| 1. |
- Islam, Md Mazharul, et al.
(författare)
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Cytogenetics and consequences of polyploidization on different biotic-abiotic stress tolerance and the potential mechanisms involved
- 2022
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Ingår i: PLANTS. - : MDPI. - 2223-7747. ; 11:20
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Forskningsöversikt (refereegranskat)abstract
- The application of polyploidy in sustainable agriculture has already brought much appreciation among researchers. Polyploidy may occur naturally or can be induced in the laboratory using chemical or gaseous agents and results in complete chromosome nondisjunction. This comprehensive review described the potential of polyploidization on plants, especially its role in crop improvement for enhanced production and host-plant resistance development against pests and diseases. An in-depth investigation on techniques used in the induction of polyploidy, cytogenetic evaluation methods of different ploidy levels, application, and current research trends is also presented. Ongoing research has mainly aimed to bring the recurrence in polyploidy, which is usually detected by flow cytometry, chromosome counting, and cytogenetic techniques such as fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). Polyploidy can bring about positive consequences in the growth and yield attributes of crops, making them more tolerant to abiotic and biotic stresses. However, the unexpected change in chromosome set and lack of knowledge on the mechanism of stress alleviation is hindering the application of polyploidy on a large scale. Moreover, a lack of cost–benefit analysis and knowledge gaps on the socio-economic implication are predominant. Further research on polyploidy coupling with modern genomic technologies will help to bring real-world market prospects in the era of changing climate. This review on polyploidy provides a solid foundation to do next-generation research on crop improvement.
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| 2. |
- Nasif, Saifullah Omar, et al.
(författare)
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Prospects of endophytic fungi as a natural resource for the sustainability of crop production in the modern era of changing climate
- 2023
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Ingår i: Symbiosis. - : Springer Science+Business Media B.V.. - 0334-5114 .- 1878-7665. ; 89, s. 1-25
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Forskningsöversikt (refereegranskat)abstract
- The world is facing severe consequences of chemical fertilizers and synthetic pesticides. As a safer and eco-friendly option for crop nutrition and pest control, endophytic fungi (EFs) are now hotpots in sustainable crop production research. This comprehensive review elucidated the potentials of EF in sustainable crop production amid various biotic and abiotic stress conditions as well as their extraordinary role in phyto- and bioremediation. A critical investigation on how climatic factors such as temperature, rainfall, nutrient level, pH and storage condition affect the survival and performance of EFs are also presented. On-going research majorly focused on the application of endophytic fungi as crop growth promoters, biocontrol agents, and stress mediators. However, a lack of in-depth understanding of the underlying mechanism is predominant. Nevertheless, challenges of successful isolation and identification of EFs hinder their commercialization. Modern genomic technologies and nanotechnology-based applications of EFs can help in overcome the barriers. This review will provide direction for future research where EFs will lead next-generation sustainable strategies to cope with climate change.
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| 3. |
- Bekele, Wondimagegne, et al.
(författare)
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Methane production from locally available ruminant feedstuffs in Ethiopia : an in vitro study
- 2024
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Ingår i: Animal Feed Science and Technology. - 0377-8401 .- 1873-2216. ; 312
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Tidskriftsartikel (refereegranskat)abstract
- Achieving optimal nutrient composition in locally sourced ruminant feeds is important, but can be challenging in resource-limited production systems. For example, improving the composition of available local feed resources is a key obstacle to efficiently mitigating enteric methane (CH4) emissions in ruminants. This study characterized the nutritional content and in vitro methane (CH4) yield of ruminant feedstuffs accessible in Ethiopia. A survey of 60 experienced farmers in two representative districts in Amhara region, Ethiopia, provided 33 feed samples, which were classified into four ruminant feed categories: Grasses (n=10); indigenous plants (trees, shrubs, herbaceous plants) (n=13); crop residues (n=5); and agro-industrial by-products (n=5). Nutritional composition was assessed by proximate and detergent methods. Methane yield (g CH4/kg feed dry matter (DM)) and total gas yield (L/kg DM) were evaluated using a fully automated in vitro gas production system. A colorimetric assay was conducted to measure condensed tannin content (CT, mg/g) in relevant feeds. Lower crude protein (CP) values were observed for the grass (mean 65.2 g/kg DM) and crop residues (mean 54.5 g/kg DM) categories. Agro-industrial by-products had the highest CP (mean 260 g/kg DM), while indigenous plants exhibited intermediate