could be playa role in growth maintenance under drought.

Wheat grain quality has a complex genetic architecture heavily influenced by the growing environment. Consistency in wheat quality not only affects the efficiency of milling and baking but also the quality of end-use products. The objectives of this study were to 1) analyze the different wheat quality parameters in Recombinant Inbred Lines (RILs) grown under different environments, and 2) to identify Quantitative Trait Loci (QTLs) associated with quality stability in RILs grown under different environments. A set of 180 RILs derived from two spring wheat lines 'Halberd' and 'Len' were grown at Uvalde and College Station TX, in the 2009/2010 growing season and at Chillicothe and College Station TX, in 2010/2011 growing seasons. The experiment was laid out in Randomized Complete Block Design (RCBD) with four replications within each location. Each line was tested for multiple quality traits that included grain hardness, protein content, dough mixing properties and bread baking quality using Single Kernel Characterization System (SKCS), Near-Infrared Reflectance Spectrometry (NIRS) analysis, mixograph and the Sodium Dodecyl Sulfate Sedimentation (SDSS) test. Genetic linkage map construction was carried out with 116 single nucleotide polymorphism (SNP) markers in the RILs. Then composite interval mapping was carried out to identify QTLs associated with quality traits. The SDSS column height was positively correlated across four environments. Similarly, it was found to have significant positive correlation with mixing tolerance and peak time within and also across locations. However, the SDSS was negatively correlated with the hardness index. The protein percent was not significant with any of the quality traits within and across environments. We were able to detect many QTLs for different quality traits but most of them were site specific. Only a few QTLs were consistent across environments. Most of the QTLs for quality traits i.e., SDSS, peak time, mixing tolerance and hardness index were identified on chromosome 1B. We were able to detect overlapped QTLs for SDSS column height and mixing tolerance on chromosome 1B. Furthermore, overlapping QTLs for mixing tolerance and peak time were detected on an unknown chromosome. We also detected overlapping QTLs for hardness index on chromosome 1B. We identified one stable QTL for SDSS column height on chromosome 4B. This QTL was detected based on the coefficient of variation (CV) for SDSS in four different environments.

Poor seed coat colour desirability in green lentil (<i>Lens culinaris</i>) costs lentil producers millions of dollars each year. The monetary value that Canadian lentil producers receive for their crop is based on the visual characteristics of the seed coat, mainly the colour. Higher value is given for samples described to have more desirable green seed coat colour. A breeding line, 1294M-23, has been noticed to consistently produce more desirable green lentil samples.<p>A cross was made between 1294M-23 and a less desirable breeding line 1048-8R with the goal of studying the heritability of green seed coat desirability measured by the Acurum® machine. The resulting progeny were taken to F7 by single seed descent. In 2005 and 2006 the recombinant inbred lines (RILs) were seeded in a randomized complete block design at three sites in the current main lentil growing region of Saskatchewan. To measure the seed coat colour of the samples, the Acurum® machine, which is a colour analyzing machine developed for grain crops, was used to consistently compare the samples. The study illustrated that the trait has large environmental effects and is quantitative with a high broad sense heritability of 0.82, using this specific cross and environments. Transgressive segregation occurred for RILs that had more desirable green seed coats and lower index scores than the desirable parent, 1294M-23. A tester that included all registered green lentil cultivars set was grown with the RILs in all environments. The seed coat colour index scores of the tester set fit into a small section of the range of index scores. They all had relatively high mean index scores, meaning less desirable, showing little genetic variation for the trait in current Canadian green lentil cultivars. <p>Chlorophyll was extracted from seed coats of some of the RILs. The amount of total chlorophyll, chlorophyll a, and chlorophyll b was compared to the Acurum® scores using regression analysis. The study found that there was significant relationship between chlorophyll a and b content and the index score, explaining 32 and 37 percent of the variation, respectively. <p>Another portion of the study was to determine if preharvest treatment of the green lentil crop has an effect on the green seed coat colour of the sample. A set of genotypes consisting of all registered green seed coat cultivars was grown at two locations in Saskatchewan in both 2005 and 2006. Prior to harvest a plot of each genotype was swathed, and a second plot was desiccated with diquat. After harvest the samples were analyzed for green seed coat colour using the Acurum® machine. In general, across most genotypes, sites, and years, swathing produced a significantly more desirable green lentil sample. The desirable green parent from the RILs, 1294M-23 produced the most desirable green lentil sample in this study. When the maturity rating was correlated to the Acurum® score a significant positive relationship was found in 2005 but not in 2006. This showed that lines with later maturity could be associated with more desirable green seed coat colour in some environments. Thus caution must be taken when selecting for more desirable phenotypes that genetic gains are being made rather than indirect selection for longer maturity.

