Submitted by Erika Demachki (erikademachki@gmail.com) on 2014-12-10T14:55:03Z No. of bitstreams: 1 Tese - Camila de Marillac Costa Nunes - 2013.pdf: 4175489 bytes, checksum: aa7c7262337f9ea945ea9fa344b873e7 (MD5) / Rejected by Erika Demachki (erikademachki@gmail.com), reason: on 2014-12-10T14:55:13Z (GMT) / Submitted by Erika Demachki (erikademachki@gmail.com) on 2014-12-15T16:28:45Z No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Tese - Camila de Marillac Costa Nunes - 2013.pdf: 4175489 bytes, checksum: aa7c7262337f9ea945ea9fa344b873e7 (MD5) / Approved for entry into archive by Erika Demachki (erikademachki@gmail.com) on 2014-12-15T16:34:36Z (GMT) No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Tese - Camila de Marillac Costa Nunes - 2013.pdf: 4175489 bytes, checksum: aa7c7262337f9ea945ea9fa344b873e7 (MD5) / Made available in DSpace on 2014-12-15T16:34:36Z (GMT). No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Tese - Camila de Marillac Costa Nunes - 2013.pdf: 4175489 bytes, checksum: aa7c7262337f9ea945ea9fa344b873e7 (MD5) Previous issue date: 2013-04-30 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / The first efforts in sugarcane breeding involved crosses between polyploid species, Saccharum spontaneum L. and Saccharum officinarum L.. These crosses produced interspecific hybrids that were successively backcrossed to S. officinarum. This strategy resulted in a considerable increase in the sugarcane genome complexity. Current varieties exhibit high levels of ploidy and heterozygosity, besides varying levels of aneuploidy. These properties make the understanding of sugarcane genome more difficult; and therefore present a challenge to the development of genetic studies with this culture. Among the different approaches to perform the genetic characterization of a species, the development of genetic maps is useful in providing information about its genomic structure. In this work, we report the first linkage maps for sugarcane using both DArT (Diversity Arrays Technology) and SSR (Single Sequence Repeat) markers. We identified markers significantly associated to characters involved in sugar production. Maps were obtained using two populations: one, consisting of 81 genotypes, was derived from the selfing of a single RB97327 plant; the other, consisting of 91 genotypes, was derived from the crossing RB97327 x RB72454. Genomic DNA was extracted from axillary buds. Genotypes for twenty pairs of SSR primers and 7680 DArT markers were identified. Using mendelian segregation analysis a total of 392 DArT and 57 SSR polymorphic markers, in the population of selfing, and 632 DArT and 79 SSR polymorphic markers, in the outcrossing population, were detected to be segregating as single-dose markers. Both maps were obtained using the OneMap software. Critical values for LOD-score of 3.5 and recombination fraction of 0.3 were chosen. In the map obtained with the selfing population, 449 polymorphic markers with 3:1 segregation were used to originate 95 linkage groups for the variety RB97327. This map had a total length of 1217.2 cM. The estimated size of the genome of RB97327 was 10540.9 cM, which suggests that the obtained coverage (11.5%) is still low. For the population derived from crossing, the 711 polymorphic markers with 3:1 and 1:1 segregation originated 136 linkage groups. The map showed a total length of 2722.2 cM. The SSR markers allowed the identification of six possible homeology groups for the female parent RB97327, and nine homeology groups for the integrated map. For each population, framework maps were produced which were then used to investigate putative associations between markers and characters involved in sugar production. QTL were found both using single marker analysis and composite interval mapping. In the population derived from selfing, using single marker analysis, 63 markers were significantly associated to six variables: number of internodes, number of stems per plant, stem length, stem diameter, stem weight and percentage of soluble solids (°Brix). Using composite interval mapping, three QTL related to stem diameter, length of stem and °Brix were identified. In the population derived from the cross RB97327 x RB724554, using single marker analysis, 60 markers were significantly associated with the same six variables. Using composite interval mapping, two QTL related to diameter and length of stem were detected. / Os primeiros trabalhos de melhoramento genético em cana-de-açúcar envolveram cruzamentos entre espécies poliplóides, Saccharum spontaneum L. e Saccharum officinarum L., os quais originaram híbridos interespecíficos que foram sucessivamente retrocruzados com S. officinarum. Essa estratégia resultou em considerável aumento da complexidade do genoma, de modo que as variedades atuais apresentem elevados níveis de ploidia e heterozigose, além de aneuploidias. Tais características dificultam a compreensão do genoma da cana-de-açúcar e, consequentemente, representam um desafio para o desenvolvimento de estudos genéticos com esta cultura. Dentre os diferentes estudos de caracterização genética, o desenvolvimento de mapas genéticos é importante por fornecer informações acerca da estrutura do genoma de uma espécie. Neste trabalho foram obtidos os primeiros mapas de ligação para cana-de-açúcar utilizando marcadores DArT (Diversity Arrays Technology) e SSR (Single Sequence Repeat). Além disso, foram identificados marcadores significativamente