1,721,054 research outputs found
Implications of structural genomic variants on agronomical traits in elite winter oilseed rape (Brassica napus L.)
Get PDFBrassica napus L. (oilseed rape) is an allotetraploid crop originated from a spontaneous hybridization event between its two diploid ancestors Brassica rapa L. (turnip) and Brassica oleracea L. (cabbage). It is assumed that this interspecific hybridization took place no more than 7,000 years ago, when turnip rape and cabbage were first cultivated in close proximity to each other. The A and C subgenomes of this relatively recent polyploid crop share highly similar homoeologous chromosomes with conserved gene order. Thus, there is a high probability of homoeologous exchanges during meiosis. Hence, highly frequent structural genome variations (SV), including deletions, insertions, inversion and translocation are expected and have already been demonstrated in several studies.
In recent years, long-read sequencing technologies have added a powerful new dimension to eukaryote genomics. Long read sequencing technologies combine great read lengths with acceptable single base accuracies and allow the detection of small- to mid-scale SV that could not be revealed by Illumina short-read sequencing datasets. Applying long-read sequencing to investigate an interconnected multiparental population of European elite winter oilseed rape revealed that ~ 5% of the annotated genes harbored a potentially functional SV event. This relatively high number of intragenic SV justified a more detailed investigation regarding the association of SV with agricultural traits.
In the present thesis, genome-wide association studies were performed to investigate flowering time modulation and quantitative blackleg resistance within a multiparental population derived from seven European elite winter oilseed rape cultivars. Several novel QTL were identified and previously known QTL regions were confirmed. Most interestingly, this work focused on SV within these QTL regions to evaluate the implications of SV on the investigated traits. The two major findings were a novel, previously undetected deletion within FLOWERING LOCUS T, a key gene of the flowering time pathway and a large, novel insertion within Rlm9, a well-investigated blackleg resistance gene. These SV were associated to quantitative phenotypic variation for flowering time and blackleg resistance, respectively. Furthermore, the results provided new insight into the suitability of long-read sequencing data for detection of single nucleotide variants and underlined the relevance of reference genome quality for SV analyses.
In summary, increasing accuracies and decreasing prices of constantly evolving long-read sequencing technologies make long-read sequencing the method of choice for detection of genomic variation. The unexpectedly high prevalence and functional relevance of SV and their association with important agronomical traits allow the recommendation for intensification of their use in commercial breeding programs and further emphasize their potential value for the development of modern, high yielding and stress tolerant cultivar.Sonstige Drittmittelgeber/-inne
Regulatory and non-coding patterns associated to genome diversification and early development in an allopolyploid crop
Get PDFOilseed rape (Brassica napus) is the third-most widely grown crop globally for vegetable oil production after soybean and oil palm. The relevance of oilseed rape relies not only in its economic value but also in its allopolyploidy and close linkage to Arabidopsis thaliana, which make it a useful model crop for other allopolyploids like wheat, cotton and sugarcane. Part of the increase of B. napus yield is due to enhanced performance in F1 hybrids, through exploitation of heterosis during the last few decades in all major oilseed rape production areas in the world. Until now, heterosis and hybrid-specific patterns have been mostly examined under allelic interaction hypotheses. Therefore, this thesis focuses on assessing genomic, transcriptomic and epigenomic features in the context of heterosis in a hybrid cross between two highly homozygous, yet genetically divergent, inbred oilseed rape accessions. Spontaneous large-scale genomic rearrangements that differed between F1 sister plants generated early and rapid gene copy number variation in a single generation. The implications of such preliminary findings suggest possible scenarios of post-polyploidization mechanisms to survive the evolutionary dead end of allopolyploidization. Furthermore, gene expression, small RNA and genome-wide methylation during seed and seedling development in the F1-hybrid were evaluated. Parental dominance was observed in transcriptomic and epigenomic patterns and key differentially expressed genes involved in reproduction and development during seed formation were detected through gene expression and microRNA analyses. Candidate epigenetic alleles with diverse core biological functions were identified and linkages between epigenomic and transcriptomic features were assessed. The insight provided through this research aims at exploring molecular patterns with potential implications in hybrids and heterosis and establishing frameworks for future multi-omics and pangenomic research in polyploid crops
