Reliable allele detection using SNP-based PCR primers containing Locked Nucleic Acid: application in genetic mapping

BACKGROUND: The diploid, Solanum caripense, a wild relative of potato and tomato, possesses valuable resistance to potato late blight and we are interested in the genetic base of this resistance. Due to extremely low levels of genetic variation within the S. caripense genome it proved impossible to generate a dense genetic map and to assign individual Solanum chromosomes through the use of conventional chromosome-specific SSR, RFLP, AFLP, as well as gene- or locus-specific markers. The ease of detection of DNA polymorphisms depends on both frequency and form of sequence variation. The narrow genetic background of close relatives and inbreds complicates the detection of persisting, reduced polymorphism and is a challenge to the development of reliable molecular markers. Nonetheless, monomorphic DNA fragments representing not directly usable conventional markers can contain considerable variation at the level of single nucleotide polymorphisms (SNPs). This can be used for the design of allele-specific molecular markers. The reproducible detection of allele-specific markers based on SNPs has been a technical challenge. RESULTS: We present a fast and cost-effective protocol for the detection of allele-specific SNPs by applying Sequence Polymorphism-Derived (SPD) markers. These markers proved highly efficient for fingerprinting of individuals possessing a homogeneous genetic background. SPD markers are obtained from within non-informative, conventional molecular marker fragments that are screened for SNPs to design allele-specific PCR primers. The method makes use of primers containing a single, 3'-terminal Locked Nucleic Acid (LNA) base. We demonstrate the applicability of the technique by successful genetic mapping of allele-specific SNP markers derived from monomorphic Conserved Ortholog Set II (COSII) markers mapped to Solanum chromosomes, in S. caripense. By using SPD markers it was possible for the first time to map the S. caripense alleles of 16 chromosome-specific COSII markers and to assign eight of the twelve linkage groups to consensus Solanum chromosomes. CONCLUSION: The method based on individual allelic variants allows for a level-of-magnitude higher resolution of genetic variation than conventional marker techniques. We show that the majority of monomorphic molecular marker fragments from organisms with reduced heterozygosity levels still contain SNPs that are sufficient to trace individual alleles

A compendium of genome-wide sequence reads from NBS (nucleotide binding site) domains of resistance genes in the common potato

SolariX is a compendium of DNA sequence tags from the nucleotide binding site (NBS) domain of disease resistance genes of the common potato, Solanum tuberosum Group Tuberosum. The sequences, which we call NBS tags, for nearly all NBS domains from 91 genomes—representing a wide range of historical and contemporary potato cultivars, 24 breeding programs and 200 years—were generated using just 16 amplification primers and high-throughput sequencing. The NBS tags were mapped to 587 NBS domains on the draft potato genome DM, where we detected an average, over all the samples, of 26 nucleotide polymorphisms on each locus. The total number of NBS domains observed, differed between potato cultivars. However, both modern and old cultivars possessed comparable levels of variability, and neither the individual breeder or country nor the generation or time appeared to correlate with the NBS domain frequencies. Our attempts to detect haplotypes (i.e., sets of linked nucleotide polymorphisms) frequently yielded more than the possible 4 alleles per domain indicating potential locus intermixing during the mapping of NBS tags to the DM reference genome. Mapping inaccuracies were likely a consequence of the differences of each cultivar to the reference genome used, coupled with high levels of NBS domain sequence similarity. We illustrate that the SolariX database is useful to search for polymorphism linked with NBS-LRR R gene alleles conferring specific disease resistance and to develop molecular markers for selection

The Open Science Fellows Program: Practicing Open Science

Der Aufsatz gibt die persönlichen Erfahrungen der Autorin mit offener Wissenschaft während des Studiums und als Fellow des Fellow-Programms Freies Wissen wieder. Einleitend wird eine kurze Einführung zum Begriff „Open Science“, offene Wissenschaft, sowie den damit zusammenhängenden Prinzipien gegeben, um anschließend über deren Anwendung in den Studiengängen Klassische Archäologie und Computerlinguistik zu reflektieren. Es folgt eine Vorstellung des Fellow-Programms und ein Überblick der Aktivitäten und die praktische Anwendung der Prinzipien anhand eines Projektes zur Erstellung einer interaktiven, offenen Online-Bibliografie während der achtmonatigen Laufzeit der Programmrunde 2018/2019.The paper presents the personal experience of the author with Open Science during her academic studies and as a fellow of the Fellow-Programm Freies Wissen. The concept “Open Science” is introduced along its accompanying principles. The author reflects upon the application of those principles during her studies of Classical Archaeology and Computational Linguistics. An introduction to the Fellow-Programme is also provided, along an overview of the author’s activities and implementation of the principles during the eight months period of the programme 2018/2019, where a project to create an interactive, open, and online bibliography was pursued

