Jahn Davik
Research Scientist
Authors
Liv Hatleli Gilpin Dag Røen Marian Schubert Jahn Davik Kimmo Rumpunen Kristina Alme Gardli Stein Harald Hjeltnes Muath K AlsheikhAbstract
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Authors
Fernanda Leiva Florent Abdelghafour Muath K Alsheikh Nina Elisabeth Nagy Jahn Davik Aakash ChawadeAbstract
Common scab (CS) is a major bacterial disease causing lesions on potato tubers, degrading their appearance and reducing their market value. To accurately grade scab-infected potato tubers, this study introduces “ScabyNet”, an image processing approach combining color-morphology analysis with deep learning techniques. ScabyNet estimates tuber quality traits and accurately detects and quantifies CS severity levels from color images. It is presented as a standalone application with a graphical user interface comprising two main modules. One module identifies and separates tubers on images and estimates quality-related morphological features. In addition, it enables the extraction of tubers as standard tiles for the deep-learning module. The deep-learning module detects and quantifies the scab infection into five severity classes related to the relative infected area. The analysis was performed on a dataset of 7154 images of individual tiles collected from field and glasshouse experiments. Combining the two modules yields essential parameters for quality and disease inspection. The first module simplifies imaging by replacing the region proposal step of instance segmentation networks. Furthermore, the approach is an operational tool for an affordable phenotyping system that selects scab-resistant genotypes while maintaining their market standards.
Authors
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 WorthingtonAbstract
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.
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Authors
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 SargentAbstract
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.
Abstract
Crown rot, caused by Phytophthora cactorum, is a devastating disease of strawberry. While most commercial octoploid strawberry cultivars (Fragaria × ananassa Duch) are generally susceptible, the diploid species Fragaria vesca is a potential source of resistance genes to P. cactorum. We previously reported several F. vesca genotypes with varying degrees of resistance to P. cactorum. To gain insights into the strawberry defence mechanisms, comparative transcriptome profiles of two resistant genotypes (NCGR1603 and Bukammen) and a susceptible genotype (NCGR1218) of F. vesca were analysed by RNA-Seq after wounding and subsequent inoculation with P. cactorum. Differential gene expression analysis identified several defence-related genes that are highly expressed in the resistant genotypes relative to the susceptible genotype in response to P. cactorum after wounding. These included putative disease resistance (R) genes encoding receptor-like proteins, receptor-like kinases, nucleotide-binding sites, leucine-rich repeat proteins, RPW8-type disease resistance proteins, and ‘pathogenesis-related protein 1’. Seven of these R-genes were expressed only in the resistant genotypes and not in the susceptible genotype, and these appeared to be present only in the genomes of the resistant genotypes, as confirmed by PCR analysis. We previously reported a single major gene locus RPc-1 (Resistance to Phytophthora cactorum 1) in F. vesca that contributed resistance to P. cactorum. Here, we report that 4–5% of the genes (35–38 of ca 800 genes) in the RPc-1 locus are differentially expressed in the resistant genotypes compared to the susceptible genotype after inoculation with P. cactorum. In particular, we identified three defence-related genes encoding wall-associated receptor-like kinase 3, receptor-like protein 12, and non-specific lipid-transfer protein 1-like that were highly expressed in the resistant genotypes compared to the susceptible one. The present study reports several novel candidate disease resistance genes that warrant further investigation for their role in plant defence against P. cactorum.
Authors
Liv Gilpin Dag Røen Marian Schubert Jahn Davik Kimmo Rumpunen Kristina Alme Gardli Stein Harald Hjeltnes Muath K AlsheikhAbstract
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.
