| 1. |
- Abreha, Kibrom Berhe, et al.
(författare)
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Article leaf apoplast of field-grown potato analyzed by quantitative proteomics and activity-based protein profiling
- 2021
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Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1661-6596 .- 1422-0067. ; 22:21
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Tidskriftsartikel (refereegranskat)abstract
- Multiple biotic and abiotic stresses challenge plants growing in agricultural fields. Most molecular studies have aimed to understand plant responses to challenges under controlled conditions. However, studies on field-grown plants are scarce, limiting application of the findings in agricultural conditions. In this study, we investigated the composition of apoplastic proteomes of potato cultivar Bintje grown under field conditions, i.e., two field sites in June–August across two years and fungicide treated and untreated, using quantitative proteomics, as well as its activity using activity-based protein profiling (ABPP). Samples were clustered and some proteins showed significant intensity and activity differences, based on their field site and sampling time (June–August), indicating differential regulation of certain proteins in response to environmental or developmental factors. Peroxidases, class II chitinases, pectinesterases, and osmotins were among the proteins more abundant later in the growing season (July–August) as compared to early in the season (June). We did not detect significant differences between fungicide Shirlan treated and untreated field samples in two growing seasons. Using ABPP, we showed differential activity of serine hydrolases and β-glycosidases under greenhouse and field conditions and across a growing season. Furthermore, the activity of serine hydrolases and β-glycosidases, including proteins related to biotic stress tolerance, decreased as the season progressed. The generated proteomics data would facilitate further studies aiming at understanding mechanisms of molecular plant physiology in agricultural fields and help applying effective strategies to mitigate biotic and abiotic stresses.
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| 2. |
- Abreha, Kibrom Berhe, et al.
(författare)
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Inoculation of Transgenic Resistant Potato by Phytophthora infestans Affects Host Plant Choice of a Generalist Moth
- 2015
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Pathogen attack and the plant's response to this attack affect herbivore oviposition preference and larval performance. Introduction of major resistance genes against Phytophthora infestans (Rpi-genes), the cause of the devastating late blight disease, from wild Solanum species into potato changes the plant-pathogen interaction dynamics completely, but little is known about the effects on non-target organisms. Thus, we examined the effect of P. infestans itself and introduction of an Rpi-gene into the crop on host plant preference of the generalist insect herbivore, Spodoptera littoralis (Lepidoptera: Noctuidae). In two choice bio-assays, S. littoralis preferred to oviposit on P. infestans-inoculated plants of both the susceptible potato (cv. Desiree) and an isogenic resistant clone (A01-22: cv. Desiree transformed with Rpi-blb1), when compared to uninoculated plants of the same genotype. Both cv. Desiree and clone A01-22 were equally preferred for oviposition by S. littoralis when uninoculated plants were used, while cv. Desiree received more eggs compared to the resistant clone when both were inoculated with the pathogen. No significant difference in larval and pupal weight was found between S. littoralis larvae reared on leaves of the susceptible potato plants inoculated or uninoculated with P. infestans. Thus, the herbivore's host plant preference in this system was not directly associated with larval performance. The results indicate that the Rpi-blb1 based resistance in itself does not influence insect behavior, but that herbivore oviposition preference is affected by a change in the plant-microbe interaction.
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| 3. |
- Abreha, Kibrom Berhe, et al.
(författare)
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Phosphite protects against potato and tomato late blight in tropical climates and has varying toxicity depending on the Phytophthora infestans isolate
- 2019
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Ingår i: Crop Protection. - : Elsevier BV. - 0261-2194 .- 1873-6904. ; 121, s. 139-146
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Tidskriftsartikel (refereegranskat)abstract
- Late blight caused by the oomycete Phytophthora infestans is one of the most severe diseases of potato (Solarium tuberosum L.) and tomato (Solarium lycopersicum L.). In this study, field trials were conducted in a cool tropical highland of Ethiopia for three consecutive years to investigate the efficacy of phosphite alone and in combination with conventional fungicide against late blight in two potato cultivars and one tomato cultivar. Phosphite alone and in combination with reduced dosages of the fungicide Ridomil (mancozeb 64% and metalaxyl-M 4% (w/w)) led to effective suppression of late blight in research plots and in farmers' fields under light-to-normal late blight pressure. However, phosphite was not as effective as the fungicide under high disease pressure. Notably, phosphite was more effective against tomato late blight than against potato late blight, and gave the same protection as the fungicide in tomato. In vitro assays showed small differences in sensitivity to phosphite among five European and two Ethiopian isolates of P. infestans in terms of radial growth, sporangium production and sporangium germination, which could affect the population structure. Since phosphite can be provided at a lower price than conventional fungicides, it can reduce expenses for Ethiopian farmers with preserved late blight control.
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| 4. |
- Alexandersson, Erik, et al.
(författare)
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Field-omics-understanding large-scale molecular data from field crops
- 2014
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- The recent advances in gene expression analysis as well as protein and metabolite quantification enable genome-scale capturing of complex biological processes at the molecular level in crop field trials. This opens up new possibilities for understanding the molecular and environmental complexity of field-based systems and thus shedding light on the black box between genotype and environment, which in agriculture always is influenced by a multi-stress environment and includes management interventions. Nevertheless, combining different types of data obtained from the field and making biological sense out of large datasets remain challenging. Here we highlight the need to create a cross-disciplinary platform for innovative experimental design, sampling and subsequent analysis of large-scale molecular data obtained in field trials. For these reasons we put forward the term field-omics: "Field-omics strives to couple information from genomes, transcriptomes, proteomes, metabolomes and metagenomes to the long-established practice in crop science of conducting field trials as well as to adapt current strategies for recording and analysing field data to facilitate integration with '-omics' data."
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| 5. |
- Alexandersson, Erik, et al.
(författare)
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Linking crop traits to transcriptome differences in a progeny population of tetraploid potato
- 2020
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Ingår i: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- Background Potato is the third most consumed crop in the world. Breeding for traits such as yield, product quality and pathogen resistance are main priorities. Identifying molecular signatures of these and other important traits is important in future breeding efforts. In this study, a progeny population from a cross between a breeding line, SW93-1015, and a cultivar, Desiree, was studied by trait analysis and RNA-seq in order to develop understanding of segregating traits at the molecular level and identify transcripts with expressional correlation to these traits. Transcript markers with predictive value for field performance applicable under controlled environments would be of great value for plant breeding. Results A total of 34 progeny lines from SW93-1015 and Desiree were phenotyped for 17 different traits in a field in Nordic climate conditions and controlled climate settings. A master transcriptome was constructed with all 34 progeny lines and the parents through a de novo assembly of RNA-seq reads. Gene expression data obtained in a controlled environment from the 34 lines was correlated to traits by different similarity indices, including Pearson and Spearman, as well as DUO, which calculates the co-occurrence between high and low values for gene expression and trait. Our study linked transcripts to traits such as yield, growth rate, high laying tubers, late and tuber blight, tuber greening and early flowering. We found several transcripts associated to late blight resistance and transcripts encoding receptors were associated to Dickeya solani susceptibility. Transcript levels of a UBX-domain protein was negatively associated to yield and a GLABRA2 expression modulator was negatively associated to growth rate. Conclusion In our study, we identify 100's of transcripts, putatively linked based on expression with 17 traits of potato, representing both well-known and novel associations. This approach can be used to link the transcriptome to traits. We explore the possibility of associating the level of transcript expression from controlled, optimal environments to traits in a progeny population with different methods introducing the application of DUO for the first time on transcriptome data. We verify the expression pattern for five of the putative transcript markers in another progeny population.
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| 6. |
- Alexandersson, Erik, et al.
