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
Xiaoyan Ma Junhua Bao Jinwei Li Xi Cheng Muhammad Mobeen Tahir Meizi Liu Xian Lu Min-Rui Wang Zhibo Hamborg Dong ZhangSammendrag
Apple stem grooving virus (ASGV) is one of the most widespread and asymptomatic main viruses, that restricts the production of apples worldwide. Establishment of rapid, simple, and effective early detection methods of apple virus is important. In this study, we established and optimized a one-step reverse transcription - recombinase polymerase amplification (RT-RPA) method, using the target-specific primers of ASGV coat protein gene sequence, and M-MLV reverse transcriptase. This method could be completed within 30 min at 40 °C, followed by a visual detection of the results within 5 min by using lateral flow dipstick (LFD). The specificity results showed that only samples infected with ASGV showed a test line, while no test line appeared in the ASGV-negative samples. In addition, when crude extract of leaves was used, the whole detection could be completed within 1 h, which was shortened by 4 to 6 times compared with the RT-PCR method. The detection made on more field samples showed that the RT-RPA-LFD method is of high stability and reliability for ASGV diagnosis, with a great potential in the rapid on-site detection of plant viruses.
Forfattere
Wiktoria Kaczmarek-DerdaSammendrag
Det er ikke registrert sammendrag
Forfattere
Wiktoria Kaczmarek-DerdaSammendrag
Det er ikke registrert sammendrag
Sammendrag
Det er ikke registrert sammendrag
Forfattere
Wiktoria Kaczmarek-DerdaSammendrag
Det er ikke registrert sammendrag
Forfattere
Wiktoria Kaczmarek-DerdaSammendrag
Det er ikke registrert sammendrag
Forfattere
Wiktoria Kaczmarek-DerdaSammendrag
Det er ikke registrert sammendrag
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.