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Sökning: WFRF:(Ramesh Vetukuri)

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1.
  • Abebe, Admas Alemu, et al. (författare)
  • Genomic selection in plant breeding: key factors shaping two decades of progress
  • 2024
  • Ingår i: Molecular Plant. - 1674-2052 .- 1752-9867. ; 17, s. 552-578
  • Forskningsöversikt (refereegranskat)abstract
    • Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in the past two decades, effectively accelerating genetic gains in plant breeding. This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period. We delved into the pivotal roles of training population size and genetic diversity, and their relationship with the breeding population, in determining GP accuracy. Special emphasis was placed on optimizing training population size. We explored its benefits and the associated diminishing returns beyond an optimum size. This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms. The density and distribution of single-nucleotide polymorphisms, level of linkage disequilibrium, genetic complexity, trait heritability, statistical machine-learning methods, and non-additive effects are the other vital factors. Using wheat, maize, and potato as examples, we summarize the effect of these factors on the accuracy of GP for various traits. The search for high accuracy in GP—theoretically reaching one when using the Pearson’s correlation as a metric—is an active research area as yet far from optimal for various traits. We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods and support from other omics approaches (transcriptomics, metabolomics and proteomics) coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy, making genomic selection an effective tool in plant breeding.
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2.
  • Abreha, Kibrom Berhe, et al. (författare)
  • Sorghum in dryland: morphological, physiological, and molecular responses of sorghum under drought stress
  • 2022
  • Ingår i: Planta. - : Springer Science and Business Media LLC. - 0032-0935 .- 1432-2048. ; 255
  • Forskningsöversikt (refereegranskat)abstract
    • Sorghum is an economically important and a staple food crop for over half a billion people in developing countries, mostly in arid and semi-arid regions where drought stress is a major limiting factor. Although sorghum is generally considered tolerant, drought stress still signifcantly hampers its productivity and nutritional quality across its major cultivation areas. Hence, understanding both the efects of the stress and plant response is indispensable for improving drought tolerance of the crop. This review aimed at enhancing our understanding and provide more insights on drought tolerance in sorghum as a contribution to the development of climate resilient sorghum cultivars. We summarized fndings on the efects of drought on the growth and development of sorghum including osmotic potential that impedes germination process and embryonic structures, photosynthetic rates, and imbalance in source-sink relations that in turn afect seed flling often manifested in the form of substantial reduction in grain yield and quality. Mechanisms of sorghum response to drought-stress involving morphological, physiological, and molecular alterations are presented. We highlighted the current understanding about the genetic basis of drought tolerance in sorghum, which is important for maximizing utilization of its germplasm for development of improved cultivars. Furthermore, we discussed interactions of drought with other abiotic stresses and biotic factors, which may increase the vulnerability of the crop or enhance its tolerance to drought stress. Based on the research reviewed in this article, it appears possible to develop locally adapted cultivars of sorghum that are drought tolerant and nutrient rich using modern plant breeding techniques.
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3.
  • Alsanius, Beatrix, et al. (författare)
  • The power of light from a non-phototrophic perspective: a phyllosphere dilemma
  • 2024
  • Ingår i: Frontiers in Photobiology. - 2813-8228. ; 2
  • Tidskriftsartikel (refereegranskat)abstract
    • Plants and crop stands are considered holobionts, colonized by both autotrophic and by non-phototrophic heterotrophic microbiota. The dilemma in the exisiting body of studies is that the focus is primarily directed towards environmental specificties relevant for phototrophic organisms (predominantly plants), but does not take into account non-phototrophs. By definition, non-phototrophic heterotrophic bacteria do not use light as an energy source. Light energy and wavelength are rather used as a signal that can provoke shifts in both their metabolism and microbial lifestyle. Reaction and recovery time can vary between organisms and is dependent on the organism’s physiological stage. The length of the lighting event affects the energy an organism is exposed to. We argue that to obtain a deeper and more distinct understanding of light exposure (irradiance, exposure length), quantity (light intensity), and quality (wavelength/spectral distribution, bandwidth at full-width half-maximum) related mechanisms on non-phototrophic bacteria in the phyllosphere, the light environment needs to be further strictly characterized. This includes information on the actual energy hitting planktonic or sessile non-phototrophic bacteria resident on and inside plants aboveground. Mapping the light environment in ecosystems aids in unraveling light-phyllosphere interactions and strengthens their transdisciplinary character. This issue is fundamental in order to revisit and repeat others’ experimental approaches and findings but also to be able to translate findings into further action.
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4.
  • Barin, Mohsen, et al. (författare)
  • Optimization of Biofertilizer Formulation for Phosphorus Solubilizing by Pseudomonas fluorescens Ur21 via Response Surface Methodology
  • 2022
  • Ingår i: Processes. - : MDPI AG. - 2227-9717. ; 10:4
  • Tidskriftsartikel (refereegranskat)abstract
    • This study aimed to analyze and quantify the effect of different ratios of vermicompost, phosphate rock, and sulfur on P solubilization and release by Pseudomonas fluorescens Ur21, and to identify optimal levels of those variables for an efficient biofertilizer. Twenty experiments were defined by surface response methodology based on a central composite design (CCD), and the effects of various quantities of vermicompost, phosphate rock, and sulfur (encoded by −1, 0, or +1) on P solubilization was explored. The results show that the CCD model had high efficiency for predicting P solubilization (R2 = 0.9035). The strongest effects of the included variables on the observed P solubilization were linear effects of sulfur and organic matter (vermicompost), a quadratic effect of phosphate rock, and an interactive effect of organic matter × phosphate rock. Statistical analysis of the coefficients in the CCD model revealed that vermicompost, vermicompost × phosphate rock, and phosphate rock × phosphate rock treatments increased P solubilization. The optimal predicted composition for maximal P solubilization by P. fluorescens Ur21 (at 1684.39 mg·kg−1, with more than 90% of the added phosphate dissolved) was 58.8% vermicompost, 35.3% phosphate rock, and 5.8% sulfur. ANOVA analysis confirmed the model’s accuracy and validity in terms of F value (10.41), p value (<0.001), and non-significant lack of fit.
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5.
  • Brhanie Mesfin, Haftom, et al. (författare)
  • Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources
  • 2022
  • Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
  • Tidskriftsartikel (refereegranskat)abstract
    • Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet’s genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Alsusceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop.
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6.
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7.
  • Burra, Dharani, et al. (författare)
  • RNAseq and Proteomics for Analysing Complex Oomycete Plant Interactions
  • 2016
  • Ingår i: Current Issues in Molecular Biology. - : MDPI AG. - 1467-3037 .- 1467-3045. ; 19, s. 73-87
  • Forskningsöversikt (refereegranskat)abstract
    • The oomycetes include some of the most devastating plant pathogens. In this review we discuss the latest results from oomycete and plant studies with emphasis on interaction studies. We focus on the outcomes of RNAseq and proteomics studies and some pitfalls of these approaches. Both pathogenic interactions and biological control are discussed. We underline the usefulness of studies at several levels of complexity from studies of one organism, up to two or more and within agricultural fields (managed settings) up to wild ecosystems. Finally we identify areas of future interest such as detailed interactome studies, dual RNAseq studies, peptide modification studies and population/meta omics with or without biological control agents.
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8.
  • Chawade, Aakash, et al. (författare)
  • Lignocellulolytic and Chitinolytic Glycoside Hydrolases: Structure, Catalytic Mechanism, Directed Evolution and Industrial Implementation
  • 2020
  • Ingår i: Industrial Applications of Glycoside Hydrolases. - Singapore : Springer Singapore. - 9789811547669 ; , s. 97-127
  • Bokkapitel (refereegranskat)abstract
    • Lignocellulolytic and chitinolytic glycoside hydrolases are commonly used enzymes in commercial processes and thus are well documented for their vital role in agriculture, textile, paper, food, biofuel and healthcare sectors. Ongoing research is targeted to further enhance the applicability of these vital enzymes in the above mentioned sectors. In this regard, an up-to-date knowledge of enzymatic structure, catalytic mechanism and several modern approaches like recombinant technology, chemical and enzymatic pre-treatment, enzyme immobilization and directed evolution for the improvement of enzymes production, activity and stability is highly required. This review provides an up-to-date information and discussion on the various lignocellulolytic and chitinolytic glycoside hydrolases regarding the vital aspects of the enzymes viz. catalytic mechanism, structural features, directed evolution approaches, current applications and under research potential applications.
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9.
  • Cleary, Michelle, et al. (författare)
  • Susceptibility of common tree species in Sweden to Phytophthora cactorum, P. cambivora and P. plurivora
  • 2017
  • Ingår i: Forest Pathology. - : Wiley. - 1437-4781 .- 1439-0329. ; 47
  • Tidskriftsartikel (refereegranskat)abstract
    • In Sweden, invasive Phytophthora pathogens have been recognized as a growing threat to urban and production forests, calling for an urgent update of regeneration strategies for infested areas. Stem inoculation tests were performed to test the relative susceptibility of common conifer and broadleaved tree species Pinus sylvestris, Picea abies, Larix x eurolepis, Betula pendula, Quercus robur, Fagus sylvatica, Populus trichocarpa and Tilia cordata to the root pathogens Phytophthora cactorum, P. cambivora and P. plurivora commonly isolated from Swedish soils. Results indicate that all the species tested were susceptible and formed lesions following stem inoculation with all three Phytophthora species, but to varying degrees. Of particular interest are the high levels of susceptibility in P. trichocarpa to all three Phytophthora species compared to other tested tree species.
