Browsing by Subject "Adaptation"

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Adaptation of model organisms and environmental bacilli to glyphosate gives insight to species-specific peculiarities of the shikimate pathway
(2024) Schwedt, Inge; Commichau, Fabian M.
Glyphosate (GS), the active ingredient of the popular herbicide Roundup, inhibits the 5-enolpyruvyl shikimate-3-phosphate (EPSP) synthase of the shikimate pathway, which is present in archaea, bacteria, Apicomplexa, algae, fungi, and plants. In these organisms, the shikimate pathway is essential for de novo synthesis of aromatic amino acids, folates, quinones and other metabolites. Therefore, the GS-dependent inhibition of the EPSP synthase results in cell death. Previously, it has been observed that isolates of the soil bacteria Burkholderia anthina and Burkholderia cenocepacia are resistant to high amounts of GS. In the framework of this PhD thesis, it could be demonstrated that B. anthina isolates are not intrinsically resistant to GS. However, B. anthina rapidly adapts to the herbicide at the genome level and the characterization of GS-resistant suppressor mutants led to the discovery of a novel GS resistance mechanism. In B. anthina, the acquisition of loss-of-function mutations in the ppsR gene increases GS resistance. The ppsR gene encodes a regulator of the phosphoenolpyruvate (PEP) synthetase PpsA. In the absence of a functional PpsR protein, the bacteria synthesize more PEP, which competes with GS for binding in the active site of the EPSP synthase, increasing GS resistance. The EPSP synthase in B. anthina probably does not allow changes in the amino acid sequence as it is the case in other organisms. Indeed, the Gram-negative model organism Escherichia coli evolves GS resistance by the acquisition of mutations that either reduce the sensitivity of the EPSP synthase or increase the cellular concentration of the enzyme. Unlike E. coli, the EPSP synthase is also critical for the viability of Gram-positive model bacterium Bacillus subtilis. This observation is surprising because the enzyme belongs to the class of GS-insensitive EPSP synthases. In fact, the EPSP synthase is essential for growth of B. subtilis. The determination of the nutritional requirements allowing the growth of B. subtilis and E. coli mutants lacking EPSP synthase activity revealed that the demand for shikimate pathway intermediates is higher in the former organism. This finding explains why laboratory as well as environmental Bacilli exclusively adapt to GS by the mutational inactivation of glutamate transporter genes. Here, it was also shown that a B. subtilis mutant lacking EPSP synthase activity grows in minimal medium only when additional mutations accumulate in genes involved in the regulation of aerobic/anaerobic metabolism and central carbon metabolism. The characterization of these additional mutants will help to elucidate the peculiarities of the shikimate pathway in B. subtilis. Moreover, the mutants could be useful to identify the aromatic amino acid transporters that still await their discovery.
Assessment of phenotypic, genomic and novel approaches for soybean breeding in Central Europe
(2022) Zhu, Xintian; Würschum, Tobias
Soybean is the economically most important leguminous crop worldwide and serves as a main source of plant protein for human nutrition and animal feed. Europe is dependent on plant protein imports and the EU protein self-sufficiency, which is an issue that has been on the political agenda for several decades, has recently received renewed interest. The protein imports are mainly in the form of soybean meal, and soybean therefore appears well-suited to mitigate the protein deficit in Europe. This, however, requires an improvement of soybean production as well as an expansion of soybean cultivation and thus breeding of new cultivars that combine agronomic performance with adaptation to the climatic conditions in Central Europe. The objective of this thesis was to characterize, evaluate and devise approaches that can improve the efficiency of soybean breeding. Breeding is essentially the generation of new genetic variation and the subsequent selection of superior genotypes as candidates for new cultivars. The process of selection can be supported by marker-assisted or genomic selection, which are both based on molecular markers. A first step towards the utilization of these approaches in breeding is the characterization of the genetic architecture underlying the target traits. In this study, we therefore performed QTL mapping for six target traits in a large population of 944 recombinant inbred lines from eight biparental families. The results showed that some major-effect QTL are present that could be utilized in marker-assisted selection, but in general the target traits are quantitatively inherited. For such traits controlled by numerous small-effect QTL, genomic selection has proven as a powerful tool to assist selection in breeding programs. We therefore also evaluated the genomic prediction accuracy and found this to be high and promising for the six traits of interest. In conclusion, these results illustrated the potential of genomic selection for soybean breeding programs, but a potential limitation of this approach are the costs required for genotyping with molecular markers. Phenomic selection is an alternative approach that uses near-infrared or other spectral data for prediction instead of the marker data used for its genomic counterpart. Here, we evaluated the phenomic predictive ability in soybean as well as in triticale and maize. Phenomic prediction based on near-infrared spectroscopy (NIRS) of seeds showed a comparable or even slightly higher predictive ability than genomic prediction. Collectively, our results illustrate the potential of phenomic selection for breeding of complex traits in soybean and other crops. The advantage of this approach is that NIRS data are often available anyhow and can be generated with much lower costs than the molecular marker data, also in high-throughput required to screen the large numbers of selection candidates in breeding programs. Soybean is a short-day plant originating from temperate China, and thus adaptation to the climatic conditions of Central Europe is a major breeding goal. In this study, we established a large diversity panel of 1,503 early-maturing soybeans, comprising of European breeding material and accessions from genebanks. This panel was evaluated in six environments, which revealed valuable genetic variation that can be introgressed into our breeding programs. In addition, we deciphered the genetic architecture of the adaptation traits flowering time and maturity. Taken together, the findings of this study show the potential of several phenotypic, genomic and novel approaches that can be integrated to improve the efficiency of soybean breeding and thus hold great promise to assist the expansion of soybean cultivation in Central Europe through breeding of adapted and agronomically improved cultivars.