Authors
May Bente Brurberg Anupam Gogoi Bikal Ghimire Erik Lysøe Mandeep Poudel Håvard Eikemo Jahn Davik Arne StensvandAbstract
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Authors
Anupam Gogoi Bikal Ghimire Erik Lysøe Mandeep Poudel Håvard Eikemo Jahn Davik Arne Stensvand May Bente BrurbergAbstract
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Authors
Anupam Gogoi Bikal Ghimire Erik Lysøe Mandeep Poudel Håvard Eikemo Jahn Davik Arne Stensvand May Bente BrurbergAbstract
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Authors
Jahn Davik Dag Røen Erik Lysøe Matteo Buti Simeon Rossmann Muath K Alsheikh Erez Lieberman Aiden Olga Dudchenko Daniel James SargentAbstract
Rubus idaeus L. (red raspberry), is a perennial woody plant species of the Rosaceae family that is widely cultivated in the temperate regions of world and is thus an economically important soft fruit species. It is prized for its flavour and aroma, as well as a high content of healthful compounds such as vitamins and antioxidants. Breeding programs exist globally for red raspberry, but variety development is a long and challenging process. Genomic and molecular tools for red raspberry are valuable resources for breeding. Here, a chromosome-length genome sequence assembly and related gene predictions for the red raspberry cultivar ‘Anitra’ are presented, comprising PacBio long read sequencing scaffolded using Hi-C sequence data. The assembled genome sequence totalled 291.7 Mbp, with 247.5 Mbp (84.8%) incorporated into seven sequencing scaffolds with an average length of 35.4 Mbp. A total of 39,448 protein-coding genes were predicted, 75% of which were functionally annotated. The seven chromosome scaffolds were anchored to a previously published genetic linkage map with a high degree of synteny and comparisons to genomes of closely related species within the Rosoideae revealed chromosome-scale rearrangements that have occurred over relatively short evolutionary periods. A chromosome-level genomic sequence of R. idaeus will be a valuable resource for the knowledge of its genome structure and function in red raspberry and will be a useful and important resource for researchers and plant breeders.
Authors
Nina Elisabeth Nagy Hans Ragnar Norli Monica Fongen Runa Berg Østby Inger Heldal Jahn Davik Ari HietalaAbstract
Tree defense against xylem pathogens involves both constitutive and induced phenylpropanoids and terpenoids. The induced defenses include compartmentalization of compromised wood with a reaction zone (RZ) characterized by polyphenol deposition, whereas the role of terpenoids has remained poorly understood. To further elucidate the tree–pathogen interaction, we profiled spatial patterns in lignan (low-molecular-weight polyphenols) and terpenoid content in Norway spruce (Picea abies) trees showing heartwood colonization by the pathogenic white-rot fungus Heterobasidion parviporum. There was pronounced variation in the amount and composition of lignans between different xylem tissue zones of diseased and healthy trees. Intact RZ at basal stem regions, where colonization is the oldest, showed the highest level and diversity of these compounds. The antioxidant properties of lignans obviously hinder oxidative degradation of wood: RZ with lignans removed by extraction showed significantly higher mass loss than unextracted RZ when subjected to Fenton degradation. The reduced diversity and amount of lignans in pathogen-compromised RZ and decaying heartwood in comparison to intact RZ and healthy heartwood suggest that α-conindendrin isomer is an intermediate metabolite in lignan decomposition by H. parviporum. Diterpenes and diterpene alcohols constituted above 90% of the terpenes detected in sapwood of healthy and diseased trees. A significant finding was that traumatic resin canals, predominated by monoterpenes, were commonly associated with RZ. The findings clarify the roles and fate of lignan during wood decay and raise questions about the potential roles of terpenoids in signal transduction, synthesis, and translocation of defense compounds upon wood compartmentalization against decay fungi.
Abstract
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Authors
Elisa Senger Sonia Osorio Klaus Olbricht Paul Shaw Béatrice Denoyes Jahn Davik Stefano Predieri Saila Karhu Sebastian Raubach Nico Lippi Monika Höfer Helen Cockerton Christophe Pradal Ebru Kafkas Suzanne Litthauer Iraida Amaya Björn Usadel Bruno MezzettiAbstract
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Authors
Isam Fattash Zachary Deitch Relindis Ghai Njah Nelson Uchechukwu Osuagwu Vera Mageney Robert Charles Wilson Jahn Davik Muath K Alsheikh Stephen RandallAbstract
Identifying and characterizing cold responsive genes in Fragaria vesca associated with or responsible for low temperature tolerance is a vital part of strawberry cultivar development. In this study we have investigated the transcript levels of eight genes, two dehydrin genes, three putative ABA-regulated genes, two cold–inducible CBF genes and the alcohol dehydrogenase gene, extracted from leaf and crown tissues of three F. vesca genotypes that vary in cold tolerance. Transcript levels of the CBF/DREB1 transcription factor FvCBF1E exhibited stronger cold up-regulation in comparison to FvCBF1B.1 in all genotypes. Transcripts of FvADH were highly up-regulated in both crown and leaf tissues from all three genotypes. In the ‘ALTA’ genotype, FvADH transcripts were significantly higher in leaf than crown tissues and more than 10 to 20-fold greater than in the less cold-tolerant ‘NCGR1363’ and ‘FDP817’ genotypes. FvGEM, containing the conserved ABRE promoter element, transcript was found to be cold-regulated in crowns. Direct comparison of the kinetics of transcript and protein accumulation of dehydrins was scrutinized. In all genotypes and organs, the changes of XERO2 transcript levels generally preceded protein changes, while levels of COR47 protein accumulation preceded the increases in COR47 RNA in ‘ALTA’ crowns.
