1,721,129 research outputs found
Genetic analysis of phenylpropanoid metabolites associated with resistance against Verticillium longisporum in Brassica napus
No full textVerticillium longisporum is a major threat to production of oilseed rape (Brassica napus) in Europe. The aim of the study was to develop new markers and obtain insights into putative mechanisms and pathways involved in the resistance reaction. A genetic approach was used to identify quantitative trait loci (QTL) for V. longisporum resistance and metabolic traits potentially influencing resistance in a B. napus mapping population. Resistance to V. longisporum was mapped in a doubled haploid (DH) population from a cross between the partially resistant winter oilseed rape variety Express 617 and a resistant resynthesized B. napus line, R53. One major resistance QTL contributed by R53 was identified on chromosome C5, while a further, minor QTL contributed by Express 617 was detected on chromosome C1. Markers flanking the QTL also significantly correlated with V. longisporum resistance in four further DH populations derived from crosses between elite oilseed rape cultivars and other resynthesized B. napus lines originating from genetically and geographically diverse brassica A and C genome donors. The tightly-linked markers developed enable the combination of favorable alleles for novel resistance loci from resynthesized B. napus materials with existing resistance loci from commercial breeding lines. HPLC analysis of hypocotyls from infected DH lines revealed that concentrations of a number of phenylpropanoids were correlated with V. longisporum resistance. QTL for some of these phenylpropanoids were also found to co-localize with the QTL for V. longisporum resistance. Genes from the phenylpropanoid pathway are suggested as candidates for V. longisporum resistance
Phenotypic and phylogenetic analysis of Verticillium longisporum strains from European and Canadian oilseed rape fields
No full textAbstract Verticillium longisporum is a vascular fungal pathogen of oilseed rape (OSR) that causes Verticillium stem striping. The pathogen segregates into three lineages originating from at least three hybridization events between four different Verticillium genomes, leading to the hybrid lineages A1/D1, A1/D2 and A1/D3. Although A1/D1 is considered the most relevant lineage in OSR, extensive studies addressing the geographical spread and phylogenetic relationships of Verticillium lineages are lacking. In the present study, the genetic diversity and relatedness of V . longisporum isolates from European and Canadian OSR fields were analysed. Based on genotyping by sequencing, genetic subgroups were identified and assigned to geographic origins and pathogenic traits. To assess the agronomic importance of different lineages, representative isolates were tested for pathogenicity and aggressiveness on OSR under greenhouse conditions. This study confirms that A1/D1 is the prevalent and most aggressive lineage of V . longisporum in European and Canadian OSR fields. Genetic clusters within the A1/D1 lineage were weakly correlated with geographic origin, but not with aggressiveness on winter OSR. Isolates from the United Kingdom, Latvia and Canada occurred only in a single and distinct subclade, indicating a more recent introduction, whereas isolates from locations where the disease has been known for a long time (France, Germany, Poland, Sweden) were less uniform and could be assigned to several subclades. Our results indicate that Verticillium stem striping in the United Kingdom, Latvia and Canada may have derived from separate and different single introductions of the pathogen in the recent past.Bundesministerium für Ernährung und Landwirtschaft https://doi.org/10.13039/50110000590
Combination of resistance to Verticillium longisporum from zero erucic acid Brassica oleracea and oilseed Brassica rapa genotypes in resynthesized rapeseed (Brassica napus) lines