Poor seed coat colour desirability in green lentil (<i>Lens culinaris</i>) costs lentil producers millions of dollars each year. The monetary value that Canadian lentil producers receive for their crop is based on the visual characteristics of the seed coat, mainly the colour. Higher value is given for samples described to have more desirable green seed coat colour. A breeding line, 1294M-23, has been noticed to consistently produce more desirable green lentil samples.<p>A cross was made between 1294M-23 and a less desirable breeding line 1048-8R with the goal of studying the heritability of green seed coat desirability measured by the Acurum® machine. The resulting progeny were taken to F7 by single seed descent. In 2005 and 2006 the recombinant inbred lines (RILs) were seeded in a randomized complete block design at three sites in the current main lentil growing region of Saskatchewan. To measure the seed coat colour of the samples, the Acurum® machine, which is a colour analyzing machine developed for grain crops, was used to consistently compare the samples. The study illustrated that the trait has large environmental effects and is quantitative with a high broad sense heritability of 0.82, using this specific cross and environments. Transgressive segregation occurred for RILs that had more desirable green seed coats and lower index scores than the desirable parent, 1294M-23. A tester that included all registered green lentil cultivars set was grown with the RILs in all environments. The seed coat colour index scores of the tester set fit into a small section of the range of index scores. They all had relatively high mean index scores, meaning less desirable, showing little genetic variation for the trait in current Canadian green lentil cultivars. <p>Chlorophyll was extracted from seed coats of some of the RILs. The amount of total chlorophyll, chlorophyll a, and chlorophyll b was compared to the Acurum® scores using regression analysis. The study found that there was significant relationship between chlorophyll a and b content and the index score, explaining 32 and 37 percent of the variation, respectively. <p>Another portion of the study was to determine if preharvest treatment of the green lentil crop has an effect on the green seed coat colour of the sample. A set of genotypes consisting of all registered green seed coat cultivars was grown at two locations in Saskatchewan in both 2005 and 2006. Prior to harvest a plot of each genotype was swathed, and a second plot was desiccated with diquat. After harvest the samples were analyzed for green seed coat colour using the Acurum® machine. In general, across most genotypes, sites, and years, swathing produced a significantly more desirable green lentil sample. The desirable green parent from the RILs, 1294M-23 produced the most desirable green lentil sample in this study. When the maturity rating was correlated to the Acurum® score a significant positive relationship was found in 2005 but not in 2006. This showed that lines with later maturity could be associated with more desirable green seed coat colour in some environments. Thus caution must be taken when selecting for more desirable phenotypes that genetic gains are being made rather than indirect selection for longer maturity.

