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In most plant species artificial polyploidy generally enhances the vigor of determinate plant parts and may be favorable where vegetative organs and biomass constitute the economic product. Furthermore, artificial polyploidy has been considered a method of increasing production potential of plants secondary metabolites. However, despite considerable research on polyploid plants, very few cases of polyploid medicinal plants have been reported. Artemisia annua L. synthesizes artemisinin, an antimalarial sesquiterpene lactone. Artemisinin can be synthesized, but it is costly compared to the naturally derived product. Hairy root cultures of Artemisia annua L. (clone YUT16) show rapid growth and produce artemisinin. This culture offers a good model system for studying artemisinin production. Others have shown that tetraploid Artemisia annua L. plants produce more artemisinin/mg DW than diploids. These yields were offset, however, by decreases in biomass productivity. Little is known about how polyploidy may affect growth production of hairy roots. Using colchicine, we have produced four stable tetraploid clones of Artemisia annua L. from YUT16 hairy root clone. Compared to the diploid clone, these tetraploid clones showed major differences in growth and development. Nevertheless, artemisinin yields of these tetraploid clones were 2-5 times higher than the diploid and their production seemed to be by the age of the inoculum. This work will prove useful in furthering our understanding of the effects of artificial polyploidy on the growth and secondary metabolite production of hairy roots.

A história de domesticação da cana-de-açúcar (Saccharum spp.) é atípica. As variedades modernas derivam de um processo que inclui hibridações entre a espécie domesticada S. officinarum e a silvestre S. spontaneum, sucessivos retrocruzamentos, no sentido de recuperar o genoma de S. officinarum e a seleção de progênies superiores. Além disso, as genealogias contemplam cruzamentos entre genótipos e eventualmente espécies, todos com elevado grau de ploidia e número de cromossomos distintos, assim como aneuploidias. Frente ao exposto, este trabalho teve como objetivos estabelecer o número de cromossomos e avaliar o comportamento meiótico da cultivar IACSP93-3046, bem como, identificar as associações cromossômicas em meiose I dos genótipos IACSP93-3046, IACSP95-3018 e de um representante de S. officinarum, Caiana Fita, pela marcação dos centrômeros usando FISH. O número de cromossomos da cultivar IACSP93-3046 foi determinado a partir de preparações do meristema radicular, pré-tratado com 8-hidroxiquinolina (0,03%, 4h), e corado pelo método de Feulgen. As células metafásicas foram analisadas sob microscopia óptica, preferencialmente intactas e com o mínimo de sobreposição de cromossomos. Para a análise do comportamento meiótico utilizou-se a técnica de esmagamento, e as células foram coradas com carmim propiônico. Foram observadas as fases meióticas desde a metáfase I até a telófase II, bem como as tétrades. O pareamento cromossômico em meiose I foi analisado usando a técnica de hibridização in situ fluorescente (FISH). Para tanto, preparações dos genótipos IACSP93-3046, IACSP95-3018 e Caiana Fita foram realizadas pelo gotejamento de uma suspensão de células em diacinese. As sondas foram obtidas por PCR a partir da amplificação da região centromérica de cana-de-açúcar, marcadas com digoxigenina-11-dUTP, por nick translation, e detectadas com anti-digoxigenina-rodamina. As lâminas foram montadas em DAPI-Vectashield e analisadas sob microscopia de fluorescência. O número diplóide 2n = 112 foi observado para a cultivar IACSP93-3046, sendo caracterizado pela primeira vez neste estudo. A microsporogênese de IACSP93-3046 apresentou elevado percentual de irregularidades (68%). De modo geral, as anormalidades foram relativas à segregação dos cromossomos, e incluíram migração precoce para os polos em metáfase I e II, cromossomos retardatários em anáfase (I e II) e em telófase (I e II), cromossomos perdidos em prófase II, e micronúcleos nas tétrades. A análise dos sítios de hibridização permitiu comprovar que os cromossomos se associam predominantemente como bivalentes em IACSP93-3046, IACSP95-3018 e Caiana Fita. As irregularidades na segregação dos cromossomos conduzem a micrósporos aneuploides, como constatado em IACSP93-3046. Sugere-se que a assincronia do processo meiótico entre os genomas que compõem a cana-de-açúcar tem papel relevante na geração dessas irregularidades. / The history of the sugarcane domestication (Saccharum spp.) is atypical. Modern varieties are derived from a hybridization process between the domestic species S. officinarum and the wild species S. spontaneum, successive backcrossings to recover the genome of S. officinarum, and the selection of superior progenies. The genealogies include crossings among genotypes, and possibly