Examining the role of genetic variability for drought stress responses in wheat (Triticum aestivum L.) and sorghum (Sorghum bicolor L. Moench.) and its implications for water and nitrogen use efficiency
No full textWheat (Triticum aestivum L. ssp. aestivum) is one of the three most important crops globally, contributing about 21% to the world's food supply. Its domestication occurred in the Fertile Crescent. Wheat's evolution is based on allopolyploidization, resulting from hybridization with Aegilops species approximately one million years ago. Diploid and tetraploid species emerged first, followed by hexaploid wheat from the hybridization of tetraploid species and diploid wild grass. Sorghum (Sorghum bicolor L. Moench) is a crucial cereal, ranking fifth in global production from 2010 to 2020. Sorghum's domestication began in Northeast Africa, in presentday Ethiopia and Sudan, around 4000-3000 BC. Disruptive selection practices led to many improved Sorghum varieties, which spread through human migration and trade to other regions of Africa, India (around 1500-1000 BC), the Middle East (around 900-700 BC), China (around 400 AD), and eventually Europe (around 1204 AD). Climate change is resulting in the emergence of erratic drought conditions in numerous growing regions. Furthermore, the excessive use of nitrogen fertilisers can have adverse environmental impacts. These include high consumption of fossil fuels and the release of carbon dioxide (CO2) during the artificial synthesis of ammonia, as well as negatively influencing ecosystems due to leaching or volatile atmospheric emissions. As a consequence of both the increasing global population and the concomitant environmental alterations induced by climate change, there is an immediate necessity for the development of a sustainable agricultural model, which will ensure the production of sufficient food and simultaneously reduce the environmental impact of agricultural practices. In the present thesis, an investigation on the physiological characteristics as well as a detailed analysis on morphological and physiological response on drought stress was performed in wheat and sorghum. Furthermore, this dissertation offers an in-depth validation of the rootgrowth associated haplotype blocks Hap-5B-RDMa and Hap-5B-RDMb with nitrogen uptake, nitrogen remobilisation as well as on water use. In Sorghum, the use of a modern gravimetrical phenotyping platform, revealed the impact of early vegetative drought on morphological and physiological response, such as on plant development, biomass and flowering time. In wheat an assessment of a low-cost phenotyping methodology in the field and under controlled conditions was performed. Normalised difference vegetation index in field as well as the digital image analysis under controlled conditions revealed, revealed a significant impact of the second leaf on the trait characteristics. Furthermore, genome-wide association studies were performed to identify genomic determination of EV, revealing 42 makers associated with vegetation index and two makers associated with projected leaf area. Additionally, the unique combination of a gravimetrical coupled with 15N tracer-based tracking revealed for all varieties, carrying the root-growth associated trait, significant higher nitrogen uptake in the root organs, compared to those not carrying such QTL. Further, lower transpiration rates were found for certain genotype – background interaction. In summary, in light of the changing climatic growing conditions and the objective of attaining more climate-neutral production systems, the development of new lines is imperative. These must be more resilient to abiotic stress factors such as drought stress, while still being able to adequately meet the demand for high-quality food under lower input factors. This dissertation provides a significant contribution to the understanding of early vegetative drought stress on morphological