Infectious Pancreatic Necrosis (IPN), due to infection with the IPN virus (IPNv), continues to cause heavy mortalities and is endemic across the major Atlantic salmon farming regions of the world. Prevalances of 0.3-0.8 or more at the freshwater stage and 0.05 to 0.3 in the seawater phase of production are typical. Partially effective injectable vaccines are available against seawater IPN but biosecurity measures remain the main methods of control. To explore the feasibility of selecting salmon for resistance to IPN, a selective breeding program was initiated in 1996, including a series of field and experimental trials challenging known full-sib families with IPNv. A total of 404,723 fish faced IPNv challenge (376,541 seawater and 28,182 freshwater) covering 14 years and 17 separate locations across 7 sites. Mortalities and survivors following IPN challenge were counted by full-sib family and analysed as binomial data (alive / dead). Initial heritabilities were obtained from expressions based on the variance and covariance of full-sib family means for the 2001 year-group, indicating heritabilities (h2) of 0.16, range 0.08 to 0.24, and genetic correlations (rg) between replicate families of 0.71 to 0.78. These results were then confirmed by residual maximum likelihood across all seawater challenged data (year-groups 1997-2003), indicating a h2 of 0.43 (s.e.0.02) across all sites, range 0.06 to 0.40 for individual sites, and a range of rg between replicates of 0.70 to 0.87 (s.e. approx 0.05). To accommodate datasets and pedigrees approaching half a million individually identified fish, an implementation of the Reduced Animal model (RAM) was used to obtain these estimates. A similar level of genetic variation for resistance to freshwater IPN (year-groups 2005-2009) was confirmed with a h2 of 0.49, (s.e. 0.03), range 0.31 to 0.59, and rg between replicates ( 0.80 to 0.95, s.e. approx 0.05), using an Individual Animal Model. When all the data were analysed together, assuming seawater and freshwater survival to be the same trait, the heritability increased to 0.67, (s.e. 0.02). On testing this assumption, the genetic correlation between freshwater and seawater survival was found to be 0.68 s.e. 0.09. Both these pooled estimates account better than those for the individual site estimates, for the known selection of superior families that was incorporated at the earliest opportunity (2001) into the selective breeding program. To further investigate if there were favourable or antagonistic relationships operating between traits under active selection, genetic correlations between IPN mortality and a range of performance and harvest traits were obtained. When restricting the harvest data to year-groups where the harvested fish had not experienced an IPN event (2003 for seawater IPN, 2005 for freshwater IPN) : fish length and flesh colour just reached significance with seawater IPN (0.27 to 0.53. s.e. 0.14), while only harvest weight (0.30 s.e 0.11) attained significance with freshwater IPN mortality. All these correlations were antagonistic. When all the data were combined, (ie both IPN and harvest events taken from all yeargroups) these became non-significant. Taken as a whole, these results indicate that selecting salmon for resistance to both seawater and freshwater IPN challenge certainly is feasible, and that adverse effects on selection for other important production traits is not expected. How these medium to high heritabilities relate to the discovery of a major QTL for IPN resistance segregating in these populations, reported in a parallel scheme of work but based on a sub-set of the same families, is discussed.

A l’échelle du globe, la diminution des ressources en eau est devenue un des principaux facteurs limitants pour les productions agricoles. Jusqu’à présent, les approches génomiques à haut débit conduites chez les espèces modèles ont permis d’identifier des centaines de gènes potentiellement impliqués dans la survie des plantes en conditions de sécheresse,mais très peu ont des effets bénéfiques sur la qualité et le rendement des cultures.Néanmoins, l’application d’un déficit hydrique bien contrôlé peut permettre d’améliorer la qualité des fruits charnus par dilution et/ou accumulation de composés gustatifs majeurs.Dans ce contexte, la première partie du travail de thèse avait pour but de déchiffrer les déterminants génétiques de la réponse au déficit hydrique chez la tomate en explorant les interactions ‘génotype x niveau d’irrigation’ (G x I) et ‘QTL x niveau d’irrigation’ (QTL x I) dans deux populations. La première population consistait en un ensemble de lignées recombinantes (RIL) issues du croisement entre deux accessions cultivées, tandis que la seconde était composée de diverses accessions à petits fruits principalement originaires d'Amérique du Sud. Les plantes ont été phénotypées pour un ensemble de caractères agronomiques (vigueur des plantes et qualité des fruits) et génotypées pour des milliers de SNP. Les données ont été analysées en utilisant les méthodologies de la cartographie de liaison et d'association, permettant l'identification de QTL et gènes candidats putatifs pour la réponse de la tomate au déficit hydrique. La deuxième partie du travail de thèse avait pour objectif d'explorer la régulation des gènes dans les fruits et les feuilles de tomates en condition de déficit hydrique. Dans ce but, des données de séquençage du transcriptome ont été recueillies sur les deux génotypes parentaux de la population RIL et leur hybride F1. Les données ont été analysées pour identifier les gènes et les allèles exprimés de manière différentielle. Puis, l'expression de 200 gènes a été mesurée dans les fruits et les feuilles de l’ensemble des lignées de la population RIL par qPCR micro-fluidique à haut débit. Des eQTL et des interactions ‘eQTL x niveau d’irrigation’ ont été identifiés pour ces gènes par cartographie de liaison. Les colocalisations entre les QTL phénotypiques et les QTL d’expression ont été analysées. Les connaissances produites au cours de cette thèse contribuent à une meilleure compréhension des interactions des plantes de tomate avec leur environnement et fournissent des bases pour l'amélioration de la qualité des fruits en conditions d’irrigation limitée. / Water scarcity will constitute a crucial constraint for agricultural productivity in a nearfuture. High throughput approaches in model species have identified hundreds of genespotentially involved in survival under drought conditions, but very few having beneficialeffects on quality and yield in crops plants. Nonetheless, controlled water deficits mayimprove fleshy fruit quality through weaker dilution and/or accumulation of nutritionalcompounds. In this context, the first part of the PhD was aimed at deciphering the geneticdeterminants of the phenotypic response to water deficit in tomato by exploring thegenotype by watering regime (G x W) and QTL by watering regime (QTL x W) interactions intwo populations. The first population consisted in recombinant inbreed lines (RIL) from across between two cultivated accessions and the second was composed of diverse small fruittomato accessions mostly native from South America. Plants were phenotyped for majorplant and fruit quality traits and genotyped for thousands of SNP. Data were analyzed withinthe linkage and association mapping frameworks allowing the identification of QTLs andputative candidate genes for response to water deficit in tomato. The second part of the PhDhad the objective to explore gene regulation in green fruit and leaves of tomato plantsstressed by water deficit. For this purpose, RNA-Seq data were collected on the two parentalgenotypes of the RIL population and their F1 hybrid. Data were analyzed to identifydifferentially expressed genes and allele specific expression (ASE). Then, the expression of200 genes was measured in leaves and fruits of the whole RIL population by high throughputmicrofluidic qPCR. eQTLs and eQTL by watering regime interactions were mapped for thosegenes using linkage mapping. Colocalisations with the phenotypic QTLs were analyzed. Theknowledge produced during this PhD will contribute to a better understanding of the tomatoplant interaction with their environment and provide bases for improvement of fruit qualityunder limited water supply.