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No. of bitstreams: 2 Dissertação - Ana Letycia Basso Garcia - 2017.pdf: 3161693 bytes, checksum: 8ea7726402d9acbdddc870e75a0b1cef (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-05-30 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Improving rice yield has been a big challenge for rice breeding programs around the world. One alternative to identify inbred lines with high yield potential, and discover genes related to yield and its components is to explore the genic pool of the population originated from crosses between cultivars not regularly used, as those introduced from another country. The objective of this study was characterizing a recombinant inbred lines population from the cross between Maninjau and Epagri 108. There were evaluated 296 RILs in experiments conducted in Goianira (GO), Boa Vista (RR) and Pelotas (RS), in 2016. In the experiments in GO and RR, the alpha lattice design (17x18) with two replications were used, and in Pelotas was applied the BAF design. Data were collected for yield (PD) and plant height (AP) in the three places, days to flowering (DF), in RR and GO, 100-grain weight (PG), in RS and GO and leaf blast resistance (BS), in GO. The data were analyzed by a mixed model with the deviance analysis. Variance components were estimated by REML/BLUP and the genetic parameters and correlation coefficients were calculated. The statistics parameters as CV e , CV g , CV r and selective accuracy were also estimated. The G x E interaction analysis was processed by the MHPRVG method. Also, the genetic distances between the progenies that had highest breeding values in each place and their relatives (Maninjau and Epagri 108), was estimated, using a 24 SSR markers panel. For Boa Vista and Goianira, most of the highest yield RILs were like the parental Epagri 108. Most of the random effects of the statistic model used in this study were significant. The RILs population showed genetic variability inside (σ g2 significant). The experimental precision in RR and GO was from good to excellent with accuracy over 90% and in RS it was moderate (~50%), probably because of the environmental effect action. Yield showed moderate heritability (0,67) and the characters DF, AP and PG showed high heritability (>0,90). Positive significant correlation was observed between the characters PD and PG, and DF and AP, however the last one showed negative correlation with yield. Nine RILs had the best performance by the MHPRVG, and it was above 30% of the general mean. They are recommended for the breeding program use. The RIL 105 were ranked as the best for stability, adaptability and yield, simultaneously. These results suggest that there is a significant genetic variation between the RILs evaluated. Therefore, this population might be used either in selection of high yield performance genotypes or for QTL mapping foragronomic traits in many environments. / O aumento da produtividade em arroz é um desafio para os programas de melhoramento do mundo todo. Uma alternativa para identificar linhagens mais produtivas, ou mesmo descobrir genes correlacionados à produtividade e seus componentes, é conhecer e explorar o pool gênico de populações provenientes de cruzamentos entre cultivares ainda pouco utilizadas, como materiais introduzidos. O objetivo desse trabalho foi caracterizar uma população de linhas puras recombinantes (RILs), provenientes do cruzamento entre Maninjau x Epagri 108. Foram avaliadas 296 RILs em experimentos conduzidos em Goianira (GO), Boa Vista (RR) e Pelotas (RS), no ano de 2016. Em GO e RR os ensaios foram implantados em delineamento alfa-látice (17x18) e em Pelotas foi utilizado BAF. Foram coletados dados referentes à produtividade (PD) e altura de plantas (AP) nos três locais, além de dias até o florescimento (DF), em RR e GO, peso de 100 grãos (PG), em RS e GO. Os dados foram analisados via modelos mistos, através da análise de deviance. Os componentes de variância foram estimados via REML/BLUP e foram estimados os parâmetros genéticos e coeficientes de correlação entre caracteres, bem como os parâmetros estatísticos CV e , CV g , CV r e acurácia seletiva. A análise de interação G x E foi feita com base no método da MHPRVG. Foram estimadas as distâncias genéticas entre as linhagens de maior valor genotípico em cada local e os parentais do cruzamento, através de um painel de 24 marcadores SSR, e para Boa Vista e Goianira, a maioria das linhagens mais produtivas foram mais similares ao genitor Epagri 108. A maioria dos efeitos aleatórios do modelo estatístico adotado foi significativa. A população de RILs apresentou variabilidade genética (σ g2 significativo). A precisão dos experimentos de RR e GO foi de boa à ótima, com acurácia maior que 90%, enquanto do RS foi moderada (~50%), provavelmente devido à maior ação do efeito ambiental. A produtividade se revelou com h2 moderada (0,67) e os caracteres DF, AP e PG apresentaram alta herdabilidade (>0,90). Foi verificada correlação positiva significativa entre os caracteres PD e PG e DF e AP, porém esses dois últimos têm correlação negativa significativa com a produtividade. Nove RILs se destacaram pela MHPRVG, com desempenho superior a 30% em relação à média geral. Elas são, portanto, recomendadas para uso do programa de melhoramento. A RIL 105 foi classificada como a de melhor estabilidade, adaptabilidade e produtividade, simultaneamente. Os resultados indicam que a população tem alta variabilidade genética e, pode ser utilizada tanto na seleção de genótipos de bom desempenho produtivo, quanto na detecção de QTLs para caracteres de interesse agronômico em múltiplos locais.