associados aos caracteres envolvidos na produção de açúcar. Para a obtenção dos mapas foram utilizadas duas populações, sendo uma constituída por 81 genótipos derivados da autofecundação de uma planta da cultivar RB97327, e outra constituída por 91 genótipos oriundos do cruzamento RB97327 x RB72454. O DNA genômico foi extraído de gemas axilares. A genotipagem foi realizada a partir de vinte pares de primers SSR e 7.680 marcadores DArT. A análise de segregação mendeliana permitiu a distinção de 392 marcas DArT e 57 marcas SSR polimórficas na população de autofecundação, e 632 DArT e 79 marcas SSR polimórficas na população de fecundação cruzada, com segregação single-dose. Ambos os mapas foram obtidos através do software OneMap utilizando-se um valor crítico de LOD-score igual a 3,5 e de fração de recombinação igual a 0,3. No mapa associado à população de autofecundação, os 449 marcadores DArT e SSR polimórficos com segregação 3:1 foram utilizados para originar 95 grupos de ligação referentes à variedade RB97327. Esse mapa apresentou um comprimento total de 1.217,2 cM. O tamanho estimado do genoma de RB97327 foi de 10.540,9 cM, o que permite afirmar que o mapa obtido apresentou baixa cobertura (11,5%). Para a população derivada de cruzamento, os 711 marcadores DArT e SSR polimórficos com segregação 3:1 e 1:1 originaram 136 grupos de ligação e o mapa apresentou um comprimento total de 2.722,2 cM. Os marcadores SSR também possibilitaram a identificação de seis possíveis grupos de homeologia no mapa referente ao genitor feminino RB97327 e nove no mapa integrado. Para cada população, foram obtidos os mapas framework nos quais foram identificados marcadores DArT e SSR associados aos caracteres envolvidos na produção de açúcar. Em ambas as populações procedeu-se à identificação de QTL a partir de análises de marcas simples e de mapeamento por intervalo composto. Na população derivada de autofecundação foram identificados, pela análise de marcas simples, 63 marcadores significativamente associados às seis variáveis avaliadas: número de entrenós, número de colmos por planta, comprimento de colmos, diâmetro de colmo, peso médio de colmo e teor de sólidos solúveis (brix). Pelo mapeamento por intervalo composto, três QTL relacionados a diâmetro de colmo, comprimento de colmo e brix foram identificados. Na população proveniente do cruzamento RB97327 x RB724554, foram identificados pela análise de marcas simples, 60 marcadores significativamente associados às seis variáveis. Pelo mapeamento por intervalo composto identificou-se dois QTL relacionados ao diâmetro e ao comprimento de colmo.

Submitted by Inês Marinho (bele_ballet@hotmail.com) on 2016-06-17T13:49:11Z No. of bitstreams: 2 Dissertação - Elizangela Farias da Silva.pdf: 725923 bytes, checksum: 334a610c50bdeda8b5392f39f6dc8ef9 (MD5) Ficha Catalografica - Elisangela Farias da Silva.pdf: 1668 bytes, checksum: 348f03e4b80e3cc81c27a3851b251ad0 (MD5) / Approved for entry into archive by Divisão de Documentação/BC Biblioteca Central (ddbc@ufam.edu.br) on 2016-06-23T20:43:00Z (GMT) No. of bitstreams: 2 Dissertação - Elizangela Farias da Silva.pdf: 725923 bytes, checksum: 334a610c50bdeda8b5392f39f6dc8ef9 (MD5) Ficha Catalografica - Elisangela Farias da Silva.pdf: 1668 bytes, checksum: 348f03e4b80e3cc81c27a3851b251ad0 (MD5) / Approved for entry into archive by Divisão de Documentação/BC Biblioteca Central (ddbc@ufam.edu.br) on 2016-06-23T20:45:40Z (GMT) No. of bitstreams: 2 Dissertação - Elizangela Farias da Silva.pdf: 725923 bytes, checksum: 334a610c50bdeda8b5392f39f6dc8ef9 (MD5) Ficha Catalografica - Elisangela Farias da Silva.pdf: 1668 bytes, checksum: 348f03e4b80e3cc81c27a3851b251ad0 (MD5) / Made available in DSpace on 2016-06-23T20:45:40Z (GMT). No. of bitstreams: 2 Dissertação - Elizangela Farias da Silva.pdf: 725923 bytes, checksum: 334a610c50bdeda8b5392f39f6dc8ef9 (MD5) Ficha Catalografica - Elisangela Farias da Silva.pdf: 1668 bytes, checksum: 348f03e4b80e3cc81c27a3851b251ad0 (MD5) Previous issue date: 2014-03-28 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The guarana (Paullinia cupana var. Sorbilis (Mart.) Ducke) is a native species from the Amazon region rich in natural caffeine. Embrapa Western Amazon develops guarana breeding program based on clonal selection and recurrent selection to obtain cultivars and progenies with desirable agronomic characteristics. The use of molecular markers has been successfully applied in breeding programs to monitor genetic diversity and assist in marker-assisted selection. Thus, the present study aims to evaluate the genetic diversity of guarana improvement program, using TRAP (Target Region Amplification Polymorphism) and the SRAP (Sequence-Related Amplification Polymorphism). The work was divided into two parts: the first to test the potential of TRAP and SRAP markers, using subsamples of 60 BAG (Active Germplasm Bank) and the second to analyze the genetic diversity six progenies of half brothers guarana. In the BAG a polymorphism observed percentage of 79% (TRAP) and 74.5% (SRAP). The Dice coefficient ranged from 0.64 to 0.87, forming four groups in the dendrogram, where one concentrated 82% of the studied material. In the progenies of half brothers, polymorphism percentage was 85% for the TRAP and 76% for SRAP. The genetic diversity of Nei (H) was 0.20 and the Shannon index (I) of 0.30. The AMOVA showed that the highest percentage of variation is within the progenies (54%). With these