Publikasjoner
NIBIOs ansatte publiserer flere hundre vitenskapelige artikler og forskningsrapporter hvert år. Her finner du referanser og lenker til publikasjoner og andre forsknings- og formidlingsaktiviteter. Samlingen oppdateres løpende med både nytt og historisk materiale. For mer informasjon om NIBIOs publikasjoner, besøk NIBIOs bibliotek.
2019
Forfattere
Finn-Arne HaugenSammendrag
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Dario Isidro Ojeda Alayon Tiina M. Mattila Tom Ruttink Sonja T. Kujala Katri Kärkkäinen Jukka-Pekka Verta Tanja PyhäjärviSammendrag
Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.
Forfattere
Atle Wehn HegnesSammendrag
Purpose An important requirement when producers apply for protected designation of origin (PDO) or protected geographical indications (PGIs) is to adapt and agree on a concise definition of the geographical boundaries and area of the product. Whereas PDO products must be both strongly ecologically and culturally embedded in the specific area, PGI products are allowed a weaker degree of embeddedness. The research question of this paper is: How are geographical boundaries becoming PDOs and PGIs? The paper aims to discuss these issues. Design/methodology/approach The analysis is based on diverse forms of empirical material. Document studies of laws, policy documents, etc. have been analyzed to uncover what kind of measures and concepts that have been important for implementation of the scheme in Norway. Interviews with producer organizations have involved the persons responsible for working out product regulations in producer organizations. Interviews have also been conducted with key informants representing public administrative bodies administering the regulation. All interviews have been semi-structured. Findings The analysis identifies a set of important conditions for the boundary work of PDO-PGI in Norway. The conditions can generally be said to be characterized by a weak understanding of the food-people-places nexus and a strong reliance on instrumentalised system logic in how to deal with the map-nature dimension in boundary work. The short answer to the research question is that geographical boundaries are becoming PDO and PGI through controversies. Originality/value The controversies are characterized by what is defined as cultural adaptation work. The actors overall adaptation work is understood as the sum of the practices that takes place in the interplay between people’s translations of language and knowledge, reorganization of social relationships and transformation of materiality. The interplay is embedded in the tension between the global and the local, the old and the new and results in both intended and unintended consequences.
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Forfattere
Joshua Cabell Eva Brod Johan Ellingsen Anne-Kristin Løes Inger Beate Standal Bendik Tordnes Henriette VivestadSammendrag
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