Le contrôle génétique et l'environnemental de l'angle des microfibrilles (MFA), les corrélations génétiques du MFA avec d'autres caractères du bois et de croissance, et par conséquent les implications pour la sélection sont très peu documentés pour les Eucalyptus. Les objectifs de cette étude étaient d'établir la variation spatiale du MFA, de la densité du bois (ρ) et de sa rigidité (E); de déterminer les relations entre MFA et propriétés du bois et enfin d'estimer le contrôle génétique et environnemental des caractères du bois et de la croissance dans le cadre de tests clonaux et de test de descendances d'Eucalyptus au Brésil et au Congo. Méthodes classiques, résonance, diffraction des rayons-X et la spectroscopie proche infrarouge ont été combinées pour évaluer les propriétés du bois. La variation du MFA représente 44% de la variation du module spécifique (E/ρ) du bois. La densité du bois est le principal déterminant de la rigidité et de la résistance du bois alors que le MFA joue un rôle secondaire. Les estimations de l'héritabilité sont de modéré à élevées pour le MFA, ρ, E, la lignine de Klason (KL) et les caractères de croissance, selon la position spatiale et le dispositif expérimental. Le contrôle génétique du MFA, ρ et E et leurs corrélations génétiques avec KL et la circonférence à 1.3 mètre des arbres varient avec l'âge. Les résultats suggèrent que les arbres à forte croissance sont génétiquement plus aptes à produire du bois de faible densité et un MFA plus faible pour assurer la rigidité du bois nécessaire à leur développement. La plupart des propriétés du bois sont génétiquement corrélées négativement avec la croissance, bien que corrélations génétiques favorables entre propriétés du bois sont observés. Les corrélations génétiques et environnementales sont parfois de signes opposés selon les caractères considérés. Ceci peut s'expliquer par l'effet pléiotropique des gènes et/ou par le déséquilibre de liaison. Les conséquences de ces résultats sur les stratégies de sélection sont discutées selon l'usage final du bois d'Eucalyptus. / The genetic and environmental control of microfibril angle (MFA), the genetic correlations with other wood and growth traits, and therefore the implications for selection are poorly documented for Eucalyptus. Thus, the objectives of this study were to determine the spatial variation of the MFA, wood density (ρ) and stiffness (E); to determine the relationship between MFA and wood traits and finally to estimate the genetic and environmental control of wood and growth traits from clonal and progeny tests of Eucalyptus in Brazil and Congo. Conventional methods, resonance, X-ray diffraction and spectroscopy were combined to evaluate the wood properties. MFA variation accounted for 44 percent of the variation in specific modulus (E/ρ) of wood. The ρ was the prime determinant on wood stiffness and strength while the MFA played a secondary role. The heritability estimates were moderate to high for the MFA, ρ, E, Klason lignin (KL) and growth traits according to the spatial position and the experimental design. Genetic control of the MFA, ρ and E and their genetic correlations with KL and circumference of 1.3 meters of trees varied with age. The results suggest that tree with potential to grow fast are genetically more likely to produce low ρ and also to decrease the MFA for ensuring stiffness required for their development. Most wood properties were genetically negatively correlated with growth, although favorable genetic correlations between many wood traits were observed. Genetic and environmental correlations were sometimes of opposite signs according to the considered trait. This can be explained by the pleiotropic effect of genes and / or linkage disequilibrium. The implications of these findings for selection strategies are discussed according to the final use of Eucalyptus wood.