results, the TRAP and SRAP markers showed potential genetic diversity studies in guarana breeding program. / O guaranazeiro (Paullinia cupana var. sorbilis (Mart.) Ducke) é uma espécie nativa da região amazônica rica em cafeína natural. A Embrapa Amazônia Ocidental desenvolve programa de melhoramento de guaranazeiro baseado em seleção clonal e seleção recorrente para obtenção de cultivares e progênies com características agronômicas desejáveis. O uso de marcadores moleculares tem sido aplicado com sucesso em programas de melhoramento para monitorar a diversidade genética e auxiliar na seleção assistida por marcadores. Com isso, a presente pesquisa visa avaliar a diversidade genética do programa de melhoramento do guaranazeiro, usando TRAP (Target Region Amplification Polymorphism) (Sequence - Related e o SRAP Amplification Polymorphism). O trabalho foi dividido em duas partes: a primeira para testar o potencial dos marcadores TRAP e SRAP, usando 60 subamostras do BAG (Banco Ativo do Germoplasma) e a segunda para análise da diversidade genética de seis progênies de meios-irmãos de guaranazeiro. No BAG observou-se um percentual de polimorfismo de 79% (TRAP) e 74,5% (SRAP). O coeficiente de Dice variou de 0,64 a 0,87, formando quatro grupos no dendrograma, onde um deles concentrou 82% do material estudado. Nas progênies de meios irmãos, o percentual de polimorfismo foi 85% para o TRAP e 76% para SRAP. A diversidade genética de Nei (H) foi de 0,20 e o índice de Shannon (I) de 0.30. A AMOVA mostrou que o maior percentual de variação se encontra dentro das progênies (54%). Com estes resultados, os marcadores TRAP e SRAP mostraram potencial em estudos de diversidade genética no programa de melhoramento de guaranazeiro.

Submitted by isabela.moljf@hotmail.com (isabela.moljf@hotmail.com) on 2017-08-17T15:02:14Z No. of bitstreams: 1 victoriarabelocampos.pdf: 2382753 bytes, checksum: c43b0ab7cfae511bfcb500d35e65da9c (MD5) / Rejected by Adriana Oliveira (adriana.oliveira@ufjf.edu.br), reason: on 2017-08-24T11:27:14Z (GMT) / Submitted by isabela.moljf@hotmail.com (isabela.moljf@hotmail.com) on 2017-08-24T12:03:07Z No. of bitstreams: 0 / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-08-24T13:01:49Z (GMT) No. of bitstreams: 0 / Made available in DSpace on 2017-08-24T13:01:49Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-02-22 / A biologia reprodutiva de uma espécie está intimamente relacionada com a base genética de uma população e constitui um dos principais fatores relacionados à dispersão e sucesso das angiospermas. Lippia alba (Verbenaceae) é conhecida por vários nomes populares como erva cidreira, falsa melissa e chá de tabuleiro, sendo amplamente utilizada na medicina popular, principalmente devido aos seus componentes do óleo essencial. A espécie pode ser facilmente encontrada desde regiões tropicais até temperadas possuindo ampla plasticidade fenotípica. Estudos recentes indicam uma possível origem autopoliploide para a espécie, sendo encontrado indivíduos diploides (2n=30), aneuploides (2n=38), triploides (2n=45), tetraploides (2n=60) e hexaploide (2n=90). Apesar da importância, poucas informações sobre o sistema reprodutivo da espécie estão disponíveis.O presente trabalho teve como objetivo estudar a estratégia reprodutiva da espécie a fim de melhor compreender a origem dos cinco citótipos descritos assim como auxiliar na elucidação da base genética da espécie. Inflorescências de 41 indivíduos foram isoladas no período de março de 2015 a dezembro de 2016. Foram comparados o número de sementes produzidas entre inflorescências isoladas e não isoladas. Sementes recém coletadas de 20 acessos foram avaliadas quanto ao comprimento e largura. Em seguida, as sementes foram colocadas para germinar em placa de petri contendo papel filtro umedecido e submetidas a temperaturas que variaram de 18ºC-25ºC-40ºC (em ciclos de 24 horas). Para avaliação da quantidade de DNA, uma única semente por vez foi macerada em tampão Marie a 4°C. A solução obtida foi filtrada em malha de 30 μm e corada com iodeto de propídeo. Para genotipagem, extraiu-se o DNA de sementes oriundas de inflorescências isoladas, não isoladas e de folhas da planta-mãe de oito acessos que foram comparados utilizando oito primers de microssatélites. Para uma análise citohistológica do desenvolvimento de botões, amostras foram coletadas anteriormente à antese e foram fixadas em solução de glutaraldeído por 24h. Análises morfológicas comparativas entre acessos diploide, triploide e tetraploide também foram realizadas, utilizando-se cinco medidas florais. Sementes oriundas de diploides apresentaram maior índice de germinação quando comparado àquelas oriundas dos poliploides. Sementes oriundas de inflorescências isoladas em geral não germinaram. O conjunto de resultados permitiu concluir que Lippia alba possui um comportamento reprodutivo preferencialmente alogâmico, com comportamento diferenciado entre diploides e poliploides. As análises citohistológicas e citométricas não permitiram excluir a ocorrência de reprodução por apomixia. Os resultados sugerem que Lippia alba possua vias alternativas de reprodução. / The reproductive biology of a species is closely related to the genetic basis of a population and is one of the main factors related to the dispersion and success of angiosperms. Lippia alba (Verbenaceae) is known by several common names as erva cidreira, falsa melissa, chá de tabuleiro, being widely used in folk