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10.
  • Gebeyehu Demissie, Adane, et al. (författare)
  • RNA-Seq Provides Novel Genomic Resources for Noug (Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome
  • 2022
  • Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
  • Tidskriftsartikel (refereegranskat)abstract
    • Genomic resources and tools are essential for improving crops and conserving their genetic resources. Guizotia abyssinica (noug), an outcrossing edible oilseed crop, has highly limited genomic resources. Hence, RNA-Seq based transcriptome sequencing of 30 noug genotypes was performed to generate novel genomic resources and assess their usefulness. The genotypes include self-compatible and self-incompatible types, which differ in maturity time, photoperiod sensitivity, or oil content and quality. RNA-Seq was performed on Illumina HiSeq 2500 platform, and the transcript was reconstructed de novo, resulting in 409,309 unigenes. The unigenes were characterized for simple sequence repeats (SSRs), and served as a reference for single nucleotide polymorphism (SNP) calling. In total, 40,776 SSRs were identified in 35,639 of the 409,309 unigenes. Of these, mono, di, tri, tetra, penta and hexanucleotide repeats accounted for 55.4, 20.8, 21.1, 2.3, 0.2, and 0.2%, respectively. The average G+C content of the unigenes and their SSRs were 40 and 22.1%, respectively. The vast majority of mononucleotide repeat SSRs (97%) were of the A/T type. AG/CT and CCA/TGG were the most frequent di and trinucleotide repeat SSRs. A different number of single nucleotide polymorphism (SNP) loci were discovered in each genotype, of which 1,687 were common to all 30 genotypes and 5,531 to 28 of them. The mean observed heterozygosity of the 5,531 SNPs was 0.22; 19.4% of them had polymorphism information content above 0.30 while 17.2% deviated significantly from Hardy-Weinberg equilibrium (P < 0.05). In both cluster and principal coordinate analyses, the genotypes were grouped into four major clusters. In terms of population structure, the genotypes are best represented by three genetic populations, with significant admixture within each. Genetic similarity between self-compatible genotypes was higher, due to the narrow genetic basis, than that between self-incompatible genotypes. The genotypes that shared desirable characteristics, such as early maturity, and high oil content were found to be genetically diverse, and hence superior cultivars with multiple desirable traits can be developed through crossbreeding. The genomic resources developed in this study are vital for advancing research in noug, such as genetic linkage mapping and genome-wide association studies, which could lead to genomic-led breeding.
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11.
  • Ghadamgahi, Farideh, et al. (författare)
  • Plant Growth-Promoting Activity of Pseudomonas aeruginosa FG106 and Its Ability to Act as a Biocontrol Agent against Potato, Tomato and Taro Pathogens
  • 2022
  • Ingår i: Biology. - : MDPI AG. - 2079-7737. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • Simple Summary Microbial bio-stimulants are attracting increasing attention in agricultural research. In particular, plant growth-promoting rhizobacteria (PGPR) have great potential to improve crops' productivity and tolerance of biotic and abiotic stresses. It is anticipated that PGPR could eventually replace synthetic fungicides in agriculture. This research evaluated Pseudomonas aeruginosa strain FG106-which was isolated from tomato plants- as a potential biocontrol agent against several plant pathogens. This strain displayed multiple plant growth-promoting attributes and high in vitro and in vivo inhibition of growth and pathogenicity of tested phytopathogens. It is thus a multifunctional PGPR with potential applications as a biocontrol agent to control fungal and bacterial pathogens. P. aeruginosa strain FG106 was isolated from the rhizosphere of tomato plants and identified through morphological analysis, 16S rRNA gene sequencing, and whole-genome sequencing. In vitro and in vivo experiments demonstrated that this strain could control several pathogens on tomato, potato, taro, and strawberry. Volatile and non-volatile metabolites produced by the strain are known to adversely affect the tested pathogens. FG106 showed clear antagonism against Alternaria alternata, Botrytis cinerea, Clavibacter michiganensis subsp. michiganensis, Phytophthora colocasiae, P. infestans, Rhizoctonia solani, and Xanthomonas euvesicatoria pv. perforans. FG106 produced proteases and lipases while also inducing high phosphate solubilization, producing siderophores, ammonia, indole acetic acid (IAA), and hydrogen cyanide (HCN) and forming biofilms that promote plant growth and facilitate biocontrol. Genome mining approaches showed that this strain harbors genes related to biocontrol and growth promotion. These results suggest that this bacterial strain provides good protection against pathogens of several agriculturally important plants via direct and indirect modes of action and could thus be a valuable bio-control agent.
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12.
  • Grenville-Briggs, Laura J, et al. (författare)
  • Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech (Fagus sylvatica)
  • 2017
  • Ingår i: Genomics Data. - : Elsevier. - 2213-5960. ; 12, s. 155-156
  • Tidskriftsartikel (refereegranskat)abstract
    • Phytophthora cactorum is a broad host range phytopathogenic oomycete. P. cactorum strain LV007 was isolated from a diseased European Beech (Fagus sylvatica) in Malmö, Sweden in 2016. The draft genome of P. cactorum strain LV007 is 67.81 Mb. It contains 15,567 contigs and 21,876 predicted protein-coding genes. As reported for other phytopathogenic Phytophthora species, cytoplasmic effector proteins including RxLR and CRN families were identified. The genome sequence has been deposited at DDBJ/ENA/GenBank under the accession NBIJ00000000. The version described in this paper is version NBIJ01000000.
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13.
  • Hanifah, Nurul Atilia Shafienaz binti, et al. (författare)
  • Comparative transcriptome profiling provides insights into the growth promotion activity of Pseudomonas fluorescens strain SLU99 in tomato and potato plants
  • 2023
  • Ingår i: Frontiers in Plant Science. - 1664-462X. ; 14
  • Tidskriftsartikel (refereegranskat)abstract
    • The use of biocontrol agents with plant growth-promoting activity has emerged as an approach to support sustainable agriculture. During our field evaluation of potato plants treated with biocontrol rhizobacteria, four bacteria were associated with increased plant height. Using two important solanaceous crop plants, tomato and potato, we carried out a comparative analysis of the growth-promoting activity of the four bacterial strains: Pseudomonas fluorescens SLU99, Serratia plymuthica S412, S. rubidaea AV10, and S. rubidaea EV23. Greenhouse and in vitro experiments showed that P. fluorescens SLU99 promoted plant height, biomass accumulation, and yield of potato and tomato plants, while EV23 promoted growth in potato but not in tomato plants. SLU99 induced the expression of plant hormone-related genes in potato and tomato, especially those involved in maintaining homeostasis of auxin, cytokinin, gibberellic acid and ethylene. Our results reveal potential mechanisms underlying the growth promotion and biocontrol effects of these rhizobacteria and suggest which strains may be best deployed for sustainably improving crop yield.
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14.
  • Iqbal, Mudassir, et al. (författare)
  • Biological control of strawberry crown rot, root rot and grey mould by the beneficial fungus Aureobasidium pullulans
  • 2021
  • Ingår i: BioControl. - : Springer Science and Business Media LLC. - 1386-6141 .- 1573-8248. ; 66, s. 535-545
  • Tidskriftsartikel (refereegranskat)abstract
    • Utilization of biocontrol agents is a sustainable approach to reduce plant diseases caused by fungal pathogens. In the present study, we tested the effect of the candidate biocontrol fungus Aureobasidium pullulans (De Bary) G. Armaud on strawberry under in vitro and in vivo conditions to control crown rot, root rot and grey mould caused by Phytophthora cactorum (Lebert and Cohn) and Botrytis cinerea Pers, respectively. A dual plate confrontation assay showed that mycelial growth of P. cactorum and B. cinerea was reduced by 33-48% when challenged by A. pullulans as compared with control treatments. Likewise, detached leaf and fruit assays showed that A. pullulans significantly reduced necrotic lesion size on leaves and disease severity on fruits caused by P. cactorum and B. cinerea. In addition, greenhouse experiments with whole plants revealed enhanced biocontrol efficacy against root rot and grey mould when treated with A. pullulans either in combination with the pathogen or pre-treated with A. pullulans followed by inoculation of the pathogens. Our results demonstrate that A. pullulans is an effective biocontrol agent to control strawberry diseases caused by fungal pathogens and can be an effective alternative to chemical-based fungicides.
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15.