and physiological growth parameters in sorghum. In addition, this work presents a cost-effective method for phenotyping leaf area and novel insights into the genetic control of early vigour and nitrogen uptake in wheat. The findings presented here can be used as potential targets for breeding to develop more efficient varieties.Weizen (Triticum aestivum L. ssp. aestivum) ist eine der drei wichtigsten Nutzpflanzen weltweit und trägt etwa 21 % zur weltweiten Nahrungsmittelversorgung bei. Seine Domestizierung fand im Fruchtbaren Halbmond statt. Die Evolution des Weizens basiert auf Allopolyploidisierung, die vor etwa einer Million Jahren durch Hybridisierung mit Aegilops-Arten entstand. Zuerst entstanden diploide und tetraploide Arten, gefolgt von hexaploidem Weizen durch die Hybridisierung von tetraploiden Arten und diploidem Wildgras. Sorghum (Sorghum bicolor L. Moench) ist ein bedeutendes Getreide und rangierte von 2010 bis 2020 weltweit an fünfter Stelle der Produktion. Die Domestizierung von Sorghum begann in Nordostafrika, im heutigen Äthiopien und Sudan, um 4000-3000 v. Chr. Disruptive Selektionspraktiken führten zur Entwicklung zahlreicher verbesserter Sorghum-Sorten, die sich durch menschliche Migration und Handelswege in andere Regionen Afrikas, nach Indien (ca. 1500-1000 v. Chr.), in den Nahen Osten (ca. 900-700 v. Chr.), nach China (ca. 400 n. Chr.) und schließlich nach Europa (ca. 1204 n. Chr.) ausbreiteten. Der Klimawandel führt, in zahlreichen Anbauregionen, zu immer häufiger erratisch auftretenden Dürrebedingungen. Darüber hinaus kann der übermäßige Einsatz von Stickstoffdüngern negative Umweltauswirkungen haben. Diese umfassen einen hohen Verbrauch fossiler Brennstoffe und die Freisetzung von Kohlendioxid (CO2) während der künstlichen Ammoniaksynthese sowie negative Einflüsse auf Ökosysteme durch Auswaschung oder volatile atmosphärische Emissionen. Aufgrund der wachsenden Weltbevölkerung und der damit einhergehenden Umweltveränderungen, die durch den Klimawandel hervorgerufen werden, besteht ein dringender Bedarf an der Entwicklung eines nachhaltigen landwirtschaftlichen Modells, das die Produktion ausreichender Nahrungsmittel sicherstellt und gleichzeitig die Umweltauswirkungen landwirtschaftlicher Praktiken verringert. In der vorliegenden Dissertation wurde eine Untersuchung der physiologischen Merkmale von Eigenschaften im Zusammenhang mit der Trockenstressresistenz sowie eine detaillierte Analyse der morphologischen und physiologischen Reaktionen auf Trockenstress bei Weizen und Sorghum durchgeführt. Darüber hinaus bietet diese Dissertation eine eingehende Validierung der mit dem Wurzelwachstum assoziierten Haploblöcke Hap-5B-RDMa und Hap- 5B-RDMb in Bezug auf Stickstoffaufnahme, Stickstoff-Remobilisierung und Wasserverbrauch. Im Sorghum zeigte der Einsatz einer modernen gravimetrischen Phänotypisierungsplattform die enormen Auswirkungen von frühem vegetativen Trockenstress auf morphologische und physiologische Reaktionen, wie beispielsweise die Pflanzenentwicklung, Biomasse und Blütezeit. Im Weizen wurde eine kostengünstige Phänotypisierungsmethode sowohl im Feld als auch unter kontrollierten Bedingungen bewertet. Der normalisierte Differenzvegetationsindex (NDVI) im Feld sowie die digitale Bildanalyse unter kontrollierten Bedingungen zeigten einen signifikanten Einfluss des zweiten Blattes auf die Merkmalscharakteristika. Darüber hinaus wurden genomweite Assoziationsstudien durchgeführt, um die genomische Bestimmung der frühen Vitalität zu identifizieren, wobei 42 Marker im Zusammenhang mit dem Vegetationsindex und zwei Marker im Zusammenhang mit der projizierten Blattfläche identifiziert wurden. Zusätzlich zeigte die einzigartige Kombination einer gravimetrischen Analyse mit der 15N-Tracer-basierten Analyse bei allen Sorten, die das mit dem Wurzelwachstum assoziierte Merkmal tragen, eine signifikant höhere Stickstoffaufnahme in den Wurzelorganen im Vergleich zu denen, die dieses QTL nicht tragen. Darüber hinaus wurden niedrigere Transpirationsraten für bestimmte Genotyp-Hintergrund-Interaktionen festgestellt. Zusammenfassend lässt sich sagen, dass angesichts der sich ändernden klimatischen Wachstumsbedingungen und des Ziels, klimaneutralere Produktionssysteme zu erreichen, die Entwicklung neuer Linien unerlässlich ist. Diese müssen widerstandsfähiger gegenüber abiotischen Stressfaktoren wie Trockenstress sein und dennoch in der Lage sein, die Nachfrage nach hochwertigen Lebensmitteln unter geringeren Inputfaktoren zu erfüllen. Diese Dissertation liefert einen wesentlichen Beitrag im Verständnis von frühen vegetativen Trockenstress auf morphologische und physiologische Wachstumsparameter bei Sorghum. Darüber hinaus stellt diese Arbeit eine kostengünstige Methode zur Phänotypisierung der Blattfläche vor, sowie neuartige Erkenntnisse zum genetischen Einfluss auf den Frühaufgang und der Stickstoffaufnahme beim Weizen. Die hier vorgestellten Erkenntnisse können als potenzielle Ziele für die Züchtung verwendet werden, um effizientere Sorten zu entwickeln
