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<p>Heterosis, or hybrid vigor, is a phenomenon observed in both plant and animal systems where hybrid offspring perform better when compared to their parents. For hybrid plants, this can result in increased biomass, crop yields, and vigor when compared to the inbred parents. Even though heterosis has been used in agriculture for over a century, the molecular mechanisms that result in hybrid vigor remain elusive even after years of investigation. A molecular understanding of heterosis is desirable because it will speed up the process of breeding compatible inbred lines for developing hybrid seeds, and it will provide us with the knowledge to potentially engineer inbred lines that can mimic the beneficial phenotypic effects of heterosis, eliminating the need for farmers to buy new hybrid seeds every year. The goal of this research project is to identify genes that are required for heterotic phenotypes in maize. Our working hypothesis is that a mutation in genes that are essential for heterosis will cause an altered heterotic phenotype in hybrid maize plants. To test this hypothesis, we applied combined approaches of EMS mutagenesis, trait phenotyping in field and controlled conditions, bulk segregant analysis, whole genome sequencing, and bioinformatics analysis. First, we applied a forward genetics approach to identify mutant hybrids with altered heterosis and detected potential causal genes <em>via</em> whole genome sequencing. We identified one mutation occurring in a protein coding gene (gene ID <em>Zm00001eb305590</em>) located in a region of interest on chromosome 7, whose genotypes across various samples assayed fit the observed segregation pattern of hybrid traits. This mutation leads to a moderate or high-level codon change, indicating that this gene may play a role in mediating heterosis in maize. By investigating this gene with further studies, the learned knowledge could speed up the process of hybrid maize breeding by selecting compatible inbred lines through sequencing or by engineering hybrids that have favorable alleles for this gene.</p>

Call number: LD2668 .T4 1985 D59 / Master of Science

Brassica napus L. is an economically important oilseed species cultivated across Western Canada. Hybrid B. napus cultivars compose the majority of the market due to their seed yield and agronomic quality. It is important to attempt to predict high-yielding parental combinations in order to conserve resources during experimental hybrid evaluation. Genetic distance between parents has been implicated in producing high-yielding hybrids and is used as one criteria for determining parental combinations.In the current study, the genetic distance between high erucic acid rapeseed (HEAR) genotypes of B. napus was established using both phenotypic and genotypic criteria. Phenotypic criteria took the form of nine agronomic and seed quality traits gathered from 318 distinct B. napus genotypes over the 2013 and 2014 field seasons in Southern Manitoba. Genotypic criteria took the form of either 291,782 SNP markers identified in 231 distinct B. napus genotypes using genotyping-by-sequencing (GBS) or 230 polymorphic sequence-related amplified polymoprhism (SRAP) markers identified in 160 B. napus genotypes. The genetic distance between available pollinators and a single male-sterile female was established using each set of criteria in an attempt to correlate genetic distance with hybrid yield. Regression analysis was conducted with yield data from hybrid genotypes gathered from 37 field sites from 2011-2014. Using the phenotypic-derived genetic distance, a significant correlation between genetic distance and hybrid yield was uncovered explaining either 22 % or 42 % of the variation in hybrid yield depending upon whether hybrids were grown at three or more, or five or more sites in the analysis, respectively. No significant link was found between GBS or SRAP-derived genetic distance and hybrid yield. These results provide evidence that that phenotypic criteria can be used to establish genetic distance with utility in the selection of high-yielding hybrid genotypes. / February 2017