(författare)
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Plant Resistance Inducers against Pathogens in Solanaceae Species-From Molecular Mechanisms to Field Application
- 2016
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Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1661-6596 .- 1422-0067. ; 17
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Forskningsöversikt (refereegranskat)abstract
- This review provides a current summary of plant resistance inducers (PRIs) that have been successfully used in the Solanaceae plant family to protect against pathogens by activating the plant's own defence. Solanaceous species include many important crops such as potato and tomato. We also present findings regarding the molecular processes after application of PRIs, even if the number of such studies still remains limited in this plant family. In general, there is a lack of patterns regarding the efficiency of induced resistance (IR) both between and within solanaceous species. In many cases, a hypersensitivity-like reaction needs to form in order for the PRI to be efficient. "-Omics" studies have already given insight in the complexity of responses, and can explain some of the differences seen in efficacy of PRIs between and within species as well as towards different pathogens. Finally, examples of field applications of PRIs for solanaceous crops are presented and discussed. We predict that PRIs will play a role in future plant protection strategies in Solanaceae crops if they are combined with other means of disease control in different spatial and temporal combinations.
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| 7. |
- Alexandersson, Erik, et al.
(författare)
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Plant secretome proteomics
- 2013
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 4
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Forskningsöversikt (refereegranskat)abstract
- The plant secretome refers to the set of proteins secreted out of the plant cell into the surrounding extracellular space commonly referred to as the apoplast. Secreted proteins maintain cell structure and acts in signaling and are crucial for stress responses where they can interact with pathogen effectors and control the extracellular environment. Typically, secreted proteins contain an N-terminal signal peptide and are directed through the endoplasmic reticulum/Golgi pathway. However, in plants many proteins found in the secretome lack such a signature and might follow alternative ways of secretion. This review covers techniques to isolate plant secretomes and how to identify and quantify their constituent proteins. Furthermore, bioinformatical tools to predict secretion signals and define the putative secretome are presented. Findings from proteomic studies and important protein families of plant secretomes, such as proteases and hydrolases, are highlighted.
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| 8. |
- Ali, Ashfaq, et al.
(författare)
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Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions
- 2014
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: In order to get global molecular understanding of one of the most important crop diseases worldwide, we investigated compatible and incompatible interactions between Phytophthora infestans and potato (Solanum tuberosum). We used the two most field-resistant potato clones under Swedish growing conditions, which have the greatest known local diversity of P. infestans populations, and a reference compatible cultivar. Results: Quantitative label-free proteomics of 51 apoplastic secretome samples (PXD000435) in combination with genome-wide transcript analysis by 42 microarrays (E-MTAB-1515) were used to capture changes in protein abundance and gene expression at 6, 24 and 72 hours after inoculation with P. infestans. To aid mass spectrometry analysis we generated cultivar-specific RNA-seq data (E-MTAB-1712), which increased peptide identifications by 17%. Components induced only during incompatible interactions, which are candidates for hypersensitive response initiation, include a Kunitz-like protease inhibitor, transcription factors and an RCR3-like protein. More secreted proteins had lower abundance in the compatible interaction compared to the incompatible interactions. Based on this observation and because the well-characterized effector-target C14 protease follows this pattern, we suggest 40 putative effector targets. Conclusions: In summary, over 17000 transcripts and 1000 secreted proteins changed in abundance in at least one time point, illustrating the dynamics of plant responses to a hemibiotroph. Half of the differentially abundant proteins showed a corresponding change at the transcript level. Many putative hypersensitive and effector-target proteins were single representatives of large gene families.
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| 9. |
- Andreasson, Erik, et al.
(författare)
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Botanicals and plant strengtheners for potato and tomato cultivation in Africa
- 2020
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Ingår i: Journal of Integrative Agriculture. - 2095-3119 .- 2352-3425. ; 19, s. 406-427
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Forskningsöversikt (refereegranskat)abstract
- This review provides a summary of botanicals and plant strengtheners that have potential uses for disease and pest management in potato and tomato cultivation in African. We discuss their possible use to prevent major diseases and pests which infest potato and tomato, such as early and late blight, bacterial wilt, potato tuber moth, and tomato leafminer. There are several examples of the successful uses of botanicals for pathogen and pest control relevant for different African climatic conditions; however, most of these studies have been conducted in vitro and often lack field verification. Plant strengtheners (substances that induce and improve crop resistance, yield, and quality) are little studied and used in Africa in comparison to North America and Europe. The possible benefits of using botanicals and plant strengtheners instead of conventional pesticides are discussed here in relation to human health and the environment as well as their modes of action and accessibility to farmers. Lack of knowledge of the composition and active ingredients of extracts, environmental concerns, uncertainties regarding stability and formulation, lack of legislation and limited support from governments, hamper the development of botanicals and plant strengtheners for use in sustainable African agriculture.
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| 10. |
- Andreasson, Erik, et al.
(författare)
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Phosphite alters the behavioral response of potato tuber moth (Phthorimaea operculella) to field-grown potato
- 2019
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Ingår i: Pest Management Science. - : Wiley. - 1526-498X .- 1526-4998. ; 75, s. 616-621
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND The potato tuber moth (PTM) (Phthorimaea operculella) is a pest of solanaceous species that causes serious damage to potato tubers and tomato fruits. Control is mainly dependent on the use of synthetic chemicals, which pose a risk to the environment and health of farmers, especially in developing countries where application safety rules are often neglected. In this study we aimed at investigating the effects of a plant resistance inducer (PRI) potassium phosphite on PTM larval population density and PTM parasitoid levels, which can be used as biocontrol agents. We also tested whether intercropping with tomato, which is less attractive to PTM, provided a spatial border to further reduce PTM numbers. RESULTS In two different locations over two seasons, we showed that foliar application of phosphite more than halved the PTM larval populations on potato, and that PTM parasitoid numbers were unaffected. No consistent reduction in PTM was achieved by intercropping potato with tomato. CONCLUSIONS Phosphite reduced PTM numbers in the field without interfering with autochthonous parasitoids, indicating its suitability as part of an Integrated Pest Management strategy. Ex situ choice tests showed that phosphite-treated potato deterred PTM, which could be a reason for the control of PTM in the field. (c) 2018 Society of Chemical Industry
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| 11. |
- Bengtsson, Therese, et al.
(författare)
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Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach
- 2014
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Induced resistance (IR) can be part of a sustainable plant protection strategy against important plant diseases. beta-aminobutyric acid (BABA) can induce resistance in a wide range of plants against several types of pathogens, including potato infected with Phytophthora infestans. However, the molecular mechanisms behind this are unclear and seem to be dependent on the system studied. To elucidate the defence responses activated by BABA in potato, a genome-wide transcript microarray analysis in combination with label-free quantitative proteomics analysis of the apoplast secretome were performed two days after treatment of the leaf canopy with BABA at two concentrations, 1 and 10 mM. Results: Over 5000 transcripts were differentially expressed and over 90 secretome proteins changed in abundance indicating a massive activation of defence mechanisms with 10 mM BABA, the concentration effective against late blight disease. To aid analysis, we present a more comprehensive functional annotation of the microarray probes and gene models by retrieving information from orthologous gene families across 26 sequenced plant genomes. The new annotation provided GO terms to 8616 previously un-annotated probes. Conclusions: BABA at 10 mM affected several processes related to plant hormones and amino acid metabolism. A major accumulation of PR proteins was also evident, and in the mevalonate pathway, genes involved in sterol biosynthesis were down-regulated, whereas several enzymes involved in the sesquiterpene phytoalexin biosynthesis were up-regulated. Interestingly, abscisic acid (ABA) responsive genes were not as clearly regulated by BABA in potato as previously reported in Arabidopsis. Together these findings provide candidates and markers for improved resistance in potato, one of the most important crops in the world.
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| 12. |
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| 13. |
- Burra, Dharani, et al.