Tesis por compendio / [EN] Fruits both produce and emit volatile chemical compounds. These are short-chained low polarity molecules involved in many processes, and they are responsible of our perception of fruit aroma and of most of their flavour. This thesis is focused on the study of volatile compounds in the tomato fruit, which is one of the most important horticultural worldwide and is a model system for the study of fruit development and ripening. Some of the analytical methods more frequently used for the analysis of tomato fruit volatiles were systematically compared. Results revealed that the observed volatile profile is highly dependent on the precise analytical method used, both for sample processing and for the technique used for volatile acquisition. It was concluded that the method of election for the comparison of large sets of samples from a multi-omics approach consists on flash freezing the biological material with liquid nitrogen at the selected ripening stage and the use of headspace solid phase microextraction coupled to gas chromatography and mass spectrometry for the subsequent analysis. This method was implemented and was used for the determination of volatile compounds in selected NILs harbouring QTLs for characters related to flavour and aroma introgressed in different genetic backgrounds. The results allowed the association of several of the organoleptic characters previously identified with modified levels of several volatiles. It was also observed that the genetic background has a major effect on the production of such metabolites. Correlation analysis between the levels of volatiles and primary metabolites led to the conclusion that the production of volatile compounds is generally not determined by the levels of their precursors. Its regulation is most likely to be due to downstream processes such as the availability of either precursors or intermediate metabolites, the variability in specific processes leading to the concersion of precursors into volatiles, or to other still unknown regulatory mechanisms. Volatile compounds were also studied in a RIL population derived from a cross between Solanum pimpinellifolium accession TO-937, the closest species to cultivated, which produces red fruits, and S. lycopersicum cv. 'Moneymaker', a tomato variety for the fresh market. This allowed the identification of 102 QTLs for 39 different volatile compounds, 76 of which had not been previously described. All these QTLs were mapped along the 12 tomato chromosomes by means of the SOLCAP SNPs molecular market map. Most of the QTLs identified were subsequently evaluated on introgression lines (ILs) generated from the same original genotypes. It was observed that almost half of the QTLs previously identified retained their effect after introgression in the 'Moneymaker' genetic background. Additionally, 12 new QTLs were identified in this IL population. Based on the existing knowledge about the effect of volatile compounds on our perception of flavour and aroma and also on their ability to maintain their effect after introgression in the cultivated tomato, some of the QTLs identified are good candidates to be used in tomato flavour breeding programs. Eventually, the comparison of the localization in the genome of the QTLs identified in the different populations studied with those already described in the literature revealed a very low degree of co-localization between the different QTLs. This implies that there exists a wide range of variability in the wild species related to tomato available for breeding tomato flavour and aroma. / [ES] Los frutos producen y emiten compuestos químicos volátiles. Estos son moléculas en general poco polares y de cadena corta que cumplen diversas funciones, y son las responsables de que percibamos el aroma y buena parte del sabor de los frutos. Esta tesis está centrada en el estudio de los volátiles del fruto del tomate, que es uno de los cultivos hortícolas más importantes y un sistema modelo para el estudio del desarrollo y maduración del fruto. Se compararon de forma sistemática los métodos analíticos más comúnmente utilizados para el análisis de volátiles en fruto de tomate, y se observó que el perfil de volátiles detectado está fuertemente condicionado por el método analítico utilizado, tanto por el proceso de preparación de la muestra como por la técnica de adquisición de los volátiles. Finalmente se concluyó que la técnica más adecuada para la comparación de grandes grupos de muestras desde una aproximación multi-ómica consiste en congelar