Submitted by JÚLIO HEBER SILVA (julioheber@yahoo.com.br) on 2016-12-07T16:22:53Z No. of bitstreams: 2 Tese - Rodrigo Soares de Castro - 2016.pdf: 5776299 bytes, checksum: 5c221af09289c691e9ae2d0146748a62 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Jaqueline Silva (jtas29@gmail.com) on 2016-12-13T15:38:02Z (GMT) No. of bitstreams: 2 Tese - Rodrigo Soares de Castro - 2016.pdf: 5776299 bytes, checksum: 5c221af09289c691e9ae2d0146748a62 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2016-12-13T15:38:02Z (GMT). No. of bitstreams: 2 Tese - Rodrigo Soares de Castro - 2016.pdf: 5776299 bytes, checksum: 5c221af09289c691e9ae2d0146748a62 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2016-05-30 / This study aimed to analyze the quantitative genetic variation within and between natural subpopulations of Hymenaea stigonocarpa (Mart. Ex Hayne), fruit tree from the Cerrado region. Six mother trees were sampled in each of the 25 subpopulations from the states of Goiás, Mato Grosso, Mato Grosso do Sul, Minas Gerais and Bahia, covering a large area of the Cerrado biome. In each tree they were collected twenty fruits, which served for evaluation of biometric data of fruits and seeds. Twenty seeds of each mother tree were sown in a nursery, with five seeds per plot in four randomized blocks, constituting a test of provenances and progenies of half sibs. Analysis of variance were performed using the hierarchical model for the characters of initial development. With the produced seedlings it was planted a germplasm collection in vivo in Escola de Agronomia of Universidade Federal de Goias.The major phenotypic variation coefficients in fruits and seeds were found in the characters number of seed (47,87%) weight of the pulp (47.74%) and fruit weight (44.06%). The analysis of variance of the physical characteristics of the fruits and seeds revealed the existence of significant variation for all characters in all levels analyzed: among subpopulations, between mother trees within subpopulations and between fruit within mother tree. Of the ten characters analyzed in six the greatest variation was found between fruit within mother tree. Significant variability was found between subpopulations and between progenies within subpopulations for most quantitative traits studied, showing a great genetic variability of the sampled material, which is important for sustainability of the species and future breeding program. The heritability estimates of traits were also high, indicating success in the selection of desirable traits in a breeding program for the species. The comparative analysis between the estimated value of the QST and FST index showed no significant difference for eight of ten characters analyzed, demonstrating that there is no evidence of the action of natural selection in the differentiation between the studied subpopulations and that the differentiation found can be explained by the action of genetic drift combined with gene flow restriction between subpopulations. The value of correlation coefficient between phenotypic and geographical matrix was 0.164 (p <0.05) by Mantel test, indicating a weak correlation between the phenotypic subpopulations means and the distances between them. / O trabalho teve o objetivo de analisar a variação genética quantitativa entre e dentro de subpopulações naturais de Hymenaea stigonocarpa (Mart. ex Hayne), árvore frutífera da região do Cerrado conhecida como jatobá, jatobá do cerrado ou jatobá do campo. Foram amostradas seis árvores matrizes em cada uma das 25 subpopulações distribuídas pelos estados de Goiás, Mato Grosso, Mato Grosso do Sul, Minas Gerias e Bahia, abrangendo uma grande área do bioma Cerrado. Em cada árvore foram coletados vinte frutos, que serviram para avaliação dos dados biométricos de frutos e sementes. Vinte sementes de cada matriz foram semeadas em uma área telada, sendo cinco sementes por parcela em quatro blocos ao acaso, constituindo um teste de progênies de meio irmãos hierarquizado. Foram feitas análises de variância e seus componentes pelo modelo hierárquico para os caracteres de desenvolvimento inicial das plântulas. Com as mudas produzidas foi plantado um banco de germoplasma in vivo na Escola de Agronomia da Universidade Federal de Goiás. Os maiores coeficientes de variação fenotípica dos frutos e sementes foram encontrados nos caracteres número de sementes (47,87%), peso da polpa (47,74%) e peso do fruto (44,06%). A análise de variância dos caracteres físicos dos frutos e sementes revelou a existência de variação significativa para todos os caracteres em todos os níveis hierárquicos analisados: entre subpopulações, entre matrizes dentro de subpopulações e entre frutos dentro de matrizes. Dos dez caracteres analisados, em seis a maior variação foi encontrada entre frutos dentro de matrizes. Foram constatadas variabilidades significativas entre subpopulações e entre progênies dentro das subpopulações para a maioria dos caracteres quantitativos de desenvolvimento inicial de plântulas estudadas. Tal resultado denota variabilidade genética do material amostrado, que é importante para a preservação da espécie e também para um futuro programa de melhoramento visando o seu aproveitamento econômico. As estimativas de herdabilidade encontradas nos caracteres estudados também foram altas e adequadas para o sucesso na seleção de caracteres desejáveis em um programa de melhoramento para a espécie. A análise comparativa entre os valores estimados dos índices QST e FST não diferiram significativamente em oito dos dez caracteres analisados, demonstrando que não existe forte evidência da ação da seleção natural na diferenciação entre as subpopulações estudadas e que a diferenciação encontrada pode ser explicada pela ação da deriva genética combinado com a restrição de fluxo gênico entre as subpopulações. O valor encontrado no teste de mantel feito entre as matrizes fenotípica e geográfica foi de 0,164 (p<0,05), denotando uma fraca correlação entre os dados fenotípicos das subpopulações avaliadas e as distâncias entre elas. Pelo correlograma de mantel verificou-se que a correlação entre as matrizes embora fraca, ela diminui constantemente através das classes de distância, chegando a zero por volta dos 500 km. Tal diminuição constante da influência da distância na diferença fenotípica entre as subpopulações caracteriza um padrão clinal.