(författare)
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Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosum leading to resistance against Phytophthora infestans
- 2014
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Ingår i: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Background: Potato late blight caused by the oomycete pathogen Phytophthora infestans can lead to immense yield loss. We investigated the transcriptome of Solanum tubersoum (cv. Desiree) and characterized the secretome by quantitative proteomics after foliar application of the protective agent phosphite. We also studied the distribution of phosphite in planta after application and tested transgenic potato lines with impaired in salicylic and jasmonic acid signaling. Results: Phosphite had a rapid and transient effect on the transcriptome, with a clear response 3 h after treatment. Strikingly this effect lasted less than 24 h, whereas protection was observed throughout all time points tested. In contrast, 67 secretome proteins predominantly associated with cell-wall processes and defense changed in abundance at 48 h after treatment. Transcripts associated with defense, wounding, and oxidative stress constituted the core of the phosphite response. We also observed changes in primary metabolism and cell wall-related processes. These changes were shown not to be due to phosphate depletion or acidification caused by phosphite treatment. Of the phosphite-regulated transcripts 40% also changed with beta-aminobutyric acid (BABA) as an elicitor, while the defence gene PR1 was only up-regulated by BABA. Although phosphite was shown to be distributed in planta to parts not directly exposed to phosphite, no protection in leaves without direct foliar application was observed. Furthermore, the analysis of transgenic potato lines indicated that the phosphite-mediated resistance was independent of the plant hormones salicylic and jasmonic acid. Conclusions: Our study suggests that a rapid phosphite-triggered response is important to confer long-lasting resistance against P. infestans and gives molecular understanding of its successful field applications.
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| 14. |
- Chawade, Aakash, et al.
(författare)
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Targeted Proteomics Approach for Precision Plant Breeding
- 2016
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 15, s. 638-646
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Tidskriftsartikel (refereegranskat)abstract
- Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that enables precise quantitation of hundreds of peptides in a single run. This technique provides new opportunities for multiplexed protein biomarker measurements. For precision plant breeding, DNA-based markers have been used extensively, but the potential of protein biomarkers has not been exploited. In this work, we developed an SRM marker panel with assays for 104 potato (Solanum tuberosum) peptides selected using univariate and multivariate statistics. Thereafter, using random forest classification, the prediction markers were identified forPhytopthora infestansresistance in leaves,P. infestansresistance in tubers, and plant yield in potato leaf secretome samples. The results suggest that the marker panel has the predictive potential for three traits, two of which have no commercial DNA markers so far. Furthermore, the marker panel was also tested and found to be applicable to potato clones not used during the marker development. The proposed workflow is thus a proof-of-concept for targeted proteomics as an efficient readout in accelerated breeding for complex and agronomically important traits.
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| 15. |
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| 16. |
- Iciar, Frades, et al.
(författare)
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A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones
- 2015
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Comparative transcriptomics between species can provide valuable understanding of plant-pathogen interactions. Here, we focus on wild Solarium species and potato clones with varying degree of resistance against Phytophthora infestans, which causes the devastating late blight disease in potato. The transcriptomes of three wild Solanurn species native to Southern Sweden, Solarium dulcamara, Solanum nigrum, and Solanurn physalifolium were compared to three potato clones, Desiree (cv.), SW93-1015 and Sarpo Mira. Desiree and S. physalifolium are susceptible to P. infestans whereas the other four have different degrees of resistance. By building transcript families based on de novo assembled RNA-seq across species and clones and correlating these to resistance phenotypes, we created a novel workflow to identify families with expanded or depleted number of transcripts in relation to the P. infestans resistance level. Analysis was facilitated by inferring functional annotations based on the family structure and semantic clustering. More transcript families were expanded in the resistant clones and species and the enriched functions of these were associated to expected gene ontology (GO) terms for resistance mechanisms such as hypersensitive response, host programmed cell death and endopeptidase activity. However, a number of unexpected functions and transcripts were also identified, for example transmembrane transport and protein acylation expanded in the susceptible group and a cluster of Zinc knuckle family proteins expanded in the resistant group. Over 400 expressed putative resistance (R)genes were identified and resistant clones Sarpo Mira and 5W93-1015 had ca 25% more expressed putative R-genes than susceptible cultivar Desiree. However, no differences in numbers of susceptibility (S)gene homologs were seen between species and clones. In addition, we identified P infestans transcripts including effectors in the early stages of P. infestans-Solanum interactions.
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| 17. |
- Iciar, Frades, et al.
(författare)
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Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case
- 2014
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Ingår i: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Background: For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, 'omics', and literature data. However, researchers encounter little guidance on how well they perform. Here, we used the recently sequenced potato genome as a case study. The potato genome was selected since its genome is newly sequenced and it is a non-model plant even if there is relatively ample information on individual potato genes, and multiple gene expression profiles are available.Results: We show that the automatic gene annotations of potato have low accuracy when compared to a "gold standard" based on experimentally validated potato genes. Furthermore, we evaluate six state-of-the-art annotation pipelines and show that their predictions are markedly dissimilar (Jaccard similarity coefficient of 0.27 between pipelines on average). To overcome this discrepancy, we introduce a simple GO structure-based algorithm that reconciles the predictions of the different pipelines. We show that the integrated annotation covers more genes, increases by over 50% the number of highly co-expressed GO processes, and obtains much higher agreement with the gold standard.Conclusions: We find that different annotation pipelines produce different results, and show how to integrate them into a unified annotation that is of higher quality than each single pipeline. We offer an improved functional annotation of both PGSC and ITAG potato gene models, as well as tools that can be applied to additional pipelines and improve annotation in other organisms. This will greatly aid future functional analysis of '-omics' datasets from potato and other organisms with newly sequenced genomes. The new potato annotations are available with this paper.
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| 18. |
- Iciar, Frades, et al.
(författare)
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Integrative Genomic Signatures Of Hepatocellular Carcinoma Derived from Nonalcoholic Fatty Liver Disease
- 2015
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Nonalcoholic fatty liver disease (NAFLD) is a risk factor for Hepatocellular carcinoma (HCC), but he transition from NAFLD to HCC is poorly understood. Feature selection algorithms in human and genetically modified mice NAFLD and HCC microarray data were applied to generate signatures of NAFLD progression and HCC differential survival. These signatures were used to study the pathogenesis of NAFLD derived HCC and explore which subtypes of cancers that can be investigated using mouse models. Our findings show that: (I) HNF4 is a common potential transcription factor mediating the transcription of NAFLD progression genes (II) mice HCC derived from NAFLD co-cluster with a less aggressive human HCC subtype of differential prognosis and mixed etiology (III) the HCC survival signature is able to correctly classify 95% of the samples and gives Fgf20 and Tgfb1i1 as the most robust genes for prediction (IV) the expression values of genes composing the signature in an independent human HCC dataset revealed different HCC subtypes showing differences in survival time by a Logrank test. In summary, we present marker signatures for NAFLD derived HCC molecular pathogenesis both at the gene and pathway level.
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| 19. |
- Lankinen, Åsa, et al.
(författare)
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Nongenetic Inheritance of Induced Resistance in a Wild Annual Plant
- 2016
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Ingår i: Phytopathology. - 0031-949X .- 1943-7684. ; 106, s. 877-883
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Tidskriftsartikel (refereegranskat)abstract
- Nongenetic inheritance (e.g., transgenerational epigenetic effects) has received increasing interest in recent years, particularly in plants. However, most studies have involved a few model species and relatively little is known about wild species in these respects. We investigated transgenerational induced resistance to infection by the devastating oomycete Phytophthora infestans in Solanum physalifolium, a wild relative of cultivated potato. We treated plants with b-aminobutyric acid (BABA), a nontoxic compound acting as an inducing agent, or infected plants with P. infestans. BABA treatment reduced lesion size in detached-leaf assays inoculated by P. infestans in two of three tested genotypes, suggesting that resistance to oomycetes can be induced by BABA within a generation not only in crops or model species but also in wild species directly collected from nature. Both BABA treatment and infection in the parental generation reduced lesions in the subsequent generation in one of two genotypes, indicating a transgenerational influence on resistance that varies among genotypes. We did not detect treatment effects on seed traits, indicating the involvement of a mechanism unrelated to maternal effects. In conclusion, our study provides data on BABA induction and nongenetic inheritance of induced resistance in a wild relative of cultivated potato, implying that this factor might be important in the ecological and agricultural landscape.
