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.
2023
Forfattere
Tomás Brůna Rishi Aryal Olga Dudchenko Daniel James Sargent Daniel Mead Matteo Buti Andrea Cavallini Timo Hytönen Javier Andrés Melanie Pham David Weisz Flavia Mascagni Gabriele Usai Lucia Natali Nahla Bassil Gina E. Fernandez Alexandre Lomsadze Mitchell Armour Bode Olukolu Thomas Poorten Caitlin Britton Jahn Davik Hamid Ashrafi Erez Lieberman Aiden Mark Borodovsky Margaret WorthingtonSammendrag
Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosomelength assembly and annotation of the diploid blackberry germplasm accession “Hillquist” (R. argutus). “Hillquist” is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The “Hillquist” assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298Mb, of which 270Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the “Hillquist” genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.
Forfattere
R. Jordan Price Jahn Davik Felicidad Fernandez Fernandez Helen J. Bates Samantha Lynn Charlotte F. Nellist Matteo Buti Dag Røen Nada Surbanovski Muath K Alsheikh Richard J. Harrison Daniel James SargentSammendrag
Red raspberry (Rubus idaeus L.) is an economically valuable soft-fruit species with a relatively small (~300 Mb) but highly heterozygous diploid (2n = 2x = 14) genome. Chromosome-scale genome sequences are a vital tool in unravelling the genetic complexity controlling traits of interest in crop plants such as red raspberry, as well as for functional genomics, evolutionary studies, and pan-genomics diversity studies. In this study, we developed genome sequences of a primocane fruiting variety (‘Autumn Bliss’) and a floricane variety (‘Malling Jewel’). The use of long-read Oxford Nanopore Technologies sequencing data yielded long read lengths that permitted well resolved genome sequences for the two cultivars to be assembled. The de novo assemblies of ‘Malling Jewel’ and ‘Autumn Bliss’ contained 79 and 136 contigs respectively, and 263.0 Mb of the ‘Autumn Bliss’ and 265.5 Mb of the ‘Malling Jewel’ assembly could be anchored unambiguously to a previously published red raspberry genome sequence of the cultivar ‘Anitra’. Single copy ortholog analysis (BUSCO) revealed high levels of completeness in both genomes sequenced, with 97.4% of sequences identified in ‘Autumn Bliss’ and 97.7% in ‘Malling Jewel’. The density of repetitive sequence contained in the ‘Autumn Bliss’ and ‘Malling Jewel’ assemblies was significantly higher than in the previously published assembly and centromeric and telomeric regions were identified in both assemblies. A total of 42,823 protein coding regions were identified in the ‘Autumn Bliss’ assembly, whilst 43,027 were identified in the ‘Malling Jewel’ assembly. These chromosome-scale genome sequences represent an excellent genomics resource for red raspberry, particularly around the highly repetitive centromeric and telomeric regions of the genome that are less complete in the previously published ‘Anitra’ genome sequence.
Forfattere
Liv Gilpin Dag Røen Marian Schubert Jahn Davik Kimmo Rumpunen Kristina Alme Gardli Stein Harald Hjeltnes Muath K AlsheikhSammendrag
Commercial fruit production in Norway is located at around latitude 60° north, demanding a careful choice of adapted cultivars. The most comprehensive collection of apple genetic resources in Norway is being kept in the Norwegian Apple Collection (NAC) at the Njøs Fruit and Berry Centre (NJØS). The collection contains around 350 accessions and was recently genotyped with a single nucleotide polymorphism (SNP) array. Curated SNP data were used for the assessment of structure and diversity, pedigree confirmation, and core collection development. In the following SNP analysis, we identified several duplicates and parent-child relationships. Across the geographic regions represented, the collection was equally diverse. Different methods for analyzing population structure were applied. K-means clustering and a Bayesian modeling approach with prior assumptions of the data revealed five subpopulations associated with geographic breeding centers. The collection has a distinct genetic structure and low relatedness among the accessions; hence, two core collections with 100 accessions in each were created. These new core collections will allow breeders and researchers to use the NAC efficiently. The results from this study suggest that several of the accessions in the Norwegian Apple Collection could be of high importance for breeding purposes.