Saccharum species, all with a high degree of ploidy and different numbers of chromosomes, as well as aneuploidies. The study aimed to establish the number of chromosomes and evaluate the meiotic behavior of cultivar IACSP93-3046, and identify chromosomal associations in meiosis I of genotypes IACSP93-3046, IACSP95-3018 and Caiana Fita (a representative of S. officinarum) by labeling centromeres using fluorescence in situ hybridization (FISH). The number of chromosomes in cultivar IACSP93-3046 was determined from the root meristem preparations, pretreated with 8-hydroxiquinoline and stained by the Feulgen method. Metaphasic cells, preferably intact and with minimum chromosome overlap, were analyzed under an optical microscope. Meiotic behavior was examined from the preparations by using squashing method and stained with propionic carmine. Meiotic phases were observed from metaphase I to telophase II, and tetrad stages. Chromosomal pairing in meiosis I was analyzed by using the FISH technique. The slides of genotypes IACSP93-3046, IACSP95-3018 and Caiana Fita were produced by dropping a suspension of meiocytes in diakinesis. The probes were obtained by PCR, with amplification of the centromere region, and labeled with digoxigenin-11-dUTP, by nick translation, and detected with anti-digoxigenin-rhodamine. The slides were mounted in DAPI-Vectashield and analyzed under a fluorescence microscope. The diploid number 2n = 112 was observed for cultivar IACSP93-3046 and characterized in this study for the first time. Microsporogenesis of IACSP93-3046 presented a high irregularity percentage regarding chromosome segregation, especially precocious migration to poles in metaphase I and II, laggard chromosomes in anaphase and telophase I and II, lost chromosomes in prophase II, and micronuclei in the tetrad stages. The analysis from the hybridization sites proved that the chromosomal pairing occurred predominantly as bivalents in IACSP93-3046, IACSP95-3018 and Caiana Fita. Chromosomal segregation irregularities led to aneuploid microspores, as confirmed in IACSP93-3046, suggesting the asynchrony in the meiotic process between the sugarcane genomes play an important role in producing these irregularities.

Dans l’alimentation humaine, le blé joue un rôle capital du fait de sa valeur nutritive. Une hausse de la production de plus de 20 % sera nécessaire d’ici 2050 simplement pour garantir aux populations les standards actuels de consommation alimentaire. Prenant en compte les bouleversements climatiques créant des contraintes environnementales conséquentes, l’amélioration du rendement en blé sans perte de qualité devient un réel défi mondial. C’est dans ce contexte que s’inscrit ma thèse.La génomique translationnelle est une approche intégrative qui fait le lien entre Recherche Fondamentale et Appliquée, où les espèces modèles jouent le rôle de pivot pour étudier les espèces d’intérêt agronomique. J’ai mis en œuvre cette approche de recherche translationnelle pour étudier finement l’histoire évolutive, l’organisation et la régulation du génome du blé. Le blé est une espèce polyploïde qui a subi des duplications chromosomiques récentes (500 000 et 10 000 ans) et anciennes (<90 millions d’années). Mes travaux ont consisté à utiliser les espèces de céréales apparentées pour étudier l’impact de ces duplications sur la plasticité structurale et expressionnelle des copies de gènes dupliqués du blé moderne. Mes travaux ont montré que la polyploïdie chez le blé est suivie d’une diploïdisation. Cette diploïdisation est en cours chez le blé moderne ; elle consiste en l’accumulation de mutations, de perte de gènes ou de modification de l’expression des gènes dupliqués. Cette diploïdisation est non aléatoire ; elle génère des blocs chromosomiques dominants à forte stabilité et d’autres plus sensibles, à forte plasticité. Au travers de l’analyse du génome du blé, la polyploïdie apparaît comme une force majeure de l’évolution, voire de l’adaptation, en permettant la spécialisation structurale et fonctionnelle des gènes surnuméraires. Cette asymétrie de plasticité structurale et expressionnelle post-polyploïdie entraine in fine la diploïdisation des phénotypes. Mes travaux de thèse l’illustre au travers de l’analyse des bases génétiques de l’inhibition du tallage, contrôlée par une insertion de 109bp codant pour un microRNA porté uniquement par la région chromosomique 1A, dite sensible. Mes travaux montrent une quasi-complète diploïdisation structurale, expressionnelle et phénotypique du blé tendre moderne ouvrant la question d’une re-définition du concept « d’espèces polyploïdes » au regard des analyses génomiques qui peuvent être conduites aujourd’hui, comme cette thèse en est une illustration. / Wheat plays a key role in Human food due to its nutritional value. Wheat production needs to be increased by more than 20% by 2050 to guarantee current human consumption standards. Taking into account climatic