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| 20. |
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| 21. |
- Liljeroth, Erland, et al.
(författare)
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Phosphite Integrated in Late Blight Treatment Strategies in Starch Potato Does Not Cause Residues in the Starch Product
- 2020
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Ingår i: Plant Disease. - 0191-2917 .- 1943-7692. ; 104, s. 3026-3032
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Tidskriftsartikel (refereegranskat)abstract
- Currently available fungicides against potato late blight are effective but there are concerns about the sustainability of frequent applications and the risks of fungicide resistance. Therefore, we investigated how potassium phosphite can be integrated into late blight control programs with reduced fungicides in field trials. Phosphite was somewhat less effective than the conventional fungicides at suppressing late blight in the foliage, and the tubers contained less starch. However, when we reduced the amount of phosphite and combined it with reduced amounts of conventional fungicides, we observed no differences in disease suppression, total yields, and tuber starch contents compared with the full treatments with conventional fungicides. The amount of phosphite detected in the harvested tubers was linearly associated with the amount of phosphite applied to the foliage. Our analyses indicate that phosphite could replace some fungicides without exceeding the current European Union standards for the maximum residue levels in potato tubers. No phosphite was detected in the starch from the tubers. In 1 of 2 years, early blight (caused by Alternaria solani) was less severe in the phosphite treatments than in the treatments without phosphite. The integration of phosphite into current treatment strategies would reduce the dependence on conventional fungicides.
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| 22. |
- Liljeroth, Erland, et al.
(författare)
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Potassium phosphite combined with reduced doses of fungicides provides efficient protection against potato late blight in large-scale field trials
- 2016
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Ingår i: Crop Protection. - : Elsevier BV. - 0261-2194 .- 1873-6904. ; 86, s. 42-55
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Tidskriftsartikel (refereegranskat)abstract
- Potato late blight caused by the oomycete Phytophthora infestans is a devastating disease of potato worldwide. Most of the potato cultivars grown in conventional agriculture are susceptible, or at best moderately resistant, and require frequent applications of fungicides to avoid heavy yield losses.In field trials spanning four years, we have investigated the effect of potassium phosphite, an inorganic salt on potato late blight. Potassium phosphite is known to induce defence responses in potato and to also have direct toxic effects on oomycetes, which in turn counteract late blight and tuber blight development. However, the use of this salt is not yet implemented and approved in European potato cultivation. We compared the effect of phosphite alone with fungicides currently used in Swedish potato cultivation. We also investigated the combined use of potassium phosphite and reduced doses of fungicides. Table potato cultivars and starch potato cultivars with different levels of resistance were used.We found that potassium phosphite in combination with reduced doses of fungicides results in the same level of protection as treatments with the recommended full dose of fungicides. These combined treatments reduce the need of traditional fungicides and may also decrease the selection pressure for fungicide resistance development in the pathogen. In relatively resistant starch potato cultivars using phosphite alone gave sufficient protection against late blight. Furthermore, in starch potato a combination of phosphite and fungicides at two-week intervals provided similar protection to weekly applications of fungicide at the recommended dose. Foliar treatment with phosphite also gave protection against tuber blight at similar levels to that of the best-performing fungicide. Our data suggests that potassium phosphite could be used in potato cultivation in temperate regions such as in Sweden, at least in combinations with reduced rates of fungicides. The implementation of the use of phosphite in practical potato crop protection as part of an IPM strategy is discussed. Doses, intervals and combinations could be adjusted to the level of cultivar resistance. (C) 2016 The Authors. Published by Elsevier Ltd.
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| 23. |
- Odilbekov, Firuz, et al.
(författare)
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Intact salicylic acid signalling is required for potato defence against the necrotrophic fungus Alternaria solani
- 2020
-
Ingår i: Plant Molecular Biology. - : Springer Science and Business Media LLC. - 0167-4412 .- 1573-5028. ; 104, s. 1-19
-
Tidskriftsartikel (refereegranskat)abstract
- Key Message Using disease bioassays and transcriptomic analysis we show that intact SA-signalling is required for potato defences against the necrotrophic fungal pathogenAlternaria solani. Early blight, caused by the necrotrophic fungusAlternaria solani,is an increasing problem in potato cultivation. Studies of the molecular components defining defence responses toA. solaniin potato are limited. Here, we investigate plant defence signalling with a focus on salicylic acid (SA) and jasmonic acid (JA) pathways in response toA. solani. Our bioassays revealed that SA is necessary to restrict pathogen growth and early blight symptom development in both potato foliage and tubers. This result is in contrast to the documented minimal role of SA in resistance ofArabidopsis thalianaagainst necrotrophic pathogens. We also present transcriptomic analysis with 36 arrays ofA. solaniinoculated SA-deficient, JA-insensitive, and wild type plant lines. A greater number of genes are differentially expressed in the SA-deficient mutant plant line compared to the wild type and JA- insensitive line. In wild type plants, genes encoding metal ion transporters, such as copper, iron and zinc transporters were upregulated and transferase-encoding genes, for example UDP-glucoronosyltransferase and Serine-glyoxylate transferase, were downregulated. The SA-deficient plants show upregulation of genes enriched in GO terms related to oxidoreductase activity, respiratory chain and other mitochondrial-related processes.Pathogenesis-relatedgenes, such as genes encoding chitinases and PR1, are upregulated in both the SA-deficient and wild type plants, but not in the JA-insensitive mutants. The combination of our bioassays and the transcriptomic analysis indicate that intact SA signalling, and not JA signalling, is required for potato defences against the necrotrophic pathogenA. solani.
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| 24. |
- Resjö, Svante, et al.
(författare)
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Comparative proteomic analyses of potato leaves from field-grown plants grown under extremely long days
- 2024
-
Ingår i: Plant Physiology and Biochemistry. - 0981-9428 .- 1873-2690. ; 215
-
Tidskriftsartikel (refereegranskat)abstract
- There are limited molecular data and few biomarkers available for studies of field-grown plants, especially for plants grown during extremely long days. In this study we present quantitative proteomics data from 3 years of field trials on potato, conducted in northern and southern Sweden and analyze over 3000 proteins per year of the study and complement the proteomic analysis with metabolomic and transcriptomic analyses. Small but consistent differences linked to the longer days (an average of four more hours of light per day) in northern Sweden (20 h light/day) compared to southern Sweden can be observed, with a high correlation between the mRNA determined by RNA-seq and protein abundances. The majority of the proteins with differential abundances between northern and southern Sweden could be divided into three groups: metabolic enzymes (especially GABA metabolism), proteins involved in redox metabolism, and hydrolytic enzymes. The observed differences in metabolic enzyme abundances corresponded well with untargeted metabolite data determined by GC and LC mass-spectrometry. We also analyzed differences in protein abundance between potato varieties that performed relatively well in northern Sweden in terms of yield with those that performed relatively less well. This comparison indicates that the proteins with higher abundance in the high-yield quotient group are more anabolic in their character, whereas the proteins with lower abundance are more catabolic. Our results create a base of information about potato "field-omics" for improved understanding of physiological and molecular processes in field-grown plants, and our data indicate that the potato plant is not generally stressed by extremely long days.
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| 25. |
- Walter, Abigail, et al.