Examining the role of genetic variability for drought stress responses in wheat (Triticum aestivum L.) and sorghum (Sorghum bicolor L. Moench.) and its implications for water and nitrogen use efficiency
No full textIn the present dissertation, an investigation of the physiological characteristics of traits related to drought stress resistance and a detailed analysis of the morphological and physiological responses to drought stress in wheat and sorghum were carried out. In addition, this dissertation provides an validation of the root growth-associated haplotypeblocks Hap-5B-RDMa and Hap-5B-RDMb in relation to nitrogen uptake, nitrogen remobilization and water use.
In sorghum, the use of a modern gravimetric phenotyping platform showed the impact of early vegetative drought stress on morphological and physiological responses, such as plant development, biomass and flowering time.
In wheat, a cost-effective phenotyping method was evaluated both in the field and under controlled conditions. Normalized difference vegetation index (NDVI) in the field as well as digital image analysis (PLA) under controlled conditions showed a significant (p < 0.05) influence of the second leaf on early plant development (early vigour). In addition, genome-wide association studies were performed to identify the genomic determination for Early Vigour, identifying 42 markers associated with NDVI and two markers associated with PLA.
Furthermore, the gravimetric measurement in combination with the 15N tracer-based analysis showed significant (p < 0.05) effects for carriers of Hap-5B-RDMa and Hap-5B-RDMb on nitrogen uptake in the root. In addition, significantly (p < 0.1) lower transpiration rates were found for certain genotype-haplotypeblock interactions.
In view of the changing climatic growing conditions and the goal of achieving more climate-neutral production systems, the development of new varieties is essential. These lines have to be more resilient to abiotic stress factors such as drought stress and must be able to meet food demand under lower input factors. This dissertation provides a significant contribution in understanding early vegetative drought stress on morphological and physiological growth parameters in sorghum. In addition, this work presents a cost-effective method for phenotyping early vigor and novel insights into the genetic influence of root-associated haplotypeblocks on nitrogen uptake in wheat. The findings presented here can be used as potential targets in pre-breeding to develop more efficient varieties
Gene presence-absence variation associates with quantitative Verticillium longisporum disease resistance in Brassica napus
No full textAlthough copy number variation (CNV) and presence-absence variation (PAV) have been discovered in selected gene families in most crop species, the global prevalence of these polymorphisms in most complex genomes is still unclear and their influence on quantitatively inherited agronomic traits is still largely unknown. Here we analyze the association of gene PAV with resistance of oilseed rape (Brassica napus) against the important fungal pathogen Verticillium longisporum, as an example for a complex, quantitative disease resistance in the strongly rearranged genome of a recent allopolyploid crop species. Using Single Nucleotide absence Polymorphism (SNaP) markers to efficiently trace PAV in breeding populations, we significantly increased the resolution of loci influencing V. longisporum resistance in biparental and multi-parental mapping populations. Gene PAV, assayed by resequencing mapping parents, was observed in 23-51% of the genes within confidence intervals of quantitative trait loci (QTL) for V. longisporum resistance, and high-priority candidate genes identified within QTL were all affected by PAV. The results demonstrate the prominent role of gene PAV in determining agronomic traits, suggesting that this important class of polymorphism should be exploited more systematically in future plant breeding
Comparative Genomic Prediction in Winter Wheat
No full textHaplotype blocks offer potential advantages over single SNP markers in genomic prediction by capturing local epistatic interactions and ancestral relationships.