medicine mainly due to its essential oil components. The species can be easily found from tropical to temperate regions, having broad phenotypic plasticity. Recent studies indicate a possible autopoliploidy origin for the species having diploids (2n = 30), aneuploids (2n = 38), triploids (2n = 45), tetraploids (2n = 60) and hexaploid (2n = 90) individuals. Despite the importance of Lippia alba, little information about the species' reproductive system is available. The goal of the present work was to study the reproduction strategy of the species to better understand the origin of the five cytotypes as well as to help the elucidation of the genetic basis of the species. Inflorescences of forty-one individuals were isolated from March 2015 to December 2016. The number of produced seeds was compared between isolated and nonisolated inflorescences. Fresh seeds from 20 accessions were collected and the measures of length and width were taken. Then the seeds were placed to germinate in petri dishes with moistened filter paper under temperatures ranging from 18°C-25°C-40°C (in 24 hour cycles). To estimate the DNA content, a single seed at a time was chopped in Marie nuclear extraction buffer at 4°C. The solution was filtered through a 30 μm filter and stained with propidium iodide. For genotyping, DNA was extracted from seeds collected in isolated and non-isolated inflorescences. Leaves were used for DNA extraction of the mother plant of eight accessions that were compared using microsatellite primers. For a cytohistological analysis of the buds’ development, samples were collected before the anthesis and were fixed in glutaraldehyde solution for 24h. Comparative morphological analyzes between diploid, triploid and tetraploid accessions were also performed, using five floral measures. Seeds originating from diploids had a higher germination index when compared to those from the polyploids and the ones originated from isolated inflorescences generally did not germinate. The set of results allowed to conclude that Lippia alba has preferentially an allogamic reproductive behavior, being different between diploids and polyploids. The cytohistological and cytometric analyzes did not allow to exclude the occurrence of apomixis reproduction. The results suggest that Lippia alba has alternative ways of reproduction.

Citrus is the main fruit crop in the world and Spain is the 6th producer and the major exporter for the fresh fruit market. Seedlessness is one of the most important fruit quality traits for this market since consumers do not accept seedy fruits. Recovery of triploid hybrids has become an important breeding strategy to develop new seedless citrus varieties and several of them have been already released from citrus breeding programs worldwide. Despite the undisputable importance of polyploidy in plant species, their genetics are much less well known than those of their diploid counterparts. Citrus triploid hybrids can be routinely recovered from sexual polyploidization (2x ¿ 2x) or interploid crosses (2x ¿ 4x and 4x ¿ 2x). In 2x ¿ 2x sexual crosses, spontaneous triploid hybrids arise from the union of an unreduced (2n) megagametophyte with haploid pollen. In the case of interploid sexual crosses (2x ¿ 4x and 4x ¿ 2x), triploid hybrids result from the fecundation of a diploid gamete arising from the tetraploid parent and a haploid gamete arising from the diploid parent. The genetic and phenotypic structures of triploid populations greatly depend on the parental heterozygosity restitution (HR) in the diploid gamete at each locus, which is mainly affected by the triploid recovery strategy. In 2x ¿ 2x crosses, HR depends on the underlying mechanism leading to the unreduced gamete formation, which are genetically equivalent to First Division Restitution (FDR) or Second Division Restitution (SDR) mechanisms. Moreover, under each restitution mechanism, HR also depends on the locus-centromere genetic distance. In the case of interploid crosses, parental heterozygosity restitution from tetraploid parents depends on the double reduction frequency. In citrus, the unreduced gamete formation mechanism is still controversial; FDR has been the mechanism proposed for sweet orange, whereas SDR has been proposed for clementine. On the other hand, inferring the allelic configurations of genetic markers is a main challenge in polyploidy crops to infer genotypic and gametic structures with the objective to analyze meiosis and inheritance mechanisms. According to this scientific context, the objectives of the thesis where: (i) to develop a new approach for allele dosis assignation when using co-dominant markers, (ii) to implement and apply methods for the analysis of 2n gametes origin and locate centromeres, and (iii) to take advantage of this knowledge to locate a major gene of resistance to Alternaria Brown Spot (ABS) which is a major constraint for triploid mandarin breeding. For microsatellite (SSR) markers, we have demonstrated that triploid progeny genotyping can be successfully performed using the microsatellite allele-counting peak ratio (MAC-PR) method. However, SSR analysis remains relatively costly and time consuming compared with actual SNP genotyping methods. Moreover, with the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers that can be selected along the entire genome. In this thesis, a new method based on competitive allele-specific PCR has been developed to assign SNP allele dosage