No full textResynthesized (RS) forms of rapeseed (Brassica napus L.; genome AACC, 2n = 38) generated from interspecific hybridization between suitable genotypes of its diploid progenitors Brassica rapa L. (syn. campestris; genome AA, 2n 20) and Brassica oleracea L. (CC, 2n 18) represent a potentially useful resource to introduce resistance against the fungal pathogen Verticillium longisporum into the gene pool of oilseed rape. Numerous cabbage (B. oleracea) accessions are known with resistance to V. longisporum; however, B. oleracea generally has high levels of erucic acid and glucosinolates in the seed, which reduces the suitability of resulting RS rapeseed lines for oilseed rape breeding. In this study resistance against V. longisporum was identified in the cabbage accession Kashirka 202 (B. oleracea convar. capitata), a zero erucic acid mutant, and RS rapeseed lines were generated by crossing the resistant genotype with two spring turnip rape accessions (B. rapa ssp. olerifera) with zero erucic acid. One of the resulting zero erucic acid RS rapeseed lines was found to have a high level of resistance to V. longisporum compared with both parental accessions and with B. napus controls. A number of other zero erucic acid RS lines showed resistance levels comparable to the parental accessions. In the most resistant RS lines the resistance and zero erucic acid traits were combined with variable seed glucosinolate contents. Erucic acid-free RS rapeseed with moderate seed glucosinolate content represents an ideal basic material for introgression of quantitative V. longisporum resistance derived from B. oleracea and B. rapa into elite oilseed rape breeding lines
Broadening the genetic basis of Verticillium longisporum resistance in Brassica napus by interspecific hybridization
No full textVerticillium wilt caused by the vascular fungal pathogen Verticillium longisporum is one of the most important pathogens of oilseed rape (Brassica napus sp. oleifera) in northern Europe. Because production of this major oilseed crop is expanding rapidly and no approved fungicides are available for V longisporum, long-term control of the disease can only be achieved with cultivars carrying effective quantitative resistance. However, very little resistance to V longisporum is available within the gene pool of oilseed rape, meaning that interspecific gene transfer from related species is the only possibility for broadening levels of resistance in current varieties. The amphidiploid species B. napus can be resyn-thesized by crossing the two progenitor species Brassica oleracea and Brassica rapa, hence resistant accessions of these two diploid species can be used as resistance donors. In this study a total of 43 potential B. rapa and B. oleracea resistance donors were tested with regard to their reaction to a mixture of two aggressive V longisporum isolates, and resistances from diverse lines were combined by embryo rescue-assisted interspecific hybridization in resynthesized rapeseed lines. Progenies from crosses of the two B. rapa gene bank accessions 13444 and 56515 to the B. oleracea gene bank accessions BRA 1008, CGN 14044, 8207, BRA 1398, and 7518 showed a broad spectrum of resistance in pathogenicity tests. Of 45 tested resynthesized lines, 41 lines exhibited a significantly higher level of resistance than the moderately V longisporum-tolerant oilseed rape cultivar Express. These lines represent a promising basis for the combination of different resistance resources in new varieties
Comparative mapping of quantitative trait loci involved in heterosis for seedling and yield traits in oilseed rape (Brassica napus L.)
Full text linkLittle is known about the genetic control of heterosis in the complex polyploid crop species oilseed rape (Brassica napus L.). In this study, two large doubled-haploid (DH) mapping populations and two corresponding sets of backcrossed test hybrids (THs) were analysed in controlled greenhouse experiments and extensive field trials for seedling biomass and yield performance traits, respectively. Genetic maps from the two populations, aligned with the help of common simple sequence repeat markers, were used to localise and compare quantitative trait loci (QTL) related to the expression of heterosis for seedling developmental traits, plant height at flowering, thousand seed mass, seeds per silique, siliques per unit area and seed yield. QTL were mapped using data from the respective DH populations, their corresponding TH populations and from mid-parent heterosis (MPH) data, allowing additive and dominance effects along with digenic epistatic interactions to be estimated. A number of genome regions containing numerous heterosis-related QTL involved in different traits and at different developmental stages were identified at corresponding map positions in the two populations. The co-localisation of per se QTL from the DH population datasets with heterosis-related QTL from the MPH data could indicate regulatory loci that may also contribute to fixed heterosis in the highly duplicated B. napus genome. Given the key role of epistatic interactions in the expression of heterosis in oilseed rape, these QTL hotspots might harbour genes involved in regulation of heterosis (including fixed heterosis) for different traits throughout the plant life cycle, including a significant overall influence on heterosis for seed yield.German Research Foundation (DFG) [SPP 1149