levels (163 g/kg DM). There was significant variation in CH4 yield (P<0.01) between grasses (12.4–24.7 g/kg DM) indigenous plants (1.8–19.3 g/kg DM), and agro-industrial by-products (8.1–26.9 g/kg DM). The indigenous plant Trifolium acaule gave the lowest in vitro CH4 yield (1.8 g/kg DM). A positive relationship was observed between in vitro dry matter digestibility (IVDMD), CH4, and total gas yield. Percentage of CH4 in total gas production varied with feed category (grasses 14.5–19.6%; indigenous plants 3.1–16.9%; crop residues 15.8–20.6%; agro-industrial by-products 12.8–18.7%), and within category, e.g., Trifolium acaule (3.1%), Acacia nilotica L. (7.1%), Ziziphus spina-christi (9.9%), brewer's spent grains (BSG) (12.8%), local liquor (areki) residues (14.1%), and local beer (tella) residues (15.1%). A negative relationship was observed between CT content and in vitro CH4 yield, with a stronger (P<0.05) correlation for soluble CTs (R2 = 0.46) than cell-bound CTs (R2 = 0.25) and total CTs (R2 = 0.29). Based on methanogenic properties and effects of CTs on in vitro CH4 yield, indigenous plants should be prioritized in ruminant rations in Ethiopia. Making nutritional composition and CH4 data publicly available could help develop environmentally sound, cost-effective rations for ruminant livestock, benefiting local farmers and leading to more sustainable and efficient livestock production in Ethiopia.
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| 4. |
- Hossain, Mohammad Anwar, et al.
(författare)
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Genetic engineering for heavy metal/metalloid stress tolerance in plants
- 2023
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Ingår i: Heavy metal toxicity and tolerance in plants. - : John Wiley & Sons. - 9781119906506 - 9781119906469 ; , s. 573-592
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Bokkapitel (refereegranskat)abstract
- Modern agricultural techniques, anthropogenic activities, fast industrialization and urbanization, and the use of fossil fuels are the sources of significant contamination of the environment with various heavy metals (HMs) and metalloids. HM pollution has an impact on agricultural output and quality. What is more, accumulation of HMs in crops poses a threat to the human health. The problem of contamination of the arable lands with HMs and metalloids has to be addressed in various ways. One of the solutions is plant genetic engineering. Developing and cultivating commercial or industrial crop plants that display increased tolerance to HM-induced stress would let to use HM-affected areas for cultivation. Moreover, HM-tolerant hyperaccumulator plants can be used for phytoremediation of contaminated land. This chapter aims to offer a comprehensive review of current advances in genome transformation for improved plant tolerance to HMs/metalloids with special reference to the overexpression of genes encoding metal transporters, sulfur metabolites, metal chelators, and components of antioxidative system and glyoxalase pathways. In addition, we have discussed the potential of using CRISPR/Cas system in developing HM tolerance in plants.
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| 5. |
- Sandhi, Arifin, et al.
(författare)
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Mercury Toxicity : Plant Response and Tolerance
- 2023
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Ingår i: Heavy Metal Toxicity and Tolerance in Plants. - : John Wiley & Sons. - 9781119906469 - 9781119906483 - 9781119906506 - 9781119906476 ; , s. 349-372
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Bokkapitel (refereegranskat)abstract
- Heavy Metal Toxicity and Tolerance in Plants provides a comprehensive overview of the physiological, biochemical, and molecular basis of heavy metal tolerance and functional omics that allow for a deeper understanding of using heavy metal tolerance for deliberate manipulation of plants. Through the authors’ unique approach, the text enables researchers to develop strategies to enhance metal toxicity and deficiency tolerance as well as crop productivity under stressful conditions, in order to better utilize natural resources to ensure future food security.The text presents the basic knowledge of plant heavy metal/metalloid tolerance using modern approaches, including omics, nanotechnology, and genetic manipulation, and covers molecular breeding, genetic engineering, and approaches for high yield and quality under metal toxicity or deficiency stress conditions.With a collection of 26 chapters contributed by the leading experts in the fields surrounding heavy metal and metalloids toxicity and tolerance in crop plants, Heavy Metal Toxicity and Tolerance in Plants includes further information on:Advanced techniques in omics research in relation to heavy metals/metalloids toxicity and toleranceHeavy metals/metalloids in food crops and their implications for human healthMolecular mechanisms of heavy metals/metalloids toxicity and tolerance in plantsMolecular breeding approaches for reducing heavy metals load in the edible plant partsHormonal regulation of heavy metals toxicity and toleranceApplications of nanotechnology for improving heavy metals stress toleranceGenetic engineering for heavy metals/metalloids stress tolerance in plantsWith comprehensive coverage of the subject, Heavy Metal Toxicity and Tolerance in Plants is an essential reference for researchers working on developing plants tolerant to metals/metalloids stress and effective strategies for reducing the risk of health hazards.