O composto GN-04 foi utilizado no presente trabalho, tendo por objetivo: a) avaliar o efeito do processo dispersivo em subpopulações de milho com diferentes tamanhos efetivos, e submetidas previamente à seleção divergente para alta e baixa produção; b) avaliar a capacidade de combinação e o potencial heterótico dessas subpopulações e c) estimar componentes da variância genética no composto GN-04, usando o esquema de cruzamento em cadeia. Um lote do referido composto foi plantado visando à obtenção de três diferentes progênies: S1, por autofecundação; irmãos germanos, cruzamento planta a planta e cruzamentos em cadeia, seguindo o esquema 1 x 2, 2 x 3 e 3 x 1. Foram obtidas 77 progênies S1, 75 de irmãos germanos e 72 cadeias, contituidas de três cruzamentos. As progênies de cada tipo foram avaliadas em ensaios distintos, em dois locais, de acordo com o delineamento em blocos casualizados, com três repetições. Os caracteres avaliados foram: altura da planta (AP), altura da espiga (AE), comprimento da espiga (CE), diâmetro da espiga (DE), peso de espigas (PE) e prolificidade (PR). Com base nos valores médios do caráter PE, foram selecionadas 10 progênies de irmãos germanos,10 de S1 e 10 cadeias, sendo cada grupo de materiais constituído das cinco progênies ou cadeias mais produtivas, e das cinco menos produtivas. A recombinação das progênies selecionadas ou cadeias ensejou a obtenção de subpopulações com diferentes tamanhos efetivos: N1, N2 e N3, que correspondem a taxas de endogamia de 50%, 25% e 17%, para S1’s, irmãos germanos e cadeias, respectivamente. Essas subpopulações foram avaliadas posteriormente com base no seu desempenho per se e em cruzamentos ‘topcrosses’ e dialélicos. Os resultados desta avaliação mostraram que o tamanho reduzido das subpopulações provocou o surgimento de valores médios inferiores ou superiores à média estimada da população original, em conseqüência da deriva genética. Os valores médios de todos os caracteres foram afetados pela redução no tamanho efetivo das subpopulações, em conseqüência da depressão por endogamia, a qual se expressou com mais intensidade no caráter PE: em subpopulações com N3 e N1, no nível de seleção positiva, o efeito da depressão foi de 5,20% e 20,07%, respectivamente, e no nível de seleção negativa, 15,98% e 55,76%, respectivamente. A seleção divergente entre subpopulações resultou em diferenciação genética suficiente para expressar heterose em cruzamentos entre subpopulações com o mesmo tamanho efetivo. As estimativas da variância aditiva do composto GN-04, com base na análise da variância conjunta dos experimentos com progênies de cruzamentos em cadeia, para os caracteres PE, CE, DE, PR, AP e AE foram, respectivamente: 128,00 (g/pl)², 1,490 (cm/esp.)², 0,1704 (cm/esp.)², 0,0200 (esp./pl)², 256,55 (cm/pl)² e 136,80 (cm/pl)². Estimativas negativas da variância aditiva foram obtidas para os caracteres CE, DE, AP e AE; para os caracteres PE e PR as estimativas foram 185,00 (g/pl)² e 0,0188 (esp./pl)², respectivamente. O delineamento de cruzamentos em cadeia de tamanho 3, tendo em vista a facilidade de execução, pode ser uma alternativa a delineamentos de execução mais complexa para estimar componentes da variância. / The composite GN-04 was used in the present work with the objetives: a) evaluation of the effect of the dispersive process in subpopulations of maize with different effective sizes, and submitted to divergent selection for higth and low yield; b) evaluation of the combining ability and heterotic potential of the subpopulations; and c) to estimate components of the genetic variance in the composite GN-04, using chain crosses. A pollination block of the base population was planted for the development of three different progenies: S1 progenies obtained by selfing, full-sib progenies obtained by plant-to-plant crosses, and chain crosses following the scheme: 1 x 2, 2 x 3 e 3 x 1. The numbers of progenies were: 77 S1´s, 75 full-sibs and 72 chains represented by three crosses in each chain. The progenies from each type were evaluated in different experiments in two locations following the randomized complete block design with three replications. The following traits were analysed: plant height (AP), ear height (AE), ear length (CE), ear diameter (DE), ear weight (PE) and prolificacy (PR). Observed means of PE were used for selection of 10 full-sib progenies, 10 S1´s progenies and 10 complete chains, each group being represented by five high yielding and five low yielding progenies or chains. The recombination of the selected progenies or chains, individually, led to the development of subpopulations with different effective sizes: N1, N2 and N3, corresponding to inbreeding rates of 50%, 25% and 17% for S1´s, full-sibs and chain crosses, respectively. The subpopulations were