Utilizing a wild barley nested association mapping (NAM) population for genome-wide association studies - [kumulative Dissertation]
No full textDie zukünftigen Getreideerträge werden maßgeblich von den prognostizierten Auswirkungen des Klimawandels beeinflusst. Die Pflanzenzüchtung nimmt bei der Bewerkstelligung dieser Herausforderungen eine Schlüsselrolle ein. Eine Hürde stellt dabei jedoch die reduzierte Anpassungsfähigkeit moderner Elitesorten an sich ändernde Umweltbedingungen dar. In den vergangenen Jahren hat sich das Konzept multiparentaler Populationen etabliert, um die Vererbung wichtiger agronomischer Merkmale zu untersuchen und die genetische Vielfalt in der modernen Pflanzenzüchtung durch exotische Allele wieder zu erhöhen. In dieser Arbeit wird die Entwicklung der weltweit ersten nested association mapping (NAM)-Population in Wildgerste, HEB-25, dargestellt. HEB-25 ist eine multiparentale Population, die auf Kreuzungen der Elitesorte Barke mit 25 diversen Wildgersten beruht. Die Vererbung entwicklungsspezifischer Merkmale, die im Hinblick auf das Vermeiden von abiotischem Stress relevant sind, wurde mittels genomweiter Assoziationsstudien (GWAS) untersucht und das Potential ausgewählter Wildallele für die zukünftige Pflanzenzüchtung untersucht.Future world crop production is expected to be severely impacted by prospected effects of climate change. Plant breeding is regarded to play a key role in facing the resulting challenges. However, one major constraint plant breeding has to deal with is a reduced adaptability of the current elite breeding germplasm to a changing environment. Therefore, in recent years the concept of multi-parental mapping populations evolved to investigate the genetic architecture of important agronomic traits and to replenish the elite breeding pool with new favorable exotic alleles. In this thesis the development of the worldwide first wild barley nested association mapping (NAM) population, HEB-25,is reported.HEB-25 is a multi-parental mapping population based on crosses of the elite barley cultivar Barke with 25 highly divergent wild barleys. The genetic architecture of plant developmental traits, which are relevant with regard to escaping a biotic stresses, were investigated via genome-wide association studies (GWAS) and the potential of selected wild alleles for future breeding was evaluated.vorgelegt von Andreas Maure
Phenotypic key factors, genetic regions and genes associated to cluster architecture in grapevine (Vitis vinifera)
Full text linkWeltweit rangieren domestizierte Reben (Vitis vinifera) unter den meistangebauten Obstkulturen. Die geernteten Trauben werden geschätzt als nahrhaftes Obst, für die Herstellung von Traubensaft und für die Vinifikation begehrter Weine. Vitis vinifera Sorten dominieren den globalen Weinbau, jedoch sind diese Sorten hoch anfällig gegenüber pilzlichen Schaderregern und müssen intensiv mit Fungiziden behandelt werden. Der Anbau pilzresistenter Sorten reduziert den Fungizideinsatz um 60 %. Grauschimmel, verursacht durch Botrytis cinerea, ist ein Hauptpathogen im Weinbau und nimmt eine gesonderte Stellung in der Resistenzzüchtung ein. Für dieses Pathogen sind derzeit keine aktiven zellulären Resistenzmechanismen bekannt. Deshalb zielt die Resistenzzüchtung auf das Einkreuzen physikalischer Eigenschaften ab, die den Infektionsmechanismus des Pathogens behindern. Lockere Traubenarchitektur hat hierbei eine zentrale Rolle. Um genetische Ursachen für lockere Traubenarchitektur zu identifizieren wurden F1 Individuen aus der Kreuzung (‘Calardis Musqué’ × ‘Villard Blanc’) und somatische Varianten der Sorte ‘Pinot Noir’ mit signifikanten Unterschieden in der Traubenkompaktheit untersucht.
Die phänotypischen Untersuchungen dieser Arbeit zeigen, dass sechs von 20 erfassten Untermerkmalen der Traubenachitektur eine herausragende Rolle für den Grad der Traubenkompaktheit spielen. Traubengewicht, Beerenanzahl, Beerenvolumen, Rachislänge, Schulterlänge und Pedicellänge sind für die Züchtung des komplexen Merkmals Lockerbeerigkeit von vorrangiger Bedeutung. Dies gilt sowohl für 149 phänotypisch diverse F1 Individuen der Kreuzugspopulation, als auch für lockere und kompakte ‘Pinot Noir’ Klone aus fünf Selektionslinien.
