Publications
NIBIOs employees contribute to several hundred scientific articles and research reports every year. You can browse or search in our collection which contains references and links to these publications as well as other research and dissemination activities. The collection is continously updated with new and historical material.
2020
Authors
Lélis A. Carlos-Júnior Joel C. Creed Rob Marrs Rob J. Lewis Timothy P. Moulton Rafael Feijó-Lima Matthew SpencerAbstract
Background Ecological communities tend to be spatially structured due to environmental gradients and/or spatially contagious processes such as growth, dispersion and species interactions. Data transformation followed by usage of algorithms such as Redundancy Analysis (RDA) is a fairly common approach in studies searching for spatial structure in ecological communities, despite recent suggestions advocating the use of Generalized Linear Models (GLMs). Here, we compared the performance of GLMs and RDA in describing spatial structure in ecological community composition data. We simulated realistic presence/absence data typical of many β-diversity studies. For model selection we used standard methods commonly used in most studies involving RDA and GLMs. Methods We simulated communities with known spatial structure, based on three real spatial community presence/absence datasets (one terrestrial, one marine and one freshwater). We used spatial eigenvectors as explanatory variables. We varied the number of non-zero coefficients of the spatial variables, and the spatial scales with which these coefficients were associated and then compared the performance of GLMs and RDA frameworks to correctly retrieve the spatial patterns contained in the simulated communities. We used two different methods for model selection, Forward Selection (FW) for RDA and the Akaike Information Criterion (AIC) for GLMs. The performance of each method was assessed by scoring overall accuracy as the proportion of variables whose inclusion/exclusion status was correct, and by distinguishing which kind of error was observed for each method. We also assessed whether errors in variable selection could affect the interpretation of spatial structure. Results Overall GLM with AIC-based model selection (GLM/AIC) performed better than RDA/FW in selecting spatial explanatory variables, although under some simulations the methods performed similarly. In general, RDA/FW performed unpredictably, often retaining too many explanatory variables and selecting variables associated with incorrect spatial scales. The spatial scale of the pattern had a negligible effect on GLM/AIC performance but consistently affected RDA’s error rates under almost all scenarios. Conclusion We encourage the use of GLM/AIC for studies searching for spatial drivers of species presence/absence patterns, since this framework outperformed RDA/FW in situations most likely to be found in natural communities. It is likely that such recommendations might extend to other types of explanatory variables.
Abstract
The Norwegian coastal goat is a national and endangered breed. Coastal goat populations are mainly divided with a large mainland and two small island populations. The objective of this study is to describe genetic diversity in the feral Skorpa island population and its relationship to the mainland coastal goat population (Selje) using the Norwegian milk goat population as a reference. Analyses were based on 96 samples genotyped by the CaprineSNP50 Beadchip from three populations; 7 Skorpa (SK), 37 Selje (SE) and 52 Norwegian milk goats (MG). The SK population had significantly less genetic variation and higher levels of inbreeding than the two other populations. It was more distant from the two mainland populations than they were from each other. The marginal contribution of the SK population to genetic diversity was small. Means of introducing genetic diversity into the SK population should be considered if the population is prioritized for conservation.
Authors
Dainis Rungis Matti W. Leino Liga Lepse Smiljana Goreta Ban Erik de Vahl Külli Annamaa Priit Põldma Terhi Suojala-Ahlfors Danguole Juskeviciene Chris Kik Ingunn M. Vågen Helena StavelikovaAbstract
Potato onions (Allium cepa var aggregatum G. Don) are multiplying or aggregating onions, very similar to shallots and have been historically cultivated throughout Europe. Currently in Northern Europe they are maintained in home gardens and ex situ field collections. Potato onions are primarily vegetatively propagated, however in Estonia, near Lake Peipsi, this species has been propagated by seed since the seventeenth century. There is increasing interest in Northern Europe in utilizing this germplasm in organic and/or sustainable farming systems. The genetic diversity and relationship between and within European potato onion collections is unclear. From historical records it is known that cultivation, exchange and trade of potato onion has occurred throughout Europe for hundreds of years. This study utilised molecular markers to assess genetic diversity, duplication of genotypes and relationships among and between Nordic, Baltic, Czech and Croatian potato onion collections. Of 264 accessions, 80 catalogued as unique had identical genotypes with one or more other accessions, and are putative duplicates. The genetic diversity within two Estonian sexually propagated accessions was comparable to that found in all of the vegetatively propagated accessions. Accessions from the Nordic countries grouped together genetically, as did Latvian and Lithuanian accessions. Croatian accessions were genetically separated. These genetic relationships suggest historical movement of potato onion germplasm in North-Eastern Europe. The results, in conjunction with other passport and characterization data, can assist in the development of potato onion core collections, facilitating the conservation and utilization of valuable potato onion genetic resources.