changes with high level of environmental constraints, yield improvement without quality loss became a big challenge. This consists in the economical and societal context of the current doctoral thesis.The integrative translational genomic approach consists in transferring fundamental knowledge gained from model species to applied practices for breeding in crops. This strategy was used here to study the evolutionary history, the organization and the regulation of the modern bread wheat genome. Modern wheat is a polypoid species deriving from two hybridization events between diploid progenitors 500 000 and 10 000 years ago, as well as a more ancient that dated back to more than 90 million years ago. The current research consisted in using cereal species closely related to wheat to study the impact of these duplications on the structural and expression plasticity of duplicated genes in wheat.My results established that the diploidization process is in progress in wheat after the successive rounds of polyploidization events. This diploidization consists in the accumulation of mutations, gene loss or expression modification between duplicated genes. This diploidization is nonrandom at the genome level; generating dominant chromosomic regions with high stability in contrast to others regions more sensitive with high plasticity. Based on such wheat genome evolutionary analysis, polyploidy appears as a major evolutionary force driving plant adaptation through structural and expressional specialization of duplicated genes.Such post-polyploidy genomic asymmetry drives finally the phenotype diploidization as illustrated in the current research with the study of genetic basis of the tiller inhibition Trait. This trait seems to be driven by a 109 pb insertion coding for a microRNA located solely on the chromosome 1A, known as a sensitive genomic fraction.The current research established that the modern bread wheat has been quasi-entirely diploidized at the structural, expressional and phenotypic levels, now requiring a new definition of the polypoid concept in line with current genomic investigations, as illustrated in the current thesis.

Submitted by (ana.araujo@ufrpe.br) on 2017-02-17T16:39:46Z No. of bitstreams: 1 Kaliny Veiga Pessoa da Silva.pdf: 1359915 bytes, checksum: de61e5532d3cfedb773fa796979687fb (MD5) / Made available in DSpace on 2017-02-17T16:39:46Z (GMT). No. of bitstreams: 1 Kaliny Veiga Pessoa da Silva.pdf: 1359915 bytes, checksum: de61e5532d3cfedb773fa796979687fb (MD5) Previous issue date: 2011-02-17 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / The Manihot genus belongs to Euphorbiaceae family, has about 98 species and native to tropical regions of the Americas, with greatest diversity center in Brazil, with 80% of Manihot species, showing a large vegetative polymorphism and a potential source for cassava breeding programs. Cassava (Manihot esculenta Crantz) is the only commercially cultivated species, with the shoots and the tuber roots used for both human food and animal feed. Cassava roots are also used in the manufacture of flour or in the composition of other products. Karyotypic analysis in mitotic or meiotic cells concerning to chromosomal homology, numerical and structural variations, polyploidy and evolution mechanisms of the karyotypes can provide useful information for breeding programs aimed at achieving improved cultivars. In addition, a karyotype study in many cases contributes to the increase cytogenetic markers that while certain aspects related to horticultural assist in the cultivars characterization. Manihot species are considered allotetraploid, with 2n=36 chromosome and x=9 as basic number. Natural interspecific crosses can be found frequently, making in some cases infertile hybrids. Infertility is not easily detected using phenotypic analysis. However, it is believed that these species undergone diploidization process along the evolution, now showing a meiotic behavior of a diploid. This work aimed the mitotic and meiotic analysis in nine species of the genus Manihot in order to confirm the karyotypic stability described at literature data. Three varieties of cassava and eight wild species were analised. The analysis revealed strong mitotic stability among species regarding the number and chromosome morphology, average size of chromosomes of 1.75 and maximum of two pairs of satellites. The meiosis was regular in wild species and irregular in varieties of M. esculenta 'manipeba', showing univalent, bivalent and trivalent at metaphase-anaphase I, showing typical behavior of a triploid and partly irregular meiosis in 'pornunça', producing polyads in microsporogenesis. An additional study was performed with molecular marker ISSR (Inter simple sequence repeat). Polymorphism was observed in 89.7% among the locus of the species, but as expected, there was a great genetic similarity between varieties of M. esculenta cultivated for the wild