Die genetischen Untersuchungen identifizieren acht Regionen des Referenzgenoms für Reben auf denen merkmalsgekoppelte quantitative Loci für bis zu vier Faktoren der Traubenarchitektur gemeinsam lokalisiert sind. Darüber hinaus können molekulare Marker mit starker Kopplung zu Faktoren der Traubenarchitektur benannt werden. Mit der Kombination aus drei der ermittelten molekularen Marker können 29 % der unerwünschten kompakten Genotypen in der Kreuzungspopulation (‘Calardis Musqué’ × ‘Villard Blanc’) selektionieret werden.
Expressionsstudien an mehreren Standorten zeigen, dass die differentielle Genexpression von 15 Kandidatengenen stabil mit Traubenarchitekturparametern von ‘Pinot Noir’ Klonen korreliert. In weiteren Studien mit, in Bezug auf Traubenarchitektur, stark unterschiedlichen Individuen aus diversem genetischem Hintergrund ergibt sich, dass das Transkriptionsfaktor kodierende Gen PRE6 und weitere sechs Gene mit Bezug zu Auxinmetabolismus, Zellwandlockerung und Strigolaktonen zwischen lockeren und kompakten Individuen differentiell exprimiert sind. Diese Gene können dazu geeignet sein um molekulare Marker für Traubenarchitektur zu entwickeln. Diese Marker können dann zur MAS von optimiertem Zuchtmaterial mit physikalischer Resilienz gegen Botrytis cinerea eingesetzt werden.Cultivated grapevine (Vitis vinifera) is one of the most widely grown fruit crops in the world and held in high regard for its nourishing fruits, sweet juices and iconic wines. Global viticulture predominantly utilizes Vitis vinifera varieties, because they convey sensory attributes corresponding to the current consumer ideal of product quality. However, they are also highly susceptible to fungal pathogens, and therefore require intense applications of plant protection products with adverse side effects. Newly bred varieties with resistances against fungal pathogens reduce the necessity for fungicide application by 60%. For grey mold, a severe threat in viticulture, an active resistance mechanism is still not feasible. Therefore, grapevine-breeding aims at introducing fungi-static physical properties. The central hub of these physical barriers is a loosely clustered variety. The enhanced available space between the berries provides the framework for the effective formation of a firm berry surface and waxy cover and is restricting the time-span with favorable moisture conditions for fungal infections.
The experimental design of this thesis draws on different sources of natural variance: Firstly, the F1 generation of the cross (‘Calardis Musqué’ × ‘Villard Blanc’) and secondly, somatic variants of the variety ‘Pinot Noir’ showing significantly different cluster compactness. The phenotypic assessment in both sources of natural variation identified six main drivers for cluster compactness. Cluster weight, berry number, berry volume, rachis length, shoulder length and pedicel length are main drivers of cluster compactness.
The genetic approach exposed eight overlapping regions with up to four quantitative trait loci for important architecture sub-traits that are physically co-located on the grapevine reference genome. In addition, several molecular markers with strong linkage to these cluster architecture sub-traits could be proposed. It was possible to exploit three of these markers for MAS against unwanted compactly clustered individuals. So, the number of undesirable compact clustered genotypes could be reduced by 29 % without selecting a single false positive in the investigated population. The gene expression of 15 candidate genes consistently correlates to cluster architecture variations of ‘Pinot Noir’ clones in a multi environmental experiment. The transcription factor gene PRE6 and six genes related to auxin metabolism, cell wall loosening, brassinosteroids and strigolactones showed differential expression in a further extended set of phenotypically divergent individuals from a genetically diverse background. The genetic approach and the gene expression experiments provide multiple lines of evidence for the reported candidate genes. Thus, the candidate genes presented here may have the capacity to be successfully involved in marker development with the aim of selecting cluster architecture traits in MAS enabling breeders to identify optimized breeding material with physical resilience to fungal pathogens such as Botrytis cinerea
Die Vorhersage der phänotypischen Leistung von Gerstenlinien mittels Modellierung von Metaboliten und Single Nucleotide Polymorphismen (SNPs) und die Aufklärung der zugrundeliegenden Genetik mittels Genomweiter Assoziationsstudie (GWAS)