con nitrógeno líquido el material vegetal una vez alcanzado el momento idóneo de recolección, y su análisis posterior mediante microextracción en fase sólida (SPME) acoplada a cromatografía de gases y espectrometría de masas. Se puso a punto esta técnica y se utilizó para la determinación de los compuestos volátiles en varias líneas NILs portadoras de QTLs de caracteres relacionados con el sabor y el aroma en distintos fondos genéticos. Los resultados permitieron asociar varios de los caracteres organolépticos identificados con alteraciones en los niveles de algunos volátiles. Igualmente se observó que el fondo genético tiene un efecto importante sobre la producción de estos metabolitos. Los análisis de correlación entre los niveles de volátiles y metabolitos primarios permitieron concluir que la producción de compuestos volátiles, en general, no está determinada por los niveles de sus precursores, sino que su regulación debe encontrarse más bien en procesos posteriores, tales como la disponibilidad de los precursores o de metabolitos intermedios, variabilidad en procesos específicos relacionados con la conversión de los precursores en volátiles, o algún otro mecanismo regulador aún desconocido. También se estudiaron los volátiles en una población de RILs derivada de un cruce entre Solanum pimpinellifolium entrada TO-937, la especie más próxima al tomate cultivado, la cual produce frutos rojos, y S. lycopersicum cv. "Moneymaker", una variedad de tomate para el mercado en fresco. Esto permitió identificar 102 QTLs para 39 volátiles diferentes, 76 de las cuales no se habían descrito previamente, las cuales se mapearon a lo largo de los 12 cromosomas del tomate utilizando el mapa de marcadores moleculares de SNPs SOLCAP. Posteriormente se evaluaron la mayoría de las QTLs identificadas mediante la determinación de los volátiles en líneas ILs generadas a partir de los mismos materiales. Se observó que casi la mitad de estas QTLs mantuvieron su efecto al ser introgresadas en el fondo genético "Moneymaker", al tiempo que 12 nuevas QTLs se identificaron en esta población de ILs. Algunas de las QTLs identificadas, en base al conocimiento existente sobre el efecto de los compuestos volátiles en nuestra percepción del sabor y el aroma, y en base a su capacidad para mantener su efecto tras su introgresión en el tomate cultivado, resultan ser candidatos prometedores para su utilización en la mejora genética del sabor del tomate. Finalmente, el análisis de la localización en el genoma de las QTLs analizadas en las distintas poblaciones objeto de estudio en esta tesis, junto con las descritas en la bibliografía disponible, puso de relieve el bajo grado de co-localización existente entre las distintas QTLs, lo cual implica que en las especies silvestres relacionadas con el tomate existe un amplio rango de variabilidad genética susceptible de ser utilizado para la mejora de su sabor y su aroma. / [CA] Els fruits produixen i emitixen compostos químics volàtils. Estos són molècules en general de baixa polarita i cadena curta que tenen diverses funcions, i són les responsables de la nostra percepció de l'aroma i de bona part del sabor dels fruits. Esta tesi està centrada a l'estudi dels volàtils del fruit de la tomata, que és un dels cultius hortícoles més importants i un sistema model per a l'estudi del desenvolupament i la maduració del fruit. Es van comparar de forma sistemática els mètodes analítics més habituals per a l'anàlisi de volàtils en fruits de tomata, i es va observar que el perfil de volàtils detectat està fortament condicionat per el mètode analític utilitzat, tant per el procés de preparació de la mostra com per la técnica d'adquisició dels volàtils. Es va concluir que la t`cnica més adequada per a la comparació de grans grups de mostres desde una aproximació multi-òmica consistix en congelar en nitrògen líquid el material vegetal en el momento idoni de recolecció, i analitzar-lo posteriorment per microextracció en fase sòlida (SPME) acoplada a cromatografía de gasos i espectrometría de masses. Es va posar a punt esta técnica i es va utilitzar per a la determinació dels composteos volàtils en varies línies NILs portadores de QTLs de caràcters relacionats en el sabor i l'aroma en fons genètics diversos. Els resultats van permetre associar alguns dels caràcters organolèptics identificats en alteracions en els nivells d'alguns compostos volàtils. També es va observar que el fons genètic té un efecte important sobre la producción d'estos metabolits. Els anàlisi de correlació entre els nivells de volàtils