  • Jahan, Sultana, et al. (författare)
  • Plant-mediated gene silencing restricts growth of the potato late blight pathogen Phytophthora infestans
  • 2015
  • Ingår i: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 66:9, s. 2785-2794
  • Tidskriftsartikel (refereegranskat)abstract
    • A host-induced gene-silencing strategy for controlling potato late blight is presented, a plant disease that conventionally requires regular application of fungicides at high rates.Phytophthora infestans is an oomycete that causes severe damage to potato, and is well known for its ability to evolve rapidly in order to overcome resistant potato varieties. An RNA silencing strategy was evaluated here to clarify if small interfering RNA homologous to selected genes in P. infestans could be targeted from the plant host to reduce the magnitude of the infection. As a proof-of-concept, a hairpin RNA (hp-RNA) construct using the GFP marker gene was designed and introduced in potato. At 72 hpi, a 55-fold reduction of the signal intensity of a corresponding GFP expressing P. infestans strain on leaf samples of transgenic plants, compared with wild-type potato, was detected. This suggests that an RNA interference construct in the potato host could be processed and target a transcript of the pathogen. Three genes important in the infection process of P. infestans, PiGPB1, PiCESA2, and PiPEC, together with PiGAPDH taking part in basic cell maintenance were subsequently tested using an analogous transgenic strategy. Out of these gene candidates, the hp-PiGPB1 targeting the G protein beta-subunit (PiGPB1) important for pathogenicity resulted in most restricted disease progress. Further, Illumina sequencing of inoculated transgenic potato leaves revealed sRNAs of 24/25 nt size homologous to the PiGPB1 gene in the transgenic plants indicating post-transcriptional silencing of the target gene. The work demonstrates that a host-induced gene-silencing approach is functional against P. infestans but is highly dependent on target gene for a successful outcome. This finding broadens the arsenal of control strategies to this important plant disease.
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16.
  • Johansson, Eva, et al. (författare)
  • A thermostable organic solvent-tolerant lipase from Brevibacillus sp.: production and integrated downstream processing using an alcohol-salt-based aqueous two-phase system
  • 2023
  • Ingår i: Frontiers in Microbiology. - 1664-302X. ; 14
  • Tidskriftsartikel (refereegranskat)abstract
    • Lipases are used for the synthesis of different compounds in the chemical, pharmaceutical, and food industries. Most of the reactions are carried out in non-aqueous media and often at elevated temperature, requiring the use of organic solvent-tolerant thermostable lipases. However, most known lipases are not stable in the presence of organic solvents and at elevated temperature. In this study, an organic solvent-tolerant thermostable lipase was obtained from Brevibacillus sp. SHI-160, a moderate thermophile isolated from a hot spring in the East African Rift Valley. The enzyme was optimally active at 65 degrees C and retained over 90% of its activity after 1 h of incubation at 70 degrees C. High lipase activity was measured in the pH range of 6.5 to 9.0 with an optimum pH of 8.5. The enzyme was stable in the presence of both polar and non-polar organic solvents. The stability of the enzyme in the presence of polar organic solvents allowed the development of an efficient downstream processing using an alcohol-salt-based aqueous two-phase system (ATPS). Thus, in the presence of 2% salt, over 98% of the enzyme partitioned to the alcohol phase. The ATPS-recovered enzyme was directly immobilized on a solid support through adsorption and successfully used to catalyze a transesterification reaction between paranitrophenyl palmitate and short-chain alcohols in non-aqueous media. This shows the potential of lipase SHI-160 to catalyze reactions in non-aqueous media for the synthesis of valuable compounds. The integrated approach developed for enzyme production and cheap and efficient downstream processing using ATPS could allow a significant reduction in enzyme production costs. The results also show the potential of extreme environments in the East African Rift Valley as sources of valuable microbial genetic resources for the isolation of novel lipases and other industrially important enzymes.
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17.
  • Kalyandurg, Pruthvi Balachandra, et al. (författare)
  • Efficient RNA silencing suppression activity of Potato Mop-Top Virus 8K protein is driven by variability and positive selection
  • 2019
  • Ingår i: Virology. - : Elsevier BV. - 0042-6822 .- 1178-122X. ; 535, s. 111-121
  • Tidskriftsartikel (refereegranskat)abstract
    • Previously, we investigated the evolution of Potato mop-top virus (PMTV) ORFs. Results indicate that positive selection acts exclusively on an ORF encoding the 8K protein, a weak viral suppressor of RNA silencing (VSR). However, how the extraordinary variability contributes to 8K-mediated RNA silencing suppression remains unknown. Here, we characterized the RNA silencing suppression activity of the 8K protein from seven diverse isolates. We show that 8K encoded by isolate P1 exhibits stronger RNA silencing suppression activity than the 8K protein from six other isolates. Mutational analyses revealed that Ser-50 is critical for these differences. By comparing small RNA profiles we found a lower abundance of siRNAs with U residue at the 5'-terminus after expression of the P1 8K compared to expression of 8K from isolate P125, an isolate with weak VSR activity. These results provide new clues as to the role of positive selection in shaping activities of VSRs.
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18.
  • Kalyandurg, Pruthvi Balachandra, et al. (författare)
  • Spray-Induced Gene Silencing as a Potential Tool to Control Potato Late Blight Disease
  • 2021
  • Ingår i: Phytopathology. - 0031-949X .- 1943-7684. ; 111, s. 2168-2175
  • Tidskriftsartikel (refereegranskat)abstract
    • Phytophthora infestans causes late blight disease on potato and tomato and is currently controlled by resistant cultivars or intensive fungicide spraying. Here, we investigated an alternative means for late blight control by spraying potato leaves with double-stranded RNAs (dsRNA) that target the P. infestans genes essential for infection. First, we showed that the sporangia of P. infestans expressing green fluorescent protein (GFP) can take up in vitro synthesized dsRNAs homologous to GFP directly from their surroundings, including leaves, which led to the reduced relative expression of GFP. We further demonstrate the potential of spray-induced gene silencing (SIGS) in controlling potato late blight disease by targeting developmentally important genes in P. infestans such as guanine-nucleotide binding protein beta-subunit (PiGPB1), haustorial membrane protein (PiHmp1), cutinase (PiCut3), and endo-1,3(4)-beta-glucanase (PiEndo3). Our results demonstrate that SIGS can potentially be used to mitigate potato late blight; however, the degree of disease control is dependent on the selection of the target genes.
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19.
  • Kelbessa, Bekele Gelena, et al. (författare)
  • Antagonistic and plant growth promotion of rhizobacteria against Phytophthora colocasiae in taro
  • 2022
  • Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
  • Tidskriftsartikel (refereegranskat)abstract
    • Taro leaf blight caused by Phytophthora colocasiae adversely affects the growth and yield of taro. The management of this disease depends heavily on synthetic fungicides. These compounds, however, pose potential hazards to human health and the environment. The present study aimed to investigate an alternative approach for plant growth promotion and disease control by evaluating seven different bacterial strains (viz., Serratia plymuthica, S412; S. plymuthica, S414; S. plymuthica, AS13; S. proteamaculans, S4; S. rubidaea, EV23; S. rubidaea, AV10; Pseudomonas fluorescens, SLU-99) and their different combinations as consortia against P. colocasiae. Antagonistic tests were performed in in vitro plate assays and the effective strains were selected for detached leaf assays and greenhouse trials. Plant growth-promoting and disease prevention traits of selected bacterial strains were also investigated in vitro. Our results indicated that some of these strains used singly (AV10, AS13, S4, and S414) and in combinations (S4+S414, AS13+AV10) reduced the growth of P. colocasiae (30−50%) in vitro and showed disease reduction ability when used singly or in combinations as consortia in greenhouse trials (88.75−99.37%). The disease-suppressing ability of these strains may be related to the production of enzymes such as chitinase, protease, cellulase, and amylase. Furthermore, all strains tested possessed plant growth-promoting traits such as indole-3-acetic acid production, siderophore formation, and phosphate solubilization. Overall, the present study revealed that bacterial strains significantly suppressed P. colocasiae disease development using in vitro, detached leaf, and greenhouse assays. Therefore, these bacterial strains can be used as an alternative strategy to minimize the use of synthetic fungicides and fertilizers to control taro blight and improve sustainable taro production.
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20.
  • Khalil, Sammar, et al. (författare)
  • Comparison of two commercial recirculated aquacultural systems and their microbial potential in plant disease suppression
  • 2021
  • Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 21
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Aquaponics are food production systems advocated for food security and health. Their sustainability from a nutritional and plant health perspective is, however, a significant challenge. Recirculated aquaculture systems (RAS) form a major part of aquaponic systems, but knowledge about their microbial potential to benefit plant growth and plant health is limited. The current study tested if the diversity and function of microbial communities in two commercial RAS were specific to the fish species used (Tilapia or Clarias) and sampling site (fish tanks and wastewaters), and whether they confer benefits to plants and have in vitro antagonistic potential towards plant pathogens. Results Microbial diversity and composition was found to be dependent on fish species and sample site. The Tilapia RAS hosted higher bacterial diversity than the Clarias RAS; but the later hosted higher fungal diversity. Both Tilapia and Clarias RAS hosted bacterial and fungal communities that promoted plant growth, inhibited plant pathogens and encouraged biodegradation. The production of extracellular enzymes, related to nutrient availability and pathogen control, by bacterial strains isolated from the Tilapia and Clarias systems, makes them a promising tool in aquaponics and in their system design. Conclusions This study explored the microbial diversity and potential of the commercial RAS with either Tilapia or Clarias as a tool to benefit the aquaponic system with respect to plant growth promotion and control of plant diseases.