species. / O gênero Manihot pertence a família Euphorbiaceae, possui cerca de 98 espécies e é nativo das regiões tropicais das Américas, apresentando um grande centro de diversidade genética no Brasil. Cerca de 80% das espécies de Manihot ocorrem no país, exibindo amplo polimorfismo vegetativo e reunindo potencial para utilização em programas de melhoramento genético do gênero. A mandioca (M. esculenta Crantz) é a única espécie comercialmente cultivada, e dela se aproveita tanto a parte aérea como suas raízes reserva para consumo humano e animal, sendo utilizada na fabricação de farinha ou como parte da composição de diversos outros produtos e subprodutos. Análise cariotípica em células mitóticas ou meióticas em relação a homologia cromossômica, variações numéricas e estruturais, poliploidia e mecanismos evolutivos dos cariótipos podem fornecer informações úteis aos programas de melhoramento que visam a obtenção de cultivares melhoradas. Além disso, um estudo cariotípico em muitos casos contribui para o aumento no número de marcadores citológicos que quando relacionados a determinados aspectos horticulturais auxiliam na caracterização de cultivares. As espécies de Manihot são consideradas alotetraplóides, com 2n=36 e um número básico x=9. Cruzamentos interespecíficos naturais podem ocorrer com certa freqüência produzindo híbridos férteis ou não e, que, nos casos de infertilidade, essa característica pode não ser facilmente detectada por análise fenotípica. No entanto, acredita-se que estas espécies sofreram processo de diploidização ao longo da evolução, apresentando hoje um comportamento meiótico típico de diplóide. Este trabalho realizou a análise mitótica e meiótica em nove espécies do gênero Manihot, a fim de confirmar a estabilidade cariotípica descrita na literatura. Para isso, três variedades de mandioca e oito espécies silvestres foram analisadas. O estudo revelou uma forte estabilidade do cariótipo mitótico entre as espécies quanto ao número e morfologia cromossômica, o tamanho médio dos cromossomos de 1,75 e máximo de dois pares de satélites. A meiose foi regular em espécies selvagens e irregular em variedades de 'manipeba‟ M. esculenta, mostrando univalentes, bivalentes e trivalentes na metáfase, anáfase I, mostrando o comportamento típico de uma meiose triplóides e parcialmente irregular em ' pornunça", produzindo políades na microsporogênese. Adicionalmente foi realizado um estudo molecular com marcador ISSR (Simples sequência interna). Foram observados polimorfismos da ordem de 89,7% entre os lócus das espécies estudadas mostrando uma ampla variabilidade genética entre as espécies do gênero que podem ser fontes importantes de genes a serem empregados em programas de melhoramento da espécie cultivada. Entretanto, como esperado, houve uma grande similaridade genética entre as variedades da espécie M. esculenta em relação as espécies silvestres.

Background: Over the relatively short period of its evolutionary history, Boechera (Brassicaceae) has undergone rapid radiation that has produced 70+ morphologically distinct, sexual diploids. However, reproductive isolation has moved more slowly than morphological divergence in this group and the diploids appear to hybridize frequently where they coexist. Boechera duchesnensis appears to be the result of hybridization between its putative parents Boechera thompsonii and Boechera formosa. Objectives: The objectives of this study are to (i) analyze and document genetic diversity patterns in the population structure, - including allelic and heterozygosity frequencies - of B. thompsonii and B. formosa in concert with their geographic distribution to determine clustering relationships within these populations, (ii) confirm and expand the morphological characteristics of B. thompsonii and B. formosa, as initially proposed in the literature, including pollen and trichome structure using Scanning Electron Microscopy (SEM) to confirm ploidy level and to determine whether both putative parent species share morphological characteristics with their apomictic diploid offspring, and (iii) use genetic and morphologic evidence to show that B. thompsoii and B. formosa are, in fact, the parents of B. duchesnensis by comparing the genetic diversity patterns, population structure, and morphological characteristics of B. duchesnensis, to those of its proposed putative parents (B. thompsonii and B. formosa) and to confirm that B. duchesnensis shares characteristics of Boechera. Methods: Microsatellite data from 14 loci previously identified in Boechera were used to reexamine the current classifications and taxonomic foundations of three Boechera spp. GenAlEx 6.501 (Peakall and Smouse, 2006, 2012) was used to analyze genetic population structures of two divergent sexual diploids in the genus Boechera: B. thompsonii and B. formosa and to later compare those with the population structure of B. duchesnensis. Geographicaldata were plotted using