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.
2012
Authors
Igor A. Yakovlev YeonKyeong Lee Bjørn Rotter Tore Skrøppa Øystein Johnsen Jorunn Elisabeth Olsen Carl Gunnar FossdalAbstract
Epigenetic memory marks establishment in Norway spruce occur exclusively during embryogenesis in response to environmental impact, and the epitype is fixated by the time the embryo is fully developed without a change in the DNA sequence. We started large scale studies aimed on identifying and characterizing of genes and regulatory elements involved in the initiation, maintenance, and heritability of epigenetic memory using candidate genes and next generation sequencing approaches. Molecular mechanisms of formation of epigenetic memory were studied on the same full-sibs family zygotic embryo in vitro cultures developed in cold (18°C) and warm (30°C) environmental conditions from proliferation till mature embryo stages. Initially we had found large set (64) of Arabidopsis epigenetic regulator gene homologs in spruce. In general, known epigenetic related genes are very well represented among spruce ESTs. Analysis of the transcription patterns of these genes using RT-PCR in epigenetically different embryogenic samples reveal specific transcription patterns on different stages of embryogenic development dependent on epitype. We are expecting to determine certain stages during embryogenesis when epigenetic memory marks are forming. At the same time, nearly no differences in transcription levels of studied genes had been found in seedlings (4 month old), originated from full-sib families clearly differed in epigenetic response. Using MACE (massive cDNA 3-end sequencing) deep mRNA sequencing on the Illumina GSII platform, we analyzed P. abies transcriptomes by comparison warm and cold originated “embryonic epitypes” developed in cold and warm environmental conditions. Significant differences in transcriptomes between epitypes revealed by high-throughput sequencing will be discussed.
Authors
Åke Olson Andrea Aerts Fred Asiegbu Lassaad Belbahri Ourdia Bouzid Anders Broberg Björn Canback Pedro M. Coutinho Dan Cullen Kerstin Dalman Giuliana Deflorio Linda T.A. van Diepen Christophe Dunand Sébastien Duplessis Mikael Durling Paolo Gonthier Jane Grimwood Carl Gunnar Fossdal David Hansson Bernard Henrissat Ari Hietala Kajsa Himmelstrand Dirk Hoffmeister Nils Högberg Timothy Y. James Magnus Karlsson Annegret Kohler Ursula Kües Yong-Hwan Lee Yao-Cheng Lin Mårten Lind Erika Lindquist Vincent Lombard Susan Lucas Karl Lundén Emmanuelle Morin Claude Murat Jongsun Park Tommaso Raffaello Pierre Rouzé Asaf Salamov Jeremy Schmutz Halvor Solheim Jerry Ståhlberg Heriberto Vélëz Ronald P. de Vries Ad Wiebenga Steve Woodward Igor A. Yakovlev Matteo Garbelotto Francis Martin Igor V. Grigoriev Jan StenlidAbstract
• Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato. • We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified. • A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production. • Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.
Authors
Igor A. Yakovlev Gustav Vaaje-Kolstad Ari Hietala Emil Stefanczyk Halvor Solheim Carl Gunnar FossdalAbstract
No abstract has been registered
Authors
Steffi Munack Kathrin Roderer Jurate Kamarauskaite Gabriele Cordara Andre van Eerde Peter Kast Ute KrengelAbstract
No abstract has been registered
Authors
DJ Sargent T Passey N Surbanovski E. Lopez Girona P Kuchta Jahn Davik R. Harrison A Passey AB Whitehouse DW SimpsonAbstract
No abstract has been registered
Authors
Jens Rohloff Muath Alsheikh Gage Koehler Robert Charles Wilson Jahn Davik Stephen K, RandallAbstract
No abstract has been registered
Abstract
The winter hardiness of strawberry cultivars used in perennial production systems varies greatly, although a strong linkage exists between transcriptional and metabolic changes during cold acclimation. Still, little information is available on how plant metabolism adapts to cold and freezing temperatures under natural temperature and light conditions. In order to examine the hardening process of overwintering meristematic tissue in Fragaria x ananassa, crown samples of field-grown cvs. ‘Polka’ and ‘Honeoye’ were consecutively collected over a period of 15 weeks, i.e. from the end of the season (week 35/ end August) until midwinter (week 50/ December). Samples were subjected to qGC MS metabolite profiling to assess the reconfiguration of central metabolism, and characterize the regulation of selected compatible solutes (amino acids, Krebs metabolites, sugars, polyols). Besides changes in amino acid patterns (glutamic acid, aspartic acid, and asparagine), monosaccharide levels (fructose) were strongly enhanced until the end of the acclimation period in cv. ‘Honeoye’ (180-fold compared to start control). In contrast, ‘Polka’ showed a concentration peak (36-fold) in week 47 and a decline towards week 50. Also sucrose levels were steadily enhanced throughout the cold hardening period with averagely 6-fold higher levels in ‘Honeoye’ compared to ‘Polka’, thus underscoring cultivar differences. However, both cultivars showed