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21.
  • Khalil, Samar, et al. (författare)
  • Disease suppression in the circular economy using spent mushroom compost
  • 2023
  • Ingår i: Acta Horticulturae. - 0567-7572 .- 2406-6168. ; 1377, s. 755-760
  • Konferensbidrag (refereegranskat)abstract
    • Mushroom (Agaricus bisporus) has gained increased attention as an alternative protein source to meat and for its beneficial nutritional and medicinal properties. However, after the harvest of edible products, mushroom cultivation generates huge amounts of used compost, known as spent mushroom compost (SMC). In Europe, more than three million tons of SMC are produced every year. Thus, the management of SMC has become an important environmental issue. Sustainable solutions are also required to replace peat as a growth medium, synthetic fertilisers and chemical plant protection products in primary food production. In this context, SMC could be utilized as a growth medium, bio-fertiliser, bioremediation material and tool to control plant diseases. This study investigates whether SMC in either a solid or water phase can suppress root diseases in horticultural production systems. The suppressive potential of SMC in a solid phase was evaluated toward the root pathogen Phytophthora cactorum (PC) in tunnel-grown strawberry plants. SMC was mixed with peat and evaluated with or without the presence of PC. The suppressive effect of SMC toward the root pathogen Pythium aphanidermatum (PA) was evaluated in dill using a SMC water extract and plants cultivated in a substrate naturally infected with PA or healthy substrate artificially infected with PA. The results indicated that disease symptoms of dill roots were less severe in peat: SMC proportions of 50%: 50% compared to 70%:30%. Moreover, disease symptoms were lowest in the naturally infected substrate treated with SMC water extract. Treatment with the SMC extract also reduced disease symptoms in the healthy substrate artificially infected with PA.
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22.
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23.
  • Kock, Teh Ooi, et al. (författare)
  • Retromer Contributes to Immunity-Associated Cell Death in Arabidopsis
  • 2015
  • Ingår i: Plant Cell. - : Oxford University Press (OUP). - 1040-4651 .- 1532-298X. ; 27, s. 463-479
  • Tidskriftsartikel (refereegranskat)abstract
    • Membrane trafficking is required during plant immune responses, but its contribution to the hypersensitive response (HR), a form of programmed cell death (PCD) associated with effector-triggered immunity, is not well understood. HR is induced by nucleotide binding-leucine-rich repeat (NB-LRR) immune receptors and can involve vacuole-mediated processes, including autophagy. We previously isolated lazarus (laz) suppressors of autoimmunity-triggered PCD in the Arabidopsis thaliana mutant accelerated cell death11 (acd11) and demonstrated that the cell death phenotype is due to ectopic activation of the LAZ5 NBLRR. We report here that laz4 is mutated in one of three VACUOLAR PROTEIN SORTING35 (VPS35) genes. We verify that LAZ4/ VPS35B is part of the retromer complex, which functions in endosomal protein sorting and vacuolar trafficking. We show that VPS35B acts in an endosomal trafficking pathway and plays a role in LAZ5-dependent acd11 cell death. Furthermore, we find that VPS35 homologs contribute to certain forms of NB-LRR protein-mediated autoimmunity as well as pathogen-triggered HR. Finally, we demonstrate that retromer deficiency causes defects in late endocytic/lytic compartments and impairs autophagy-associated vacuolar processes. Our findings indicate important roles of retromer-mediated trafficking during the HR; these may include endosomal sorting of immune components and targeting of vacuolar cargo.
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24.
  • Kushwaha, Sandeep Kumar, et al. (författare)
  • Differential Gene Expression Analysis of Wheat Breeding Lines Reveal Molecular Insights in Yellow Rust Resistance under Field Conditions
  • 2020
  • Ingår i: Agronomy. - : MDPI AG. - 2073-4395. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • The evolution of pathogens in the changing climate raises new challenges for wheat production. Yellow rust is one of the major wheat diseases worldwide, leading to an increased use of fungicides to prevent significant yield losses. The enhancement of the resistance potential of wheat cultivars is a necessary and environmentally friendly solution for sustainable wheat production. In this study, we aimed to identify the differentially expressed genes induced upon yellow rust infection in the field. Reference and de novo based transcriptome analysis was performed among the resistant and susceptible lines of a bi-parental population to study the global transcriptome changes in contrasting wheat genotypes. Based on the analysis, the de novo transcriptome analysis approach was found to be more supportive for field studies. Expression profiles, gene ontology, KEGG pathway analysis and enrichment studies indicated the relation between differentially expressed genes of wheat and yellow rust infection. The h0igh expression of genes related to non-race specific resistance along with pathogen-specific resistance might be a reason for the better resistance ability of a resistant wheat genotype in the field. The targeted metagenomic analysis of wheat samples revealed that Puccinia striiformis tritici was the most dominant pathogen along with other pathogens on the collected leaf material and validating the disease scoring carried out in the field and transcriptomics analyses.
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25.
  • Kushwaha, Sandeep Kumar, et al. (författare)
  • Draft Genome of Biocontrol Agent Pythium periplocum Strain CBS 532.74
  • 2017
  • Ingår i: Genome Announcements. - 2169-8287. ; 5
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • The oomycete Pythium periplocum is an aggressive mycoparasite of a number of plant pathogenic fungi and oomycetes and therefore has potential as a biological control agent. Here, we report the first draft genome sequence of P. periplocum, which comprises 35.89 Mb. It contains 1,043 scaffolds and 14,399 predicted protein-coding genes.
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26.
  • Kushwaha, Sandeep Kumar, et al. (författare)
  • Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum Strain CBS 530.74
  • 2017
  • Ingår i: Genome Announcements. - 2169-8287. ; 5
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • The oomycete Pythium oligandrum is a mycoparasite and licenced biological control agent. Here, we report the draft genome sequence of P. oligandrum strain CBS 530.74, which is 36.80 Mb. It contains 341 scaffolds and 11,647 predicted protein-coding genes. As reported for plant-pathogenic Pythium species, RXLR-type effector sequences are absent.
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27.
  • Larsson Herrera, Sebastian, et al. (författare)
  • Monitoring and discrimination of Pandemis moths in apple orchards using semiochemicals, wing pattern morphology and DNA barcoding
  • 2020
  • Ingår i: Crop Protection. - : Elsevier BV. - 0261-2194 .- 1873-6904. ; 132
  • Tidskriftsartikel (refereegranskat)abstract
    • Non-phemmonal insect attractants of plant and microbial origin are often classified as kairomones. They differ from moth pheromones in that they can attract both sexes of several insect species. Kairomones are nowadays the object of several studies, due to their promising properties for monitoring and selective control of agricultural pests. Here we report on field trapping experiments carried out in apple orchards to quantify the response of the two leafroller species Pandemis heparana (Denis & Schiffermuller) and Pandemis cerasana (Hubner) to potential kairomones (acetic acid (AA), 2-phenyl ethanol (2-PET), pear ester (PE) and benzyl cyanide (BC)) in apple orchards. Specimens of the two species were sexed and classified to the species level using a morphological key based on wing traits. DNA barcoding was used to validate the discrimination between the two species through the morphological key. A two-component blend of AA and 2-PET was effective in catching significant numbers of females of P. heparana and P. cerasana. The addition of PE increased male but not female catches of only P. heparana. For P. heparana blends containing AA and BC with or without PE caught significantly fewer males and females than blends with PET and the AA/BC combination was as effective as PET releasing blends in trapping P. cerasana females. Morphological identification of Pandemis by wing pattern was in agreement with the DNA barcoding in the majority of cases. Additional studies are now required to establish an economic threshold to correlate moth catches with fruit damage and to the possibility that attract and kill based on the identified kairomones can be used to reduce damage.
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28.
  • Liang, Dong, et al. (författare)
  • Horizontal Gene Transfer and Tandem Duplication Shape the Unique CAZyme Complement of the Mycoparasitic Oomycetes Pythium oligandrum and Pythium periplocum
  • 2020
  • Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • Crop protection strategies that are effective but that reduce our reliance on chemical pesticides are urgently needed to meet the UN sustainable development goals for global food security. Mycoparasitic oomycetes such as Pythium oligandrum and Pythium periplocum, have potential for the biological control of plant diseases that threaten crops and have attracted much attention due to their abilities to antagonize plant pathogens and modulate plant immunity. Studies of the molecular and genetic determinants of mycoparasitism in these species have been less well developed than those of their fungal counterparts. Carbohydrate-active enzymes (CAZymes) from P. oligandrum and P. periplocum are predicted to be important components of mycoparasitism, being involved in the degradation of the cell wall of their oomycete and fungal prey species. To explore the evolution of CAZymes of these species we performed an in silico identification and comparison of the full CAZyme complement (CAZyome) of the two mycoparasitic Pythium species (P. oligandrum and P. periplocum), with seven other Pythium species, and four Phytophthora species. Twenty CAZy gene families involved in the degradation of cellulose, hemicellulose, glucan, and chitin were expanded in, or unique to, mycoparasitic Pythium species and several of these genes were expressed during mycoparasitic interactions with either oomycete or fungal prey, as revealed by RNA sequencing and quantitative qRT-PCR. Genes from three of the cellulose and chitin degrading CAZy families (namely AA9, GH5_14, and GH19) were expanded via tandem duplication and predominantly located in gene sparse regions of the genome, suggesting these enzymes are putative pathogenicity factors able to undergo rapid evolution. In addition, five of the CAZy gene families were likely to have been obtained from other microbes by horizontal gene transfer events. The mycoparasitic species are able to utilize complex carbohydrates present in fungal cell walls, namely chitin and N-acetylglucosamine for growth, in contrast to their phytopathogenic counterparts. Nonetheless, a preference for the utilization of simple sugars for growth appears to be a common trait within the oomycete lineage.