Authors
T. Haikonen Jahn Davik M. Rantanen P. Parikka J. Näkkilä S. Karhu Muath K Alsheikh S. H. HjeltnesAbstract
Climate change may result in increased root system stresses in strawberry cultivation, requiring cultivars with root and crown-related resistance and resiliency traits. Approaches to widen the genetic basis and improve tools for the incorporation of novel variation are relevant to plant breeding for changing climate. The pre-breeding project NORDFRUIT is a Nordic public-private-partnership project that aims to introduce novel genetic variation from new sources, support the use of existing genetic resources adapted to Nordic and Baltic cultivation conditions, and develop efficient tools to speed up germplasm evaluation in breeding programs for climate adaptation. Pre-evaluated genotypes of Fragaria chiloensis or Fragaria virginiana were used as parents in interspecific (species hybridization) crosses, re-creating the garden strawberry hybrid species, F. ×ananassa. The created F1 hybrid seedlings were propagated by runners for replicated phenotyping trials. A greenhouse assay to test root-shoot biomass partition, growth vigour and Phytophthora cactorum resistance in these small plants was scaled up from an earlier assay based on nutrient film technology (NFT). The observed variation in disease symptom appearance, root-shoot ratio, and root proliferation indicated promising traits in the strawberry hybrid material, to be exploited further in genomic studies and to develop genome-assisted resistance breeding. The on-going work also includes field testing of the same hybrid material to evaluate winter hardiness, powdery mildew incidence, and fruit traits.
Authors
Jahn Davik Robert Charles Wilson Relindis Ghai Njah Paul Eivind Grini Stephen K. Randall Muath K Alsheikh Daniel James SargentAbstract
Extreme cold and frost cause significant stress to plants which can potentially be lethal. Low temperature freezing stress can cause significant and irreversible damage to plant cells and can induce physiological and metabolic changes that impact on growth and development. Low temperatures cause physiological responses including winter dormancy and autumn cold hardening in strawberry (Fragaria) species, and some diploid F. vesca accessions have been shown to have adapted to low-temperature stresses. To study the genetics of freezing tolerance, a F. vesca mapping population of 143 seedlings segregating for differential responses to freezing stress was raised. The progeny was mapped using ‘Genotyping-by-Sequencing’ and a linkage map of 2,918 markers at 851 loci was resolved. The mapping population was phenotyped for freezing tolerance response under controlled and replicated laboratory conditions and subsequent quantitative trait loci analysis using interval mapping revealed a single significant quantitative trait locus on Fvb2 in the physical interval 10.6 Mb and 15.73 Mb on the F. vesca v4.0 genome sequence. This physical interval contained 896 predicted genes, several of which had putative roles associated with tolerance to abiotic stresses including freezing. Differential expression analysis of the 896 QTL-associated gene predictions in the leaves and crowns from ‘Alta’ and ‘NCGR1363’ parental genotypes revealed genotype-specific changes in transcript accumulation in response to low temperature treatment as well as expression differences between genotypes prior to treatment for many of the genes. The putative roles, and significant interparental differential expression levels of several of the genes reported here identified them as good candidates for the control of the effects of freezing tolerance at the QTL identified in this investigation and the possible role of these candidate genes in response to freezing stress is discussed.