(författare)
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GENE TRANSCRIPTION CHANGES DURING COMPATIBLE AND INCOMPATIBLE INFECTIONS OF POTATO BY GLOBODERA ROSTOCHIENSIS
- 2014
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Ingår i: Journal of Nematology. - 0022-300X. ; 46, s. 253-253
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The golden potato cyst nematode,Globodera rostochiensis, is one of the most important pests of potato in Sweden. Several pathotypes of the nematode exist, and they may be controlled by one of several sources of single-gene resistance in potato. Here we report that SW93-1015, a breeding line from the potato breeding program at SLU Alnarp, has phenotypic resistance to the Ro1/4 pathotype ofG. rostochiensis. Reproduction ofG. rostochiensispathotype Ro1/4 on SW93-1015 is approximately 5% of reproduction on the susceptible cultivar Desiree. To further investigate the interaction between potato cyst nematodes and susceptible and resistant host plants, changes in gene transcription were monitored just after root penetration and during syncytium formation in Desiree and SW93-1015 potato plants infected with Ro1/4G. rostochiensis.RNA expression in root tissue was analysed on a microarray at 0, 8, and 48 h post-infection, corresponding to pre-infection, root penetration, and early syncytium formation. Changes in gene transcription over the process of infection in susceptible and resistant genotypes are discussed. The resistance will be further investigated using a crossing population if Desiree and SW93-1015.
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| 26. |
- Alexandersson, Erik, et al.
(författare)
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Arabidopsis Plasma Membrane Proteomics Identifies Components of Transport, Signal Transduction and Membrane Trafficking
- 2004
-
Ingår i: Plant and Cell Physiology. - : Oxford University Press (OUP). - 1471-9053 .- 0032-0781. ; 45:11, s. 1543-1556
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Tidskriftsartikel (refereegranskat)abstract
- In order to identify integral proteins and peripheral proteins associated with the plasma membrane, highly purified Arabidopsis plasma membranes from green tissue (leaves and petioles) were analyzed by mass spectrometry. Plasma membranes were isolated by aqueous two-phase partitioning, which yields plasma membrane vesicles with a cytoplasmic-side-in orientation and with a purity of 95%. These vesicles were turned inside-out by treatment with Brij 58 to remove soluble contaminating proteins enclosed in the vesicles and to remove loosely bound contaminating proteins. In total, 238 putative plasma membrane proteins were identified, of which 114 are predicted to have transmembrane domains or to be glycosyl phosphatidylinositol anchored. About two-thirds of the identified integral proteins have not previously been shown to be plasma membrane proteins. Of the 238 identified proteins, 76% could be classified according to function. Major classes are proteins involved in transport (17%), signal transduction (16%), membrane trafficking (9%) and stress responses (9%). Almost a quarter of the proteins identified in the present study are functionally unclassified and more than half of these are predicted to be integral.
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| 27. |
- Alexandersson, Erik
(författare)
-
Computer Vision and Less Complex Image Analyses to Monitor Potato Traits in Fields
- 2021
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Ingår i: Solanum tuberosum : Methods and Protocols. - New York, NY : Springer US. - 9781071616086 ; 2354:2354, s. 273-299
-
Bokkapitel (refereegranskat)abstract
- Field phenotyping of crops has recently gained considerable attention leading to the development of new protocols for recording plant traits of interest. Phenotyping in field conditions can be performed by various cameras, sensors, and imaging platforms. In this chapter, practical aspects as well as advantages and disadvantages of aboveground phenotyping platforms are highlighted with a focus on drone-based imaging and relevant image analysis for field conditions. It includes useful planning tips for experimental design as well as protocols, sources, and tools for image acquisition, preprocessing, feature extraction, and machine learning highlighting the possibilities with computer vision. Several open and free resources are given to speed up data analysis for biologists. This chapter targets professionals and researchers with limited computational background performing or wishing to perform phenotyping of field crops, especially with a drone-based platform. The advice and methods described focus on potato but can mostly be used for field phenotyping of any crops.
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| 28. |
- Alexandersson, Erik
(författare)
-
Cross-domain transfer learning for weed segmentation and mapping in precision farming using ground and UAV images
- 2024
-
Ingår i: Expert Systems with Applications. - 0957-4174. ; 246
-
Tidskriftsartikel (refereegranskat)abstract
- Weed and crop segmentation is becoming an increasingly integral part of precision farming that leverages the current computer vision and deep learning technologies. Research has been extensively carried out based on images captured with a camera from various platforms. Unmanned aerial vehicles (UAVs) and ground-based vehicles including agricultural robots are the two popular platforms for data collection in fields. They all contribute to site-specific weed management (SSWM) to maintain crop yield. Currently, the data from these two platforms is processed separately, though sharing the same semantic objects (weed and crop). In our paper, we have proposed a novel method with a new deep learning-based model and the enhanced data augmentation pipeline to train field images alone and subsequently predict both field images and UAV images for weed segmentation and mapping. The network learning process is visualized by feature maps at shallow and deep layers. The results show that the mean intersection of union (IOU) values of the segmentation for the crop (maize), weeds, and soil background in the developed model for the field dataset are 0.744, 0.577, 0.979, respectively, and the performance of aerial images from an UAV with the same model, the IOU values of the segmentation for the crop (maize), weeds and soil background are 0.596, 0.407, and 0.875, respectively. To estimate the effect on the use of plant protection agents, we quantify the relationship between herbicide spraying saving rate and grid size (spraying resolution) based on the predicted weed map. The spraying saving rate is up to 90 % when the spraying resolution is at 1.78 × 1.78 cm2 . The study shows that the developed deep convolutional neural network could be used to classify weeds from both field and aerial images and delivers satisfactory results. To achieve this performance, it is crucial to perform preprocessing techniques that reduce dataset differences between two distinct domains.
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| 29. |
- Alexandersson, Erik, et al.
(författare)
-
Nordic research infrastructures for plant phenotyping
- 2018
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Ingår i: Agricultural and Food Science. - : Agricultural and Food Science. - 1459-6067 .- 1795-1895. ; 27, s. 7-16
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Forskningsöversikt (refereegranskat)abstract
- Plant phenomics refers to the systematic study of plant phenotypes. Together with closely monitored, controlled climates, it provides an essential component for the integrated analysis of genotype-phenotype-environment interactions. Currently, several plant growth and phenotyping facilities are under establishment globally, and numerous facilities are already in use. Alongside the development of the research infrastructures, several national and international networks have been established to support shared use of the new methodology. In this review, an overview is given of the Nordic plant phenotyping and climate control facilities. Since many areas of phenomics such as sensor-based phenotyping, image analysis and data standards are still developing, promotion of educational and networking activities is especially important. These facilities and networks will be instrumental in tackling plant breeding and plant protection challenges. They will also provide possibilities to study wild species and their ecological interactions under changing Nordic climate conditions.
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| 30. |
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| 31. |
- Alexandersson, Erik, et al.
(författare)
-
Plasma membrane proteomics
- 2006
-
Ingår i: Plant Proteomics. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783540726166 - 9783540726173 ; , s. 186-206
-
Bokkapitel (refereegranskat)abstract
- Proteins residing in the plasma membrane have key functions in transport, signal transduction, vesicle trafficking and many other important processes. To better understand these processes it is necessary to reveal the identity of plasma membrane proteins and to monitor modifications and regulation of their expression. This chapter is an overview of the methods used in plant plasma membrane proteomic studies and the results obtained so far. It focuses on studies using mass spectrometry for identification and includes aspects of plasma membrane fractionation, extraction and washing treatments, assessment of purity, separation methods for plasma membrane proteins and choice of techniques for protein cleavage. Finally, the results of plasma membrane proteomic studies are compared and problems with contaminating proteins are discussed.