in an accurate, simple, and cost effective way. Combining the MAC-PR and the new developed SNP genotyping methods offers the possibility to utilize a broad range of molecular markers in genotyping triploid genotypes. Both methods have been used in further works included in this thesis. SDR has been demonstrated as the mechanism underlying unreduced gamete production in `Fortune¿ mandarin by genotyping triploid progenies with SSR markers. In addition, a new method to locate the centromere, based on the best fit between observed heterozygosity restitution within a linkage group and theoretical functions under either partial or no chiasma interference hypotheses has been developed and successfully applied. To expand the knowledge of the mechanism underlying unreduced gamete formation to other citrus genotypes besides clementines and `Fortune¿ mandarin, a maximum likelihood method based on parental heterozygosity restitution of centromeric loci was developed and successfully applied in sixteen mandarin cultivars. The new method developed in the study allows inferring the restitution mechanism both at population level and even at individual level. Maternal origin of 2n gametes was confirmed for all triploid hybrids and SDR was proposed as the restitution mechanism for all analyzed progenies. The information acquired from the mode of heterozygosity restitution in citrus was useful to determine the genetic and phenotypic structures of new triploid populations arising from different breeding strategies. We studied these structures for the resistance to Alternaria brown spot (ABS), a serious fungal disease producing necrotic lesions on fruits and young leaves in susceptible citrus genotypes. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from SDR to map a genome region linked to ABS resistance in triploid citrus progeny. The monolocus dominant inheritance of the susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. A 3.3 Mb genomic region linked to ABS resistance was located near the centromere on chromosome III, which includes clusters of resistance genes. SSR and SNP markers were developed for an efficient early selection of ABS resistant hybrids and they are currently used in our breeding program to perform marker assisted selection. The knowledge obtained in this thesis on the mechanism of sexual polyploidization and inheritance of concrete traits in citrus will allow implementing much more efficient triploid breeding programs on the basis of current and future needs. Indeed, applied outcomes of this PhD are already routinely used in the IVIA triploid breeding program. / Cuenca Ibáñez, J. (2013). Mechanisms of sexual polyploidization and inheritance in triploid citrus populations [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/34671 / TESIS / Premios Extraordinarios de tesis doctorales

Penstemon is the largest genus in North America with more than 270 reported species. However, little is known about the genome size of this genus and how this information may be useful in selecting species in developing hybrids for landscape use. Using flow cytometry, we estimated the genome size of approximately 40% of the genus (117 specimens from 104 different species.) Genome sizes for the putative diploids ranged from 2C = 0.94 – 1.89 pg (1C = 462 – 924 Mbp) and the putative polyploids ranged from 2.57 – 6.54 pg (1C = 1,257 – 3,156 Mbp). Chromosome counts were compiled and compared with the flow cytometry results for the species within this publication. Ploidy within the genus ranged from diploid to dodecaploid. These data were compared and contrasted with the current taxonomy of Penstemon and previously published ITS and cpDNA phylogenetic work. Based on genome size, reassigning P. montanus, P. cardinalis, and P. uintahensis to the subgenus Penstemon and P. personatus to the subgenus Dasanthera, would better reflect the phylogeny of the genus. Both auto- and allo-polyploidization are plausible mechanisms for increasing ploidy within the genus. The diploid species within the subgenus Saccanthera contain on average 1.09 pg (1C = 532 Mbp); however, two species within this subgenus are tetraploid and octaploid. The DNA content of subgenus Penstemon exhibits high plasticity and spans a six-fold increase. Our study found flow cytometry to be useful in species identification and verification. This represents the first published work on the genome size of Penstemon. This research will aid in future DNA sequencing experiments and breeding programs.

Allopolyploids are formed by interspecific hybridization and whole genome duplication, with the resulting organism contains multiple distinct subgenomes in one nucleus. Subgenomic interactions result in massive genetic and epigenetic reconstruction, contributing to variable phenotypic traits noted in newly formed allopolyploids. To better understand these mechanisms in the context of molecular biology, evolution, and plant breeding, plant biologists study the model organism Brassica napus (farmed as canola or oilseed rape). With white-flowering and yellow-flowering progenitors, flower color phenotype of B. napus presents an opportunity to examine subgenomic interactions. CAROTENOID CLEAVAGE DIOXYGENASE 4 (CCD4) is known to play a major role in determining flower color phenotype of carotenoid-synthesizing angiosperms. Here, we investigate the genetic and epigenetic role of CCD4 orthologs and their role in flower color phenotype of B. napus.