Forfattere
Monica Sanden Eirill Ager-Wick Johanna Eva Bodin Nur Duale Anne-Marthe Ganes Jevnaker Kristian Prydz Ville Erling Sipinen Volha Shapaval Tage ThorstensenSammendrag
Det er ikke registrert sammendrag
Forfattere
Monica Sanden Eirill Ager-Wick Johanna Eva Bodin Nur Duale Anne-Marthe Ganes Jevnaker Kristian Prydz Ville Erling Sipinen Volha Shapaval Tage ThorstensenSammendrag
Genetically modified maize DP41149 x MON 890349 x MON 874119 x DAS-40278-9 was developed by crossing to combine four single events: DP4114, MON 89034, MON 87411 and DAS-40278-9. DP4114 express the Cry1F protein to confer protection against certain lepidopteran pests, the Cry34Ab1 and Cry35Ab1 proteins to confer protection against certain coleopteran pests and PAT protein to confer tolerance to glufosinate-ammonium-containing herbicides. MON 89034 express the Cry1A.105 and Cry2Ab2 proteins to confer protection against certain lepidopteran pests. MON 87411 express the Cry3Bb1 protein to confer protection against certain coleopteran larvae and the DvSnf7 dsRNA confer protection against western corn rootworm, and the CP4 EPSPS protein for tolerance to glyphosate containing herbicides. DAS-40278-9 express the AAD-1 protein to catalyse the degradation of the general class ofherbicides known as aryloxyphenoxypropionates (AOPP) and to confer tolerance to 2,4- dichlorophenoxyacetic acid (2,4-D) herbicides.
Forfattere
Monica Sanden Eirill Ager-Wick Johanna Eva Bodin Nur Duale Kristian Prydz Volha Shapaval Tage ThorstensenSammendrag
Bt11 x MIR162 x MIR604 x MON 89034 x 5307 x GA21 was produced by conventional breeding of the GM maize events Bt11, MIR162, MIR604, MON 89034, 5307 and GA21. Accordingly, Bt11 x MIR162 x MIR604 x MON 89034 x 5307 x GA21 maize produces the transgenic proteins in the individual GM maize events (Cry1Ab, PAT, Vip3Aa20, PMI, mCry3A, MIR604 PMI, Cry1A.105, Cry2Ab2, eCry3.1Ab and mEPSPS). Event Bt11 maize expresses the insecticidal protein Cry1Ab that protects against feeding damage caused by certain lepidopteran pests and the phosphinothricin acetyltransferase (PAT) protein for weed control by providing tolerance to herbicide products containing glufosinate ammonium. Event MIR162 maize expresses the insecticidal protein Vip3Aa20 that protects against feeding damage caused by certain lepidopteran pests and the PMI protein which enables transformed plant cells to utilise mannose as a primary carbon source and therefore used as a selectable marker in the development of the MIR162 maize. Event MIR604 maize expresses the insecticidal protein mCry3A that protects against feeding damage caused by certain coleopteran pests and the MIR604 PMI protein which enables transformed plant cells to utilise mannose as a primary carbon source and therefore used as a selectable marker in the development of the MIR604 maize. Event MON 89034 maize expresses the insecticidal proteins Cry1A.105 and Cry2Ab2 that protect against feeding damage caused by certain lepidopteran pests. Event 5307 maize expresses the insecticidal protein eCry3.1Ab that protects against feeding damage caused by certain coleopteran pests and the PMI protein which enables transformed plant cells to utilise mannose as a primary carbon source and therefore used as a selectable marker in the development of the 5307 maize. Event GA21 expresses the double-mutated 5-enolpyruvylshikimate-3-phosphate synthase enzyme (mEPSPS) for weed control by providing tolerance to herbicide products containing glyphosate.The scientific documentation provided in the application for genetically modified maize Bt11 x MIR162 x MIR604 x MON 89034 x 5307 x GA21 is adequate for risk assessment, and in accordance with EFSA guidance on risk assessment of genetically modified plants for use in food or feed. The VKM GMO panel does not consider the introduced modifications in maize Bt11 x MIR162 x MIR604 x MON 89034 x 5307 x GA21 to imply potential specific health or environmental risks in Norway, compared to EU-countries The EFSA opinion is adequate also for Norwegian considerations. Therefore, a full risk assessment of maize Bt11 x MIR162 x MIR604 x MON 89034 x 5307 x GA21 was not performed by the VKM GMO Panel.