a clear decline in sucrose levels after week 47. Particularly, the raffinose pathway was affected leading to strongly and transiently increased levels of the precursor galactinol (week 42/ mid October) and the trisaccharide raffinose (weeks 43 to 47/ end October to mid November). While galactinol biosynthesis was obviously earlier induced in cv. ‘Polka’ (week 38) compared to ‘Honeoye’ (week 39), subsequent raffinose production and concentration peaks were clearly delayed in ‘Polka’ (week 47) in contrast to ‘Honeoye’ (week 45). Major metabolic changes in both cultivars coincided with a decrease in daylength below 14 h after week 37 (mid September), and a consistent drop below 10°C average day temperature in week 39 (end September). The effect of temperature and light conditions on metabolic cold acclimation in field-grown strawberry is discussed. Keywords: Winter hardiness, metabolite profiling, quadrupole gas chromatography-mass spectrometry (qGC-MS), temperature, light
Authors
Jens Rohloff Joachim Kopka Alexander Erban Per Winge Robert Charles Wilson Atle M. Bones Jahn Davik Stephen K, Randall Muath AlsheikhAbstract
Winter freezing damage is a crucial factor in overwintering crops such as the octoploid strawberry (Fragaria × ananassa Duch.) when grown in a perennial cultivation system. Our study aimed at assessing metabolic processes and regulatory mechanisms in the close-related diploid model woodland strawberry (Fragaria vesca L.) during a 10-days cold acclimation experiment. Based on gas chromatography/ time-of-flight-mass spectrometry (GC/TOF-MS) metabolite profiling of three F. vesca genotypes, clear distinctions could be made between leaves and non-photosynthesizing roots, underscoring the evolvement of organ-dependent cold acclimation strategies. Carbohydrate and amino acid metabolism, photosynthetic acclimation, and antioxidant and detoxification systems (ascorbate pathway) were strongly affected. Metabolic changes in F. vesca included the strong modulation of central metabolism, and induction of osmotically-active sugars (fructose, glucose), amino acids (aspartatic acid), and amines (putrescine). In contrast, a distinct impact on the amino acid proline, known to be cold-induced in other plant systems, was conspicuously absent. Levels of galactinol and raffinose, key metabolites of the cold-inducible raffinose pathway, were drastically enhanced in both leaves and roots throughout the cold acclimation period of 10 days. Furthermore, initial freezing tests and multifaceted GC/TOF-MS data processing (Venn diagrams, Independent Component Analysis, Hierarchical Clustering) showed that changes in metabolite pools of cold-acclimated F. vesca were clearly influenced by genotype.
Authors
Jens Rohloff Pankaj Barah Per Winge Jahn Davik Robert Wilson Stephen K, Randall Atle M. Bones Muath Alsheikh-YousefAbstract
Freezing damage is a crucial factor in the cultivation of perennial crops. Overwintering plants acclimate to decreasing temperatures in their environment and thus, prevent freezing damage of plant tissue. To assess transcriptional and metabolic changes in meristematic tissue (crowns) of octoploid strawberry (Fragaria × ananassa Duch.), acclimation experiments were carried out at above-zero temperature (2 °C) using three cultivars with contrasting cold tolerance: ‘Elsanta’ < ‘Frida’ < ‘Jonsok’. Crowns were sampled after 1 day (d), 2d, 2 weeks (w) and 6w in order to detect short- and long-term metabolic shifts. GC/MS-based metabolite profiling revealed more than 140 metabolites (identified structures, not-annotated mass spectral tags, and unidentified metabolites). Transcriptional changes were assessed at two time points (2d and 6w) using a customized Fragaria microarray chip developed as a joint collaboration between Graminor Breeding Ltd. and NTNU. A total of 4061 differentially regulated transcripts (unique 60-mer probes) with a p-value≤0.05 were detected in all hybridizations. Microarray analysis revealed the up-regulation of ~100 cold-responsive transcripts (TFs and dehydrins), also including enzymes involved in starch breakdown and raffinose biosynthesis. Gene-metabolite correlation analysis revealed strong connectivity in components of Krebs-cycle (citric and succinic acid), amino acids (isoleucine, aspartic acid, glutamic acid, valine and phenylalanine) and the raffinose pathway. Metabolite levels of hexoses (fructose and glucose), trisaccharides (raffinose), amino acids (aspartic acid, alanine and serine), phenols (gallic acid) and several polyphenols still increased during long-term acclimation phase. Varietal differences could be clearly explained by Venn diagrams: frost-tolerant ‘Jonsok’ showed least individual up- or down-regulated transcripts (2 d), and least commonly shared transcripts with frost-sensitive ‘Elsanta’ (2d and 6w). Further multivariate statistics and network analyses underscored genotype-dependent cold responses, and might further guide in the identification of frost-tolerant vs. sensitive plants in diverse Fragaria accessions or cross-breeding populations .
Abstract
No abstract has been registered