En 1996, la FAO a reconnu le rôle des agriculteurs dans la construction des ressources génétiques. Dans ce contexte, l'objectif général du projet PLANTADIV, dans lequel s'inscrit cette thèse, est d'appréhender comment les facteurs anthropiques et biologiques interagissent et façonnent la diversité génétique des plantes cultivées dans le bassin du lac Tchad. Dans cette région, les populations ont mis au point une innovation agricole originale : l'utilisation en contre-saison de terres argileuses inondées pour repiquer du sorgho. Les variétés de sorgho repiqué sont capables de puiser dans les réserves hydriques du sol pour accomplir leur cycle végétatif en saison sèche sans autre apport d'eau. Le sorgho repiqué connaît un large développement dans la région depuis la moitié du XXe siècle. Le projet de thèse se focalise sur l'estimation de la diversité génétique des sorghos repiqués et sur les mécanismes biologiques et génétiques qui ont pu contribuer à sa structuration intra et inter variétale. Nous avons également entrepris de retracer l'histoire évolutive des sorghos repiqués en nous appuyant essentiellement sur des outils de génétique des populations pour discuter les hypothèses géographiques et historiques existantes. Cette étude a mis en évidence qu'au moins deux événements de dessaisonalisation avaient eu lieu à partir de sorghos pluviaux provenant de deux groupes génétiques différents. Les sorghos repiqués sont plus différenciés que les sorghos pluviaux. Ceci peut s'expliquer en partie par les pratiques paysannes : les sorghos pluviaux sont échangés plutôt via les amis, la famille et les voisins, alors que les sorghos repiqués le sont plutôt via les marchés. De par les nombreux échanges de semence entre les différentes populations humaines dans cette région, l'étude phylogénétique n'a pas permis de mettre en évidence le(s) lieu(x) d'origine de dessaisonalisation.La seconde partie de ce travail a été consacré à la biologie de la reproduction du sorgho repiqué. Les méthodes de calcul indirectes et directes ont montrées que le sorgho repiqué est, comme le sorgho pluvial, préférentiellement autofécondé. Le taux moyen chez le sorgho repiqué est cependant plus faible (1,8%) que pour le sorgho pluvial (12%). De même, les variations d'allofécondation entre des panicules d'un même type nommé semblent plus faibles que pour le sorgho pluvial. La dernière partie de la thèse est consacrée aux impacts des pratiques agricoles sur la structuration de la diversité génétique des sorghos repiqués à une échelle locale. Les analyses génétiques ont montré, que ce soit pour le village de Djongdong ou celui de Bouzar, situés à l'extrême Nord du Cameroun, que pour un agriculteur donné, chaque type nommé correspond à une entité génétique. De plus, un même morphotype chez différents agriculteurs correspond aussi à une entité génétique. Les modes de gestion des semences et les pratiques culturales ont été analysés, elles influencent peu la structuration de la diversité génétique du sorgho repiqué. / In 1996, FAO has recognized the role of farmers in building and managing genetic resources. This work is part of the project PLANTADIV which main objective is to understand how biological and anthropogenic factors interact and shape diversity of cultivated plants in the Lake Chad Basin. In this region, people have developed an original agricultural innovation: the use in dry-season of flooded clay soils for transplanting sorghum. Transplanted sorghum varieties are able to tap into soil moisture reserves to complete their growth cycle in the dry-season without any water supply. Transplanted sorghum cultivation undertook a large development in the region since the middle of the XX century.The thesis project focuses on the estimation of the genetic diversity of planted sorghum and on biological and genetic mechanisms that may have contributed to its structuration both within and between landraces. We also undertook to trace the evolutionary history of planted sorghum by relying primarily on population genetics approaches to elaborate over geographical and historical hypotheses.This study revealed that at least two events of deseasonalization occurred from rain- sorghum pools from two different genetic groups. Differentiation of dry-season sorghum is stronger than that of rain-sorghum. This may be partially due to social practices: rainy sorghum are mainly exchanged through friends, families and neighbors as planted sorghum seeds are often obtain from markets. Extensive seed exchange between different human populations across the region may have blurred the geographical pattern of the genetic diversity, not allowing us to identify potential sites for deseasonalization.The second part of this work is devoted to the reproductive biology of dry-season sorghum. Direct and indirect estimation methods have shown that dry-season sorghum is, as rain sorghum, preferably selfing. Average level of out crossing is nevertheless lower in dry-season sorghum (1.8%) than it is in rain-sorghum (12%). Within landraces, variations are also smaller for dry-season sorghum than for rain-sorghum.The last part of the thesis is devoted to the impacts of agricultural practices on the structure of the genetic diversity of dry-season sorghum at a local scale. Genetic analyzes have shown that in both studied villages of Djongdong and Bouzar, located in the extreme north of Cameroon, each landrace named by a farmer corresponds to a genetic entity. In addition, the same morphological type among different farmers corresponds to a genetic entity. Modes of seed management and cultural practices were analyzed; they seem to have little influence on the structure of the genetic diversity of dry-season sorghum.

Com a finalidade de avaliar o programa de melhoramento da cana-de-açúcar, este trabalho teve como objetivos: determinar o grau da interação famílias x ambientes (FA); comparar métodos de seleção na etapa inicial em termos de resposta esperada à seleção; e propor o método de seleção sequencial modificado. Para isso, foram avaliados 4752 'seedlings' pertencentes a 33 famílias (irmãs germanas e meia irmãs), em dois locais do Estado de São Paulo, Piracicaba e Jaú. Os caracteres estimados foram altura e diâmetro dos colmos, número de perfilhos, Brix % caldo da cana, toneladas de cana por hectare (TCH) e toneladas de Brix por hectare (TBH). Para validar a resposta esperada à seleção sequencial modificada, 40 famílias foram selecionadas por este método e os clones foram multiplicados até a etapa III do programa de melhoramento, a fim de fornecer a resposta realizada à seleção. Os resultados mostraram interação FA significativa para todos os caracteres avaliados. A opção por uma seleção específica implicou em aumentos de ganhos de 4,1% e 5,8% para TBH, para Piracicaba e Jaú, respectivamente, em relação à seleção de famílias generalistas, ou seja, baseada na média dos dois locais. A seleção sequencial modificada, proposta neste trabalho e a seleção combinada através de índices apresentaram pouca vantagem em relação à seleção massal, na condição de seleção direta (sem avaliação visual). Nessas mesmas condições, a seleção sequencial tradicional e a australiana foram inferiores à seleção massal, em termos de progresso esperado, para todos os caracteres. Incluindo a seleção indireta (com avaliação visual) o método sequencial modificado foi sempre superior à seleção massal, para os principais caracteres avaliados (TCH e TBH). Para os métodos australiano e tradicional, houve vantagem apenas quando a correlação genética entre a avaliação visual e o caráter principal foi igual ou inferior a 0,7. Dessa