Metabolic potential of endophytic bacteria

The bacterial endophytic microbiome promotes plant growth and health and beneficial effects are in many cases mediated and characterized by metabolic interactions. Recent advances have been made in regard to metabolite production by plant microsymbionts showing that they may produce a range of different types of metabolites. These substances play a role in defense and competition, but may also be needed for specific interaction and communication with the plant host. Furthermore, few examples of bilateral metabolite production are known and endophytes may modulate plant metabolite synthesis as well. We have just started to understand such metabolic interactions between plants and endophytes, however, further research is needed to more efficiently make use of beneficial plant-microbe interactions and to reduce pathogen infestation as well as to reveal novel bioactive substances of commercial interest

One Schema to Rule them All. The Inner Workings of the Digital Archive ARCHE

A Resource Centre for the HumanitiEs (ARCHE) ist ein digitales Archiv, das vom Austrian Centre for Digital Humanities an der Österreichischen Akademie der Wissenschaften betrieben wird. Das Archiv speichert Daten aus dem gesamten Bereich der Geisteswissenschaften und bietet eine persistente Aufbewahrung und Bereitstellung von Ressourcen. Es wird der technische Aufbau von ARCHE beschrieben, wobei das Augenmerk auf das für die Auffindbarkeit, den Zugriff und die Nachnutzung von Daten maßgeschneiderte Metadatenschema gelegt wird. Darüberhinaus verbindet das Schema die verschiedenen Systemkomponenten, enthält Mappings auf andere wohlbekannte Schemata, stellt mehrsprachige Label für die GUI-Ansicht bereit und wird verwendet, um ein Metadatenformular zu generieren.A Resource Centre for the HumanitiEs (ARCHE) is a digital archive provided by the Austrian Centre for Digital Humanities, which is part of the Austrian Academy of Sciences. The archive welcomes data from all humanities fields and offers persistent hosting as well as dissemination of resources. The technical setup of ARCHE is described, focusing on the bespoke metadata schema that was created to help in finding, accessing, and reusing data. Beyond that the schema binds together the different system components, contains mappings to other well-known schemas, provides multilingual labels for GUI display, and is used to generate a metadata form

One Schema to Rule them All. The Inner Workings of the Digital Archive ARCHE

A Resource Centre for the HumanitiEs (ARCHE) is a digital archive provided by the Austrian Centre for Digital Humanities, which is part of the Austrian Academy of Sciences. The archive welcomes data from all humanities fields and offers persistent hosting as well as dissemination of resources. The technical setup of ARCHE is described, focusing on the bespoke metadata schema that was created to help in finding, accessing, and reusing data. Beyond that the schema binds together the different system components, contains mappings to other well-known schemas, provides multilingual labels for GUI display, and is used to generate a metadata form

One schema to rule them all. The inner workings of the digital archive Arche

A Resource Centre for the HumanitiEs (ARCHE) is a digital archive provided by the Austrian Centre for Digital Humanities, which is part of the Austrian Academy of Sciences. The archive welcomes data from all humanities fields and offers persistent hosting as well as dissemination of resources. The technical setup of ARCHE is described, focusing on the bespoke metadata schema that was created to help in finding, accessing, and reusing data. Beyond that the schema binds together the different system components, contains mappings to other well-known schemas, provides multilingual labels for GUI display, and is used to generate a metadata form

Data Curation: How and Why. A Showcase with Re-use Scenarios.