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29.
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30.
  • Lukhovitskaya, Nina, et al. (författare)
  • A viral transcription factor exhibits antiviral RNA silencing suppression activity independent of its nuclear localization
  • 2014
  • Ingår i: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 95, s. 2831-2837
  • Tidskriftsartikel (refereegranskat)abstract
    • Viral suppressors of RNA silencing (VSRs) are critical for the success of virus infection and efficient accumulation of virus progeny. The chrysanthemum virus B p12 protein acts as a transcription factor to regulate cell size and proliferation favourable for virus infection. Here, we showed that the p12 protein suppressed RNA silencing and was able to complement a VSR-deficient unrelated virus. Moreover, p12 counter-silencing activity could be uncoupled from its function as a transcription factor in the nucleus. The altered p12 protein, which lacked a nuclear localization signal and was not imported into the nucleus, was able to suppress RNA silencing as efficiently as the native protein. The data revealed new aspects of p12 functioning and identified a novel role for this viral zinc-finger transcription factor. The results provided a general insight into one of the activities of the p12 protein, which appeared to possess more than one function.
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31.
  • Lukhovitskaya, Nina, et al. (författare)
  • Importin-alpha-Mediated Nucleolar Localization of Potato Mop-Top Virus TRIPLE GENE BLOCK1 (TGB1) Protein Facilitates Virus Systemic Movement, Whereas TGB1 Self-Interaction Is Required for Cell-to-Cell Movement in Nicotiana benthamiana
  • 2015
  • Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 167, s. 738-752
  • Tidskriftsartikel (refereegranskat)abstract
    • Recently, it has become evident that nucleolar passage of movement proteins occurs commonly in a number of plant RNA viruses that replicate in the cytoplasm. Systemic movement of Potato mop-top virus (PMTV) involves two viral transport forms represented by a complex of viral RNA and TRIPLE GENE BLOCK1 (TGB1) movement protein and by polar virions that contain the minor coat protein and TGB1 attached to one extremity. The integrity of polar virions ensures the efficient movement of RNA-CP, which encodes the virus coat protein. Here, we report the involvement of nuclear transport receptors belonging to the importin-alpha family in nucleolar accumulation of the PMTV TGB1 protein and, subsequently, in the systemic movement of the virus. Virus-induced gene silencing of two importin-alpha paralogs in Nicotiana benthamiana resulted in significant reduction of TGB1 accumulation in the nucleus, decreasing the accumulation of the virus progeny in upper leaves and the loss of systemic movement of RNA-CP. PMTV TGB1 interacted with importin-alpha in N. benthamiana, which was detected by bimolecular fluorescence complementation in the nucleoplasm and nucleolus. The interaction was mediated by two nucleolar localization signals identified by bioinformatics and mutagenesis in the TGB1 amino-terminal domain. Our results showed that while TGB1 self-interaction is needed for cell-to-cell movement, importin-alpha-mediated nucleolar targeting of TGB1 is an essential step in establishing the efficient systemic infection of the entire plant. These results enabled the identification of two separate domains in TGB1: an internal domain required for TGB1 self-interaction and cell-to-cell movement and the amino-terminal domain required for importin-a interaction in plants, nucleolar targeting, and long-distance movement.
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32.
  • Löbmann, Michael, et al. (författare)
  • The occurrence of pathogen suppressive soils in Sweden in relation soil biota, soil properties, and farming practices
  • 2016
  • Ingår i: Applied Soil Ecology. - : Elsevier BV. - 0929-1393 .- 1873-0272. ; 107, s. 57-65
  • Tidskriftsartikel (refereegranskat)abstract
    • Despite more than 50 years of research and their great potential for sustainable pest management, pathogen suppressive soils remain poorly understood. We conducted a study on suppression of root rot disease symptoms associated with Pythium ultimum in untreated and heat-sterilized soil from ten southern Swedish farms with six different cropping and management regimes. Physical and chemical soil properties, soil nematodes belonging to different trophic guilds, and the predominant soil oomycetes were analyzed for their potential as indicators of soil suppressiveness. Six of the ten sampled soils were suppressive to P. ultimum disease symptoms. Suppressive or conducive properties of the soils from sites with permanent soil cover were related to the presence of live soil biota, while soils from sites with interrupted soil cover had suppressive or conducive effects unrelated to live soil biota. In soils with biologically conducive effects, soils had high or low cation nutrient content, while biologically suppressive soils had intermediate nutrient levels. No relationship was found between disease symptoms and the soil nematode trophic community or the predominant soil oomycetes. Permanent soil cover and a balanced nutrient supply were correlated with biologically suppressive effects on P. ultimum disease symptoms. (C) 2016 The Authors. Published by Elsevier B.V.
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33.
  • Minina, Alyona, et al. (författare)
  • Transcriptional stimulation of rate-limiting components of the autophagic pathway improves plant fitness
  • 2018
  • Ingår i: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 69, s. 1415-1432
  • Tidskriftsartikel (refereegranskat)abstract
    • Autophagy is a major catabolic process whereby autophagosomes deliver cytoplasmic content to the lytic compartment for recycling. Autophagosome formation requires two ubiquitin-like systems conjugating Atg12 with Atg5, and Atg8 with lipid phosphatidylethanolamine (PE), respectively. Genetic suppression of these systems causes autophagy-deficient phenotypes with reduced fitness and longevity. We show that Atg5 and the E1-like enzyme, Atg7, are rate-limiting components of Atg8-PE conjugation in Arabidopsis. Overexpression of ATG5 or ATG7 stimulates Atg8 lipidation, autophagosome formation, and autophagic flux. It also induces transcriptional changes opposite to those observed in atg5 and atg7 mutants, favoring stress resistance and growth. As a result, ATG5-or ATG7-over-expressing plants exhibit increased resistance to necrotrophic pathogens and oxidative stress, delayed aging and enhanced growth, seed set, and seed oil content. This work provides an experimental paradigm and mechanistic insight into genetic stimulation of autophagy in planta and shows its efficiency for improving plant productivity.
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34.
  • Muthusamy, Sarala Devi, et al. (författare)
  • Transient expression and purification of β-caryophyllene synthase in Nicotiana benthamiana to produce β-caryophyllene in vitro
  • 2020
  • Ingår i: PeerJ. - : PeerJ Inc. - 2167-8359. ; 8, s. 1-21
  • Tidskriftsartikel (refereegranskat)abstract
    • The sesquiterpene beta-caryophyllene is an ubiquitous component in many plants that has commercially been used as an aroma in cosmetics and perfumes. Recent studies have shown its potential use as a therapeutic agent and biofuel. Currently, beta-caryophyllene is isolated from large amounts of plant material. Molecular farming based on the Nicotiana benthamiana transient expression system may be used for a more sustainable production of beta-caryophyllene. In this study, a full-length cDNA of a new duplicated beta-caryophyllene synthase from Artemisia annua (AaCPS1) was isolated and functionally characterized. In order to produce beta-caryophyllene in vitro, the AaCPS1 was cloned into a plant viral-based vector pEAQ-HT. Subsequently, the plasmid was transferred into the Agrobacterium and agroinfiltrated into N. benthamiana leaves. The AaCPS1 expression was analyzed by quantitative PCR at different time points after agroinfiltration. The highest level of transcripts was observed at 9 days post infiltration (dpi). The AaCPS1 protein was extracted from the leaves at 9 dpi and purified by cobalt-nitrilotriacetate (Co-NTA) affinity chromatography using histidine tag with a yield of 89 mg kg(-1). fresh weight of leaves. The protein expression of AaCPS1 was also confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and western blot analyses. AaCPS1 protein uses farnesyl diphosphate (FPP) as a substrate to produce p-caryophyllene. Product identification and determination of the activity of purified AaCPS1 were done by gas chromatography-mass spectrometry (GC-MS). GC-MS results revealed that the AaCPS1 produced maximum 26.5 +/- 1 mg of P-caryophyllene per kilogram fresh weight of leaves after assaying with FPP for 6 h. Using AaCPS1 as a proof of concept, we demonstrate that N. benthamiana can be considered as an expression system for production of plant proteins that catalyze the formation of valuable chemicals for industrial applications.
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35.