forma, e devido à dificuldade prática de utilizar índices (seleção combinada), concluiu-se que o método proposto de seleção sequencial modificada é perfeitamente viável, sendo, portanto, recomendado. Na comparação entre as respostas estimada e a realizada com a seleção sequencial modificada, houve concordância dos resultados, na condição de correlação genética igual a 0,62. Isso veio reforçar a confiabilidade das estimativas obtidas no trabalho, bem como assegurar as vantagens do método proposto sobre os demais aqui apresentados. Se considerada uma correlação genética entre o critério de avaliação visual e o caráter principal variando entre 0,5 a 0,7, a superioridade do método proposto em relação ao massal é da ordem de 3% a 5%, em termos de ganho esperado para TCH, em um ciclo de seleção. Para alcançar estes mesmos ganhos com a seleção massal, ter-se-ia que aumentar a população inicial entre 36% a 100%. Alternativamente, mantendo os mesmos tamanhos populacionais, o número provável de clones no final do processo seletivo seria aumentado em 85% a 150%, apenas com a substituição do método de seleção massal pelo sequencial modificado na etapa inicial. / Aiming at the evaluation of the sugarcane breeding program, this study had the following objectives: to determine the degree of the family x environments interaction (FE); to compare selection methods in the initial phase, in terms of expected response to selection, and to propose the modified sequential selection method. For this, 4752 seedlings, originated from 33 families (full-sibs and half-sibs), were evaluated in two sites of the State of São Paulo: Piracicaba and Jaú. The traits evaluated were stalk height and diameter, number of stalks, Brix % cane juice, tons of cane per hectare (TCH) and tons of brix per hectare (TBH). To validate the expected response to the modified sequential selection, 40 families were selected by this method and the clones were multiplied until phase III of the breeding program and the realized gains in selection measured. The results showed significant FE interaction for all evaluated traits. The option for a site specific selection would increase gains by 4.1% and 5.8% for TBH in Piracicaba and Jau, respectively, in relation to the generalized family selections, that is, based on the average of the two sites. The proposed modified sequential selection and the combined selection using indices showed little advantage over the mass selection using direct selection (without visual selection). In these conditions, the traditional sequential selection and the Australian one were inferior to the mass selection, in terms of expected progress, for all traits. Allowing for the indirect selection (with visual selection) the modified sequential method was always superior to the mass for the main traits evaluated (TCH and TBH). The Australian method and the Traditional one, were advantageous in relation to the mass selection only when the genetic correlation between visual selection and the main trait was equal or inferior to 0.7. For this reason, and given the practical difficulty of applying indices (combined selection), it was concluded that the proposed method of modified sequential is perfectly viable and was reccommended. Comparing the estimated and realized response of the modified sequential selection, there was correspondence of results, given rG equals to 0.62. This result confirmed the reliance of the estimates obtained in this study, and assured the advantages of the proposed method over those compared. Considering a genetic correlation (rG), between the visual selection criterion and the main character, varying from 0.5 to 0.7, the superiority of the proposed method over the mass one, varies from 3 to 5%, in terms of expected gain, for TCH in one selection cycle. To obtain these same gains with mass selection, one would have to increase the initial population between 36% and 100%. Alternatively, keeping the same population sizes, the likely number in the end of the selection process would be increased in 85% to 150%, just with the substitution of the method of mass selection by the modified sequential one, in the initial phase.

Com a finalidade de avaliar o programa de melhoramento da cana-de-açúcar, este trabalho teve como objetivos: determinar o grau da interação famílias x ambientes (FA); comparar métodos de seleção na etapa inicial em termos de resposta esperada à seleção; e propor o método de seleção sequencial modificado. Para isso, foram avaliados 4752 'seedlings' pertencentes a 33 famílias (irmãs germanas e meia irmãs), em dois locais do Estado de São Paulo, Piracicaba e Jaú. Os caracteres estimados foram altura e diâmetro dos colmos, número de perfilhos, Brix % caldo da cana, toneladas de cana por hectare (TCH) e toneladas de Brix por hectare (TBH). Para validar a resposta esperada à seleção sequencial modificada, 40 famílias foram selecionadas por este método e os clones foram multiplicados até a etapa III do programa de melhoramento, a fim de fornecer a resposta realizada à seleção. Os resultados mostraram interação FA significativa para todos os caracteres avaliados. A opção por uma seleção específica implicou em aumentos de ganhos de 4,1% e 5,8% para TBH, para Piracicaba e Jaú, respectivamente, em relação à seleção de famílias generalistas, ou seja, baseada na média dos dois locais. A seleção sequencial modificada, proposta neste trabalho e a seleção combinada através de índices apresentaram pouca vantagem em relação à seleção massal, na condição de seleção direta (sem avaliação visual). Nessas mesmas condições, a seleção sequencial tradicional e a australiana foram inferiores à seleção massal, em termos de progresso esperado, para todos os caracteres. Incluindo a seleção indireta (com avaliação visual) o método sequencial modificado foi sempre superior à seleção massal, para os principais caracteres avaliados (TCH e TBH). Para os métodos australiano e tradicional, houve vantagem apenas quando a correlação genética entre a avaliação visual e o caráter principal foi igual ou inferior a 0,7. Dessa forma, e devido à dificuldade prática de utilizar índices (seleção combinada), concluiu-se que o método proposto de seleção sequencial modificada é perfeitamente viável, sendo, portanto, recomendado. Na comparação entre as respostas estimada e a realizada com a seleção sequencial modificada, houve concordância dos resultados, na condição de correlação genética igual a 0,62. Isso veio reforçar a confiabilidade das estimativas obtidas no trabalho, bem como assegurar as vantagens do método proposto sobre os demais aqui apresentados. Se considerada uma correlação genética entre o critério de avaliação visual e o caráter principal variando entre 0,5 a 0,7, a superioridade do método proposto em relação ao massal é da ordem de 3% a 5%, em termos de ganho esperado para TCH, em um ciclo de seleção. Para alcançar estes mesmos ganhos com a seleção massal, ter-se-ia que aumentar a população inicial entre 36% a 100%. Alternativamente, mantendo os mesmos tamanhos populacionais, o número provável de clones no final do processo seletivo seria aumentado em 85% a 150%, apenas com a substituição do método de seleção massal pelo sequencial modificado na etapa inicial. / Aiming at the evaluation of the sugarcane breeding program, this study had the following objectives: to determine the degree of the family x environments interaction (FE); to compare selection methods in the initial phase, in terms of expected response to selection, and to propose the modified sequential selection method. For this, 4752 seedlings, originated from 33 families (full-sibs