Forfattere
Monica Sanden Eirill Ager-Wick Johanna Eva Bodin Nur Duale Anne-Marthe Ganes Jevnaker Kristian Prydz Volha Shapaval Ville Erling Sipinen Tage ThorstensenSammendrag
Det er ikke registrert sammendrag
Forfattere
Monica Sanden Eirill Ager-Wick Johanna Eva Bodin Nur Duale Anne-Marthe Ganes Jevnaker Kristian Prydz Volha Shapaval Ville Erling Sipinen Tage ThorstensenSammendrag
Det er ikke registrert sammendrag
Forfattere
Monica Sanden Eirill Ager-Wick Johanna Eva Bodin Nur Duale Anne-Marthe Ganes Jevnaker Kristian Prydz Ville Erling Sipinen Volha Shapaval Tage ThorstensenSammendrag
Event MON 87429 is a genetically modified maize developed via Agrobacterium tumefaciens transformation. MON 87429 plants contain the transgenes pat, dmo, ft_t and cp4 epsps. Maize MON 87429 encodes the DMO, PAT and FT_T proteins. In addition, maize MON 87429 encodes the CP4 EPSPS protein and utilises an endogenous maize RNAi regulatory element to suppress its expression in pollen. This results in a lack of viable pollen and thus male sterility when MON 87429 plants are exposed to glyphosate-containing herbicides at growth stages ranging from V8 to V13. This is part of a hybridisation system to be used in inbred lines to facilitate the hybrid seeds production. This is not considered an agronomic trait since the application of glyphosate outside the specific growth stages does not lead to male sterile plants but reduces plant yield compared to plants not expressing the same trait. The scientific documentation provided in the application for genetically modified maize MON 87429 is adequate for risk assessment, and in accordance with EFSA guidance on risk assessment of genetically modified plants for use in food or feed. The VKM GMO panel does not consider the introduced modifications in event MON 87429 to imply potential specific health or environmental risks in Norway, compared to EU-countries. The EFSA opinion is adequate also for Norwegian considerations. Therefore, a full risk assessment of event MON87429 was not performed by the VKM GMO Panel
Sammendrag
Stacked event MON 89034 × 1507 × MIR162 × NK603 × DAS‐40278‐9 (EFSA‐GMO‐NL‐2018‐151) is a genetically modified maize developed via conventional breeding. MON 89034× 1507 × MIR162 × NK603 × DAS‐40278‐9 plants contain the transgenes cry1A.105, cry2Ab2, cry1F, Vip3Aa20, cp4 epsps, pat, aad-1 and the phosphomannose isomerase (PMI) used as a selectable marker in the production of MIR162. MON89034 x 1507 x MIR162 x NK603 x DAS-40278-9 maize provides distinct sources for insect resistance combined with three distinct modes of herbicide tolerance: 2,4-D, glufosinate, and glyphosate. The scientific documentation provided in the application for genetically modified maize is adequate for risk assessment, and in accordance with EFSA guidance on risk assessment of genetically modified plants for use in food or feed. The VKM GMO panel does not consider the introduced modifications in event maize to imply potential specific health or environmental risks in Norway, compared to EU-countries. The EFSA opinion is adequate also for Norwegian considerations. Therefore, a full risk assessment of event MON 89034 × 1507 × MIR162 × NK603 × DAS‐40278‐9 was not performed by the VKM GMO Panel.