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| 32. |
- Alexandersson, Erik
(författare)
-
Plasma Membrane Proteomics and Functional Characterization & Expression Profiling of Plant Aquaporins
- 2006
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In order to identify integral and peripheral proteins associated with the plasma membrane (PM), highly purified Arabidopsis PMs were analyzed by mass spectrometry. In total, 238 putative PM proteins were identified, of which 114 were predicted to have transmembrane domains or to be PM-anchored. Identified proteins were involved in transport, signal transduction, membrane trafficking and stress responses. Almost 25% of the proteins were functionally unclassified and more than half of these were predicted to be integral. In this proteomic study, ten aquaporin (AQP) isoforms were identified. AQPs (also referred to as major intrinsic proteins, MIPs) are integral proteins that facilitate transport of water and other small neutral solutes. In plants, AQPs form a large family with 35 members in Arabidopsis. The number of genes is about the same in moncots. Based on sequence similarity, plant AQPs are divided in four subfamilies: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), Nod26-like intrinsic proteins (NIPs) and small basic intrinsic proteins (SIPs). By in-house designed cDNA microarrays and quantitative PCR, the expression patterns of all 35 Arabidopsis AQP genes were monitored in leaves, roots and flowers. This showed that many AQP genes were pre-dominantly expressed in either root or flower organs, but none seemed to be leaf-specific. Most PIP and some TIP genes had a high level of expression, while NIP genes were present at a low level. During gradual drought stress of soil-grown plants, PIP transcripts were generally down-regulated in leaves, with the exception of AtPIP1;4 and AtPIP2;5, which were up-regulated. AtPIP2;6 was constitutively expressed. These three PIP genes were therefore further characterized by promoter-beta-glucuronidase (GUS)- and green florescence protein (GFP)-fusions. Also, expression profiling upon drought stress of PIP genes in different Arabidopsis ecotypes was done. No major differences in expression between ecotypes were detected. Instead expression of many PIP genes correlated with plant water content. Since little is known about the role of AQPs in the elongation zone of growing leaves, an AQP, HvPIP1;6, was cloned from this tissue and characterized by expression in Xenopus oocytes, in-situ PCR and Northern and Western blotting. The gating of the AQP SoPIP2;1 is caused by phosphorylation at Ser115 and Ser274. Two protein kinases acting on these two sites were purified and characterized. The Ser115 kinase was soluble and Ca2+- independent, whereas the Ser274 kinase was PM-associated and Ca2+-dependent.
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| 33. |
- Alexandersson, Erik, et al.
(författare)
-
Purification and proteomic analysis of plant plasma membranes.
- 2008
-
Ingår i: Methods in Molecular Biology. - Totowa, NJ : Humana Press. - 1940-6029. ; 432, s. 161-173
-
Tidskriftsartikel (refereegranskat)abstract
- All techniques needed for proteomic analyses of plant plasma membranes are described in detail, from isolation of plasma membranes to protein identification by mass spectrometry (MS). Plasma membranes are isolated by aqueous two-phase partitioning yielding vesicles with a cytoplasmic side-in orientation and a purity of about 95%. These vesicles are turned inside-out by treatment with Brij 58, which removes soluble contaminating proteins enclosed in the vesicles as well as loosely attached proteins. The final plasma membrane preparation thus retains all integral proteins and many peripheral proteins. Proteins are separated by one-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), and protein bands are excised and digested with trypsin. Peptides in tryptic digests are separated by nanoflow liquid chromatography and either fed directly into an ESI-MS or spotted onto matrix-assisted laser desorption ionization (MALDI) plates for analysis with MALDI-MS. Finally, data processing and database searching are used for protein identification to define a plasma membrane proteome.
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| 34. |
- Alexandersson, Erik
(författare)
-
Smallholder farmers' knowledge, attitudes, and practices (KAP) regarding agricultural inputs with a focus on agricultural biologicals
- 2024
-
Ingår i: Heliyon. - 2405-8440. ; 10
-
Tidskriftsartikel (refereegranskat)abstract
- There is a general drive to reduce pesticide use owing to the potential negative effects of pesticides on the environment and human health. The EU Commission, for example, through its "Farm to Fork Strategy," has proposed to decrease the use of hazardous chemical pesticides by 50% by 2030. In addition, smallholder farmers in low-income countries do not always follow pesticide safety precautions. This necessitates the introduction of low-risk crop protection strategies also suited for these farmers. Agricultural biologicals can substitute for, or at least partially replace hazardous chemical pesticides. While the market for and use of biologicals is growing quickly in industrialized countries, this practice remains limited in sub-Saharan Africa. To understand the reason behind the low adoption of biologicals, this study examined the knowledge, attitudes, and practices toward biologicals among 150 smallholder farmers in the Chole district in Ethiopia. All farmers used chemical pesticides and/or inorganic fertilizers to protect crops, improve yields, and comply with government regulations. The use of biologicals was, however, restricted to one group of biologicals, bio-fertilizers, which approximately 60% of farmers used, and no use of biologicals for plant protection was reported. Even though the understanding of the concept of biologicals was deemed high among respondents, the majority (90%) did not identify biologicals as safer alternatives to conventional agricultural inputs. More than half of the respondents (54%) did not recommend biologicals as safer alternatives to their colleagues. Nevertheless, even if the responding farmers did not perceive biologicals as risk-free, they had a positive attitude towards biologicals when it came to producing healthy food and increasing crop yields and incomes. In comparison to the positive attitude, farmers' knowledge and practice of biologicals were generally low; thus, efforts are needed to create awareness among farmers.
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| 35. |
- Alexandersson, Erik
(författare)
-
The genes and enzymes of the carotenoid metabolic pathway in Vitis vinifera L.
- 2012
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 13
-
Tidskriftsartikel (refereegranskat)abstract
- Conclusions: The carotenoid metabolic pathway is well characterised, and the genes and enzymes have been studied in a number of plants. The study of the 42 carotenoid pathway genes of grapevine showed that they share a high degree of similarity with other eudicots. Expression and pigment profiling of developing berries provided insights into the most complete grapevine carotenoid pathway representation. This study represents an important reference study for further characterisation of carotenoid biosynthesis and catabolism in grapevine.
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| 36. |
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| 37. |
- Alexandersson, Erik, et al.
(författare)
-
Transcriptional regulation of aquaporins in accessions of Arabidopsis in response to drought stress.
- 2010
-
Ingår i: Plant Journal. - 1365-313X. ; 61, s. 650-660
-
Tidskriftsartikel (refereegranskat)abstract
- Summary Aquaporins facilitate water transport over cellular membranes and are therefore believed to play an important role in water homeostasis. In higher plants aquaporin-like proteins, also called major intrinsic proteins (MIPs), are divided into 5 subfamilies. We have previously shown that MIP transcription in Arabidopsis thaliana generally is down-regulated in leaves upon drought stress, apart from two members of the Plasma membrane Intrinsic Protein (PIP) subfamily, AtPIP1;4 and AtPIP2;5, which are up-regulated. In order to assess if this regulation is general or accession-specific we monitored gene expression of all PIPs in five Arabidopsis accessions. Overall drought regulation of PIPs was well conserved for all five accessions tested suggesting a general and fundamental physiological role of this drought response. In addition, significant differences among accessions were identified for transcripts of three PIP genes. Principal component analysis showed that most of the PIP transcriptional variation during drought stress could be explained by one variable linked to leaf water content. Promoter-GUS constructs of AtPIP1;4, AtPIP2;5 and also AtPIP2;6, which is unresponsive to drought stress, had distinct expression patterns concentrated to the base of the leaf petioles and parts of the flowers. The presence of drought stress response elements within the 1.6 kb promoter regions of AtPIP1;4 and AtPIP2;5, was demonstrated by comparing transcription of the promoter reporter construct and the endogenous gene upon drought stress. Analysis by ATTED-II and other web-based bioinformatical tools showed that several of the MIPs down-regulated upon drought are strongly co-expressed, whereas AtPIP1;4, AtPIP2;5 and AtPIP2;6 are not co-expressed.