and half-sibs), were evaluated in two sites of the State of São Paulo: Piracicaba and Jaú. The traits evaluated were stalk height and diameter, number of stalks, Brix % cane juice, tons of cane per hectare (TCH) and tons of brix per hectare (TBH). To validate the expected response to the modified sequential selection, 40 families were selected by this method and the clones were multiplied until phase III of the breeding program and the realized gains in selection measured. The results showed significant FE interaction for all evaluated traits. The option for a site specific selection would increase gains by 4.1% and 5.8% for TBH in Piracicaba and Jau, respectively, in relation to the generalized family selections, that is, based on the average of the two sites. The proposed modified sequential selection and the combined selection using indices showed little advantage over the mass selection using direct selection (without visual selection). In these conditions, the traditional sequential selection and the Australian one were inferior to the mass selection, in terms of expected progress, for all traits. Allowing for the indirect selection (with visual selection) the modified sequential method was always superior to the mass for the main traits evaluated (TCH and TBH). The Australian method and the Traditional one, were advantageous in relation to the mass selection only when the genetic correlation between visual selection and the main trait was equal or inferior to 0.7. For this reason, and given the practical difficulty of applying indices (combined selection), it was concluded that the proposed method of modified sequential is perfectly viable and was reccommended. Comparing the estimated and realized response of the modified sequential selection, there was correspondence of results, given rG equals to 0.62. This result confirmed the reliance of the estimates obtained in this study, and assured the advantages of the proposed method over those compared. Considering a genetic correlation (rG), between the visual selection criterion and the main character, varying from 0.5 to 0.7, the superiority of the proposed method over the mass one, varies from 3 to 5%, in terms of expected gain, for TCH in one selection cycle. To obtain these same gains with mass selection, one would have to increase the initial population between 36% and 100%. Alternatively, keeping the same population sizes, the likely number in the end of the selection process would be increased in 85% to 150%, just with the substitution of the method of mass selection by the modified sequential one, in the initial phase.

Robinia pseudoacacia L. est un arbre nordaméricain qui est largement répandu à travers l’Europe. Afin d’évaluer les mécanismes évolutifs pouvant expliquer son potentiel invasif, il est indispensable d’identifier les populations sources de l’introduction et de comprendre quels traits ont contribué à son succès dans l’aire européenne Une étude de génétique des populations a été réalisée, un large échantillonnage a été conduit au sein des deux aires et 818 individus provenant de 63 populations ont été génotypés grâce à 113 marqueurs SNPS. En premier lieu, nous avons démontré que le robinier européen provenait d’un nombre restreint de populations situées au nord du plateau des Appalaches, ce qui est en accord avec les données historiques. Au sein des ÉtatsUnis la structure reflète des processus évolutifs au long cours tandis qu’en Europe, la structure est plus ténue et pourrait être due à l’activité humaine, notamment aux programmes de sélection entrepris en Europe centrale depuis le 18ème siècle. En deuxième lieu, un goulot d’étranglement génétique associé à une perte de diversité a été mis en évidence dans l’aire d’introduction. Enfin un plus fort taux de clonalité a été observé au sein des populations d’Europe Conjointement à cette étude de génétique des populations. Une expérimentation de génétique quantitative a été réalisée afin d’évaluer la différenciation de traits juvéniles entre populations des deux aires (3000 individus de 20 populations) cultivées dans 3 conditions de température différentes (18°C ; 22°C et 31°C). Les résultats ont révélé une augmentation du taux de germination parmi les populations européennes par rapport aux américaines (88% vs 60%) quelles que soient les conditions environnementales. Un scénario possible est que l’Homme aurait sélectionné et propagé les meilleures graines en Europe favorisant alors l’évolution du taux de germination. De plus, les traits phénotypiques juvéniles sont extrêmement plastiques à la température avec une tendance générale à l’augmentation de la valeur du trait avec la température. Cela suggère qu’un réchauffement climatique favoriserait le développement de l’espèce, au moins en conditions d’alimentation en eau non limitante. Cependant, seules les populations américaines montrent un signal une adaptation locale à la température d’origine Dans tous les cas, ils semblent que l’action de l’Homme sur le potentiel reproductif, sexué ou asexué, a probablement influencé le potentiel invasif du robinier en Europe / Robinia pseudoacacia L. is a North American tree which has now broadly spread in Europe. In order to evaluate the evolutionary mechanisms behind its invasiveness, it is crucial to identify the population sources of the introduction and to understand which traits contributed to its success in the European range. To undertake a population genetics study, we performed a large sampling both in the invasive and native ranges; 818 individuals from 63 populations were genotyped using 113 SNPs. First, we demonstrated that European black locust was introduced from only a limited number of populations located in the Northern plateau of the Appalachians Mountains; this is in agreement with historical records. Within America, population structure reflected long time evolutionary processes whereas in Europe, it was largely impacted by human activities. In the European range, the genetic clustering may be a signal of evolution caused by artificial selection due to human oriented mass selection or tree breeding initiated in Central Europe since the 18th century. Second, we evidenced a genetic bottleneck among ranges with a decrease in allelic richness and in the total number of alleles in Europe. Lastly, we found more clonality within the European populations. Conjointly to the population genetic analysis, we conducted a quantitative genetics experiment to evaluate juvenile traits of both native and invasive black locust populations (3000 individuals from 20 populations) grown under 3 different temperature conditions. Results revealed an enhanced germination rate among European populations compared to that of the native American populations whatever the environmental condition (88% vs 60%). Thus a possible scenario may be that Man would have selected and propagated the best seeds in the new range that would have favored an evolution of germination rate through European populations. Phenotypic traits of juvenile development are extremely plastic in response to temperature (18/22/31°C), with a general tendency to increasing trait values with increasing temperature. This suggests that global warming would favor the development of the species, at least under nonlimiting water supply conditions. However, only American populations demonstrated a signal of local adaptation to the temperature at the sampling location. In any case, the human role on the reproductive potential, both sexual and asexual, within the introduced rangewould likely be a key process in the success of black locust dynamics in Europe.

