ORCID Profile
0000-0002-3178-523X
Current Organisation
Sveriges lantbruksuniversitet
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Publisher: MDPI AG
Date: 21-01-2022
DOI: 10.3390/APP12031136
Abstract: High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for ex le, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the s les, the marker genes selected, and the number of environmental s les. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes s led 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 s le-specific index primers, and we then optimized the lification with these composite Ps for 380 s les. The fungal DNA concentration in the s les 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 subs les and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required lification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected licon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully lified this region for every s le (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of s le-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an licon library in order to subject the intended 380 environmental s les to HTS.
Publisher: Springer Science and Business Media LLC
Date: 30-12-2023
Publisher: MDPI AG
Date: 12-10-2022
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.
No related grants have been discovered for Abu Bakar Siddique.