Nitrogen (N) is a central nutrient in cropping systems. However, a considerable N fraction is lost through runoffs and leaching with detrimental consequences for environment and controversial effects on human health. Increasing the plant N uptake by optimizing the degree of root branching for exploring a larger soil volume in search of the mobile nitrate resource may contribute to limit soil leaching and subsequently to rely more efficiently on the soil mineralization and fertilizer inputs. Rapeseed (Brassica napus L.) is a major oil crop that highly depends on N fertilization. This doctoral thesis aims at exploring the diversity of root morphology in recently selected cultivars and in a large set of rapeseed inbred lines, and at understanding the genetic control on root morphology and how it is impacted by N nutrition.Firstly, a panel of twenty-eight European recently selected cultivars of winter oilseed rape were tested in laboratory and field conditions. Upon hydroponic culture, these hybrids showed a great diversity for biomass production and root morphological traits. Differences in root and shoot dry biomasses and lateral root length were mainly explained by the genotype, while differences in primary root length by the nutrition. The cultivars were tested in a pluriannual field trial. The observed variation for yield and seed quality traits attributed to the genotype was more important than the year or the genotype x year interaction effects. The total root length measured in laboratory could predict the proportion of nitrogen taken-up from the field and reallocated to the seeds. The genetic interrelationship between cultivars, established with polymorphic markers, indicated a very narrow genetic base. Positive correlations were found between the genetic distance measures, root morphological trait distances during nitrogen depletion conditions, and agronomic performance. Secondly, three cultivars previously selected from a root morphology screen at a young developmental stage were field tested with two nitrogen applications. The purpose was to examine the relationship between root morphology and Nitrogen Uptake Efficiency (NUpE) and to test the predictiveness of canopy optical indices for seed quality and yield. A tube-rhizotron system was used to incorporate below-ground root growth information. One-meter length clear tubes were installed in soil at an angle of 45°. The root development was followed with a camera at key growth stages in autumn (leaf development) and spring (stem elongation and flowering). Autumn was a critical time window to observe the root development and exploration in deeper horizons (36-48 cm) was faster without any fertilization treatment. Analysis of the rhizotron images was challenging and it was not possible to clearly discriminate between cultivars. Canopy reflectance and leaf optical indices were measured with proximal sensors. The Normalized Difference Vegetation Index (NDVI) was a positive indicator of biomass and seed yield while the Nitrogen Balance Index (NBI) was a positive indicator of above-ground biomass N concentration at flowering and seed N concentration at harvest.Thirdly, the natural variability offered by a diversity set of 392 inbred lines was screened to apprehend the genetic control of root morphology in rapeseed and how it is impacted by nitrogen nutrition. Seedlings grew hydroponically with low (0.2 mM) or elevated (5 mM) nitrate supplies. Low nitrate supply triggered the primary root and lateral root growth, while elevated supply promoted shoot biomass production. A considerable variation degree in the root morphological traits was observed across the diversity set, and there was no trade-off between abundant lateral root branching and shoot biomass production. Root traits were mainly dependent on the genotype and highly heritable. A genome wide association study identified some genomic regions associated with biomass production and root morphological traits. A total of fifty-nine QTLs were identified and thirty of them were integrated into seven clusters on chromosomes A01 and C07. Some candidate genes were identified with Arabidopsis orthologs related to root growth and development, nitrogen nutrition or hormone regulation.This study provides promising routes for redesigning the root system architecture by uncovering nitrogen-interactive genomic regions shaping root morphology. A perspective is to develop genetic markers associated with root morphological traits that could be used for assisted breeding. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