  • Ortiz Rios, Rodomiro Octavio, et al. (författare)
  • Genomic Prediction for Inbred and Hybrid Polysomic Tetraploid Potato Offspring
  • 2024
  • Ingår i: Agriculture. - 2077-0472. ; 14
  • Tidskriftsartikel (refereegranskat)abstract
    • Potato genetic improvement begins with crossing cultivars or breeding clones which often have complementary characteristics for producing heritable variation in segregating offspring, in which phenotypic selection is used thereafter across various vegetative generations (Ti ). The aim of this research was to determine whether tetrasomic genomic best linear unbiased predictors (GBLUPs) may facilitate selecting for tuber yield across early Ti within and across breeding sites in inbred (S1 ) and hybrid (F1 ) tetraploid potato offspring. This research used 858 breeding clones for a T1 trial at Umeå (Norrland, 63◦4903000 N 20◦1505000 E) in 2021, as well as 829 and 671 clones from the breeding population for T2 trials during 2022 at Umeå and Helgegården (Skåne, 56◦0104600 N 14◦0902400 E), respectively, along with their parents (S0 ) and check cultivars. The S1 and F1 were derived from selfing and crossing four S0 . The experimental layout was an augmented design of four-plant plots across testing sites, where breeding clones were non-replicated, and the parents and cultivars were placed in all blocks between the former. The genomic prediction abilities (r) for tuber weight per plant were 0.5944 and 0.6776 in T2 at Helgegården and Umeå, respectively, when T1 at Umeå was used as the training population. On average, r was larger in inbred than in hybrid offspring at both breeding sites. The r was also estimated using multi-environment data (involving at least one S1 and one F1 ) for T2 performance at both breeding sites. The r was strongly influenced by the genotype in both S1 and F1 offspring irrespective of the breeding site.
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36.
  • Ortiz Rios, Rodomiro Octavio, et al. (författare)
  • Inbreeding Effects on the Performance and Genomic Prediction for Polysomic Tetraploid Potato Offspring Grown at High Nordic Latitudes
  • 2023
  • Ingår i: Genes. - 2073-4425. ; 14
  • Tidskriftsartikel (refereegranskat)abstract
    • Inbreeding depression (ID) is caused by increased homozygosity in the offspring after selfing. Although the self-compatible, highly heterozygous, tetrasomic polyploid potato (Solanum tuberosum L.) suffers from ID, some argue that the potential genetic gains from using inbred lines in a sexual propagation system of potato are too large to be ignored. The aim of this research was to assess the effects of inbreeding on potato offspring performance under a high latitude and the accuracy of the genomic prediction of breeding values (GEBVs) for further use in selection. Four inbred (S-1) and two hybrid (F-1) offspring and their parents (S-0) were used in the experiment, with a field layout of an augmented design with the four S-0 replicated in nine incomplete blocks comprising 100, four-plant plots at Umea (63 & DEG;49 & PRIME;30 & DPRIME; N 20 & DEG;15 & PRIME;50 & DPRIME; E), Sweden. S-0 was significantly (p < 0.01) better than both S-1 and F-1 offspring for tuber weight (total and according to five grading sizes), tuber shape and size uniformity, tuber eye depth and reducing sugars in the tuber flesh, while F-1 was significantly (p < 0.01) better than S-1 for all tuber weight and uniformity traits. Some F-1 hybrid offspring (15-19%) had better total tuber yield than the best-performing parent. The GEBV accuracy ranged from -0.3928 to 0.4436. Overall, tuber shape uniformity had the highest GEBV accuracy, while tuber weight traits exhibited the lowest accuracy. The F-1 full sib's GEBV accuracy was higher, on average, than that of S-1. Genomic prediction may facilitate eliminating undesired inbred or hybrid offspring for further use in the genetic betterment of potato.
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37.
  • Ortiz Rios, Rodomiro Octavio, et al. (författare)
  • Optimizing multi-environment testing in potato breeding: using heritability estimates to determine number of replications, sites, and years for field trials
  • 2023
  • Ingår i: Euphytica. - : Springer Science and Business Media LLC. - 0014-2336 .- 1573-5060. ; 219
  • Tidskriftsartikel (refereegranskat)abstract
    • Multi-environment trials (METs) of potato breeding clones and cultivars allow to precisely determine their performance across testing sites over years. However, these METs may be affected by the genotype × environment interaction (GEI) as noted in tuber yield. Furthermore, trials are replicated several times to optimize the predictive value of the data collected because knowledge on spatial and temporal variability of testing environments is often lacking. Hence, the objectives of this research were to use components of variance from METs to estimate broad sense heritability (H2) based on best linear unbiased predictors and use these estimates to determine the optimum number of sites, years, and replications for testing potato breeding clones along with cultivars. The data were taken from METs in southern and northern Sweden comprising up to 256 breeding clones and cultivars that underwent testing using a simple lattice design of 10-plant plots across three sites over 2 years. Percentage starch in the tuber flesh had the largest H2 in each testing environment (0.850–0.976) or across testing environments (0.905–0.921). Total tuber weight per plot also exhibited high H2 (0.720–0.919) in each testing environment or across them (0.726–0.852), despite a significant GEI. Reducing sugar content in the tuber flesh had the lowest, but still medium H2 (0.426–0.883 in each testing environment; 0.718–0.818 across testing environments). The H2 estimates were smaller when their variance components were disaggregated by year and site, instead of lumping them as environments. Simulating H2 with genetic, site, year, site × year, genetic × site, genetic × year, genetic × site × year, and residual variance components led to establish that two replicates at each of two sites in 2-year trials will suffice for testing tuber yield, starch and reducing sugars. This article provides a methodology to optimize the number of testing size and years for METs of potato breeding materials, as well as tabulated information for choosing the appropriate number of trials in same target population of environments.
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38.
  • Piombo, Edoardo, et al. (författare)
  • Comparative Small RNA and Degradome Sequencing Provides Insights into Antagonistic Interactions in the Biocontrol Fungus Clonostachys rosea
  • 2022
  • Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 88
  • Tidskriftsartikel (refereegranskat)abstract
    • Necrotrophic mycoparasitism is an intricate process involving recognition, physical mycelial contact, and killing of host fungi (mycohosts). During such interactions, mycoparasites undergo a complex developmental process involving massive regulatory changes of gene expression to produce a range of chemical compounds and proteins that contribute to the parasitism of the mycohosts. Small RNAs (sRNAs) are vital components of posttranscriptional gene regulation, although their role in gene expression regulation during mycoparasitisms remain understudied. Here, we investigated the role of sRNA-mediated gene regulation in mycoparasitism by performing sRNA and degradome tag sequencing of the mycoparasitic fungus Clonostachys rosea interacting with the plant-pathogenic mycohosts Botrytis cinerea and Fusarium graminearum at two time points. The majority of differentially expressed sRNAs were downregulated during the interactions with the mycohosts compared to a C. rosea self-interaction control, thus allowing desuppression (upregulation) of mycohost-responsive genes. Degradome analysis showed a positive correlation between high degradome counts and antisense sRNA mapping and led to the identification of 201 sRNA-mediated potential gene targets for 282 differentially expressed sRNAs. Analysis of sRNA potential gene targets revealed that the regulation of genes coding for membrane proteins was a common response against both mycohosts. The regulation of genes involved in oxidative stress tolerance and cellular metabolic and biosynthetic processes was exclusive against F. graminearum, highlighting common and mycohost-specific gene regulation of C. rosea. By combining these results with transcriptome data collected during a previous study, we expand the understanding of the role of sRNA in regulating interspecific fungal interactions and mycoparasitism. IMPORTANCE Small RNAs (sRNAs) are emerging as key players in pathogenic and mutualistic fungus-plant interactions; however, their role in fungus-fungus interactions remains elusive. In this study, we employed the necrotrophic mycoparasite Clonostachys rosea and the plant-pathogenic mycohosts Botrytis cinerea and Fusarium graminearum and investigated the sRNA-mediated gene regulation in mycoparasitic interactions. The combined approach of sRNA and degradome tag sequencing identified 201 sRNA-mediated putative gene targets for 282 differentially expressed sRNAs, highlighting the role of sRNA-mediated regulation of mycoparasitism in C. rosea. We also identified 36 known and 13 novel microRNAs (miRNAs) and their potential gene targets at the endogenous level and at a cross-species level in B. cinerea and F. graminearum, indicating a role of cross-species RNA interference (RNAi) in mycoparasitism, representing a novel mechanism in biocontrol interactions. Furthermore, we showed that C. rosea adapts its transcriptional response, and thereby its interaction mechanisms, based on the interaction stages and identity of the mycohost.Small RNAs (sRNAs) are emerging as key players in pathogenic and mutualistic fungus-plant interactions; however, their role in fungus-fungus interactions remains elusive. In this study, we employed the necrotrophic mycoparasite Clonostachys rosea and the plant-pathogenic mycohosts Botrytis cinerea and Fusarium graminearum and investigated the sRNA-mediated gene regulation in mycoparasitic interactions.
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39.