Full text linkGerste (Hordeum vulgare ssp. vulgare) ist die viertwichtigste Kulturpflanze weltweit. Wie andere Nutzpflanzenarten leidet Gerste unter dem genetischen Flaschenhalseffekt, durch den weitere Leistungssteigerungen durch klassische Züchtungsmethoden zunehmend schwieriger werden. Deshalb sind indirekte Selektionsmethoden von großem Interesse. In dieser Arbeit wurden genomische Vorhersagen (GV) auf der Grundlage von 33.005 SNP-Markern und alternativ metabolische Vorhersagen (MV) auf der Grundlage von 128 Metaboliten berechnet. Es wurden mehrjährige agronomische Merkmale in der Nested Association Mapping (NAM)-Population HEB-25 vorhergesagt. Vorhersagefähigkeiten von bis zu 0,93 für die Pflanzenhöhe mit SNP-Markern und bis zu 0,59 für den Blühzeitpunkt mit Metaboliten wurden realisiert. Im zweiten Teil der Arbeit wurde eine genomweite Assoziationsstudie (GWAS) in HEB-25 durchgeführt, um metabolische quantitative Merkmalsloci (mQTL) zu identifizieren. Dabei wurden signifikante mQTL für mehrere Metaboliten gefunden. Alle diese Metaboliten konnten als Zucker klassifiziert werden. Zucker sind an der Signalinduktion, dem Pflanzenwachstum und der Pflanzenentwicklung beteiligt. Zucker-assoziierte Gene, die hauptsächlich für Zuckertransporter kodieren, wurden als Kandidatengene für die meisten mQTL identifiziert.Like other crops, barley (Hordeum vulgare ssp. vulgare), the fourth most important crop in the world, suffers from the genetic bottleneck effect, which makes further performance improvements through classical breeding methods difficult. Therefore, indirect selection methods are of great interest. In this work genomic prediction (GP) based on 33,005 SNP markers and alternatively, metabolic prediction (MP) based on 128 metabolites were applied. Multi-year agronomic traits in the Nested Association Mapping (NAM) population HEB-25 were predicted. Predictive abilities of up to 0.93 for plant height with SNP markers and up to 0.59 for flowering time with metabolites were realized. In the second part of this work, a genome-wide association study (GWAS) was conducted in HEB-25 to identify metabolic quantitative trait loci (mQTL). Significant mQTL were found for several metabolites. All these metabolites could be classified as sugars. Sugars are known to be involved in signal induction, plant growth and plant development. Sugar-associated genes, which mainly code for sugar transporters, have been identified as candidate genes for most mQTL
Predictive Modelling with Machine Learning in Plant Breeding
Full text linkGenomic prediction, originally proposed as a solution to the limitations of marker-assisted selection for complex traits, has become the standard for estimating breeding values in both inbred and hybrid crops. While linear models such as GBLUP and RR-BLUP remain effective in many cases, especially when assuming an additive genetic architecture, recent years have seen a growing interest in applying machine learning (ML) methods to overcome some of their constraints, including their limited capacity to model non-additive effects and nonlinear interactions. This thesis explored the influence of three key aspects on the success of genomic prediction: The choice of input features, the statistical model used, and the target trait or crop.
In terms of input features, marker data was compared to minimalist parentage-based models, haplotype blocks, and features generated using autoencoders. It was shown that even simple ML models using parentage-based information can rival marker-based GBLUP under certain conditions, which holds potential for small breeding programs with large amounts of historical, but ungenotyped, records. At the same time, dimensionality reduction techniques, especially a novel haplotype-based autoencoder that was developed during this thesis, were introduced to compress genomic data while preserving prediction accuracy and successfully accelerated model training.
Concerning the model aspect, a variety of ML algorithms were benchmarked using different approaches for hyperparameter tuning. Although no single model outperformed others across all traits and crops, ensemble approaches typically performed better than the individual models they were based on. Support vector machines seemed to be relatively unstable when compared to other ML based algorithms, such as tree-based models.
Finally, results showed that the accuracy of the genomic predictions was strongly dependent on differences between traits, crops with different breeding schemes, and different populations. For hybrids, ML performed well when SCA was more important for determining the hybrid yield than GCA. Large differences were observed for different fungal diseases in wheat, while differences among methods for the same disease were relatively similar.