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| 38. |
- Alexandersson, Erik, et al.
(författare)
-
Tro får inte ersätta vetenskap
- 2014
-
Ingår i: Svenska dagbladet. - 1101-2412.
-
Tidskriftsartikel (populärvet., debatt m.m.)
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| 39. |
- Alexandersson, Erik, et al.
(författare)
-
Whole gene family expression and drought stress regulation of aquaporins
- 2005
-
Ingår i: Plant Molecular Biology. - : Springer Science and Business Media LLC. - 1573-5028 .- 0167-4412. ; 59:3, s. 469-484
-
Tidskriftsartikel (refereegranskat)abstract
- Since many aquaporins (AQPs) act as water channels, they are thought to play an important role in plant water relations. It is therefore of interest to study the expression patterns of AQP isoforms in order to further elucidate their involvement in plant water transport. We have monitored the expression patterns of all 35 Arabidopsis AQPs in leaves, roots and flowers by cDNA microarrays, specially designed for AQPs, and by quantitative real-time reverse transcriptase PCR (Q-RT-PCR). This showed that many AQPs are pre-dominantly expressed in either root or flower organs, whereas no AQP isoform seem to be leaf specific. Looking at the AQP subfamilies, most plasma membrane intrinsic proteins (PIPs) and some tonoplast intrinsic proteins (TIPs) have a high level of expression, while NOD26-like proteins (NIPs) are present at a much lower level. In addition, we show that PIP transcripts are generally down-regulated upon gradual drought stress in leaves, with the exception of AtPIP1;4 and AtPIP2;5, which are up-regulated. AtPIP2;6 and AtSIP1;1 are constitutively expressed and not significantly affected by the drought stress. The transcriptional down-regulation of PIP genes upon drought stress could also be observed on the protein level.
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| 40. |
- Araujo Sandroni, Murilo, et al.
(författare)
-
In-field classification of the asymptomatic biotrophic phase of potato late blight based on deep learning and proximal hyperspectral imaging
- 2023
-
Ingår i: Computers and Electronics in Agriculture. - : Elsevier BV. - 0168-1699 .- 1872-7107. ; 205
-
Tidskriftsartikel (refereegranskat)abstract
- Effective detection of potato late blight (PLB) is an essential aspect of potato cultivation. However, it is a challenge to detect late blight in asymptomatic biotrophic phase in fields with conventional imaging approaches because of the lack of visual symptoms in the canopy. Hyperspectral imaging can capture spectral signals from a wide range of wavelengths also outside the visual wavelengths. Here, we propose a deep learning classification architecture for hyperspectral images by combining 2D convolutional neural network (2D-CNN) and 3D-CNN with deep cooperative attention networks (PLB-2D-3D-A). First, 2D-CNN and 3D-CNN are used to extract rich spectral space features, and then the attention mechanism AttentionBlock and SE-ResNet are used to emphasize the salient features in the feature maps and increase the generalization ability of the model. The dataset is built with 15,360 images (64x64x204), cropped from 240 raw images captured in an experimental field with over 20 potato genotypes. The accuracy in the test dataset of 2000 images reached 0.739 in the full band and 0.790 in the specific bands (492 nm, 519 nm, 560 nm, 592 nm, 717 nm and 765 nm). This study shows an encouraging result for classification of the asymptomatic biotrophic phase of PLB disease with deep learning and proximal hyperspectral imaging.
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| 41. |
- Araujo Sandroni, Murilo, et al.
(författare)
-
Plant resistance inducers (PRIs): perspectives for future disease management in the field
- 2020
-
Ingår i: Cab Reviews: Perspectives In Agriculture, Veterinary Science, Nutrition And Natural Resources. - 1749-8848. ; 15, s. 10-
-
Forskningsöversikt (refereegranskat)abstract
- Plants are confronted with numerous biotic stresses that may affect productivity. Besides their constitutive defence, plants can activate specific metabolic processes to enhance resistance upon stress detection. These defence mechanisms can also be activated through the recognition of plant resistance inducers (PRIs). This review highlights some of the current challenges that prevent the adoption of PRIs in agriculture, and explore research topics and knowledge gaps to be addressed for bringing PRIs closer to practice. First, we present studies on the variance of induced defence responses and examine the possibility of employing inducibility in breeding strategies as well as the possible role of epigenetics. We also discuss the efficiency of PRIs in future climate and knowledge gaps on this subject. Remote sensing, high-throughput phenotyping and modelling in combination with PRIs as part of decision support systems and integrated pest management are further possibilities to advance the use of PRIs. Finally, we discuss the challenges which need to be addressed to make PRIs available for small-scale farmers in low-income countries. Although PRIs have successfully presented significant rates of disease prevention under controlled conditions, converting these findings into field application still depends on more studies, e.g. on how they can be integrated into disease management programmes. Better mechanistic understanding of IR together with the coupling of PRIs to new disease monitoring and protection strategies can give PRIs a stronger role in future agricultural practice.
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| 42. |
- Axell, Erik, et al.
(författare)
-
Jamming detection in GNSS receivers: Performance evaluation of field trials
- 2013
-
Ingår i: Proceedings of the 26th international technical meeting of the Satellite Division of The Institute of Navigation, ION GNSS+ 2013, Sept. 16 - 20, 2013, Nashville Convention Cener, Nashville, Tennessee. - Manassas, VA : Institute of Navigation, The. ; , s. 2542-2551
-
Konferensbidrag (refereegranskat)abstract
- In this work, we evaluate the detection performance of a number of commercial interference detectors and, in addition, of a detector that uses the automatic gain control (AGC) levels as test statistic. The AGC detector has been implemented on a Novatel GPS receiver and on a Universal Software Radio Peripheral (USRP). The evaluations are based on actual measurements of GPS signals and different types of jamming signals, which have been performed at the Vidsel test range in northern Sweden. The AGC detector was shown to work well for all types of jamming signals, in particular the one implemented on the USRP. The Chronos CTL-3500 was also shown to perform quite well for all kinds of signals, although not as good as the USRP with an AGC detector. Quite surprisingly, the J-alert was only able to detect the wideband (20 MHz) signal but not the narrow band (<2MHz) signals. By contrast, the jamming indicator on the Ublox 6 receiver was only able to detect a slowly varying modulated CW (MCW) signal, but not the signals with larger bandwidth (2 and 20 MHz). We confirmed that C/N0-based detectors could work well in a static scenario, but are not suitable in a dynamic scenario, since they cannot distinguish between decreased GPS signal strength (e.g. indoors) and an increased interference level.
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| 43. |
- Axell, Erik, et al.
(författare)
-
Jamming Detection in GNSS Receivers: Performance Evaluation of Field Trials
- 2015
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Ingår i: Navigation. - : Institute of Navigation. - 0028-1522 .- 2161-4296. ; 62:1, s. 73-82
-
Tidskriftsartikel (refereegranskat)abstract
- We evaluate the detection performance of several commercial interference detectors and of a detector that uses the automatic gain control (AGC) level as a test statistic. The evaluations are based on actual measurements of GPS signals and different types of jamming signals, and were performed at the Vidsel test range in northern Sweden.The AGC detector and the Chronos CTL-3500 were shown to work well for all types of jamming signals. The J-alert was able to detect a wideband (20 MHz) signal but not the narrow band (<2 MHz) signals. By contrast, the jamming indicator on a Ublox 6H receiver was only able to detect a slowly varying modulated CW signal, but not signals with larger bandwidth (>2 MHz). We confirmed that C/N0-based Android application detectors could work well in static scenarios but are not suitable in dynamic scenarios, since they cannot distinguish between decreased GPS signal strength and increased interference
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| 44. |
- Chawade, Aakash, et al.