  • Piombo, Edoardo, et al. (författare)
  • RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents
  • 2023
  • Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 14
  • Tidskriftsartikel (refereegranskat)abstract
    • IntroductionOomycetes cause several damaging diseases of plants and animals, and some species also act as biocontrol agents on insects, fungi, and other oomycetes. RNA silencing is increasingly being shown to play a role in the pathogenicity of Phytophthora species, either through trans-boundary movement of small RNAs (sRNAs) or through expression regulation of infection promoting effectors. MethodsTo gain a wider understanding of RNA silencing in oomycete species with more diverse hosts, we mined genome assemblies for Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDRP) proteins from Phytophthora plurivora, Ph. cactorum, Ph. colocasiae, Pythium oligandrum, Py. periplocum, and Lagenidium giganteum. Moreover, we sequenced small RNAs from the mycelium stage in each of these species. Results and discussionEach of the species possessed a single DCL protein, but they differed in the number and sequence of AGOs and RDRPs. SRNAs of 21nt, 25nt, and 26nt were prevalent in all oomycetes analyzed, but the relative abundance and 5' base preference of these classes differed markedly between genera. Most sRNAs mapped to transposons and other repeats, signifying that the major role for RNA silencing in oomycetes is to limit the expansion of these elements. We also found that sRNAs may act to regulate the expression of duplicated genes. Other sRNAs mapped to several gene families, and this number was higher in Pythium spp., suggesting a role of RNA silencing in regulating gene expression. Genes for most effector classes were the source of sRNAs of variable size, but some gene families showed a preference for specific classes of sRNAs, such as 25/26 nt sRNAs targeting RxLR effector genes in Phytophthora species. Novel miRNA-like RNAs (milRNAs) were discovered in all species, and two were predicted to target transcripts for RxLR effectors in Ph. plurivora and Ph. cactorum, indicating a putative role in regulating infection. Moreover, milRNAs from the biocontrol Pythium species had matches in the predicted transcriptome of Phytophthora infestans and Botrytis cinerea, and L. giganteum milRNAs matched candidate genes in the mosquito Aedes aegypti. This suggests that trans-boundary RNA silencing may have a role in the biocontrol action of these oomycetes.
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40.
  • Piombo, Edoardo, et al. (författare)
  • Small RNAs: A new paradigm in fungal-fungal interactions used for biocontrol
  • 2024
  • Ingår i: Fungal Biology Reviews. - 1749-4613 .- 1878-0253. ; 48
  • Tidskriftsartikel (refereegranskat)abstract
    • In many eukaryotes, small RNAs (sRNAs) can mediate gene expression regulation through a mechanism known as RNA silencing. In fungi, RNA silencing plays a crucial role in numerous biological processes, including parasitic and mutualistic fungus-plant interactions. This review summarizes recent findings on the role of RNA silencing in parasitic fungus-fungus and fungus-insect interactions in relation to their use for the biological control (biocontrol) of fungal plant diseases and insect damage. Genes belonging to the RNA silencing machinery are identified in the genomes of almost all known fungal and oomycete biocontrol organisms. However, recent functional genetic studies in Ascomycota species of the Hypocreales order, such as Trichoderma atroviride and Clonostachys rosea, show how RNA silencing can have family-specific effects, as conidiation is affected differently in the two organisms when the same elements of the RNA silencing machinery are deleted. The size of sRNAs regulated by RNA silencing can also vary between organisms. Cross-species RNA silencing represents a new field in the study of antagonistic interactions. For example, a microRNA (miRNA) of another hypocrealean fungus, Beauveria bassiana, was proven to target genes involved in the immune response of mosquitoes, and there are indications that miRNAs from the mycoparasitic C. rosea may target factors of virulence in its plant-pathogenic host fungi. Accumulating evidence from many species shows that the number of endogenous genes affected by the disruption of the RNA silencing mechanism is always much higher than the number of predicted direct target genes. As several putative targets of fungal sRNAs are transcription factors, it is possible that specific sRNAs have a role as master regulators of gene expression, affecting the transcription of a high number of genes through cascading regulating effects. The challenges faced when studying cross-species RNA silencing, including sRNA trafficking during mycoparasitism, are also discussed. This includes the difficulties in separating the extracellular vesicles of mycoparasitic fungi from those of their hosts, the high amount of sequencing reads lost in bioinformatics filtering steps, imprecise target prediction and the lack of a streamlined accepted way of reporting results.
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41.
  • Prado Fortuna Macan, Giovana, et al. (författare)
  • A Detached Leaf Assay for Rapidly Screening Plant Pathogen-Biological Control Agents
  • 2022
  • Ingår i: Plant Pathology : Method and Protocols. - New York, NY : Springer US. - 9781071625163 ; 2536:2536, s. 449-458
  • Bokkapitel (refereegranskat)abstract
    • The detached leaf assay (DLA) is a nondestructive method for evaluating interactions between plants and disease-causing agents that allows quick characterization of potential pathogens’ infectivity and plants’ resistance to them. Here we show its utility for also assessing potential biological control agents (BCAs), by demonstrating its applicability for screening potential BCAs for the strawberry (Fragaria × ananassa) pathogen Phytophtora cactorum.
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42.
  • Ramesh, Vetukuri (författare)
  • Antifungal compounds, GC-MS analysis and toxicity assessment of methanolic extracts of Trichoderma species in an animal model
  • 2022
  • Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 17
  • Tidskriftsartikel (refereegranskat)abstract
    • Fungi of the genus Trichoderma have been marketed for the management of diseases of crops. However, some Trichoderma species may produce toxic secondary metabolites and it should receive due attention to ensure human safety. In this study, we investigated the in vitro antagonistic potential of T. asperellum AU131 and T. longibrachiatum AU158 as microbial biocontrol agents (MBCAs) against Fusarium xylarioides and the associated antagonistic mechanism with bioactive substances. Swiss albino mice were used to evaluate the in vivo toxicity and pathogenicity of T. asperellum AU131 and T. longibrachiatum AU158 methanolic extracts and spore suspensions, respectively, in a preliminary safety assessment for use as biofungicides. Gas Chromatography-Mass Spectrometry (GC-MS) was used to profile volatile organic metabolites (VOCs) present in the methanolic extracts. The agar diffusion assay of the methanolic extracts from both T. asperellum AU131 and T. longibrachiatum AU158 were effective at a concentration of 200 mu g/mL (1x10(7) spores/mL), causing 62.5%, and 74.3% inhibition, respectively. A GC-MS analysis of methanolic extracts from both bioagents identified 23 VOCs which classified as alcohols, acids, sesquiterpenes, ketones and aromatic compounds. The oral administration of methanolic extracts and spore suspensions of each Trichoderma species to female Swiss albino mice over 14 days did not show any significant signs of toxicity, mortality or changes to body weight. It can be concluded that the tested spore suspensions and methanolic extracts were not pathogenic or toxic, respectively, when administered to Swiss albino mice at various doses.
  •  
43.
  • Ramesh, Vetukuri (författare)
  • Assessment of the effects of liquid and granular fertilizers on maize yield in Rwanda
  • 2021
  • Ingår i: African Journal of Food, Agriculture, Nutrition and Development. - : African Journal of Food, Agriculture, Nutrition and Development. - 1684-5358 .- 1684-5374. ; 21, s. 17787-17800
  • Tidskriftsartikel (refereegranskat)abstract
    • Maize (Zea mays L.) is the most widely grown cereal in the world, accounting for 1,116.34 MT of production in 2019/2020. In Africa, this crop represented approximately 56% of the total cultivated area from 1990 to 2005. About 50% of the African population depends on maize as a staple food and source of carbohydrates, protein, iron, vitamin B, and minerals. Lately, maize has become a cash crop which contributes to the improvement of farmers' livelihoods. For example, the Strategic Plan for Agricultural Transformation (SPAT) III outlined that fertilizer availability in Rwanda should increase to 55,000 MT per year, while fertilizer use should increase from 30 kg/ha in 2013 to 45 kg/ha for the 2017/18 cropping season. Only inorganic fertilizers are currently being used in maize production in Rwanda. This research was conducted to assess the effects of liquid (CBX: Complete Biological Extract) and granular fertilizers on maize crop yields in Rwanda. The study was conducted in the fields of the Rwanda Agriculture and Animal Resources Development Board (Rubona Station) during the 2018/2019 cropping season. Analysis of variance (ANOVA) was used to determine whether differences between treatments were statistically significant, with the threshold for statistical significance set at p < 0.05. Aboveground biomass differed significantly between treatments, with maximum and minimum values of 11,475 kg and 7,850 kg, respectively, being observed. Furthermore, the harvest index differed significantly between treatments, with minimum and maximum values of 0.2136 and 0.33, respectively, being observed. Grain yield also differed significantly between treatments, with the highest value (3,053 kg/ha) observed for a treatment which applied liquid and granular fertilizer at equal proportions (treatment 8), and the lowest one was found in treatment 3 with 1,852 kg/ha. In this study, the gap between the lowest and highest grain yields was about 39.3%. In conclusion, the combination of organic liquid fertilizer and granular fertilizer can significantly increase the grain yield of maize in Rwanda.
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44.