Molecular evidence of intraclonal variation and implications for adaptational traits of grape phylloxera populations (Daktulosphaira vitifoliae, Fitch)
(2007) Vorwerk, Sonja; Blaich, Rolf
Grape phylloxera (Daktulosphaira vitifoliae Fitch; Homoptera: Phylloxeridae) is an economical important insect pest of grapevine (Vitis spp.) worldwide. The insect was introduced with contaminated plant material from North America in the 1850s and spread rapidly across all European viticultural regions. In the 19th century, nearly three-forths of the ungrafted and highly susceptible European grape species were destroyed by the insect pest. European viticulture did not recover until the development of grafting, combining European Vitis vinifera varieties with resistant rootstocks, bred from American Vitis species. Grape phylloxera is still present in viticulture. Today, grape phylloxera populations mainly persist in abandoned vineyards and rootstock nurseries. Grape phylloxera populations seem to be variable in terms of genotypic composition and host adaptability. The lifecycle described by Fitch (1854) and others in the 19th century does not seem to match actual conditions anymore. This thesis aimed at redefining the genetic structure of European grape phylloxera populations by employing genetic markers. It was shown, that the insect has turned away from its classical holocycle and now mainly reproduces asexually, as already demonstrated for Australian grape phylloxera populations. Despite asexual reproduction, all examined populations revealed a high grade of genotypic diversity. The reports on the emergence of new and more aggressive strains raised the question, how a population composed of asexually reproducing organisms would change and adapt to such an extent. Using a multilocus marker system, eight single founder lineages were genetically monitored over at least 15 generations. All lineages revealed a high grade of intraclonal variation. Sequencing of polymorphic fragments showed, that the genetic variation was not due to contaminating plant or bacterial DNA, but was due to variation within the insect genome. Furthermore, mutations occured already in early generations and were not observed to accumulate in later generations. Mutations were rather generated constantly and only few mutation specific markers were identified to be stable over all following generations. The here documentated genetic variation reveals the great adaptational potential of this insect pest. The adaptability of single founder lineages was further assessed by measuring physiological parameters in single isolation chambers in the greenhouse. Parameters as the number of surviving individuals per generation, the number of eggs or the number of ovarioles per generation exposed differences in performance among the lineages and also within the lineages a high grade of intraclonal variation. A direct correlation of specific multilocus markers and particularly adapted individuals or lineages was not possible in this assay. Two markers, though, were observed to occure in several lineages which performed well on the new host plant. These markers may be a first step to the development of adaptation-related markers and need to be tested on further populations and host plants. When analysing intraclonal variation, the question of putative contaminating factors within the system arises. Symbiotic bacteria occuring in nearly all aphid species certainly are the first to be suspected as a source of genetic variation among single individuals tested. Endosymbiotic bacteria, as Buchnera aphidicola in other aphid species, influencing nutritional condition and fitness of the insect population, were not identified in D. vitifoliae. A bacterium, closely related to Pantoea agglomerans, however, was identified in several grape phylloxera populations, using universal 16S rDNA primers and later specifically developed markers, which were also employed for in situ hybridization. The bacterium was localized in the salivary pump of D. vitifoliae. PCR analysis of in vitro reared populations revealed that the bacterium is present in root- and leaf-feeding parthenogenetic populations of grape phylloxera and, moreover, seems to be transmitted from generation to generation. In other insect species, this bacterium has been demonstrated to produce antifungal and antibacterial substances, which were also found in first in vitro tests with grape phylloxera associated bacteria. The insect may benefit from the antagonistic potential of these bacteria. P. agglomerans may be a further participant in the certainly complex interaction of grape phylloxera and grapevine. This thesis represents a broad approach to elucidate the development of grape phylloxera populations in Europe. Using new molecular marker systems, it has become possible to gain more information on the genetic structure of the insect and its adaptational potential. The predominant clonal reproduction mode of the insect confronts grapevine breeders and pest management with the task to continously develop new resistant rootstocks and to keep up with new pest management systems.