later evaluated based on their performance per se, in the topcrosses and in diallel crosses. Results showed that the reduced size of the subpopulations led to changes in the means of the evaluated traits, which were smaller or higher than the original means as a consequence of genetic drift. On the average, all traits showed a decrease in the mean as a consequence of inbreeding depression. The most depressive trait was PE and the depression effects in subpopulations with N3 and N1 were 7.17% and 22.94% in the positive selection and 16.85% and 55.91% in the negative selection. The divergent selection among subpopulations led to a genetic differentiation sufficient for the expression of heterosis in crosses between subpopulations in the same level of effective size. The estimates of the additive genetic variance in the composite GN-04 were obtained from the analysis of chain crosses. The estimates for the traits PE, CE, DE, PR, AP and AE were, respectively: 128.00 (g/pl)², 1.490 (cm/esp.)², 0.1704 (cm/esp.)², 0.0200 (esp./pl)², 256.55 (cm/pl)² and 136.80 (cm/pl)². Negative estimates of the dominance variance were obtained for the traits CE, DE, AP and AE; for the traits PE and PR, the estimates were 185.00 (g/pl)² and 0.0188 (esp./pl)², respectively. The mating design based on chain crosses with size 3 was considered feasible and easy to be used and can be a reliable alternative as compared with other more complex designs.

La sélection génomique (GS) est un outil puissant pour prédire les phénotypes ou les valeurs génétiques d'individus encore non observés, sur la base d'un panel à la fois phénotypé et génotypé. Les modèles mixtes GBLUP habituellement utilisés prennent en compte tous les marqueurs simultanément, en postulant que leurs effets suivent tous la même distribution gaussienne. Les connaissances des mécanismes biologiques sous-jacent à la variation phénotypique ne sont donc pas pris en compte dans une telle modélisation. Le but de cette thèse est d'intégrer dans des modèles GBLUP des connaissances a priori, comme des régions génomique impliquées dans la variation des caractères d'intérêt ou encore des réseaux de gènes, afin d'évaluer le potentiel d'amélioration de la précision de prédiction. Ces modèles ont été appliqués à l'espèce de tournesol Helianthus annuus L., sur trois caractères (la floraison, le rendement et la sénescence foliaire) dans 13 environnements différents. L'un des principaux défis des études sur les hybrides de tournesol est de modéliser la vigueur hybride, ou hétérosis. Différentes hypothèses, incluant la dominance, la superdominance et l'épistasie ont été proposées pour clarifier les mécanismes génétiques sous-jacents au phénomène de l'hétérosis, mais leur importance n'est pas clairement connue. Dans ce contexte, la première partie de cette étude a eu pour but de tester l'efficacité de la GS dans une population d'hybrides provenant du croisement de 36 lignées femelles avec 36 lignées mâles. Pour cela des modèles prenant en compte des effets non-additifs ont été expérimentés, et les résultats validés expérimentalement en champ sur deux années. La prédiction des valeurs génétiques des hybrides ayant été concluante, nous avons ensuite cherché des informations a priori à intégrer à ces modèles. Des SNPs impliqués dans la variation des trois caractères d'intérêt ont été recherchés à l'aide de plusieurs modèles de GWAS (additifs et non-additifs). De plus, dans la perspective de tester des modèles prenant en compte des interactions épistatiques, des SNPs localisés dans des réseaux de gènes connus ont été recherchés. La dernière partie de cette thèse a eu pour but d'intégrer aux modèles GBLUP ces régions génomiques impliquées dans la variation des caractères. Deux méthodes ont été utilisées pour cela, à savoir la modélisation des informations a priori dans la partie aléatoire (modèle MultiBLUP) ou dans la partie fixe des modèles. Ces méthodes ne montrent pas d'amélioration significative des précisions de prédiction par rapport aux modèles GBLUP sans information a priori. / Genomic selection is a powerful tool for predicting phenotypes or genetic values of non-observed individuals, based on a panel both phenotyped and genotyped. The mixed models GBLUP usually utilized take into account all markers simultaneously, assuming that all their effects all follow the same Gaussian distribution. Knowledge of the biological mechanisms underlying phenotypic variation is therefore not taken into account in such