De nombreuses études mettent en évidence un effet positif de la diversité spécifique sur la productivité des communautés végétales et la biodiversité associée. Mais l’effet de la diversité génétique sur la communauté d’espèces reste encore peu étudié en dépit des rares études montrant un effet positif avec des perspectives d’application dans le domaine de l’amélioration des plantes. C’est dans ce contexte que cette thèse s’interroge sur l’effet de la diversité génétique sur les communautés prairiales et la biodiversité du sol associée. Cette thèse repose sur une situation réelle via un dispositif d’évaluation de mélanges prairiaux installé par et chez un sélectionneur de plantes fourragères. Les résultats majeurs de cette thèse sont un effet positif de la diversité génétique des espèces sur la production de biomasse du mélange, particulièrement lors d’épisodes de sècheresse, et sur l’équilibre d’abondance des espèces. Ces effets positifs semblent être le résultat d’une différenciation de niches des espèces qui est à la base de la complémentarité des espèces en écologie. Il a été mis en évidence une complémentarité temporelle des espèces par une asynchronie des dynamiques de croissance, mais aussi une complémentarité sur l’acquisition de la lumière par des mécanismes de sélection et de plasticité. Enfin, des effets de la diversité génétique ont été observés sur la diversité microbienne avec des rétroactions potentielles sur les plantes. Au vu de ces résultats, il apparait que la diversité génétique occupe une place centrale dans l’assemblage et la structuration des communautés végétales et microbiennes, nous amenant à réfléchir quant à sa valorisation en amélioration des plantes. / Many studies highlight a positive effect of species diversity on plant community productivity and associated biodiversity. But genetic diversity effect on species community is still poorly studied despite the rare studies showing a positive effect with prospects for application in the field of plant breeding. It is in this context that this thesis examines the genetic diversity effect on grassland communities and associated soil biodiversity. This thesis is based on a real situation via an evaluation design of grassland mixtures installed by and in a plants breeding company. The major results of this thesis are a positive effect of the species genetic diversity on mixture biomass production, especially during drought episodes, and on species abundance equilibrium. These positive effects seem to be the result of a niche differentiation of species which is at the basis of species complementarity in ecology. Temporal complementarity of species has been demonstrated by asynchronous growth dynamics, but also by a complementarity for light acquisition via selection and plasticity mechanisms. Finally, genetic diversity effects have been observed on microbial diversity with plants feedbacks. In view of these results, it appears that genetic diversity occupies a central role in the assembly and structure of plant and microbial communities, leading us to consider how it could be integrated into plant breeding program.

<p>  </p> <p>Rapid climate change on a global scale is posing a considerable threat to forest biodiversity. Assessing physiological and genomic backgrounds of each tree is crucial for informing conservation and mitigation strategies to evaluate species or populations' vulnerability and adaptive capacity under climate change. The goal of my dissertation research was to use morpho-physiological and molecular approaches in combination with genomic background, as a backbone knowledge for enhancing the restoration and conservation of different hardwood tree species. The same approaches also led to a better understanding of mitigation strategies of tree species to evaluate their vulnerability and adaptability under climate change. To do so, the native <em>Juglans</em> species (<em>J. cinerea</em> and <em>J. nigra</em>), local species (Arizona walnut<em>; J. major, </em>California walnut; <em>J. hindsii</em>), exotic species (Persian walnut, <em>J. regia</em>) and its F1 interspecific hybrids were used as a case study to evaluate the level of cold hardiness in <em>Juglans</em>. Hybridization can integrate biotic and abiotic tolerance in plants and could be a potential forest restoration and conservation tool. Evidence from past studies in some F1 interspecific hybrids indicates that naturalized hybrids of Persian walnut with black walnut or butternut have higher level of tolerance to lower temperature than Persian walnut. The potential cold tolerance of native, local, exotic <em>Juglans</em> species and F1 interspecific hybrid using field, electrolyte leakage, qPCR, and genome analysis was investigated, and results presented in chapter 2. Differences in cold hardiness were observed in tested <em>Juglans</em> species, <em>J. regia</em> as an exotic species and <em>J. major</em> from Arizona maladapted in West Lafayette, Indiana. No sign of cold damage was observed in F1 interspecific hybrids or native species. Using morpho-physiological, molecular, and genome data, we