| 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. |
- 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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| 3. |
- 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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| 4. |
- 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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| 5. |
- 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
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Ingår i: Plant Molecular Biology. - : Springer Science and Business Media LLC. - 0167-4412 .- 1573-5028. ; 104, s. 1-19
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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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| 6. |
- 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
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Ingår i: Plant Physiology and Biochemistry. - 0981-9428 .- 1873-2690. ; 215
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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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| 7. |
- Alexandersson, Erik
(författare)
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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
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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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| 8. |
- Alexandersson, Erik
(författare)
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Cross-domain transfer learning for weed segmentation and mapping in precision farming using ground and UAV images
- 2024
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Ingår i: Expert Systems with Applications. - 0957-4174. ; 246
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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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| 9. |
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| 10. |
- Alexandersson, Erik
(författare)
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Smallholder farmers' knowledge, attitudes, and practices (KAP) regarding agricultural inputs with a focus on agricultural biologicals
- 2024
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Ingår i: Heliyon. - 2405-8440. ; 10
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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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