modeling. The aim of this thesis is to integrate in GBLUP models a priori knowledge, such as genomic regions involved in the variation of the traits of interest or networks of genes, in order to evaluate the potential for improvement of accuracies. These models were applied to the Helianthus annuus L. sunflower specie on three traits (flowering time, yield and leaf senescence) in 13 several environments. One of the main challenges of genetic studies on sunflower hybrids is to model hybrid vigor, or heterosis. Different hypotheses, including dominance, over-dominance and epistasis have been proposed to clarify the genetic mechanisms underlying the heterosis phenomenon, but their importance is not clearly known. In this context, the first part of this study aimed to test the efficiency of the GS in an hybrid population from the crossing of 36 female lines with 36 male lines. For this purpose, models taking into account non-additive effects were experimented, and the results validated experimentally in field over two years. The prediction of the genetic values of the hybrids was conclusive, so we looked for a priori information to integrate with these models. SNPs involved in the variation of the three traits of interest were searched using several models of GWAS (additive and non-additive). Moreover, in order to test models taking into account epistatic interactions, SNPs located in known gene networks have been sought. Finally the integration of the genomic regions involved in the variation of the traits, into the GBLUP models, was conducted. Two methods were implemented for this, namely the modeling of a priori information in the random part (MultiBLUP model) or in the fixed part of the models. These methods do not show significant improvement in accuracies compared to GBLUP models without a priori information.

Heterosis, or hybrid vigor, refers to the superiority of F₁hybrid performance over the mean of its parents (mid-parent heterosis) theoretically, or the performance of better parents. It has been discovered in many species of plants and animals as well as in humans, and played an important role in enhanced agricultural production, especially in maize, rice and sorghum although the mechanism have not been elucidated. We studied the molecular basis of heterosis with a combined genomics and systems biology approach using model organism maize. We profiled the expression of 39 genes that were most differentially expressed (DG) between the mid-parents and their F1 hybrid (Mo17 x B73) in the 13V-satged, developed whole ear shoots of 13 inbred lines and their 22 F1 hybrids grown in the field trails and phenotyped their 13 traits significant for grain yield. The results showed that gene expression varies significantly among inbreds, among hybrids and in heterosis. The gene clustering heat map and gene action networks in inbreds and hybrids were constructed respectively based on their gene expression profile. According to these pattern analyses, we find dramatically difference between inbreds and their hybrids, although the differential expression varies across different hybrids. Our results also suggest that gene networks are altered from inbreds to hybrids, including their gene contents and wire structures. Last but not least, we have determined the genetic variation correlations between the gene expression and trait performance and constructed the gene networks for the development of 12 of the 13 traits that varied significantly among genotypes. This has led to identification of genes significantly contributing to the performances of the traits, with 1 – 16 genes per trait. These results have indicated that heterosis results not only from altered expression level of corresponding genes between inbreds and their hybrids, importantly, also from the altered gene action networks and expression patterns. These alternations could be derived from gene actions in a manner of additivity, dominance, over dominance, pseudo-overdominance, epistasis and/or their combinations. Therefore, our findings provide a better understanding of the underlying molecular basis of heterosis. The genes identified for the traits will provide tools for advanced studies of the trait heterosis and could be used as tools for their heterosis breeding in maize. The strategy developed in this study will provide an effective tool for studies of other complicated, quantitative traits in maize and other species.

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