While ML has not yet provided a significant improvement over traditional methods in many scenarios, its flexibility and potential for multi-modal data integration remain promising. The development of plant breeding-specific model architectures, such as haplotype-based autoencoders, may represent a more promising path than the general application of standard ML models.Sonstige Drittmittelgeber/-inne
Genetic dissection of cold tolerance in sorghum (Sorghum bicolor L. Moench)
Full text linkSorghum (Sorghum bicolor L. Moench), the 5th most important cereal crop belongs to the Poaceae grass family. According to records, it originated around 7000-5000 BC in the north-eastern part of Africa from where it traveled across the different parts of Africa, the middle east, India, China and eventually Americas, Australia, and finally Europe. As a result of multiple complex genomic interactions and selection, pressure can be broadly subdivided into the botanical classification of S. halepense, S. propinquum, and S. bicolor, and classification of cultivated forms of S. bicolor subsp. bicolor into five races, namely bicolor, guinea, caudatum, kafir, and durra. It is mainly grown in the lowlands and semi-arid regions of the tropics and subtropics and has been adapted to various contrasting environments for different end-products leading to an increase in morphological and genetic diversity. For example, in African countries, it is primarily grown as food grain and stalk, and leaves are valued as forage and building material. In the USA, its mainly used for livestock feed and ethanol production, whereas, in China, it is popular for manufacturing traditional alcoholic beverages.
Sorghum’s remarkable ability to survive and produce yields under extreme climatic conditions compared to most other grain crops makes it an important 'failsafe' source of food, feed, fiber, and fuel in the global agroecosystem. Future projections regarding changing climate and its negative effect on yield traits, highlight the urgency to harness new genetic resources and the ability of breeding programs to develop the required adaptations promptly. Sorghum has numerous agro- ecological advantages over other crops like maize when it comes to temperate climates. But few of the biggest hurdles for sorghum adaptation to cooler climates are juvenile and reproductive cold stress.
The present study reported a genetic characterization of the diverse, previously uncharacterized S.bicolor collection of the Uganda National Genebank, representing different agro-ecological zones of the country. High-resolution genotyping using reduced representation sequencing was used to characterize the material and study population genetics. More than 3000 S. bicolor accessions were genotyped using a panel of around 20,000 genome-wide DArTseq SNP markers and co-analyzed with a global sorghum collection genotyped previously with the same panel of markers for genetic diversity analysis and studying different interesting traits. The results revealed the presence of extensive genetic and racial diversity in predominantly admixed accessions and a unique, genetically isolated group of accessions from the southwestern Ugandan highlands, a region which low temperatures which potentially harbors genes of interest for breeding of sorghum in Germany and other temperate climate zones.
A representative core set of the novel Ugandan sorghum germplasm was analyzed to study juvenile cold tolerance. Data was collected from multi-year field trials and controlled climate chamber experiments. Genome-wide association studies were used to identify genomic regions involved in adaptation to cooler climatic conditions that could be of interest for the expansion of sorghum
production into temperate latitudes. This thesis can be considered a case study to illustrate the potential of genebank genomics to screen valuable, underutilized germplasm collections to evaluate various biological and agro-economical traits and alleles.
While farmers can avoid early-stage cold stress by later sowing (albeit at the expense of maturity and yield potential), there is no escape strategy for reproductive stage cold stress. This trait was analysed in another broad diversity panel consisting of 330 inbred lines of different origin, types of use, and subspecies from multi-location field trials including tropical high-altitude and temperate environments. In this study, several significant marker-trait associations were identified. This was further combined with local LD analysis, previously curated QTL data, and synteny to potential candidate genes in rice and maize to narrow down to interesting marker-trait associations to specific genomic regions involved in cold stress response.
This thesis can be considered a basis for selecting accessions for genetic diversity preservation and management, utilization in breeding programs, and establishing genetic relationships with other existing germplasm collections. The results provide important new insights for adaptive crop breeding in the face of climate change and the expansion of sorghum production to different regions. This will facilitate sorghum from being a "plant of the future" to transforming into a real-life major agricultural alternative
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