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| 6. |
- Siddique, Abu Bakar, First research engineer, et al.
(författare)
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A cost-effective and efficient strategy for Illumina sequencing of fungal communities: A case study of beech endophytes identified elevation as main explanatory factor for diversity and community composition
- 2016
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Ingår i: Fungal ecology. - : Elsevier. - 1754-5048 .- 1878-0083. ; 20, s. 175-185
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Tidskriftsartikel (refereegranskat)abstract
- We describe an accurate and efficient workflow for highly multiplexed paired-end Illumina sequencing of fungal full-length ITS amplicons. The impact of habitat and substratum conditions on leaf-inhabiting fungal communities was analysed. Fully vital and clearly senescent leaves of European beech (Fagus sylvatica) were sampled along an elevation gradient of about 1000 m in the Bavarian Alps, Germany, in autumn 2013. Surface-sterilised leaves were used for genomic DNA extraction, tagging-by-amplification and high-throughput sequencing. Significant correlation of community composition with elevation was observed. The mycobiome was little affected by the physiological state of the leaves, because only a partial shift of taxonomic composition was observed from vital towards clearly senescent leaves.
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| 7. |
- Siddique, Abu Bakar, First research engineer, et al.
(författare)
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Molecular studies of rust on European aspen suggest an autochthonous relationship shaped by genotype
- 2023
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT). At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances. Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.
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| 8. |
- Siddique, Abu Bakar, First research engineer, et al.
(författare)
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Optimization of Protocol for Construction of Fungal ITS Amplicon Library for High-Throughput Illumina Sequencing to Study the Mycobiome of Aspen Leaves
- 2022
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Ingår i: Applied Sciences. - : MDPI. - 2076-3417. ; 12:3
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Tidskriftsartikel (refereegranskat)abstract
- High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/µL to 1526 ng/µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63–2.04 and 0.26–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS.
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| 9. |
- Siddique, Abu Bakar, First research engineer, et al.
(författare)
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What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions
- 2017
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 20, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- Comparative simultaneous studies of environmental high-throughput sequencing (HTS) and cultivation of plant-associated fungi have rarely been conducted in the past years. For the present contribution, HTS and extinction culturing were applied for the same leaf samples of European beech (Fagus sylvatica) in order to trace both “real” environmental drivers as well as method-dependent signals of the observed mycobiomes. Both approaches resulted in non-overlapping community composition and pronounced differences in taxonomic classification and trophic stages. However, both methods revealed similar correlations of the fungal communities with local environmental conditions. Our results indicate undeniable advantages of HTS over cultivation in terms of revealing a good representation of the major functional guilds, rare taxa and biodiversity signals of leaf-inhabiting fungi. On the other hand our results demonstrate that the immense body of literature about cultivable endophytic fungi can and should be used for the interpretation of community signals and environmental correlations obtained from HTS studies and that cultivation studies should be continued at the highest standards, e.g. when sequencing facilities are not available or if such surveys are expanded into functional aspects with experiments on living isolates.
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| 10. |
- Unterseher, Martin, et al.
(författare)
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Diversity and Composition of the Leaf Mycobiome of Beech (Fagus sylvatica) Are Affected by Local Habitat Conditions and Leaf Biochemistry
- 2016
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 11:4
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Tidskriftsartikel (refereegranskat)abstract
- Comparative investigations of plant-associated fungal communities (mycobiomes) in distinct habitats and under distinct climate regimes have been rarely conducted in the past. Nowadays, high-throughput sequencing allows routine examination of mycobiome responses to environmental changes and results at an unprecedented level of detail. In the present study, we analysed Illumina-generated fungal ITS1 sequences from European beech (Fagus sylvatica) originating from natural habitats at two different altitudes in the German Alps and from a managed tree nursery in northern Germany. In general, leaf-inhabiting mycobiome diversity and composition correlated significantly with the origin of the trees. Under natural condition the mycobiome was more diverse at lower than at higher elevation, whereas fungal diversity was lowest in the artificial habitat of the tree nursery. We further identified significant correlation of leaf chlorophylls and flavonoids with both habitat parameters and mycobiome biodiversity. The present results clearly point towards a pronounced importance of local stand conditions for the structure of beech leaf mycobiomes and for a close interrelation of phyllosphere fungi and leaf physiology.
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