| 1. |
- Armoniené, Rita, et al.
(författare)
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Affordable Imaging Lab for Noninvasive Analysis of Biomass and Early Vigour in Cereal Crops
- 2018
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Ingår i: BioMed Research International. - : Hindawi Limited. - 2314-6133 .- 2314-6141.
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Tidskriftsartikel (refereegranskat)abstract
- Plant phenotyping by imaging allows automated analysis of plants for various morphological and physiological traits. In this work, we developed a low-cost RGB imaging phenotyping lab (LCP lab) for low-throughput imaging and analysis using affordable imaging equipment and freely available software. LCP lab comprising RGB imaging and analysis pipeline is set up and demonstrated with early vigour analysis in wheat. Using this lab, a few hundred pots can be photographed in a day and the pots are tracked with QR codes. The software pipeline for both imaging and analysis is built from freely available software. The LCP lab was evaluated for early vigour analysis of five wheat cultivars. A high coefficient of determination (R-2 0.94) was obtained between the dry weight and the projected leaf area of 20-day-old wheat plants and R-2 of 0.9 for the relative growth rate between 10 and 20 days of plant growth. Detailed description for setting up such a lab is provided together with custom scripts built for imaging and analysis. The LCP lab is an affordable alternative for analysis of cereal crops when access to a high-throughput phenotyping facility is unavailable or when the experiments require growing plants in highly controlled climate chambers. The protocols described in this work are useful for building affordable imaging system for small-scale research projects and for education.
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| 2. |
- Edin, Eva, et al.
(författare)
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Genetic diversity and occurrence of the F129L substitutions among isolates of Alternaria solani in south-eastern Sweden
- 2016
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Ingår i: Hereditas. - : Springer Science and Business Media LLC. - 0018-0661 .- 1601-5223. ; 153
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Tidskriftsartikel (refereegranskat)abstract
- Background: Early blight, caused by the fungus Alternaria solani, occurs on potato mainly in the south-eastern part of Sweden, but also in other parts of the country. The aim of this study was to investigate the genetic diversity of A. solani populations from different potato growing regions in south-eastern Sweden using AFLP marker analysis. In addition, the cultured isolates were examined for substitutions in the gene encoding cytochrome b, associated with loss of sensitivity against QoI fungicides.Results: Nei's gene diversity index for the Swedish populations of A. solani revealed a gene diversity of up to 0.20. Also genetic differentiation was observed among populations of A. solani from different locations in south-eastern Sweden. The mitochondrial genotype of the isolates of A. solani was determined and both known genotypes, GI (genotype 1) and GII (genotype 2), were found among the isolates. The occurrence of the F129L substitution associated with a loss of sensitivity to strobilurins was confirmed among the GII isolates. In vitro conidial germination tests verified that isolates containing the F129L substitution had reduced sensitivity to azoxystrobin and, at a lower extent, to pyraclostrobin.Conclusions: Genetic diversity was relatively high among isolates of A. solani in south-eastern part of Sweden. F129L substitutions, leading to reduced sensitivity to strobilurins, have been established in field populations, which may have implications for the future efficacy of QoI fungicides.
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| 5. |
- Odilbekov, Firuz, et al.
(författare)
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GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage
- 2019
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Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Septoria tritici blotch (STB) disease caused by Zymoseptoria tritici is one of the most damaging diseases of wheat causing significant yield losses worldwide. Identification and employment of resistant germplasm is the most cost-effective method to control STB. In this study, we characterized seedling stage resistance to STB in 175 winter wheat landraces and old cultivars of Nordic origin. The study revealed significant (p < 0.05) phenotypic differences in STB severity in the germplasm. Genome-wide association analysis (GWAS) using five different algorithms identified ten significant markers on five chromosomes. Six markers were localized within a region of 2 cM that contained seven candidate genes on chromosome 1B. Genomic prediction (GP) analysis resulted in a model with an accuracy of 0.47. To further improve the prediction efficiency, significant markers identified by GWAS were included as fixed effects in the GP model. Depending on the number of fixed effect markers, the prediction accuracy improved from 0.47 (without fixed effects) to 0.62 (all non-redundant GWAS markers as fixed effects), respectively. The resistant genotypes and single-nucleotide polymorphism (SNP) markers identified in the present study will serve as a valuable resource for future breeding for STB resistance in wheat. The results also highlight the benefits of integrating GWAS with GP to further improve the accuracy of GP.
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| 6. |
- Odilbekov, Firuz, et al.
(författare)
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Proximal Phenotyping and Machine Learning Methods to Identify Septoria Tritici Blotch Disease Symptoms in Wheat
- 2018
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Phenotyping with proximal sensors allow high-precision measurements of plant traits both in the controlled conditions and in the field. In this work, using machine learning, an integrated analysis was done from the data obtained from spectroradiometer, infrared thermometer, and chlorophyll fluorescence measurements to identify most predictive proxy measurements for studying Septoria tritici blotch (STB) disease of wheat. The random forest (RF) models for chlorosis and necrosis identified photosystem II quantum yield (QY) and vegetative indices (Ms) associated with the biochemical composition of leaves as the top predictive variables for identifying disease symptoms. The RF model for chlorosis was validated with a validation set (R-2: 0.80) and in an independent test set (R-2: 0.55). Based on the results, it can be concluded that the proxy measurements for photosystem II, chlorophyll content, carotenoid, and anthocyanin levels and leaf surface temperature can be successfully used to detect STB. Further validation of these results in the field will enable application of these predictive variables for detection of STB in the field.
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| 7. |
- Odilbekov, Firuz, et al.