Authors
Jahn Davik Kjersti Aaby Matteo Buti Muath K Alsheikh Nada Surbanovski Stefan Martens Dag Røen Daniel James SargentAbstract
Strawberries are rich in polyphenols which impart health benefits when metabolized by the gut microbiome, including anti-inflammatory, neuroprotective, and antiproliferative effects. In addition, polyphenolic anthocyanins contribute to the attractive color of strawberry fruits. However, the genetic basis of polyphenol biosynthesis has not been extensively studied in strawberry. In this investigation, ripe fruits from three cultivated strawberry populations were characterized for polyphenol content using HPLC-DAD-MSn and genotyped using the iStraw35k array. GWAS and QTL analyses identified genetic loci controlling polyphenol biosynthesis. QTL were identified on four chromosomes for pelargonidin-3-O-malonylglucoside, pelargonidin-3-O-acetylglucoside, cinnamoyl glucose, and ellagic acid deoxyhexoside biosynthesis. Presence/absence of ellagic acid deoxyhexoside and pelargonidin-3-O-malonylglucoside was found to be under the control of major gene loci on LG1X2 and LG6b, respectively, on the F. × ananassa linkage maps. Interrogation of gene predictions in the F. vesca reference genome sequence identified a single candidate gene for ellagic acid deoxyhexoside biosynthesis, while seven malonyltransferase genes were identified as candidates for pelargonidin-3-O-malonylglucoside biosynthesis. Homologous malonyltransferase genes were identified in the F. × ananassa ‘Camarosa’ genome sequence but the candidate for ellagic acid deoxyhexoside biosynthesis was absent from the ‘Camarosa’ sequence. This study demonstrated that polyphenol biosynthesis in strawberry is, in some cases,under simple genetic control, supporting previous observations of the presence or absence of these compounds in strawberry fruits. It has also shed light on the mechanisms controlling polyphenol biosynthesis and enhanced the knowledge of these biosynthesis pathways in strawberry. The above findings will facilitate breeding for strawberries enriched in compounds with beneficial health effects.
Authors
Daniel J. Sargent Matteo Buti Nada Surbanovski May Bente Brurberg Muath K Alsheikh Matthew Peter Kent Jahn DavikAbstract
Strawberry powdery mildew (Podosphaera aphanis Wallr.) is a pathogen which infects the leaves, fruit, stolon and flowers of the cultivated strawberry (Fragaria ×ananassa), causing major yield losses, primarily through unmarketable fruit. The primary commercial control of the disease is the application of fungicidal sprays. However, as the use of key active ingredients of commercial fungicides is becoming increasingly restricted, interest in developing novel strawberry cultivars exhibiting resistance to the pathogen is growing rapidly. In this study, a mapping population derived from a cross between two commercial strawberry cultivars (‘Sonata’ and ‘Babette’) was genotyped with single nucleotide polymorphism (SNP) markers from the Axiom iStraw90k genotyping array and phenotyped for powdery mildew susceptibility in both glasshouse and field environments. Three distinct, significant QTLs for powdery mildew resistance were identified across the two experiments. Through comparison with previous studies and scrutiny of the F. vesca genome sequence, candidate genes underlying the genetic control of this trait were identified.
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Authors
Jahn Davik Daniel J. Sargent May Bente Brurberg Sigbjørn Lien Matthew Peter Kent Muath K AlsheikhAbstract
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Authors
Gage Koehler Jens Rohloff Robert Charles Wilson Joachim Kopka Alexander Erban Per Winge Atle M. Bones Jahn Davik Muath K Alsheikh Stephen K. RandallAbstract
To assess underlying metabolic processes and regulatory mechanisms during cold exposure of strawberry, integrative “omic” approaches were applied to F. ananassa ‘Korona’. Analysis of leaf tissue was emphasized because of its immediate and early responses in the cold acclimation processes. Levels of metabolites, proteins, and transcripts in tissues from plants grown at 20°C were compared to those following 1 to 10 days of cold exposure. When leaves and roots were subjected to GC/TOF-MS-based metabolite profiling, about 160 compounds comprising mostly structurally annotated primary metabolites and secondary metabolites, were found. Overall, ‘Korona’ showed a modest increase of protective metabolites such as amino acids (aspartic acid, leucine, isoleucine, and valine), pentoses, phosphorylated and non-phosphorylated hexoses, and distinct compounds of the raffinose pathway (galactinol and raffinose). Distinctive responses were observed in roots and leaves. By 2DE proteomics a total of 845 spots were observed in leaves; 4.6% changed significantly in response to cold. Twenty-one proteins were identified, many of which were associated with general metabolism or photosynthesis. Transcript levels in leaves were determined by microarray, where dozens of cold associated transcripts were quantitatively characterized, and levels of several potential key contributors (e.g., the dehydrin COR47 and GADb) to cold tolerance were confirmed by qRT-PCR. Cold responses are placed within the existing knowledge base of low temperature stress change in plants, allowing an evaluation of the uniqueness or generality of Fragaria responses in photosynthetic tissues. Overall, the cold response characteristics of ‘Korona’ are consistent with a moderately cold tolerant plant.