i els metabolits primaris ens van permetre concluir que la producción de compostos volàtils, en general, no està determinada per els nivells dels seus precursors. La seua regulació és deguda a procesos posteriors, com la disponibilitat dels precursors o de metabolits intermediaris, la variabilitat en processos específics relacionats en la conversió dels precursors en volàtils, o en algún altre mecanisme regulador encara desconegut. També es van estudiar els volàtils en una población de RILs rerivada d'un creuament entre Solanum pimpinellifolium entrada TO-937, la espècie silvestre més próxima a la tomatera cultivada i que produix fruits rojos, i S. lycopersicum cv. Moneymaker, una varietat de tomata per al mercat en fresc. Açò va permetre l'identificació de 102 QTLs de 39 volàtils diferents, 76 de les quals no s'havien descrit prèviament, i que es van mapejar al llarg dels 12 cromosomes de la tomatera mitjançant el mapa de marcadors moleculars de SNPs SOLCAP. Posteriorment es van evaluar la majoria de les QTLs identificades mitjançant la determinació dels volàtils en línies ILs generades a partir dels mateixos materials. Es va observar que quasi la meitat de estes QTLs van mantindre el seu efecte al ser introgressades en el fons genètic "Moneymaker". Adicionalment, 12 noves QTLs es van identificar en esta población d'ILs. Algunes de les QTLs identificades, en base al coneiximent existent respecte a l'efecte dels volàtils en la nostra percepció del sabor i l'aroma, i tenin en cónter la seua capacitat de mantindre el seu efecte al ser introgressats en la tomata cultivada, són candidats prometedors per a ser utilitzats en la millora genética del sabor de les tomates. Finalment, l'anàlisi de la localització en el genoma de les QTLs analitzades en les distintes poblacions objecte d'aquesta tesi, junt a les descrites en la bibliografía disponible, va evidenciar que existix una baixa freqüència de co-localització entre les distintes QTLs. Açò implica que existix molta variabilitat genética en les espècies silvestres relacionades en la tomatera, que pot ser utilitzada per a la millora del sabor i l'aroma dels seus fruits. / Rambla Nebot, JL. (2016). GENES AND GENOMIC REGIONS RELATED TO THE PRODUCTION OF VOLATILE COMPOUNDS IN THE TOMATO FRUIT [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/61768 / Premios Extraordinarios de tesis doctorales / Compendio

Des génotypes adaptés à des environnements contrastés ont de grandes chances de se comporter différemment lorsqu’ils sont placés dans des conditions similaires et contrôlées, notamment si leur sensibilité aux signaux environnementaux et/ou leur croissance intrinsèque sont limitées à différents niveaux. De ce fait, la variabilité observée dans les populations naturelles peut être utilisée comme une source illimitée de nouveaux allèles ou gènes pour l’étude des bases génétiques de la variation des traits quantitatifs. Mon travail de doctorat a consisté en l’analyse de la variabilité naturelle pour la croissance et la réponse à l’environnement chez Arabidopsis thaliana. Le but des approches de génétique quantitative est de comprendre comment la diversité génétique et épigénétique contrôle la variabilité phénotypique observée dans les populations à différentes échelles, au cours du développement et sous différentes contraintes environnementales. De plus, ces analyses ont pour objectif de comprendre comment les processus adaptatifs et démographiques influencent la fréquence de ces variants dans les populations en fonction de leur environnement local. Ainsi, l’étude de la variabilité naturelle peut être appréhendée en utilisant diverses approches, de la génétique et des méthodes de biologie moléculaire aux études écologiques et évolutives. Au cours de mon doctorat, j’ai eu la chance de travailler sur plusieurs de ces aspects au travers de trois projets indépendants qui exploitent tous la variabilité naturelle d’A. thaliana.Le premier projet a consisté en l’analyse du pattern de polymorphisme observé dans des populations d’A. thaliana au gène MOT1 qui code pour un transporteur de molybdate (la forme assimilable du molybdène (Mo), un micro-élément essentiel) et qui est responsable d’une partie des variations de croissance et de fitness observées à l’échelle de l’espèce en fonction de la disponibilité en Mo des sols. J’ai montré à différentes échelles géographiques que le pattern de polymorphisme à MOT1 ne reflète pas une évolution neutre mais présente plutôt des traces de sélection diversifiante. Ce travail a contribué à renforcer l’hypothèse selon