(författare)
-
Functional phenomics for improved climate resilience in Nordic agriculture
- 2022
-
Ingår i: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431.
-
Forskningsöversikt (refereegranskat)abstract
- The five Nordic countries span the most northern region for field cultivation in the world. This presents challenges per se, with short growing seasons, long days, and a need for frost tolerance. Climate change has additionally increased risks for micro-droughts and water logging, as well as pathogens and pests expanding northwards. Thus, Nordic agriculture demands crops that are adapted to the specific Nordic growth conditions and future climate scenarios. A focus on crop varieties and traits important to Nordic agriculture, including the unique resource of nutritious wild crops, can meet these needs. In fact, with a future longer growing season due to climate change, the region could contribute proportionally more to global agricultural production. This also applies to other northern regions, including the Arctic. To address current growth conditions, mitigate impacts of climate change, and meet market demands, the adaptive capacity of crops that both perform well in northern latitudes and are more climate resilient has to be increased, and better crop management systems need to be built. This requires functional phenomics approaches that integrate versatile high-throughput phenotyping, physiology, and bioinformatics. This review stresses key target traits, the opportunities of latitudinal studies, and infrastructure needs for phenotyping to support Nordic agriculture.
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| 45. |
- Chawade, Aakash, et al.
(författare)
-
High-Throughput Field-Phenotyping Tools for Plant Breeding and Precision Agriculture
- 2019
-
Ingår i: Agronomy. - : MDPI AG. - 2073-4395. ; 9
-
Forskningsöversikt (refereegranskat)abstract
- High-throughput field phenotyping has garnered major attention in recent years leading to the development of several new protocols for recording various plant traits of interest. Phenotyping of plants for breeding and for precision agriculture have different requirements due to different sizes of the plots and fields, differing purposes and the urgency of the action required after phenotyping. While in plant breeding phenotyping is done on several thousand small plots mainly to evaluate them for various traits, in plant cultivation, phenotyping is done in large fields to detect the occurrence of plant stresses and weeds at an early stage. The aim of this review is to highlight how various high-throughput phenotyping methods are used for plant breeding and farming and the key differences in the applications of such methods. Thus, various techniques for plant phenotyping are presented together with applications of these techniques for breeding and cultivation. Several examples from the literature using these techniques are summarized and the key technical aspects are highlighted.
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| 46. |
- Chawade, Aakash, et al.
(författare)
-
Normalyzer: A Tool for Rapid Evaluation of Normalization Methods for Omics Data Sets
- 2014
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 13:6, s. 3114-3120
-
Tidskriftsartikel (refereegranskat)abstract
- High-throughput omics data often contain systematic biases introduced during various steps of sample processing and data generation. As the source of these biases is usually unknown, it is difficult to select an optimal normalization method for a given data set. To facilitate this process, we introduce the open-source tool "Normalyzer". It normalizes the data with 12 different normalization methods and generates a report with several quantitative and qualitative plots for comparative evaluation of different methods. The usefulness of Normalyzer is demonstrated with three different case studies from quantitative proteomics and transcriptomics. The results from these case studies show that the choice of normalization method strongly influences the outcome of downstream quantitative comparisons. Normalyzer is an R package and can be used locally or through the online implementation at http://quantitativeproteomics.org/normalyzer.
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| 47. |
- Delshammar, Tim, et al.
(författare)
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Stadsodling – reflektioner och perspektiv från SLU Alnarp
- 2012
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Det är uppenbart att det mediala intresset för stadsodling har vuxit påtagligt de senaste åren. En sökning i databasen Retriever visar en ökande användning av begreppet ”urban odling” och en starkt ökande användning av ordet “stadsodling”. Olika medier påverkar så klart varandra. Radioprogrammet Odla med stadsgrönt började sändas våren 2009. Medier påverkar politiken som i sin tur påverkar medier. Den förste oktober 2009 lämnades motionen ”Stadsodling viktig i hållbara städer” in till riksdagen. Såväl media som politik påverkar och påverkas av praktiken. Våren 2009 började projektet Barn i stan odla i stadsdelen Seved i Malmö, ett projekt som uppmärksammats flitigt i media. Samma år började organisationen Stadsjord odla i stadsdelen Högsbo i Göteborg, även det flitigt uppmärksammat i media. Den statliga Delegationen för hållbara städer har beviljat bidrag till åtminstone fyra planeringsprojekt med inriktning mot stadsodling: SLU (sökt 2009), Plantagon (två projekt sökta 2010) samt Falun kommun (sökt 2012). Även investeringsprojekt har haft inslag av stadsodling, till exempel Malmö stads ansökan “Hållbar stadsomvandling Malmö, Fokus Rosengård” ( sökt 2010). Stadsodling finns med som ett inslag i flera aktuella stadsförnyelse- och stadsbyggnadsprojekt. Det har fått fungera som en symbol för kombinationen av ekologisk och social hållbarhet. En viktig fråga att reflektera över är därför hur hållbar stadsodling är. Vad kan vi ha för nytta av stadsodling? Hur kan odling ta plats i städerna? Hur kan vi stadsodla på ett hållbart sätt?
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| 48. |
- Eliasson, Karolina, 1977-
(författare)
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The Use of Case-Based Reasoning in a Human-Robot Dialog System
- 2006
-
Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- As long as there have been computers, one goal has been to be able to communicate with them using natural language. It has turned out to be very hard to implement a dialog system that performs as well as a human being in an unrestricted domain, hence most dialog systems today work in small, restricted domains where the permitted dialog is fully controlled by the system.In this thesis we present two dialog systems for communicating with an autonomous agent:The first system, the WITAS RDE, focuses on constructing a simple and failsafe dialog system including a graphical user interface with multimodality features, a dialog manager, a simulator, and development infrastructures that provides the services that are needed for the development, demonstration, and validation of the dialog system. The system has been tested during an actual flight connected to an unmanned aerial vehicle.The second system, CEDERIC, is a successor of the dialog manager in the WITAS RDE. It is equipped with a built-in machine learning algorithm to be able to learn new phrases and dialogs over time using past experiences, hence the dialog is not necessarily fully controlled by the system. It also includes a discourse model to be able to keep track of the dialog history and topics, to resolve references and maintain subdialogs. CEDERIC has been evaluated through simulation tests and user tests with good results.
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| 49. |
- Eriksson, Erik, 1977-, et al.
(författare)
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Public management in turbulent times : COVID-19 as an ecosystem disruptor
- 2021
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Ingår i: Australian journal of public administration. - : John Wiley and Sons Inc. - 0313-6647 .- 1467-8500. ; 80:4, s. 732-747
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Tidskriftsartikel (refereegranskat)abstract
- The decentralisation of Swedish healthcare closer to citizens has been slow. Drawing from empirical material of the reform prior and amidst the COVID-19 pandemic, this paper argues that the pandemic has disrupted the healthcare ecosystem. Consequently, citizen-centred collaborations have accelerated integration of resources (such as knowledge and skills) across organisational, hierarchical and professional borders. However, collaborations have been delimited to traditional healthcare providers, neglecting the resources of citizens and other actors to be used to improve service delivery. The pandemic has revealed strengths and weaknesses with the prevailing healthcare ecosystem that post-COVID-19 public management must address, both theoretically and practically. Theoretically, the paper contributes to the development of a public service logic, addressing both strengths and difficulties with the logic in turbulent times. Practically, the empirical descriptions contribute to improved understanding of public service delivery reform and how it is impacted during the pandemic. © 2021 The Authors. Australian Journal of Public Administration published by John Wiley & Sons Australia, Ltd on behalf of Institute of Public Administration Australia.
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| 50. |
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