However, their effectiveness varies by trait and block construction method. This study evaluates genomic prediction for 11 traits in winter wheat using haplotype blocks constructed based on linkage disequilibrium (LD), fixed SNP numbers, fixed lengths in cM, and HaploBlocker, alongside single SNP markers. Data from 361 genotypes and single-year field trials were analyzed using ridge regression best linear unbiased prediction (RR-BLUP), restricted maximum likelihood ANOVA (RMLA), and genomic and variance component based on haplotype blocks (GVCHAP) in a cross-validation study. LD-based blocks showed the highest prediction accuracies for resistance traits (Blumeria graminis, Puccinia triticina, and Fusarium graminearum), while HaploBlocker outperformed other methods for protein concentration and resistances to Septoria tritici and P. striiformis. Machine learning methods were also assessed for their potential to improve prediction accuracy and resistance genotype identification. Nineteen prediction approaches, combining different models (RR-BLUP, RMLA, Bayesian ordinal regression, support vector machine, gradient boosting machine, and random forest), predictors (SNPs, LD-based blocks, autoencoder variables, and GWAS-selected SNPs), and response values (untransformed and logit transformed scores), were evaluated using cross-validation and Cohen’s κ.
While RR-BLUP consistently performed well, gradient boosting machine and random forest achieved higher accuracy for P. triticina (0.71 vs. 0.64 for RR-BLUP). Cohen’s κ was used to assess the ability of each method to correctly identify the most resistant genotypes, demonstrating that machine learning models offered improvements in resistance identification, especially for P. triticina. A major finding is that no single method or predictor set universally outperforms others. The choice of model and predictors must be tailored to the genetic architecture of the trait being studied. Logit transformation proves particularly useful for resistance scores, ensuring that predicted genotypic values remain within an interpretable range. This thesis underscores the importance of a trait-specific approach to genomic prediction, emphasizing that effective prediction relies on selecting models and predictors that align with the unique characteristics of the traits.Federal State
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Unraveling the impact on agronomic traits of the genetic architecture underlying plant-density responses in canola
No full textPlant density defines vegetative architecture and the competition for light between individuals. Brassica napus (canola, rapeseed) presents a radically different plant architecture compared to traditional crops commonly cultivated at high density, and can act as a model system of indeterminate growth. Using a panel of 152 spring-type accessions and a double-haploid population of 99 lines from a cross between the cultivars Lynx and Monty, we performed genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping for 12 growth and yield traits at two contrasting plant densities of 15 and 60 plants m-2. The most significant associations were found for time to flowering, biomass at harvest, plant height, silique and seed numbers, and seed yield. These were generally independent of plant density, but some density-dependent associations were found in low-density populations. RNA-seq transcriptomic analysis revealed distinctive latent gene-regulatory responses to simulated shade between Lynx and Monty. Having identified candidate genes within the canola QTLs, we further examined their influence on density responses in Arabidopsis lines mutated in certain homologous genes. The results suggested that TCP1 might promote growth independently of plant density, while HY5 could increase biomass and seed yield specifically at high plant density. For flowering time, the results suggested that PIN genes might accelerate flowering in plant a density-dependent manner whilst FT, HY5, and TCP1 might accelerate it in a density-independent. This work highlights the advantages of using agronomic field experiments together with genetic and transcriptomic approaches to decipher quantitative complex traits that potentially mediate improved crop productivity.Fil: Menendez, Yesica Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Sanchez, Diego Hernan. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Snowdon, Rod J.. Justus Liebig Universitat Giessen.; AlemaniaFil: Rondanini, Deborah Paola. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Botto, Javier Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentin
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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