ArcGIS 10.1 (Esri, 2012) to map heterozygosity distribution. Cluster analysis was run with STRUCTURE 2.3.3 (Pritchard et al., 2000; Falush et al., 2003, 2007) and distribution of allelic diversity and heterozygosity was subsequently compared within each taxon and correlated with geographic distribution characteristics. Resultant data were then compared with B. duchesnensis data to document genetic diversity patterns, population structure, and morphological characteristics. Key Results: Analysis of genetic diversity patterns, allelic distribution of the populations, and heterozygosity of B. thompsonii and B. formosa across their geographic range identified four genetically distinct clusters within B. thompsonii, and one genetically distinct cluster in B. formosa. Allelic frequencies in all four discrete population clusters of B. thompsonii and in one discrete population cluster of B. formosa were close to values found in species on the decline. Reproductive isolation, genetic variability, and allelic frequencies were determined, specimen elevations reported, and morphological characteristics reported in the literature were confirmed and expanded. A codominant genetic analysis performed for 14 different loci for B. duchesnensis against those of its parents showed that B. duchesnensis inherits alleles from both putative parents and confirms B. thompsonii and B. formosa as the parents of B. duchesnensis. Observed levels of heterozygosity of B. thompsonii and B. formosa were lower than expected levels and lower than those of other outcrossing diploids. The mean overall observed heterozygosities for each cluster were determined and documented by geographic location. A substantially higher level of observed heterozygosity in B. duchesnensis (Ho = 0.908) consistent with genetic fixation of a heterozygote and apomixis, supports hybridization as a speciation mechanism and apomixis as a mode of reproduction accounting for genotypic and phenotypic diversity. Morphological characteristics, especially those of pollen and trichomes were confirmed, expanded, and documented with SEM imagery. Discussion: This study provides an analysis of the genetic diversity patterns inherent in the population structure, allelic frequencies, allelic variation among individuals of the rare sexual diploids B. thompsonii, B. formosa, and the apomictic diploid B. duchesnensis in correlation with their geographic distribution. There is an implication of a reproductive barrier, within populations of the same species, that contributes to genetic isolation between clusters. I analyze the tendency of reduced heterozygosity to lead to genetic fixation, reproductive isolation, and how the heightened heterozygosity supports the classification of B. duchesnensis as an apomict. Assessing potential populations that might exist based on similar characteristics could possibly provide inferences about where future research might find similar examples of this hybridization. Reproductive isolation is hypothesized to limit gene flow between identified clusters of B. thompsonii and B. formosa exacerbating low observed heterozygosity levels and low allelic frequency levels. Population studies and cluster analysis have implications for offering future conservation strategies for both taxa.

Conservation and restoration of quaking aspen in the western United States requires an understanding of how and when aspen clones became established, how clones adapt to environmental challenges, and how individual clones interact within stands. I used molecular tools to identify individual clones in a natural population of aspen in southern Utah and detected high and low levels of clonal diversity within stands. Stands with high clonal diversity were located in areas with a more frequent fire history, indicating that fires may have prepared sites for seed germination and establishment over time. Conversely, areas of low clonal diversity corresponded to areas with less frequent fire. The same molecular tools were then used to investigate clonal interactions/succession over relatively recent time. For this portion of the study I sampled small, medium, and large aspen ramets (stems) at 25 subplots within spatially separated one-hectare plots, and mapped the clonal identities. I found that approximately 25% of the clones appeared to be spreading into adjacent clones, while 75% of the clones had a stationary pattern. In the final portion of the study, I again used molecular tools to identify aspen clones and investigated tradeoffs between growth and defense chemistry in mature, naturally-occurring trees. Growth was estimated using a ten-year basal area increment, and the percent dry weight of salicortin, tremulacin, and condensed tannins was measured in the same trees. Overall I discovered evidence for a tradeoff between growth and salicortin/tremulacin, and a marginally significant but positive relationship between growth and condensed tannins.