L'arachide (Arachis hypogaea L.) est une plante allotétraploïde (2n = 4x = 40) issue d'un événement récent d'hybridation entre deux espèces sauvages suivi d'un doublement spontané des chromosomes. La variabilité génétique existant dans le compartiment cultivé est faible. Les espèces diploïdes sauvages apparentées à l'arachide cultivée représentent un important réservoir d'allèles nouveaux utilisables pour élargir le pool génique du cultigène. L'objectif général de cette thèse est d'augmenter les marges de progression en amélioration de l'arachide par recours aux ressources génétiques sauvages. Nous avons développé une population BC1F1 à partir du croisement entre Fleur11 et un amphidiploïde synthétique (A. ipaensis x A. duranensis)x4 qui associe les génomes des plus probables progéniteurs sauvages de l'espèce cultivée. Nous avons d'abord construit une carte génétique comprenant 298 loci positionnés sur 21 groupes de liaison avec une taille totale de 1843.7 cM. Nous avons ensuite conduit une analyse AB-QTL pour plusieurs caractères impliqués dans la productivité, l'adaptation et la domestication de l'arachide. Au total, nous avons cartographié 95 QTL. Pour plusieurs QTL, les effets positifs sont associés aux allèles provenant des espèces sauvages. Nous avons aussi identifié trois régions du génome qui portent des empreintes de la domestication. Nous avons enfin développé une population de 122 lignées d'introgression à l'aide d'une stratégie de sélection assistée par marqueurs. L'ensemble des groupes de liaison sont couverts avec des frag ments chevauchants, issus des donneurs sauvages, d'une taille moyenne de 39.2 cM et chaque lignée comprend en moyenne 1.2 fragments. Nous avons par ailleurs discuté l'utilisation de cette collection de lignées d'introgression pour des applications de sélection et de recherche. Nos résultats ouvrent de nouvelles perspectives pour l'amélioration de l'arachide par croisement avec les espèces sauvages apparentées. / Peanut (Arachis hypogaea L.) is considered to be an allotetraploid (2n = 4x = 40) originated from a single hybridization event between two wild diploids followed by spontaneous chromosomes duplication. Cultivated peanut harbours a limited genetic diversity. Peanut wild relatives represent an important source of novel alleles that could be used to broaden the gene pool of the cultigen. The general objective of this work is to enhance the rate of progress in peanut breeding using wild species resources.We developed a BC1F1 population from the cross between Fleur11 and a synthetic amphidiploid (A. ipaensis x A. duranensis)x4 that combines the genomes of the most probable wild progenitors of the cultigen. We first developed a SSR based genetic map of 298 loci on 21 linkage groups, spanning a total map distance of 1843.7 cM. We then conducted a detailed AB-QTL analysis for several traits involved in peanut productivity and adaptation as well as in the domestication syndrome. We mapped a total of 95 QTLs. About half of the QTL positive effects were associated with alleles of the wild parents and several QTLs involved in yield components were specific to the water-limited treatment. We identified three genomic regions which bear footprints of domestication. We finally developed, through a marker assisted backcross strategy, an exotic introgression library of 122 lines. This population, which has in average 1.2 fragments per line, allows covering all linkage groups with overlappi ng wild donor fragments of in average 39.2 cM length. The utilization of the exotic introgression lines library for breeding and research is discussed. Our findings open new avenues for peanut improvement using wild relatives.

Intensive cytotype screening in the primary contact zone of relict serpentine Knautia arvensis agg. revealed a striking predominance of the derivative tetraploid (81 % of subpopulations) over the diploid maternal race. Eleven mixed-ploidy subpopulations with the close spatial proximity of both cytotypes were identified. Flow cytometric analyses of almost 5 000 individuals led to discovery of two extremely rare minority cytotypes (3x, 6x). Vegetation analyses were made at two different spatial scales and in both cases confirmed the absence of distinctions in habitat preferences of cytotypes. Slight microhabitat segregation of cytotypes was however apparent at the finest spatial scales. Cytotype distribution within mixed-ploidy sites was not random. Striking patterns of cytotype clumping into cytotype uniform patches and negative spatial correlations between diploid and tetraploid individuals were apparent at all sites. Distribution of life cycle stages of diploids and tetraploids within the mixed-ploidy subpopulations were significantly different. The clonality was the most common mode of reproduction in the subpopulations of both cytotypes. Seedlings accounted for only 7 % of new plants. Significant distinctions in the plant vigour between the cytotypes were showed during the in situ comparison in...