(författare)
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QTL Mapping and Transcriptome Analysis to Identify Differentially Expressed Genes Induced by Septoria Tritici Blotch Disease of Wheat
- 2019
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Ingår i: Agronomy. - : MDPI AG. - 2073-4395. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Resistance to Septoria tritici blotch (STB) is an economically important trait in many wheat-breeding programs across the world. Several quantitative trait loci (QTL) for STB resistance were identified in wheat but due to the dynamic pathogen population it is necessary to continuously identify new resistance genes/QTL and determine the underlying resistance mechanism. In this work, we integrated QTL mapping and transcriptome profiling to identify candidate genes underlying QTL associated with STB resistance in bread wheat at the seedling stage. The results revealed four QTL on chromosomes 1BS, 1BL, 3AS and 3DL for STB resistance. Among these, two QTL on 2BL and 3DL were mapped for chlorosis, necrosis and pycnidia while the other two on 1BS and 3AS were associated with necrosis and pycnidia. Among the four identified QTL, genes were identified in three QTL (1BS, 2BL and 3DL). In total, 238 differentially expressed genes (DEGs) were localized in 1BS, 16 DEGs in 2BL and 80 DEGs in 3DL QTL region respectively. F-box protein, NBS-LRR disease resistance genes and receptor-like protein kinase were the most over-represented. The results emphasize the importance of integrating QTL and transcriptome analysis to accelerate the identification of key genes underlying the traits of interest.
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| 8. |
- Odilbekov, Firuz
(författare)
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Resistance to early blight in potato and genetic structure of the pathogen population in Southeast Sweden
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Potato early blight caused by the necrotrophic fungus Alternaria solani is a common foliar disease in many potato-growing regions. Application of fungicides is commonly used to effectively control the disease, although they are undesirable due to environmental consequences. Use of resistant cultivars would be the most optimal solution, but there are no cultivars with high level of resistance available on the market. In the present thesis, assessments of early blight resistance both in leaves and tubers of potato cultivars/clones were performed by applying different screening methods (field and greenhouse). Plant defence signalling in response to A. solani infection with main emphasis on salicylic (SA) and jasmonic acid (JA) hormones, was also studied. Furthermore, the genetic variability in A. solani populations from different potato growing regions of southeast Sweden was investigated. The fungal isolates were analysed for the F129L substitutions, which are associated with loss of sensitivity to QoI fungicides. In addition, field experiments were conducted to determine the occurrence of the F129L substitution and genetic shifts in the population during one growing season in response to two different fungicide strategies. Cultivars/clones revealed significant differences in resistance to A. solani both in leaves and tubers irrespective of screening method. Results from field and intact plant inoculation experiments were significantly correlated but there were no correlations observed between these two methods and detached leaf assays. Some cultivars/clones showed relatively higher level of resistance to the pathogen. Results from the data suggested that SA appears to be responsible for regulating symptom development while JA dependent COI1 defense signaling is important to inhibit fungal growth during early stages of infection. Microarray analysis showed rapid defense responses to A. solani infection mediated by partially overlapping SA and COI1 dependent jasmonic acid (JA) signaling. It was also observed that JA/ethylene signaling responses dominate at later time points. The genetic variability was relatively high among isolates of A. solani and significant genetic differentiation was found among populations from different locations in southeast Sweden. Two mitochondrial genotypes (GI and GII) were found among the isolates but the F129L substitution was only detected in GII isolates. Results from the field experiment showed that application of azoxystrobin (QoI fungicide) alone did not control the disease; better disease control was achieved with boscalid combined with pyraclostrobin. Similar results were obtained for yield. Moreover, results of sensitivity tests showed that isolates with the F129L substitution were less sensitive to azoxystrobin. AFLP analysis indicated within season changes in the A.solani population, especially at the end of the season.
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| 9. |
- Odilbekov, Firuz, et al.
(författare)
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Within-season changes in Alternaria solani populations in potato in response to fungicide application strategies
- 2019
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Ingår i: European Journal of Plant Pathology. - : Springer Science and Business Media LLC. - 0929-1873 .- 1573-8469. ; 155, s. 953-965
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Tidskriftsartikel (refereegranskat)abstract
- Early blight, caused by the fungus Alternaria solani, is a common foliar disease in potato. Quinone outside inhibitor (QoIs) fungicides have commonly been used against A. solani. To avoid or delay development of fungicide resistance it is recommended to alternate or combine fungicides with different modes of action. Therefore, we compared two different fungicide programs against early blight in field trials and studied within season changes in the pathogen population. An untreated control was compared with treatments using azoxystrobin alone and with a program involving difenoconazole followed by boscalid and pyraclostrobin combined. Isolates of A. solani were collected during the growing season and changes in the population structure was investigated. We also screened for the amino acid substitution in the cytochrome b gene and investigated changes in sensitivity to azoxystrobin. Treatment with azoxystrobin alone did not improve disease control in 2014 when the disease pressure was high. However, lower severity of the disease was observed after combined use of difenoconazole, boscalid and pyraclostrobin. The efficacy of both fungicide treatments were similar during the field trial in 2017. Two mitochondrial genotypes (GI and GII) were found among isolates, where all isolates, except two, were GII. All GII isolates had the F129 L substitution while the two GI isolates were wild type. Population structure analysis and principal component analysis (PCA) of amplified fragment length polymorphisms (AFLP) data revealed within season changes in the A. solani populations in response to fungicide application. Isolates with the F129 L substitution had reduced sensitivity to azoxystrobin in vitro and their sensitivity tended to decrease with time.
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