Des changements de méthylation de l’ADN peuvent affecter l’expression des gènes et pour certains être transmis au travers des générations. De telles « épimutations » qui concernent des groupes de cytosines à proximité ou dans les gènes sont donc une source potentielle de variation phénotypique héritable en absence de changements de la séquence de l’ADN. Chez les plantes la méthylation de l’ADN est cependant principalement observée au niveau des séquences répétées. Il reste à déterminer dans quelle mesure les changements de méthylation au niveau de ce type de séquences peuvent être héritées et affecter les phénotypes. Afin de répondre à ces questions, plus de 500 épiRIL (epigenetic Recombinant Inbred Lines) quasi-isogéniques a été générée chez Arabidopsis thaliana. Cette population a été obtenue par le croisement d’un parent sauvage et d’un parent mutant pour le gène DDM1 présentant une très forte réduction du taux de méthylation de l’ADN. Après un rétrocroisement de la F1 avec une plante sauvage, les individus sauvages pour le gène DDM1 ont été sélectionnés et propagées sur 6 générations par autofécondation. Nous avons montré par l’analyse du méthylome de plus de 100 épiRIL que l’hypométhylation induite par ddm1 présente selon les séquences affectées différents degrés de transmission au travers des générations. La réversion de l’hypométhylation concerne des régions associées à une abondance élevée en sRNA de 24 nt. Nous avons utilisé l’hypométhylation stablement transmise dans les épiRIL induite par ddm1 afin de détecter des QTL (Quantitative Trait Loci) affectant le temps de floraison et la longueur de la racine primaire, deux caractères pour lesquels les variations observées dans les épiRIL présentent une héritabilité importante. En dernier lieu, nous avons recherché par différentes approches les variations causales de ces QTL. / Loss or gain of DNA methylation can affect gene expression and is sometimes transmitted across generations. Such epigenetic alterations, which concern clusters of cytosines located near or within genes, are thus a source of heritable phenotypic variation in the absence of DNA sequence change. In plants however, DNA methylation targets repeat elements predominantly and it remains unclear to which extent DNA methylation changes over repeat sequences can be inherited and affect phenotypes. To address these issues, a population of near-isogenic, epigenetic Recombinant Inbred Lines (epiRILs) was generated in Arabidopsis thaliana. These were derived from a cross between a wild type and an isogenic ddm1 mutant line, in which DNA methylation is compromised specifically over repeat elements. After backcrossing of the F1 and selection of the progeny homozygous for wild-type DDM1, the epiRILs were propagated through six rounds of selfing. Analysis of the methylomes of more than 100 epiRILs and of the parents, indicates that ddm1-induced hypomethylation exhibit different patterns of inheritance through generations. Reversion of ddm1-induced hypomethylation is observed for regions associated with high level of 24 nt siRNA. Based on these findings, stable ddm1-induced hypomethylated regions were used to map quantitative trait loci (QTL) for flowering time and primary root length, two complex traits for which substantial heritable variation is observed in the epiRIL population. We finally analysed these QTL by different approaches to find their causal variations.