IANUS is funded by the German Research Foundation (DFG) with the objective to build up a digital archive for archaeology and ancient studies in Germany. A first three year phase of conceptual work is now being followed by a second, in which the concepts get implemented and the data centre begins its operational work. Data curation is essential for preservation of digital data and helps to detect errors, aggregate documentation, ensure the reusability of data and in some cases even add further functionality and additional files. This paper will present the workflow of data curation based on a data collection about European vertebrate fauna and will exemplify the different data processing stages at IANUS according to the OAIS model – from its initial submission until its final presentation on the recently established data portal. One aspect of this will be the discussion of the archival information package. To enable and ease the reusability of research data, it is useful to enrich the data. This includes the GIS integration of geographic informations and reutilisation of bibliography. Finally a re-use scenario of research data stored in the IANUS repository will be presented that offers researchers a unified search and discovery facilities over several distributed and heterogeneous datasets by using Semantic Web technologies.  

Genetic Population Structure of Cacao Plantings within a Young Production Area in Nicaragua

Significant cocoa production in the municipality of Waslala, Nicaragua, began in 1961. Since the 1980s, its economic importance to rural smallholders increased, and the region now contributes more than 50% of national cocoa bean production. This research aimed to assist local farmers to develop production of high-value cocoa based on optimal use of cacao biodiversity. Using microsatellite markers, the allelic composition and genetic structure of cacao was assessed from 44 representative plantings and two unmanaged trees. The population at Waslala consists of only three putative founder genotype spectra (lineages). Two (B and R) were introduced during the past 50 years and occur in >95% of all trees sampled, indicating high rates of outcrossing. Based on intermediate allelic diversity, there was large farm-to-farm multilocus genotypic variation. GIS analysis revealed unequal distribution of the genotype spectra, with R being frequent within a 2 km corridor along roads, and B at more remote sites with lower precipitation. The third lineage, Y, was detected in the two forest trees. For explaining the spatial stratification of the genotype spectra, both human intervention and a combination of management and selection driven by environmental conditions, appear responsible. Genotypes of individual trees were highly diverse across plantings, thus enabling selection for farm-specific qualities. On-farm populations can currently be most clearly recognized by the degree of the contribution of the three genotype spectra. Of two possible strategies for future development of cacao in Waslala, i.e. introducing more unrelated germplasm, or working with existing on-site diversity, the latter seems most appropriate. Superior genotypes could be selected by their specific composite genotype spectra as soon as associations with desired quality traits are established, and clonally multiplied. The two Y trees from the forest share a single multilocus genotype, possibly representing the Mayan, ‘ancient Criollo’ cacao

Diversity of cacao trees in Waslala, Nicaragua: Associations between genotype spectra, product quality and yield potential

The sensory quality and the contents of quality-determining chemical compounds in unfermented and fermented cocoa from 100 cacao trees (individual genotypes) representing groups of nine genotype spectra (GG), grown at smallholder plantings in the municipality of Waslala, Nicaragua, were evaluated for two successive harvest periods. Cocoa samples were fermented using a technique mimicking recommended on-farm practices. The sensory cocoa quality was assessed by experienced tasters, and seven major chemical taste compounds were quantified by near infrared spectrometry (NIRS). The association of the nine, partially admixed, genotype spectra with the analytical and sensory quality parameters was tested. The individual parameters were analyzed as a function of the factors GG and harvest (including the date of fermentation), individual trees within a single GG were used as replications. In fermented cocoa, significant GG-specific differences were observed for methylxanthines, theobromine-to-caffeine (T/C) ratio, total fat, procyanidin B5 and epicatechin, as well as the sensory attributes global score, astringency, and dry fruit aroma, but differences related to harvest were also apparent. The potential cocoa yield was also highly determined by the individual GG, although there was significant tree-to-tree variation within every single GG. Non-fermented samples showed large harvest-to-harvest variation of their chemical composition, while differences between GG were insignificant. These results suggest that selection by the genetic background, represented here by groups of partially admixed genotype spectra, would be a useful strategy toward enhancing quality and yield of cocoa in Nicaragua. Selection by the GG within the local, genetically segregating populations of seedpropagated cacao, followed by clonal propagation of best-performing individuals of the selected GG could be a viable alternative to traditional propagation of cacao by seed from open pollination. Fast and gentle air-drying of the fermented beans and their permanent dry storage were an efficient and comparatively easy precondition for high cocoa quality. (Résumé d'auteur