confirmed that molecular and morpho-physiological data were highly correlated and thus can be used to characterize cold hardy trait in <em>Juglans</em> species. </p> <p>Although the native <em>Juglans</em> species are cold tolerant, with current trend of climate change and rapid tree migration to the northern range, it is not easy to predict how <em>Juglans</em> species may adapt to new environments and response to other biotic and abiotic stresses in future. A reference-genome assembly for nuclear and chloroplast genomes and cold hardy genes is presented in chapter 3. We used re-sequence genomes of 170 individuals collected from 20 <em>Juglans</em> species and <em>Carya</em> (as an outgroup) of the Juglandaceae family distributed in temperate-tropical forests of America and Asia. We integrate genome and temperature variables to identify a set of associated single-nucleotide polymorphisms (SNP), structural variations, and the geographical distribution of the variants in the genes related to local adaptation of <em>Juglans</em> across latitudes. Phylogeny analyses revealed that <em>Juglans</em> species were sorted based on their origin using the nuclear genome, cold-hardy genes, and organellar genome. <em>Juglans regia</em>, a native species of Asia and Europe, was distinct from other species and exhibited less genetic diversity than <em>Juglans</em> spp. of North America, based on whole genome and cold-hardy gene analysis. We identified the black walnut as a more diverse species and the California walnut and Persian walnut (<em>J. regia</em>) as less diverse species using selective sweep and heterozygosity analysis. Within <em>Juglans </em>species, those from colder areas exhibited higher diversity of cold hardy genes compared to the ones from warmer regions. Differences in genetic diversity among continents and latitudes did not follow a clear trend. Still, the level of gene diversity of <em>Juglans</em> from North America is higher than the species that originated in eastern Asia. We can use 65,000 nuclear SNPs variants in an ecological modeling system to predict genetic diversity and spatiotemporal shift of <em>Juglans</em> species in response to future climate change. These SNPs variants are helpful for forest tree breeding programs with aims such as marker-assisted selection (MAS), conservation or assisted migration in future.  </p> <p>Based on the findings of chapter 2 and 3, black walnut is the most diverse species with high genetic diversity in comparison with other <em>Juglans</em> species distributing across eastern forest of the USA. However, deeper knowledge of how this genetically diverse species will be affected by climate change is crucial. In chapter 3, we projected black walnut's current and future basal area. Utilizing machine learning, we tested different models using more than 1.4 million tree records from 10,162 Forest Inventory and Analysis (FIA) sample plots and 42 spatially explicit bioclimate and other environmental attributes. Ultimately, we used random forests (RF) model to estimate the basal area of black walnut under climate change. The mean of annual temperature and precipitation, potential evapotranspiration, topology, and human footprint were the most significant variables in prediction of basal area. Under two emission scenarios (Representative Concentration Pathway 4.5 and 8.5), the RF model projected that black walnut stocking will increase in the northern part of the current range in the USA by 2080, with a potential shift of species distribution range. However, uncertainty remains due to unpredictable events, including extreme abiotic (heat, drought) and biotic (pests, disease) occurrences. Our models can be adapted to other hardwood tree species to predict tree changes in the basal area based on future climate scenarios.  </p> <p>A similar approach of chapter 2, with a slightly different freeze test (whole plant freezing test) and use of cold-acclimated seedling was used in chapter 4. For cold acclimation, seedlings exposed to air temperatures progressively lowered for eight weeks (from 25.6/22.2 ºC to 8/4 ºC, day/night) and non-acclimated seedlings from sea level to 2,300 m, in tropical Hawaiʻi, USA to evaluate cold tolerance of koa. We also investigated gene expression using qPCR and wideseq sequencing in this study. Freezing tolerance varied significantly in non-acclimated versus cold-acclimated treatments across the elevation cline using the whole plant physiology-freezing test and gene expression. The level of freezing tolerance and the elevation at which seeds were collected were consistent with the frequency of freezing tolerance genes to facilitate variation interpretation in cold-hardy phenotypes. Findings of physiology and molecular data analysis for freezing tolerance of koa across the elevation gradient of the Hawaiian Islands provides insight into natural selection processes and will help to support forest restoration efforts. </p> <p>  </p>