Abstract
Key message A locus on wheat chromosome 2A was found to control feld resistance to both leaf and glume blotch caused by the necrotrophic fungal pathogen Parastagonospora nodorum. Abstract The necrotrophic fungal pathogen Parastagonospora nodorum is the causal agent of Septoria nodorum leaf blotch and glume blotch, which are common wheat (Triticum aestivum L.) diseases in humid and temperate areas. Susceptibility to Septoria nodorum leaf blotch can partly be explained by sensitivity to corresponding P. nodorum necrotrophic efectors (NEs). Susceptibility to glume blotch is also quantitative; however, the underlying genetics have not been studied in detail. Here, we genetically map resistance/susceptibility loci to leaf and glume blotch using an eight-founder wheat multiparent advanced generation intercross population. The population was assessed in six feld trials across two sites and 4 years. Seedling infltration and inoculation assays using three P. nodorum isolates were also carried out, in order to compare quantitative trait loci (QTL) identifed under controlled conditions with those identifed in the feld. Three signifcant feld resistance QTL were identifed on chromosomes 2A and 6A, while four signifcant seedling resistance QTL were detected on chromosomes 2D, 5B and 7D. Among these, QSnb.niab-2A.3 for feld resistance to both leaf blotch and glume blotch was detected in Norway and the UK. Colocation with a QTL for seedling reactions against culture fltrate from a Norwegian P. nodorum isolate indicated the QTL could be caused by a novel NE sensitivity. The consistency of this QTL for leaf blotch at the seedling and adult plant stages and culture fltrate infltration was confrmed by haplotype analysis. However, opposite efects for the leaf blotch and glume blotch reactions suggest that diferent genetic mechanisms may be involved.
Abstract
Understanding how populations are structured in space and time is a central question in evolutionary biology. Parasites and their hosts are assumed to evolve together, however, detailed understanding of mechanisms leading to genetic structuring of parasites and their hosts are lacking. As a parasite depends on its host, studying the genetic structure of both parasite and host can reveal important insights into these mechanisms. Here, genetic structure of the monogenean parasite Gyrodactylus thymalli and its host the European grayling (Thymallus thymallus) was investigated in 10 tributaries draining into the large Lake Mjøsa in Norway. The population genetic structure of spawning grayling was studied using microsatellite genotyping, while G. thymalli was studied by sequencing a mitochondrial DNA gene (dehydrogenase subunit 5). Two main genetic clusters were revealed in grayling, one cluster comprising grayling from the largest spawning population, while the remaining tributaries formed the second cluster. For both taxa, some genetic differentiation was observed among tributaries, but there was no clear isolation-by-distance signature. The structuring was stronger for the host than for the parasite. These results imply that moderate to high levels of gene flow occur among the sub-populations of both taxa. The high parasite exchange among tributaries could result from a lack of strong homing behavior in grayling as well as interactions among individual fish outside of the spawning season, leading to frequent mixing of both host and parasite.