Abstract
The woodland strawberry (Fragaria vesca) has become the model plant for the economically important, but genetically complex, octoploid F. × ananassa. Crown rot caused by the oomycete Phytophthora cactorum is a major problem for the strawberry industry and the identification and incorporation of efficient resistance genes into superior cultivars are important for breeding. In the present study, two experimental populations were used in inoculation experiments under controlled greenhouse condition. Studies of a sparse diallel cross between resistant and susceptible F. vesca genotypes concluded that resistance to crown rot is inherited as a dominant trait under nuclear control. Subsequently, an F2 population derived from the grandparents Bukammen (resistant) and Haugastøl 3 (susceptible) collected in Norway, were phenotyped in infection experiments and genotyped using genotyping-by-sequencing. A 416.2-cM linkage map was constructed, and a single major gene locus was identified on linkage group 6 that we attributed to resistance to Phytopthora infection. We propose to name the resistance locus RPc-1 (Resistance to Phytophthora cactorum 1). Gene prediction of the 3.3 Mb QTL recovered 801 genes of which 69 had a potential role in plant disease resistance.
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The winter hardiness of strawberry varieties used in perennial production systems varies greatly. 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 ananassa, crown samples of field-grown var. ‘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. Besides changes in amino acid patterns (glutamic acid, aspartic acid, and asparagine), monosaccharide levels (fructose) increased strongly in ‘Honeoye’ (180 fold compared to start control) towards the end of the acclimation period. In contrast, ‘Polka’ showed a concentration peak (36-fold) in week 47 and a decline towards week 50. Also sucrose levels were steadily increased throughout the cold hardening period with averagely 6-fold higher levels in ‘Honeoye’ compared to ‘Polka’, thus underscoring cultivar-dependent differences. However, both varieties showed a 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 earlier induced in ‘Polka’ (week 38) compared to ‘Honeoye’ (week 39), subsequent raffinose production was delayed in ‘Polka’ (week 47) compared to ‘Honeoye’ (week 45). Major metabolic changes in both varieties coincided with a decrease in day length below 14 h in mid-September, and a consistent drop below 10°C average day temperature by the end of September.
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Authors
DJ Sargent T Passey N Surbanovski E. Lopez Girona P Kuchta Jahn Davik R. Harrison A Passey AB Whitehouse DW SimpsonAbstract
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Authors
Jahn Davik Gage Koehler Britta From Torfinn Torp Jens Rohloff Petter Eidem Robert Wilson Anita Sønsteby Stephen K, Randall Muath Alsheikh-YousefAbstract
The use of artificial freezing tests, identification of biomarkers linked to or directly involved in the low-temperature tolerance processes, could prove useful in applied strawberry breeding. This study was conducted to identify genotypes of diploid strawberry that differ in their tolerance to low-temperature stress and to investigate whether a set of candidate proteins and metabolites correlate with the level of tolerance. 17 Fragaria vesca, 2 F. nilgerrensis, 2 F. nubicola, and 1 F. pentaphylla genotypes were evaluated for low-temperature tolerance. Estimates of temperatures where 50 % of the plants survived (LT50) ranged from −4.7 to −12.0 °C between the genotypes. Among the F. vesca genotypes, the LT50 varied from −7.7 °C to −12.0 °C. Among the most tolerant were three F. vesca ssp. bracteata genotypes (FDP821, NCGR424, and NCGR502), while a F. vesca ssp. californica genotype (FDP817) was the least tolerant (LT50 −7.7 °C). Alcohol dehydrogenase (ADH), total dehydrin expression, and content of central metabolism constituents were assayed in select plants acclimated at 2 °C. The LT50 estimates and the expression of ADH and total dehydrins were highly correlated (r adh = −0.87, r dehyd = −0.82). Compounds related to the citric acid cycle were quantified in the leaves during acclimation. While several sugars and acids were significantly correlated to the LT50 estimates early in the acclimation period, only galactinol proved to be a good LT50 predictor after 28 days of acclimation (r galact = 0.79). It is concluded that ADH, dehydrins, and galactinol show great potential to serve as biomarkers for cold tolerance in diploid strawberry.
