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
Abstract
This chapter emphasizes the need for active stakeholder engagement right through from strategy development to planning and implementation, to realize the benefits of sustainable bioeconomy development. In general, this varies between regions and countries. In the EU, it is considered important to engage stakeholders at all stages, whereas in developing countries engaging stakeholders so far has not been given much importance when launching new strategies. Stakeholders, including the private sector, research institutions, farmers organizations, the government and non-governmental organizations, all have important roles to play. The chapter focuses on the why, how and what type of stakeholders should be engaged, and the relevant benefits and challenges. It discusses experiences from the EU and other regions where stakeholder engagement (both formal and informal) and participative governance have led to or are necessary for successful and sustainable bioeconomy development.
Authors
Erik J. M. Koenen Dario Isidro Ojeda Alayon Freek T. Bakker Jan J. Wieringa Catherine Kidner Olivier J. Hardy R. Toby Pennington Patrick S. Herendeen Anne Bruneau Colin E. HughesAbstract
The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous–Paleogene (K–Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events]
Authors
Paal KrokeneAbstract
No abstract has been registered
Abstract
Recent discoveries have highlighted multiple mitotically and meiotically inherited alterations in gene expression that could not be explained solely by changes in the DNA sequence but were acknowledged as epigenetic. The modern view on epigenetics considers it as an integral part of genetics. Epigenetic mechanisms are encoded by genes in the genome and contribute to an essential part of genomic diversity, significantly extending its regulatory abilities. Epigenetic mechanisms involve molecular chromatin alterations through DNA methylation and histone modifications, as well as, complex non-coding RNAs and related enzyme machinery leading to changes in gene expression and resulting in changing phenotypes. In plants, epigenetic mechanisms may occur over their lifetime and across multiple generations, and can contribute substantially to phenotypic plasticity, stress responses, disease resistance, acclimation and adaptation to habitat conditions. In this review, we summarize recent advances with regards to Norway spruce epigenomics. We first consider the large size of the spruce genome that is linked to epigenetic mechanisms and why epigenomics is vitally important for spruce. Then, we discuss the molecular machinery supporting epigenetic mechanisms in Norway spruce and putative gene models involved. We presume substantial extension of gene families of epigenetic regulators and non-coding RNAs, especially in reproductive tissues. Norway spruce was the first species among forest trees in which epigenetic memory and epigenetic mechanisms were studied. The induction of an epigenetic memory during sexual reproduction and somatic embryogenesis has been described in Norway spruce. We discuss the latest results of epigenomic variation and epigenetic memory studies in Norway spruce and define the future perspectives for epigenetic studies. However, there is still a long way to decipher how the epigenetic mechanisms are involved in maintaining the stability of the spruce epigenome, how the epigenome is set to produce the epigenetic memory phenomenon and how these may result in an increased rate of adaptation to a changing environment.
Authors
Rosemary Collier Dominique Mazzi Annette Folkedal Schjøll Quentin Schorpp Gunda Thöming Tor J. Johansen Richard Meadow Nicolai Vitt Meyling Anne-Marie Cortesero Ute Vogler Michael T. Gaffney Martin HommesAbstract
Several important vegetable crops grown outdoors in temperate climates in Europe can be damaged by the root-feeding larvae of Diptera (Delia radicum, Delia floralis, Chamaepsila rosae, Delia platura, Delia florilega, Delia antiqua). Knowledge of pest insect phenology is a key component of any Integrated Pest Management (IPM) strategy, and this review considers the methods used to monitor and forecast the occurrence of root-feeding flies as a basis for decision-making by growers and the ways that such information can be applied. It has highlighted some current management approaches where such information is very useful for decision support, for example, the management of C. rosae with insecticidal sprays and the management of all of these pests using crop covers. There are other approaches, particularly those that need to be applied at sowing or transplanting, where knowledge of pest phenology and abundance is less necessary. Going forward, it is likely that the number of insecticidal control options available to European vegetable growers will diminish and they will need to move from a strategy which often involves using a single ‘silver bullet’ to a combination of approaches/tools with partial effects (applied within an IPM framework). For the less-effective, combined methods, accurate information about pest phenology and abundance and reliable decision support are likely to be extremely important.
Abstract
Genetic selection in commercial sheep production has mainly focussed on production traits and to a large extent ignoring behavioural traits, such as response towards predators. The Icelandic leadersheep is a sheep breed selected and known for its special behavioural traits, such as leading the flock and bringing it home from pasture in case of danger. Those traits are also said to be beneficial in areas with a high predator pressure. In this study, it was investigated if there are behavioural differences in sheep flocks with and without a leadersheep present. Behaviour of sheep flocks was observed before, during and after a predator test, in small groups of Icelandic sheep with or without a leadersheep in the group. Eleven groups of Icelandic sheep with six ewes in each group were observed in a test arena while a human, a dog and a drone passed through the pasture. Six of the groups included a leadersheep and the remaining five did not. Groups including a leadersheep spent more time grazing after both the human and dog test, indicating a faster recovering to normal behaviour. They were also located close to the exit during the dog test compared to groups without a leadersheep, fitting well with the assertion that leadersheep bring the flock home in case of danger. During the drone test, groups with a leadersheep however spent more time moving around compared to the other groups. Since the sheep had experienced both humans and dogs before, but not drones, this may indicate that groups with leadersheep recovered quickly from the figurants they had experienced before, but tended to react more in the test which was a new situation. In conclusion, it appears likely that the earlier selection for leader traits in the leadersheep have indeed changed both their own behaviour and also that this has an effect on the behaviour of group members.