The Atlantic salmon (Salmo salar) is an iconic species that dominates the global finfish production sector with increasing market demand. The Scottish industry and government alone aspires for expansion of the sector to 210,000 t by 2020 with 154, 000 t produced in 2013. As such, there are pressures to improve sustainable development in particular to minimise the genetic impact of escapees on wild populations and reduce sea lice infection which are required for the granting of “green licenses” in Norway. The use of triploidy has been tested in the 1980’s with little success owing to suboptimal rearing conditions leading to elevated mortalities, poorer growth and a higher prevalence of deformities, in particular of the skeleton. Collectively: recent success of triploid trout farming, expansion to the salmon production sector and potential resulting pressure on wild stocks through escapee increases have reinstated interest to implement artificially induced triploid Atlantic salmon in commercial production. As diploid Atlantic salmon have undertaken extensive domestication to achieve the high quality production and welfare standards observed to date, triploid conspecifics too require husbandry optimisation to realise potential. In particular, industrialisation requires that higher observations of deformities and inconsistent growth trajectories during seawater ongrowing be resolved through optimisation of rearing regimes and subsequent standardization of husbandry protocols. Triploids possess additional genomic material and increased cell size yet reduced frequency that reflects known differences in physiology and supports that, in effect, triploids should be considered as a new species relative to diploid conspecifics. Therefore, this doctoral thesis aimed to study nutrition and temperature effects on triploid Atlantic salmon traits throughout the production cycle from ‘egg to plate’. Nutrition trials aimed to improve growth potential and mitigate skeletal deformities both in freshwater (FW) and saltwater (SW) whilst attempts were made to define a window of smoltification to ensure optimal ongrowing performance. Finally, impacts of embryonic temperature regimes that are known to impact long term performance and deformity development in triploids, were examined in relation to DNA regulation and yolk composition in an attempt to underpin potential mechanisms for the environmental impact of temperature on developmental phenotype. One of the main restrictions to triploid Atlantic salmon implementation is the increased prevalence and severity of skeletal deformities, particularly after the maring phase. The work performed in this thesis first demonstrated that protein and/or phosphorous (P) supplementation throughout SW ongrowing not only reduced the level of severely deformed (≥ 10 deformed vertebrae observable by x-radiography) individuals by 30 % but also sustained 6.8 % faster growth and improved harvest grade compared to triploids fed a standard grower diet (chapter 2). Comparison of x-radiography and severely deformed individuals between harvest and sea transfer highlighted that protein and P supplementation arrested deformity development whereas prevalence increased in triploids fed a standard grower diet. This implied that severe deformities were of FW origin and strongly suggest requirement for improved nutrition in FW to optimise SW performance. Therefore investigation of higher dietary P inclusion in FW was investigated and results showed significantly reduced number of deformed vertebrae and no severely deformed individuals in those fed 19.7 g total P Kg-1 compared with those fed 13.0 & 16.7 g total P Kg-1 (chapter 3). Most deformities were localised in the central (vertebrae 27 – 31) and caudal (vertebrae 52 – 57) regions for all treatments. However, triploids fed lower dietary P displayed a particular increase in prevalence within the tail region (vertebrae 32- 47) which is consistent with SW ongrowing reports and results from chapter 2, further highlighting FW origin of higher vertebral deformities reported in SW ongrowing in triploids. Higher P supplementation in FW also significantly improved growth in triploid parr compared to diploids and lower supplementation. However, this effect did not transpire in later FW smolt stages where weights were significantly higher in triploids fed lower compared to higher P supplementation. Expression of target genes involved in osteogenesis and bone P homeostasis in vertebrates were then analysed and a ploidy effect of osteogenic genes alp, igf1r and opn as well as a dietary effect on P homeostasis gene fgf23 was apparent in the parr stages but not smolt. In addition, stronger ploidy-diet effects were also observed in parr stages for whole body mineral concentrations. Collectively, growth, gene expression and whole body mineral content results indicate these earlier parr life stages may be more sensitive to P supplementation. This pronounced effect may be a consequence of seasonal accelerated growth associated with this period, where higher temperatures were also observed. The potential for shorter P supplementation windows in commercial production was addressed in chapter 4 with hope to cut economic cost to raw mineral inclusion in feed and also mitigate potential anthropogenic eutrophication on the environment that may be induced by P leached through uneaten feed and faeces. Triploids were fed higher dietary P (17.4 g total P Kg-1) until either early (5 g) or later (20 g) parr stages, or smolt (83 g) and monitored for performance throughout freshwater (FW) development. During later parr development (30 g), x-radiography assessment demonstrated that increased dietary P reduced the number of deformities and severely deformed individuals with no indication that feeding P for shorter windows improved skeletal integrity. Hence, P supplementation may be required throughout FW development for optimal skeletal performance. In addition, no differences in deformities were observed between triploid treatments at smolt. An effect of dietary P supplementation on whole body mineral concentration was observed in the early and later parr stages that was not as pronounced as smolt, which is consistent with results in chapter 3. Together, these results indicate that skeletal assessment during early developmental stages may not reflect smolt performance most likely as a consequence of seasonal effects of improved linear growth in the cooler winter temperatures prior to smolt where reversible deformities observed at parr may also be alleviated. In the same study (chapter 4), the inclusion of the probiotic Pediococcus acidilactici (Bactocell™) was also tested as a means to enhance gut assimilation as suggested in previous studies and therefore reduce the levels of P supplementation. Results clearly indicate superior skeletal performance in parr (30 g) as well as significantly less deformed vertebrae and no severely deformed individuals. However, at smolt (~83g), no effects of the dietary probiotic treatment were observed which may also be attributed to seasonal effects. Overall, nutritional research clearly indicate triploids require higher dietary P for optimal growth and skeletal development, which although is not consistent between life stages, is ultimately required throughout FW for optimal skeletal development at smolt. The use of probiotics offer a promising avenue for reduced P requirement in FW feed and further research should verify results and assess long-term performance. Timing of SW transfer according to correct parr-smolt transformation (PST) is essential for survival and growth performance in ongrowing where feeding and growth rate accelerate post-transfer. So far, SW transfer regimes and in particular the smoltification ‘window’ remains loosely defined in triploid Atlantic salmon and it is crucial that this be addressed to ensure optimal ongrowing survival and performance.