Authors
Muath Alsheikh-Yousef Gage Koehler Robert Wilson Jens Rohloff Anita Sønsteby Jahn Davik Stephen K, RandallAbstract
A crucial consideration for strawberry producers in Norway and other northern countries is winter freezing damage. A long-term goal of the Norwegian strawberry breeding is to increase winter hardiness and to improve fruit quality. Due to the complexity involved in regulating and enhancing freezing tolerance, the progress in the improvement of cultivars using traditional screening methods have had limited success. Thus, the development of molecular markers for freezing hardiness would facilitate the selection work for this trait. In this effort, we have developed and adopted state-of-art molecular tools to investigate cold response in strawberry plants during the acclimation phase resulting in the identification of a large number of genes, proteins, and distinct metabolites that correspond to cold/freezing tolerance in strawberry. To identify proteins responsible for freezing tolerance in strawberry we have examined alterations in protein levels in strawberry varieties that differ in cold tolerance using either 2-DE gel analysis followed by LC-MS/MS analysis or a shotgun MS/MS approach. Proteomic analysis suggested 30 potential biomarkers that showed significant changes in the cultivated strawberry in response to cold. In addition, GC-MS-based metabolite profiling revealed the up-regulation of carbohydrates, polyols, amino acids, TCA intermediates, and other distinct secondary metabolites after cold treatment. Transcriptional analysis of the cold acclimated samples also confirmed the regulation upon cold-treatment with varietal differences in strawberry. Moreover, several F2-populations from the model F. vesca parents diverging in cold tolerance have been developed in order to facilitate mapping of QTLs by performing GBS analyses. The knowledge attained from these endeavors is expected to expedite breeding of strawberries to achieve freezing tolerant lines and provide an integrative understanding of the molecular pathways that underlie this characteristic. * Rohloff et al. (2012) Metabolite profiling reveals novel multi-level cold responses in the model Fragaria vesca. Phytochemistry 79:99-109. * Koehler et al. (2012) Proteomic study of low temperature responses in strawberry cultivars (Fragaria x ananassa) that differ in cold tolerance. Plant Physiology 159:1787–1805 * Davik et al., (2012) Low temperature tolerance in diploid strawberry species (Fragaria ssp.) and its correlation to alcohol dehydrogenase levels, dehydrin levels, and central metabolism constituents. Planta (in press; DOI: 10.1007/s00425-012-1771-2).
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 .
Authors
Vladimir Shulaev DJ Sargent RN Crowhurst TC Mockler O Folkerts AL Delcher P Jaiswal K Mockaitis A Liston SP Mane P Burns TM Davis JP Slovin N Bassil RP Hellens C Evans T Harkins C Kodira B Desany OR Crasta RV Jensen AC Allan TP Michael JC Setubal JM Celton DJG Rees KP Williams SH Holt JJR Rojas M Chatterjee B Liu H Silva L Meisel A Adato SA Filichkin M Troggio R Viola TL Ashman H Wang P Dharmawardhana J Elser R Raja HD Priest DW Bryant SE Fox SA Givan LJ Wilhelm S Naithani A Christoffels DY Salama J Carter EL Girona A Zdepski WQ Wang RA Kerstetter W Schwab SS Korban Jahn Davik A Monfort B Denoyes-Rothan P Arus R Mittler B Flinn A Aharoni JL Bennetzen SL Salzberg AW Dickerman R Velasco M Borodovsky RE Veilleux Kevin M. FoltaAbstract
No abstract has been registered
Abstract
No abstract has been registered