Abstract
The necrotrophic fungal pathogen Parastagonospora nodorum causes Septoria nodorum blotch (SNB), which is one of the dominating leaf blotch diseases of wheat in Norway. A total of 165 P. nodorum isolates were collected from three wheat growing regions in Norway from 2015 to 2017. These isolates, as well as nine isolates from other countries, were analyzed for genetic variation using 20 simple sequence repeat (SSR) markers. Genetic analysis of the isolate collection indicated that the P. nodorum pathogen population infecting Norwegian spring and winter wheat underwent regular sexual reproduction and exhibited a high level of genetic diversity, with no genetic subdivisions between sampled locations, years or host cultivars. A high frequency of the presence of necrotrophic effector (NE) gene SnToxA was found in Norwegian P. nodorum isolates compared to other parts of Europe, and we hypothesize that the SnToxA gene is the major virulence factor among the three known P. nodorum NE genes (SnToxA, SnTox1, and SnTox3) in the Norwegian pathogen population. While the importance of SNB has declined in much of Europe, Norway has remained as a P. nodorum hotspot, likely due at least in part to local adaptation of the pathogen population to ToxA sensitive Norwegian spring wheat cultivars.
Authors
Cornelya KlutschAbstract
No abstract has been registered
Authors
Simo Maduna Adam Vivian-Smith Ólöf Dóra Bartels Jónsdóttir Albert Imsland Cornelya Klutsch Tommi Nyman Hans Geir Eiken Snorre HagenAbstract
The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as linkage mapping, parentage analysis, marker-assisted selection (MAS), quantitative trait loci (QTL) analysis, and assessing adaptive genetic diversity are currently available for the species. Here, we identify both genome- and transcriptome-derived microsatellites loci from C. lumpus to facilitate such applications. Across 2,346 genomic contigs, we detected a total of 3,067 microsatellite loci, of which 723 were the most suitable ones for primer design. From 116,555 transcriptomic unigenes, we identified a total of 231,556 microsatellite loci, which may indicate a high coverage of the available STRs. Out of these, primer pairs could only be designed for 6,203 loci. Dinucleotide repeats accounted for 89 percent and 52 percent of the genome- and transcriptome-derived microsatellites, respectively. The genetic composition of the dominant repeat motif types showed differences from other investigated fish species. In the genome-derived microsatellites AC/GT (67.8 percent), followed by AG/CT (15.1 percent) and AT/AT (5.6 percent) were the major motifs. Transcriptome-derived microsatellites showed also most dominantly the AC/GT repeat motif (33 percent), followed by A/T (26.6 percent) and AG/CT (11 percent). Functional annotation of microsatellite-containing transcriptomic sequences showed that the majority of the expressed sequence tags encode proteins involved in cellular and metabolic processes, binding activity and catalytic reactions. Importantly, STRs linked to genes involved in immune system process, growth, locomotion and reproduction were discovered in the present study. The extensive genomic marker information reported here will facilitate molecular ecology studies, conservation initiatives and will benefit many aspects of the breeding programmes of C. lumpus.
Authors
Gillian Butler Carsten Malisch Elisabet Nadeau Anna Woodhouse Bjørn Egil Flø Tomasz Sakowski Flaviana Gottardo Giorgia Riuzzi Hannah Davis Håvard SteinshamnAbstract
No abstract has been registered
Authors
Gillian Butler Carsten Malisch Elisabet Nadeau Anna Woodhouse Bjørn Egil Flø Tomasz Sakowski Flaviana Gottardo Giorgia Riuzzi Hannah Davis Håvard SteinshamnAbstract
The SusCatt project investigates alternative systems to improve sustainability in European cattle production, taking different approaches in Norway, Sweden, Germany, Poland, UK and Italy – all making greater use of pasture and forage, reducing damaging or external inputs. Rather than us deciding on how we tell everybody about findings, one project task is to ask potential audiences about their sources of information – how they gain knowledge? Ideally, this will offer guidance on an effective dissemination strategy. Project messages are relevant to multiple sectors: farmers, extension workers, consumers and policy makers. Attempts were made to survey these multiple stakeholders. We collected 236 opinions and found considerable variation, not only between groups but also between the same sectors in different countries. The most popular and highest-ranking sources overall were traditional press formats of newspapers and magazines. On the other hand, accessing information from social media was very polarised; almost non-existent for German and Polish stakeholders but widely used by UK farmers (possibly skewed by the dominance of face-to-face rather than on-line data collection). Findings suggest that each message from research projects needs a customized approach in dissemination, depending on the target audience and their regular habits of sourcing information