The trajectory of evolutionary adaptation can be influenced both by the interactions of organisms with their environments as well as by the biological characteristics of the organisms themselves. My dissertation research uses the New Zealand freshwater snail Potamopyrgus antipodarum to 1) gain important insight into how coevolutionary interactions between hosts and parasites influence patterns of gene expression and genetic differentiation of hosts and, 2) evaluate how reproductive mode, and ploidy level affect patterns of adaptive molecular evolution. Coevolutionary interactions between hosts and parasites are a primary source of strong natural selection that can lead to rapid evolutionary change. Here, I used evaluation of patterns of gene expression and genetic differentiation to take critical steps towards characterizing the genomic basis of coevolutionary interactions between P. antipodarum and Microphallus livelyi. I found that M. livelyi-infected P. antipodarum exhibit systematic downregulation of genes relative to uninfected P. antipodarum. The specific genes involved in response to parasites differ markedly across lakes, consistent with population-specific host-parasite interactions leading to population-specific evolutionary trajectories. I also identified a set of rapidly evolving loci that represent promising candidates for targets of parasite-mediated selection across lakes as well as within each lake population. These results constitute the first genomic evidence for population-specific responses to coevolving infection in the P. antipodarum-M. livelyi interaction and provide new insights into the genomic basis of coevolutionary interactions in nature. I also generated and characterized the first transcriptomic resources for Microphallus parasites collected from two species of Potamopyrgus snails (P. antipodarum and P. estuarinus). These data both revealed that these parasites appear to represent distinct genetic lineages, which is interesting in light of the tight coevolutionary interactions between P. antipodarum and M. livelyi, and lay the groundwork for future research. Polyploidy has the potential to facilitate adaptive evolution by providing redundant genome copies that are free to evolve new functions. By contrast, asexuality, with which polyploidy is often associated, is expected to restrict adaptive evolution by decreasing the efficacy of natural selection and access to new genetic variation. I evaluated whether and how ploidy level and reproductive mode influence patterns of adaptive molecular evolution in P. antipodarum to assess 1) the potential evolutionary genomic benefits of recent polyploidy, and 2) how patterns of adaptive molecular evolution in asexuals are influenced by polyploidy. I compared patterns of positive selection in 60 genes across 27 P. antipodarum lineages (10 diploid sexuals, 12 triploid asexuals, 5 tetraploid asexuals) and a diploid sexual outgroup, Potamopyrgus estuarinus. I found little evidence that ploidy level and/or reproductive mode influence patterns of positive selection in P. antipodarum. Even so, this study provides initial steps in evaluating whether ploidy level and reproductive mode influence patterns of adaptive molecular evolution. Taken together, my dissertation work contributes new insights to the field of host-parasite coevolutionary interactions and will inform future studies into how ploidy level and reproductive mode influence patterns of adaptive molecular evolution.

Thesis (Ph. D.)--University of Missouri-Columbia, 2000. / Typescript. Vita. Includes bibliographical references. Also available on the Internet.

Hybrid plants and animals, like corn and the domestic dog, grow larger and more vigorously than their parents, a common phenomenon known as hybrid vigor or heterosis. In hybrids between Arabidopsis ecotypes or species (in allotetraploids), altered expression of circadian clock genes leads to increased starch and chlorophyll content and greater biomass. In plants and animals, circadian clock regulation plays a key role in optimizing metabolic pathways, increasing fitness, and controlling responses to biotic and abiotic stresses. In the allotetraploids, the increased level of heterosis is likely caused by interspecific hybridization as well as genome doubling. However, it is unknown how genome dosage and allelic effects influence heterosis, and whether additional clock output traits, such as stress responses, are altered in hybrids. In three related projects, the effects of genomic hybridization (including parent-of-origin effects) and genome dosage on heterosis were elucidated. In my first project, I found that although ploidy influenced many traits, including seed and cell size, biomass and circadian clock gene expression were most strongly influenced by hybridization. Additionally, parent-of-origin effects between reciprocal hybrids were frequently observed for many traits. In my second project, I described a unique role for RNA-directed DNA methylation (mainly CHH methylation) in mediating the parent-of-origin effect on expression of the circadian clock gene CCA1 in reciprocal hybrids. Altered CCA1 expression peaks were associated with heterosis of biomass accumulation in the reciprocal hybrids. Lastly, I used transcriptome sequencing in hybrids at different times of day to examine changes in downstream clock-regulated pathways. In the hybrids, many genes in photosynthetic pathways were upregulated, while many genes involved in biotic and abiotic stresses were repressed during the morning and afternoon, respectively. Additionally, natural variation between parents in stress-responsive gene expression was found to be crucial for producing vigorous hybrids. These conceptual advances increase the mechanistic understanding of heterosis, and may guide selection of parents for making better hybrids. / text