laquelle des mutations au niveau du gène MOT1 pourraient avoir été sélectionnées dans certaines populations pour faire face aux niveaux élevés de Mo observés dans certains sols et potentiellement délétères malgré leur effet négatif sur des milieux pauvres en Mo.Le deuxième projet portait sur la caractérisation et l’analyse fonctionnelle de deux récepteur-kinase putatifs (RLK) identifiés de part leurs effets sur la croissance foliaire spécifiquement en réponse à un stress induit par du mannitol mais pas sous d’autres contraintes osmotiques. La fonction de ces récepteurs chez A. thaliana -qui n’est pas connu pour produire du mannitol- peut paraître intrigante. Les différentes expériences réalisées au cours de cette thèse nous ont cependant permis de construire un modèle selon lequel ces récepteurs pourraient être activés par le mannitol produit par certains pathogènes tel que les champignons et participer aux réponses de défense de la plante.Le troisième projet a été réalisé en collaboration avec l’équipe de Michel Vincentz (CBMEG, Brésil) et de Vincent Colot (IBENS, Paris) et consiste en l’analyse de l’occurrence de variants épigénétiques naturels au gène QQS dans différentes populations d’Asie Centrale et de leurs possibles conséquences phénotypique et adaptative.En conclusion, l’analyse des variants génétiques et épigénétiques naturels à l’origine des variations de biomasse en interaction avec l’environnement permet de comprendre comment l’évolution façonne la variabilité naturelle. / Genotypes adapted to contrasting environments are expected to behave differently when placed in common controlled conditions, if their sensitivity to environmental cues or intrinsic growth behaviour are set to different thresholds, or are limited at distinct levels. This allows natural variation to be exploited as an unlimited source of new alleles or genes for the study of the genetic basis of quantitative trait variation. My doctoral work focuses on analysing natural variation for shoot growth and response to the environment in A. thaliana. Natural variation analyses aim at understanding how molecular genetic or epigenetic diversity controls phenotypic variation at different scales and times of plant development and under different environmental conditions, and how selection or demographic processes influence the frequency of those molecular variants in populations for them to get adapted to their local environment. As such, the analysis of A. thaliana natural variation can be addressed using a variety of approaches, from genetics and molecular methods to ecology and evolutionary questions. During my PhD, I got the chance to tackle several of those aspects through my contributions to three independent projects which have in common to exploit A. thaliana natural variation. The first one is the analysis of the pattern of polymorphism from a set of 102 A. thaliana accessions at the MOT1 gene coding for a molybdate transporter (an essential micronutrient) and responsible for contrasted growth and fitness among accessions in response to Mo availability in the soil. I showed at different geographical scales that MOT1 pattern of polymorphisms is not consistent with neutral evolution and shows signs of diversifying selection. This work helped reinforce the hypothesis that in some populations, mutations in MOT1 have been selected to face soils rich in Mo and potentially deleterious despite their negative effect on Mo-limiting soils. The second project consists in the characterisation and functional analysis of two putative receptor-like kinases (RLKs) identified from their effect on shoot growth specifically under mannitol-supplemented media and not in response to other osmotic constraints. The function of such RLKs in A. thaliana, which is not known to synthesize mannitol was intriguing at first but, through different experiments, we built the hypothesis that those RLKs could be activated by the mannitol produced by some pathogens such as fungi and participate to plant defensive response. The third project, in collaboration with Michel Vincentz’s team from CBMEG (Brasil) and Vincent Colot (IBENS, Paris), consists in the analysis of the occurrence of natural epigenetic variants of the QQS gene in different populations from Central Asia and their possible phenotypic and adaptive consequences. Overall, these analyses of the genetic and epigenetic molecular variation leading to the biomass phenotype(s) in interaction with the environment provide clues as to how and where in the pathways adaptation is shaping natural variation.