Authors
Aurita Butkeviciute Mindaugas Liaudanskas Darius Kviklys Dalia Gelvonauskiene Valdimaras JanulisAbstract
As the interest in heirloom cultivars of apple trees, their fruit, and processed products is growing worldwide, studies of the qualitative and quantitative composition of biological compounds are important for the evaluation of the quality and nutritional properties of the apples. Studies on the variations in the chemical composition of phenolic compounds characterized by a versatile biological effect are important when researching the genetic heritage of the heirloom cultivars in order to increase the cultivation of such cultivars in orchards. A variation in the qualitative and quantitative composition of phenolic compounds was found in apple samples of cultivars included in the Lithuanian collection of genetic resources. By the high-performance liquid chromatography (HPLC) method flavan-3-ols (procyanidin B1, procyanidin B2, procyanidin C2, (+)-catechin and (−)-epicatechin), flavonols (rutin, hyperoside, quercitrin, isoquercitrin, reynoutrin and avicularin), chlorogenic acids and phloridzin were identified and quantified in fruit samples of heirloom apple cultivars grown in Lithuania. The highest sum of the identified phenolic compounds (3.82 ± 0.53 mg/g) was found in apple fruit samples of the ‘Koštelė’ cultivar
Authors
Michal SposobAbstract
No abstract has been registered
Authors
Ahto Agan Rein Drenkhan Kalev Adamson Leho Tedersoo Halvor Solheim Isabella Børja Iryna Matsiakh Volkmar Timmermann Nina Elisabeth Nagy Ari HietalaAbstract
European ash (Fraxinus excelsior) is threatened by the invasive ascomycete Hymenoscyphus fraxineus originating from Asia. Ash leaf tissues serve as a route for shoot infection but also as a sporulation substrate for this pathogen. Knowledge of the leaf niche partitioning by indigenous fungi and H. fraxineus is needed to understand the fungal community receptiveness to the invasion. We subjected DNA extracted from unwashed and washed leaflets of healthy and diseased European ash to PacBio sequencing of the fungal ITS1-5.8S-ITS2 rDNA region. Leaflets from co-inhabiting rowan trees (Sorbus aucuparia) served as a reference. The overlap in leaflet mycobiomes between ash and rowan was remarkably high, but unlike in rowan, in ash leaflets the sequence read proportion, and the qPCR-based DNA amount estimates of H. fraxineus increased vigorously towards autumn, concomitant with a significant decline in overall fungal richness. The niche of ash and rowan leaves was dominated by epiphytic propagules (Vishniacozyma yeasts, the dimorphic fungus Aureobasidion pullulans and the dematiaceous hyphomycete Cladosporium ramotenellum and H. fraxineus), and endophytic thalli of biotrophs (Phyllactinia and Taphrina species), the indigenous necrotroph Venturia fraxini and H. fraxineus. Mycobiome comparison between healthy and symptomatic European ash leaflets revealed no significant differences in relative abundance of H. fraxineus, but A. pullulans was more prevalent in symptomatic trees. The impacts of host specificity, spatiotemporal niche partitioning, species carbon utilization profiles and life cycle traits are discussed to understand the ecological success of H. fraxineus in Europe. Further, the inherent limitations of different experimental approaches in the profiling of foliicolous fungi are addressed.
Abstract
An understanding of the relationship between volume increment and stand density (basal area, stand density index, etc.) is of utmost importance for properly managing stand density to achieve specific management objectives. There are two main approaches to analyse growth–density relationships. The first relates volume increment to stand density through a basic relationship, which can vary with site productivity, age, and potentially incorporates treatment effects. The second is to relate the volume increment and density of thinned experimental plots relative to that of an unthinned experimental plot on the same site. Using a dataset of 229 thinned and unthinned experimental plots of Norway spruce, a growth model is developed describing the relationship between gross or net volume increment and basal area. The models indicate that gross volume increases with increasing basal area up to 50 m2 and thereafter becomes constant out to the maximum basal area. Alternatively, net volume increment was maximized at a basal area of 43 m2 and decreased with further increases in basal area. However, the models indicated a wide range where net volume increment was essentially constant, varying by less than 1 m3 ha−1 year−1. An analysis of different thinning scenarios indicated that the relative relationship between volume increment and stand density was dynamic and changed over the course of a rotation.