Orientadores: Anete Pereira de Souza, Antonio Augusto Franco Garcia / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-17T01:28:45Z (GMT). No. of bitstreams: 1 Vigna_BiancaBacciliZanotto_D.pdf: 11101038 bytes, checksum: 673b1f6718032badeb8a155d352235ed (MD5) Previous issue date: 2010 / Resumo: As pastagens cultivadas constituem a forma mais econômica de fornecer alimentação abundante e de qualidade aos animais. As gramíneas do gênero Brachiaria representam as forrageiras mais utilizadas no Brasil, dentre as quais a espécie B. humidicola caracteriza-se por ser tolerante à solos úmidos, à cigarrinha-das-pastagens, principal praga das pastagens, e apresentar elevada produção. O conhecimento da extensão da variabilidade genética contida dentro dos bancos de germoplasma pode auxiliar no planejamento de estratégias para maximizar os ganhos genéticos em programas de melhoramento. Além disso, a construção de mapas de ligação é uma importante fonte de informações a respeito da estrutura do genoma e da genética de características de interesse agronômico. Nesse contexto, foram isolados e caracterizados marcadores microssatélites para a espécie como ferramenta para o estudo da diversidade genética de acessos do banco de germoplasma de B. humidicola e a construção de um mapa genético e posterior mapeamento do modo de reprodução por apomixia do tipo aposporia Foram desenvolvidos 154 marcadores microssatélites para a espécie. Os resultados da análise do banco de germoplasma revelaram quatro grupos de acessos que apresentam diferenças significativas entre si, além do único acesso sexual, o qual ficou isolado dos demais acessos, mostrando-se bem distante geneticamente. Esses dados fornecem importantes subsídios para o programa de melhoramento da espécie, orientando cruzamentos e futuras coletas de acessos. O mapa genético desenvolvido conta com 124 marcas em dose-única (geradas a partir de 79 locos microssatélites polimórficos na população de mapeamento) distribuídas em 38 grupos de ligação, com uma cobertura de 1.543,8cM do genoma hexaplóide (2n=6x=36) da espécie, com uma densidade de 12,3cM. O modo de reprodução por aposporia foi mapeado em um único grupo de ligação, de acordo com o esperado, por provavelmente estar associada a uma região genômica específica associada à aposporia (ASGR). Com base no perfil de amplificação dos locos microssatélite e em dados sobre o comportamento meiótico de 45 desses híbridos, pode-se sugerir que os genótipos hexaplóides desta espécie tenham origem autoalopoliplóide, corroborando alguns estudos citogenéticos e moleculares para a espécie / Abstract: Cultivated pastures are the most economic way to produce quality feed in abundance to the animal herd. Grasses from the genus Brachiaria are the ones most plants for pastures in Brazil. Among those, the species B. humidicola is the most adapted to poor drained soils, is tolerant to spittlebugs, the major pest of the tropical forage grasses and is very productive. The knowledge about extension of the genetic variability in the germplasm banks can help to plan out strategies to maximize the gains in breeding programs. The construction of genetic maps is an important source of information about the genome structure and the genetics of characteristics that are important to agronomic studies. Based on this, microsatellite loci have been isolated and characterized for this species as a tool to study genetic diversity in the germplasm bank and the construction of a linkage map and apospory mapping. In total, 154 microsatellite loci were developed for this species. The results obtained from the germplasm analysis show that the germplasm is divided into four major groups and the only sexual accession was keep separated, showing its high divergence from the other accessions. These data are important to the breeding program of the species to define crosses and for future collections. The genetic map developed is formed by 124 single-dose markers (generated from 79 polymorphic SSR loci in the mapping population) distributed in 38 linkage groups, covering 1.543,8cM of the hexaploid genome (2n=6x=36) of the species, with a density of 12,3cM. The reproductive mode hrough apospory has been mapped in only one linkage group, as expected, as it is probably linked to an apospory-specific genomic region (ASGR), described in other grasses. Based on the amplification pattern of the microsatellite loci and in meiotic behaviour data of 45 hybrids from the mapping population, an autoallopolyploid origin can be suggested for the hexaploid genotypes of this species, corroborating some molecular and cytogenetics studies in B. humidicola / Doutorado / Doutor em Genetica e Biologia Molecular