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Stagonospora nodorum blotch (SNB), is a major foliar disease of wheat in the mid-Atlantic U.S., is caused by the necrotrophic fungus Parastagonospora nodorum. SNB is managed using cultural practices, resistant varieties, and foliar fungicides. There are increasing trends of severity and incidence of SNB in Virginia and the surrounding mid-Atlantic region, but it is not known if changes in the pathogen population are contributing to this trend. The overall goal of this research was to 1) determine the occurrence of quinone outside inhibitor (QoI) resistance in Virginia populations of P. nodorum infecting wheat, 2) quantify the distribution of G143A mutations conferring fungicide resistance in Virginia populations of P. nodorum, and 3) characterize genetic diversity of P. nodorum populations in Virginia and assess influences of cultivars and environments on population structure and SNB severity. For Objective 1, QoI resistant isolates of P. nodorum were identified from Virginia wheat fields, and this was the first report of QoI resistant P. nodorum in the United States. The G143A substitution in the cytochrome b gene of P. nodorum was associated with reduced QoI sensitivity, and in Objective 2, a state-wide, two-year survey of P. nodorum populations in Virginia determined that the G143A mutation was widespread in the state and among sampled fields the frequency ranged from 5-32% (mean = 19%). For Objective 3, P. nodorum was isolated from five different wheat cultivars across seven locations over two years in Virginia. SNB severity varied by cultivar but greater differences in disease severity were observed among locations and years suggesting environment plays an important role in SNB development. Among the necrotrophic effector (NE) genes examined, SnTox1 was predominant followed by SnTox3, and frequencies of NE genes did not vary by cultivar or location. P. nodorum populations in Virginia had high genetic diversity, but there was no genetic subdivision among locations or wheat cultivars from which individuals were isolated. Results also indicated that the P. nodorum population in Virginia undergoes a mixed mode of reproduction, but sexual reproduction made the greatest contribution to population structure. Overall, this work provides insights into the population biology of P. nodorum in Virginia and information on variability in fungicide sensitivity and cultivar susceptibility to SNB that has implications for the current and future efficacy of fungicides and host resistance for management of SNB. / Doctor of Philosophy / Wheat (Triticum aestivum L.) is one of the major cereal crops grown worldwide for food, feed, and other products. However, yields of this crop are often limited by fungal diseases including Stagonospora nodorum blotch (SNB) caused by Parastagonospora nodorum. Increasing trends of severity and incidence of SNB may be due to reduced sensitivity of P. nodorum to fungicides or increased virulence of P. nodorum populations on commonly grown cultivars. Fungicides such as quinone outside inhibitors (QoIs) are one of the major classes of fungicides used for disease control and G143A substitution is the most common point mutation associated with complete resistance to QoIs. Therefore, the overall goal of this research was to better understand genotypic and phenotypic variation in Virginia populations of P. nodorum in the context of fungicide sensitivity and susceptibility of wheat cultivars to SNB. The specific objectives were to 1) determine the occurrence of quinone outside inhibitor (QoI) fungicide resistance in Virginia populations of P. nodorum infecting wheat, 2) quantify the distribution of G143A mutations conferring QoI fungicide resistance in Virginia populations of P. nodorum, and 3) characterize genetic diversity of P. nodorum populations in Virginia and assess influences of cultivars and environments on population structure and SNB severity. Results from this research indicate that QoI fungicide resistance occurs in Virginia populations of P. nodorum due to a target site mutation (G143A substitution in the cytochrome b gene), and this mutation is widespread and relatively common in Virginia wheat fields. Based on a multi-year multilocation study, P. nodorum populations were genetically diverse, but there was no genetic subdivision among locations or wheat cultivars. SNB severity varied by location and cultivar, but disease severity was greatest at site-years with moderate springtime temperatures and high rainfall. Overall, this work contributes to a better understanding of P. nodorum populations including the current efficacy of fungicides and host resistance for management of SNB in the region.