  • Ramesh, Vetukuri (författare)
  • Biological management of coffee wilt disease (Fusarium xylarioides) using antagonistic Trichoderma isolates
  • 2023
  • Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 14
  • Tidskriftsartikel (refereegranskat)abstract
    • Coffee wilt disease (CWD) is a serious threat to the food security of small-scale farmers in Ethiopia, causing significant reductions in coffee yield. Currently, there are no effective control measures available against the causative agent of CWD, Fusarium xylarioides. The main objective of this study was therefore to develop, formulate, and evaluate a range of biofungicides against F. xylarioides, derived from Trichoderma species and tested under in vitro, greenhouse, and field conditions. In total, 175 Trichoderma isolates were screened as microbial biocontrol agents against F. xylarioides. The efficacy of two biofungicide formulations, wettable powder and water dispensable granules, were tested on the susceptible Geisha coffee variety in three different agro-ecological zones in southwestern Ethiopia over three years. The greenhouse experiments were set up using a complete block design, while in the field a randomized complete block design was used, with twice yearly applications of biofungicide. The test pathogen spore suspension was applied to the coffee seedlings by soil drenching, and the subsequent incidence and severity of CWD evaluated annually. The mycelial growth inhibition profiles of the Trichoderma isolates against F. xylarioides ranged from 44.5% to 84.8%. In vitro experiments revealed that T. asperelloides AU71, T. asperellum AU131 and T. longibrachiatum AU158 reduced the mycelial growth of F. xylarioides by over 80%. The greenhouse study indicated that wettable powder (WP) of T. asperellum AU131 had the highest biocontrol efficacy (84.3%), followed by T. longibrachiatum AU158 (77.9%) and T. asperelloides AU71 (71.2%); they also had a significant positive impact on plant growth. The pathogen-treated control plants had a disease severity index of 100% across all the field experiments, and of 76.7% in the greenhouse experiments. In comparison to untreated controls, the annual and cumulative disease incidence over the three years of the study period varied from 46.2 to 90%, 51.6 to 84.5%, and 58.2 to 91%, at the Teppi, Gera and Jimma field experimental locations. Overall, the greenhouse and field experiments and in vitro assays support the biocontrol potential of Trichoderma isolates, and T. asperellum AU131 and T. longibrachiatum AU158 in particular are recommended for the management of CWD under field conditions.
  •  
45.
  • Ramesh, Vetukuri, et al. (författare)
  • Can silencing of transposons contribute to variation in effector gene expression in Phytophthora infestans?
  • 2012
  • Ingår i: Landes Bioscience. - : Informa UK Limited. ; 2, s. 110-114
  • Tidskriftsartikel (refereegranskat)abstract
    • Transposable elements are ubiquitous residents in eukaryotic genomes. Often considered to be genomic parasites, they can lead to dramatic changes in genome organization, gene expression, and gene evolution. The oomycete plant pathogen Phytophthora infestans has evolved a genome organization where core biology genes are predominantly located in genome regions that have relatively few resident transposons. In contrast, disease effector-encoding genes are most frequently located in rapidly evolving genomic regions that are rich in transposons. P. infestans, as a eukaryote, likely uses RNA silencing to minimize the activity of transposons. We have shown that fusion of a short interspersed element (SINE) to an effector gene in P. infestans leads to the silencing of both the introduced fusion and endogenous homologous sequences. This is also likely to occur naturally in the genome of P. infestans, as transcriptional inactivation of effectors is known to occur, and over half of the translocated “RXLR class” of effectors are located within 2 kb of transposon sequences in the P. infestans genome. In this commentary, we review the diverse transposon inventory of P. infestans, its control by RNA silencing, and consequences for expression modulation of nearby effector genes in this economically important plant pathogen.
  •  
46.
  • Ramesh, Vetukuri (författare)
  • Constitutive and Inducible Expression of Genes Related to Salicylic Acid and Ethylene Pathways in a Moderately Resistant Tomato Cultivar Leads to Delayed Development of Meloidogyne javanica
  • 2022
  • Ingår i: Agriculture. - : MDPI AG. - 2077-0472. ; 12
  • Tidskriftsartikel (refereegranskat)abstract
    • Knowledge of the molecular changes in resistant and susceptible cultivars during nematode attack is essential for developing plant resistance. Increased expression of genes related to the synthesis and signaling of salicylic acid, jasmonic acid, and ethylene is known to induce expression of genes related to defense against plant parasitic nematodes. Here, we inoculated approximately 3000 s-stage juveniles (J2s) of Meloidogyne javanica to moderately resistant and highly susceptible tomato cultivars (ALYSTE F-1 and Dutch Mobil, respectively) to compare the developmental disease stages. The roots of each cultivar were collected daily until 30 days after inoculation (DAI). The roots were stained with acid-fuchsin and dissected under a microscope. The results showed that a few parasitic J2s were converted to J3s in the moderately resistant cultivar at 14 DAI, at which time, the highly susceptible cultivar had the highest number of J3s. Comparison of hormonal pathways in the two cultivars revealed that the expression of genes related to the ethylene pathway in ALYSTE F-1 was more strongly upregulated than in Dutch Mobil at 14 DAI. Moreover, the jasmonic acid pathway in the roots of both cultivars decreased at 14 DAI. The expression of genes related to salicylic acid synthesis and signaling was not significantly different between the two cultivars with regard to their non-inoculated controls, respectively, but ALYSTE F-1 in general showed constitutively higher levels of these genes compared to Dutch Mobil at 14 DAI. These results suggest that constitutive and induced expression of genes related to the salicylic acid pathway and ethylene pathway, respectively, delay the development of M. javanica J2s in ALYSTE F-1.
  •  
47.
  • Ramesh, Vetukuri (författare)
  • Draft genome assemblies for tree pathogens Phytophthora pseudosyringae and Phytophthora boehmeriae
  • 2021
  • Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • Species of Phytophthora, plant pathogenic eukaryotic microbes, can cause disease on many tree species. Genome sequencing of species from this genus has helped to determine components of their pathogenicity arsenal. Here, we sequenced genomes for two widely distributed species, Phytophthora pseudosyringae and Phytophthora boehmeriae, yielding genome assemblies of 49 and 40Mb, respectively. We identified more than 270 candidate disease promoting RXLR effector coding genes for each species, and hundreds of genes encoding candidate plant cell wall degrading carbohydrate active enzymes (CAZymes). These data boost genome sequence representation across the Phytophthora genus, and form resources for further study of Phytophthora pathogenesis.
  •  
48.
  • Ramesh, Vetukuri, et al. (författare)
  • Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora
  • 2018
  • Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 10:9, s. 2432-2442
  • Tidskriftsartikel (refereegranskat)abstract
    • Species from the genus Phytophthora are well represented among organisms causing serious diseases on trees. Phytophthora plurivora has been implicated in long-term decline of woodland trees across Europe. Here we present a draft genome sequence of P. plurivora, originally isolated from diseased European beech (Fagus sylvatica) in Malmö, Sweden. When compared with other sequenced Phytophthora species, the P. plurivora genome assembly is relatively compact, spanning 41 Mb. This is organized in 1,919 contigs and 1,898 scaffolds, encompassing 11,741 predicted genes, and has a repeat content of approximately 15%. Comparison of allele frequencies revealed evidence for tetraploidy in the sequenced isolate. As in other sequenced Phytophthora species, P. plurivora possesses genes for pathogenicity-associated RXLR and Crinkle and Necrosis effectors, predominantly located in gene-sparse genomic regions. Comparison of the P. plurivora RXLR effectors with orthologs in other sequenced species in the same clade (Phytophthora multivora and Phytophthora capsici) revealed that the orthologs were likely to be under neutral or purifying selection.
  •  
49.
  •  
50.
  • Ramesh, Vetukuri (författare)
  • Effect of Biochar and Microbial Inoculation on P, Fe, and Zn Bioavailability in a Calcareous Soil
  • 2022
  • Ingår i: Processes. - : MDPI AG. - 2227-9717. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • To identify effective ways of increasing the yield of crops grown in nutrient-poor calcareous soils, the combined effects of biochar addition and inoculation with plant growth promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) on wheat growth and soil properties were investigated under rhizobox conditions. Measured soil properties included pH, electrical conductivity (EC), organic matter content (OM), the availability of P, Fe, and Zn in the rhizosphere, and the uptake of these elements by plants. Combined biochar addition and microbial inoculation were shown to significantly increase the concentration of available forms of P, Fe, and Zn in the soil when compared to non-biochar treatments. The highest soil pH (7.82) was observed following biochar addition without microbial inoculation. The EC following biochar addition and PGPR inoculation was significantly higher than the other treatments, and the soil OM content was highest when combining AMF inoculation with biochar addition. The available P content after AMF inoculation combined with biochar addition was 27.81% higher than the control conditions, and AMF inoculation increased Fe and Zn bioavailability by factors of 2.38 and 1.29, respectively, when combined with biochar addition relative to AMF inoculation alone. The simultaneous biochar addition and PGPR inoculation significantly increased P uptake by the plants. The highest shoot Fe and Zn uptake rates were observed after a simultaneous application of biochar and PGPR inoculation. Under these conditions, shoot uptake was higher than seen when combining biochar addition with AMF inoculation by factors of 1.64 and 1.21, respectively. In general, it can be concluded that combining inoculation with growth-promoting bacteria and biochar addition can effectively improve nutrient availability to plant and soil conditions.
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