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No. of bitstreams: 2 Dissertação - Odilon Peixoto de Morais Júnior - 2013.pdf: 2379319 bytes, checksum: e48602a211183d753b05be7362d82c91 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2013-03-14 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Rice (Oryza sativa L.) is the most important cereal in the world as a major component of the staple food of the world’s population. The increase of the yield potential of new upland rice cultivars has been became highlighted as a main challenge for the plant breeding in this millennium. The increasing mean yield of cultivars becomes more difficult to identify superior genotypes, because the contrasts among elite-lines are becoming smaller. This highlights the importance of developing improved populations with high frequency of favorable alleles and genetic variability. The recurrent selection is a method based on population breeding and the main characteristic is obtaining long-term results. Using the recurrent selection population CNA6 of upland rice, the objectives of this study were: (i) to obtain estimates of genetic and phenotypic parameters among S0:2 progenies for grain yield (PG, in kg ha-1) and plant height (AP, in cm), in four selection cycles; (ii) to determine the influence of the progeny x location interaction on estimates of genetic and phenotypic parameters; (iii) to estimate the genetic progress of the population along the four cycles of recurrent selection for PG, AP and days-to-flowering (DF, in days); and (iv) to evaluate the genetic potential of this population through the expected proportion of superior lines after each selection cycle. It was used the data set from yield trials of S0:2 progenies in the years 2000/01, 2003/04, 2006/07 and 2009/10 from Brazilian Agricultural Research Corporation (Embrapa). In each cycle, the trials were carried out in some locations (Santo Antônio de Goiás-GO; Paragominas-PA; Primavera do Leste, MT; Sinop-MT; Teresina-PI and Vilhena-RO). The experimental design was augmented block of Federer, without replicate within location and with at least three checks. The plots were composed by four rows with five meters long, spacing of 0.30 m, and density of 60 seeds per meter. In each cycle, the data set from PG and AP were subjected to individual analysis of variance for Santo Antônio de Goiás-GO, the unique common location in all cycles, and joint analysis of variance for all locations. Estimates of phenotypic, genotypic and environment correlations among three traits studied was obtained. The average gains per cycle, and average annual gains and total were estimated, as also the weighted coefficients of determination and gains among cycles and the total gain based on contrasts among estimated averages for each cycle. In addition, the expected proportions of superior inbred lines after each selection cycle were obtained, using the average of the checks as standard. Estimates of genetic correlations between PG and AP were -0.42 and between AP and DF the -0.11 , both significant (p0,01), and no correlation was detected among PG and DF. Thus, within this population progenies with higher grain yield had lower plant height, and cycle may be early, medium or late. Estimates of genetic variance among S0:2 progenies suggested that genetic variability was maintained along the cycles of selection for the traits PG and AP. After unfolding of the genotype x location interaction (GxL) was observed predominance of the crossover interaction for PG and AP. Finally, it was found that the GxL interaction affected the estimates of genetic and phenotypic parameters for both traits, due to the wide geographic distribution of the target environments, which the recurrent selection program aims to obtain genetic gains in medium and long term. The results show clearly the efficiency of recurrent selection program in the progress of the population mean for grain yield and plant height, with significant genetic gains observed during the four cycles of selection. The genetic potential of the population to develop superior inbred lines increased during to selection cycles for grain yield and plant height. Despite the absence of genetic gain for days-to-flowering, the genetic potential for this trait was kept in the population during the four cycles elapsed. / O arroz (Oryza sativa L.) é o cereal mais importante do mundo, sendo o componente principal da dieta básica da população mundial. O incremento do potencial produtivo em novas cultivares de arroz de terras altas vem se destacando como um dos principais desafios para o melhoramento genético da cultura neste milênio. À medida que se aumenta a produção média das cultivares, torna-se mais difícil identificar genótipos superiores, visto que as diferenças a serem detectadas são cada vez menores. Isto ressalta a importância do desenvolvimento de populações melhoradas com alta frequência de alelos favoráveis e variabilidade genética. A seleção recorrente apresenta-se como um método que tem como base funcional o melhoramento populacional, sendo sua principal característica a obtenção de resultados em longo prazo. A partir da população de seleção recorrente CNA6 de arroz de terras altas, este trabalho teve como objetivos (i) obter estimativas de parâmetros genéticos e fenotípicos entre progênies S0:2 para produção de grãos (PG, em kg ha-1) e altura de plantas (AP, em cm), em quatro ciclos de seleção; (ii) determinar a influência do componente da interação entre progênies e locais sobre as estimativas de parâmetros genéticos e fenotípicos; (iii) estimar o progresso genético da população ao longo de quatro ciclos de seleção recorrente para PG, AP e dias para florescimento (DF, em dias); e (iv) avaliar o potencial genético dessa população por meio da probabilidade de se gerar linhagens superiores após cada ciclo de seleção. Foi utilizado um conjunto de dados provenientes de ensaios de rendimentos de progênies S0:2 nos anos agrícolas de 2000/01, 2003/04, 2006/07 e 2009/10 da Empresa Brasileira de Pesquisa Agropecuária (Embrapa). Em cada ciclo de seleção foram conduzidos ensaios em diferentes locais (Santo Antônio de Goiás-GO; Paragominas-PA; Primavera do Leste-MT; Sinop-MT; Teresina-PI e Vilhena-RO). O delineamento experimental adotado foi em blocos aumentados de Federer, sem repetição dentro de local e com mínimo de três testemunhas em cada ciclo. Em cada ciclo de seleção, os dados de PG e AP foram submetidos à análise de variância individual para Santo Antônio de Goiás-GO, o único local comum em todos os ciclos, e análise de variância conjunta com todos os locais. Foram obtidas estimativas de correlações fenotípicas, genéticas e ambientais entre os três caracteres estudados. Foram estimados os ganhos genéticos médios relativos por ciclo, ganhos médios anuais e totais relativos, como também os coeficientes de determinação ponderados e os ganhos entre ciclos e o ganho total com base nos contrastes entre as médias estimadas para cada ciclo. Além disso, foram obtidas as proporções esperadas de linhagens superiores após cada ciclo de seleção, adotando a média das testemunhas como padrão. As estimativas de correlações genéticas entre PG e AP foram -0,42 e entre AP e DF de -0.11, ambas significativas (p0,01), e nenhuma correlação foi detectada entre PG e DF. Assim, dentro dessa população as progênies mais produtivas apresentavam menor porte, podendo ser de ciclo precoce, médio ou tardio. As estimativas de variância genética entre progênies S0:2 sugeriram que a variabilidade genética foi mantida ao longo dos ciclos de seleção para os caracteres PG e AP. Pela decomposição da interação genótipo x local (GxL) foi verificado predominância da parte complexa da interação para os caracteres PG e AP. Por fim, verificou-se que a interação GxL afetou as estimativas de parâmetros genéticos e fenotípicos para ambos os caracteres, em função da ampla distribuição geográfica dos ambientes alvos, os quais o programa de seleção recorrente do arroz de terras altas visa obter ganhos com seleção a médio e longo prazo. Os resultados revelaram claramente a eficiência do programa de seleção recorrente no progresso da média da população, para PG e AP, com ganhos genéticos significativos observados durante os quatro ciclos de seleção. O potencial genético da população em gerar linhagens superiores aumentou ao longo dos ciclos de seleção para PG e AP. Apesar da ausência de ganho genético em DF, o potencial genético para este caráter foi mantido na população durante os quatro ciclos decorridos.