Citrus es el género de la subfamilia Aurantioideae de mayor importancia económica. Su origen es la región sureste de Asia, en un área que incluye China, India y la península de Indochina y los archipiélagos de los alrededores. Aunque se han realizado múltiples estudios, la taxonomía del género Citrus aun no está bien definida, debido al alto nivel de diversidad morfológica encontrado en este grupo, la compatibilidad sexual entre sus especies y la apomixis de muchos genotipos. En la presente tesis doctoral se ha estudiado una amplia diversidad del género Citrus, especies relacionadas y otros taxones de la subfamilia Aurantioideae, para poder aclarar su organización y filogenia mediante el empleo de diferentes tipos de marcadores moleculares y métodos de genotipado. Más concretamente, el germoplasma de mandarino juega un papel muy importante en la mejora de variedades y patrones, pero su organización genética no está bien definida. Por lo tanto, se ha realizado un análisis en profundidad de su diversidad y organización genética. El desarrollo de marcadores moleculares de Inserción-Deleción (indel), por primera vez en cítricos, ha permitido demostrar su utilidad para estudios de diversidad y filogenia en el género Citrus. En combinación con los marcadores de tipo microsatélite (SSR), se ha cuantificado la contribución de los tres principales taxones de cítricos (C. reticulata, C. maxima and C. medica) a los genomas de las especies secundarias y cultivares modernos. También se ha definido su estructura genética a partir de los datos obtenidos en la secuenciación de 27 fragmentos de genes nucleares relacionados con la biosíntesis de compuestos que determinan la calidad de los cítricos y genes relacionados con la respuesta de la planta a estreses abióticos. El análisis de la filogenia nuclear ha permitido determinar la relación existente entre la especie C. reticulata y Fortunella, que se diferencian claramente del grupo formado por las otras dos principales especies de cítricos (C. maxima y C. medica). Este resultado está en concordancia con el origen geográfico de las especies estudiadas. A partir de este estudio, se han desarrollado marcadores moleculares de tipo SNP con un alto valor filogenético, que han sido transferidos a géneros relacionados de los cítricos. Estos marcadores han dado un resultado muy positivo en el género Citrus y serán de gran utilidad para el establecimiento de la huella genética del germoplasma en un nivel de diversidad más amplio. Se ha estudiado la organización genética dentro del germoplasma mandarino (198 genotipos de tipo mandarino pertenecientes a dos colecciones, INRA-CIRAD e IVIA), así como la introgresión de otros genomas mediante el uso de 50 y 24 marcadores de tipo SSR y indel, respectivamente, además de cuatro marcadores InDel mitocondrial (ADNmt). Se ha observado que muchos genotipos, que se creía que eran mandarinos puros, presentan introgresión de otros genomas ancestrales. Dentro del germoplasma de mandarino, se han identificado a nivel nuclear cinco grupos parentales, a partir de los cuales se originaron muchos genotipos, dando lugar a estructuras hibridas complejas. Se ha observado incluso, genotipos con un origen maternal no mandarino, determinado por los marcadores de ADNmt. La presente tesis doctoral ha aportado nueva información sobre las relaciones filogenéticas entre las especies del género Citrus, géneros cercanos, así como de las especies secundarias. Además, se han desarrollado nuevos marcadores moleculares que se complementan entre sí. Se ha establecido una nueva organización genética del germoplasma mandarino y se han caracterizado adecuadamente las dos colecciones de cítricos en estudio. Por lo tanto, todas estas contribuciones, ayudarán a los programas de mejora para la obtención de nuevas variedades de cítricos de alta calidad y permitirán optimizar la conservación y uso de los recursos genéticos existentes, así como su caracterización genética y fenotípica. / García Lor, A. (2013). Organización de la diversidad genética de los cítricos [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/31518

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The accurate assessment of forest persistence under environmental change is dependent on the fundamental understanding of the genetic consequences of human intervention and its comparison to that of natural processes, as declines in genetic diversity and changes in its structuring can compromise the adaptive ability of a population. The European beech, Fagus sylvatica, has experienced prolonged human impact over its 14 million ha range with contemporary forests harbouring high ecological, economic, and cultural value. Historical traditional management practices, such as coppicing and pollarding, have impacted a large portion of Europe’s forests. This form of management encouraged vegetative regeneration, prolonging the longevity of individual trees. In several cases, the structure and function of managed trees and their associated ecosystems were significantly altered. Specifically, coppiced beech forests in Europe displayed significantly larger extents of spatial genetic structuring compared to their natural counterparts, revealing a change in the genetic composition of the population due to decades of management. Humans have also aided in the dispersal of beech within and outside of its natural range. In Great Britain, the putative native range retained signals of past colonisation dynamics. However, these signals were obscured by the wide-spread translocation of the species throughout the country. Evidence of post-glacial colonisation dynamics can be found in Sweden as well. In contrast to Britain, the structure of this natural leading range edge displays a gradual reduction in population size where isolation was found to have acted as an effective barrier to gene flow reducing the genetic diversity of populations.