Phenotypic and genomics-assisted breeding of soybean for Central Europe : from environmental adaptation to tofu traits
(2022) Kurasch, Alena; Würschum, Tobias
Soybean (Glycine max Merr.) is one of the major crops in the world providing an important source of protein and oil for food and feed; however it is still a minor crop in Central Europe. Soybean cultivation can play an important role in a more sustainable agricultural system by increasing local and regional protein production in Europe. The demand for locally produced soybean products is still growing in Europe. The key for a successful establishment of soybean cultivation in Europe is adaptation of soybean varieties to the Central European growing conditions. For the latitudinal adaptation to long-day conditions in Central to Northern Europe, an adapted early flowering and maturity time is of crucial importance for a profitable cultivation. The key traits flowering and maturity are quantitatively inherited and mainly affected by photoperiod responsiveness and temperature sensitivity. The most important loci for an early flowering and maturity are E1-E4 and the various allelic combinations condition soybean flowering and maturity time and therefore strongly contribute to the wide adaptability (Jiang et al., 2014; Tsubokura et al., 2014; M. Xu et al., 2013). Besides the main usage as protein source for animal feeding, soybean is also a very valuable source for human consumption. Tofu is enjoying ever greater popularity in Europe, as it is one of the best sources of plant protein with additional health benefits, rich in essential amino acids, beneficial lipids, vitamins, and minerals, as well as other bioactive compounds, such as isoflavones, soyasaponin, and others, (Lima et al., 2017; Zhang et al., 2018). Thus, plant breeding has to provide not only well-adapted varieties with good agronomic and quality properties, but also provide varieties well-suited to the further processing into soymilk and tofu. Therefore, a good knowledge about the breeding target, how to assess it and how it is inherited is crucial. The conducted studies covered a broad range of aspects relevant to improve a soybean breeding program. By combining environmental analysis, E-gene analysis, genomic approaches (QTL mapping and genomic prediction), and tofu phenotyping, breeder decisions become more accurate and targeted in the way of selection thereby increasing the genetic gain. In addition, combining the results of the different aspects helps to optimize the resources of a breeding program. Increasing the knowledge about the different aspects from environment to tofu QTL enables a breeder to be more precise and focused. But the more targeted and specific, the more complex a breeding program gets, which requires adequate tools to handle all the different information in a meaningful and efficient way to enable a quick and precise breeding decision.
Studies on flowering time and photoperiod sensitivity in domesticated and wild amaranth species (Amaranthus spp.)
(2023) Baturaygil, Ali; Schmid, Karl J.
Flowering time plays fundamental roles in the local adaptation and agricultural productivity of the crops. Photoperiodic response regulates the time of flowering by adjusting the response of plant circadian rhythm to environmental signals. Amaranth (Amaranthus spp.) is a short-day crop native to Central and South America, and mainly used as grain and vegetable. Hence, photoperiod sensitivity is a pivotal trait for grain amaranths in Central Europe climatic and long-day conditions, as it determines the local adaptability and the cultivation purpose of the crop i.e., grain or biomass production. However, the knowledge on the different aspects such as breeding, domestication history and adaptation genetics is very limited in grain amaranths. In this project, we studied such different aspects of grain amaranths by addressing the elucidative photoperiod sensitivity trait. In the first study, the phenotypic evaluation of biomass yield components revealed two distinct growth types. Of those, our ten biomass genotypes showed mild to high photoperiod sensitivity, flowered late or completely rejected flowering, reached long final plant heights and low dry matter content. In contrast, the only grain type variety showed photoperiod insensitivity, flowered early, and reached a short final plant height and a relatively higher dry matter content. Our results suggested that selection for both high dry matter yield and content requires a trade-off between photoperiod sensitivity and early flowering, due to the negative correlation between these traits. In the second study, characterization of genebank accessions from the three major grain species (A. caudatus, A. cruentus, A. hypochondriacus) and their wild relative species (A. hybridus and A. quitensis) for adaptive traits such as flowering time and seed setting under long-day conditions discovered a larger photoperiodic variation in the Central American accessions ranging from insensitivity to high sensitivity, whereas South American accessions showed a more narrow variation, limited by mild sensitivity. This result suggests the Central American origin of the wild relative A. hybridus, which might have migrated from Central to South America, and potentially has been selected against high photoperiod sensitivity. Moreover, we studied the environmental variables that may influence seed setting. Photoperiod insensitive accessions set seed regardless of their origin. However, mild photoperiod-sensitive accessions set seed, only if they were from warm center of origin. In the third study, we investigated the genetic architecture of photoperiod sensitivity. The bimodal-like flowering time distributions, and the linkage and association mapping studies using three different populations revealed that photoperiod sensitivity trait is controlled in an oligogenic manner. In particular, all three populations consistently found the same ‘consensus region’ that includes a very promising candidate gene called ‘response regulator of two-component system’. The homologs of this candidate gene are responsible for photoperiodic response in a variety of different crops and the model species Arabidopsis thaliana. In addition, the phenotypic analyses, and the marker data (i) showed photoperiod sensitivity guided pleiotropic relationships between the traits, (ii) revealed a potential epistatic behavior of the genomic region controlling photoperiod sensitivity, and (iii) showed the dominance of photoperiod sensitivity over insensitivity in that region.