Brief Note Rapid plant DNA and RNA extraction protocol using a bench drill

Ferreira, Cláudia Fortes; Gutiérrez, D.Alonso; Kreuze, Jan; Caruana, Marie-Line; Chabannes, Matthieu; Barbosa, Ana Cláudia Oliveira; Santos, Taís Araújo; Silva, A.G.S.; Santos, Renata; Amorim, Édson Perito; Oliveira, S. A. S. de; Jesus, O. N. de

doi:10.4238/gmr18394

Cited by 10 publications

(4 citation statements)

References 2 publications

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“…DNA and RNA were extracted from leaves of common bean using a bench drill according to cetyltrimethylammonium bromide (CTAB) protocol (Doyle & Doyle, 1990) and (Ferreira et al, 2019) for DNA and RNA extractions, respectively. The grinded plant tissues were dissolved inside the plastic bags (20 × 10 × 0.01 cm of virgin, low-density polyethylene) at rotation of 2,500 rpm, until tissue is fully dissolved.…”

Section: Measurementsmentioning

confidence: 99%

Coupling effects of phosphorus fertilization source and rate on growth and ion accumulation of common bean under salinity stress

Mohamed

El-Sayed

Rady

et al. 2021

PeerJ

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Many agricultural regions in arid and semiarid climate zone need to deal with increased soil salinity. Legumes are classified as salt-sensitive crops. A field experiment was performed to examine the application of phosphorus (P) fertilizer source and rate on growth, chlorophylls and carotenoid content, DNA and RNA content and ion accumulation in common bean (Phaseolus vulgaris L.) cultivated under salinity stress. An experimental design was split-plot with three replicates. The main plots included two P sources, namely single superphosphate (SP) and urea phosphate (UP). The sub-plots covered four P rates, i.e., 0.0, 17.5, 35.0, and 52.5 kg P ha–1. All applied P fertilization rates, in both forms, increased plant height, leaf area, dry weight of shoots and roots per plant, and total dry weight (TDW) in t ha−1. The highest accumulation of N, P, K+, Mg2+, Mn2+, Zn2+, and Cu2+ was determined in the shoot and root of common bean, while 35 kg of P per ha−1 was used compared to the other levels of P fertilizer. The highest P rate (52.5 kg ha−1) resulted in a significant reduction in Na+ in shoot and root of common bean. The response curve of TDW (t ha–1) to different rates of P (kg ha–1) proved that the quadratic model fit better than the linear model for both P sources. Under SP, the expected TDW was 1.675 t ha–1 if P was applied at 51.5 kg ha–1, while under UP, the maximum expected TDW was 1.875 t ha–1 if P was supplied at 42.5 kg ha–1. In conclusion, the 35.0 kg P ha–1 could be considered the best effective P level imposed. The application of P fertilizer as urea phosphate is generally more effective than single superphosphate in enhancing plant growth and alleviating common bean plants against salinity stress.

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Section: Measurementsmentioning

confidence: 99%

Coupling effects of phosphorus fertilization source and rate on growth and ion accumulation of common bean under salinity stress

Mohamed

El-Sayed

Rady

et al. 2021

PeerJ

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“…RNA extraction was conducted using the CTAB (2% CTAB; 100 mM Tris–HCl pH 8.0; 50 mM EDTA pH 8.0; 1.4 M NaCl) 104 protocol with modifications 105 . Total RNA was extracted from the roots of inoculated and non-inoculated cassava plants.…”

Section: Methodsmentioning

confidence: 99%

Comparative analysis of infected cassava root transcriptomics reveals candidate genes for root rot disease resistance

Hohenfeld,

de Oliveira,

Ferreira

et al. 2024

Sci Rep

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Cassava root-rot incited by soil-borne pathogens is one of the major diseases that reduces root yield. Although the use of resistant cultivars is the most effective method of management, the genetic basis for root-rot resistance remains poorly understood. Therefore, our work analyzed the transcriptome of two contrasting genotypes (BRS Kiriris/resistant and BGM-1345/susceptible) using RNA-Seq to understand the molecular response and identify candidate genes for resistance. Cassava seedlings (resistant and susceptible to root-rot) were both planted in infested and sterilized soil and samples from Initial-time and Final-time periods, pooled. Two controls were used: (i) seedlings collected before planting in infested soil (absolute control) and, (ii) plants grown in sterilized soil (mock treatments). For the differentially expressed genes (DEGs) analysis 23.912 were expressed in the resistant genotype, where 10.307 were differentially expressed in the control treatment, 15 DEGs in the Initial Time-period and 366 DEGs in the Final Time-period. Eighteen candidate genes from the resistant genotype were related to plant defense, such as the MLP-like protein 31 and the peroxidase A2-like gene. This is the first model of resistance at the transcriptional level proposed for the cassava × root-rot pathosystem. Gene validation will contribute to screening for resistance of germplasm, segregating populations and/or use in gene editing in the pursuit to develop most promising cassava clones with resistance to root-rot.

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“…DNA was extracted from the young leaves of the 150 banana accessions as described by Doyle and Doyle [28], with modifications proposed by Ferreira et al [29]. The samples of young banana leaves (300 mg) were immediately placed in plastic bags (20 × 10 cm) with 2 mL extraction buffer (2% CTAB; 100 mM Tris-HCl, pH 8.0; 50 mM EDTA, pH 8.0; 1.4 M NaCl; 2% PVP-40; and 1% sodium sulfite).…”

Section: Dna Extraction and Pcr Conditionsmentioning

confidence: 99%

Phytoene Desaturase (PDS) Gene-Derived Markers Identify “A” and “B” Genomes in Banana (Musa spp.)

Nascimento,

Mascarenhas,

Boaventura

et al. 2024

Horticulturae

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Phytoene desaturase (PDS) is a plant enzyme involved in carotenoid biosynthesis. The PDS gene has been used as a selective marker for genome editing in several plant species, including banana (Musa spp.). Its knockout promotes dwarfism and albinism, characteristics that are easily recognizable and highly favorable. In Musa spp., the A genome increases fruit production and quality, whereas the B genome is associated with tolerance to biotic and abiotic stresses. The objective of this study was to identify a molecular marker in the PDS gene to easily discriminate the A and B genomes of banana. A 2166 bp fragment for the “PDSMa” marker was identified as polymorphic for the A genome (identification accuracy of 99.33%), whereas ~332 and ~225 bp fragments were detected for the “PDSMb” marker with 100% accuracy using MedCalc software. In this study, we used genotypes with A and B genomes that are used in the genetic improvement of bananas and an accession with the BT genome. It was not possible to differentiate the accession with the BT genome from the others, suggesting that the markers do not have the capacity to separate the T genome from the A and B genomes. To the best of our knowledge, this is the first study to use the PDS gene to determine doses of the A genome and identify the B genome in Musa spp., which will aid in evaluating the genomic constitution of banana hybrids and accessions at the seedling stage and accelerating their classification in crop genetic improvement programs.

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Brief Note Rapid plant DNA and RNA extraction protocol using a bench drill

Cited by 10 publications

References 2 publications

Coupling effects of phosphorus fertilization source and rate on growth and ion accumulation of common bean under salinity stress

Coupling effects of phosphorus fertilization source and rate on growth and ion accumulation of common bean under salinity stress

Comparative analysis of infected cassava root transcriptomics reveals candidate genes for root rot disease resistance

Phytoene Desaturase (PDS) Gene-Derived Markers Identify “A” and “B” Genomes in Banana (Musa spp.)

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