Determining the optimal method for DNA isolation from fruit jams

Sovová, Tereza; Barbora, Křížová; Ovesná, Jaroslava

doi:10.17221/340/2017-cjfs

Cited by 7 publications

(3 citation statements)

References 28 publications

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“…There is no universal protocol for DNA extraction yet; the most appropriate extraction method should be chosen on a matrix basis. Thus, the amplification capability of the DNA isolated from a food sample needs to be verified because the DNA extract may contain PCR inhibitors [29,30,[40][41][42]. For this purpose, universally amplifiable (conservative) DNA sequences of the actin gene were used.…”

Section: Discussionmentioning

confidence: 99%

cor1 Gene: A Suitable Marker for Identification of Opium Poppy (Papaver somniferum L.)

Čermáková,

Svoboda,

Ovesná

et al. 2024

Foods

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This paper discusses the development of rapid, reliable, and accurate polymerase chain reaction (PCR) assays for detecting opium poppy (Papaver somniferum L.) in food. Endpoint, quantitative, and digital PCRs were compared based on the amplification of a newly developed DNA marker targeting the NADPH-dependent codeinone reductase (COR) gene. Designed assays were shown to be highly specific and sensitive in discriminating opium poppy from other plant species, even in heat-treated and food samples. Digital PCR was the most sensitive, with a detection limit of up to 5 copies, i.e., approximately 14 pg of target DNA per reaction. Quantitative and digital PCR further allowed the quantification of opium poppy in up to 1.5 ng and 42 pg (15 copies) of target DNA in a sample, respectively. In addition, two duplex PCRs have been developed for the simultaneous detection of opium poppy DNA and representatives of (i) the Papaveraceae family or (ii) the Plantae kingdom. Finally, all designed assays were successfully applied for analysis of 15 commercial foodstuffs; two were suspected of being adulterated. The study results have an important impact on addressing food fraud and ensuring the safety and authenticity of food products. Beyond food adulteration, the study may also have significant implications for forensics and law enforcement.

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Section: Discussionmentioning

confidence: 99%

cor1 Gene: A Suitable Marker for Identification of Opium Poppy (Papaver somniferum L.)

Čermáková,

Svoboda,

Ovesná

et al. 2024

Foods

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“…These biomolecule can be isolated from any biological material for subsequent downstream processes, analytical, or preparative purposes [1,2]. There are many different protocols and, kits commercially available for DNA extraction from different plant materials [2][3][4][5][6][7][8][9][10]. Varying amounts and integrity of DNA are obtained due to the inherent properties as it were, and, differences in the optimization of the protocols for DNA extraction [11,12].…”

Section: Introductionmentioning

confidence: 99%

“…In addition, there are different DNA extraction kits in phase with the outstanding discrepancy [8,9]. This study addressed the differences in the incubation temperatures and effect of salt concentration optimal for the extraction of DNA, particularly from banana fruits.…”

Section: Introductionmentioning

confidence: 99%

Protocol Optimization of DNA Extraction from Banana Fruits

Omara

Barugahare²

2022

JABB

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Background: DNA extraction is the process by which the DNA is extracted and purified from the living or dead cells or tissues. There are many different kits commercially available for DNA extraction, with varying protocols. This study aimed at determining the optimal conditions for the extraction of high yield DNA from banana fruits. Methodology: DNA was extracted from banana fruits by precipitation method. The DNA yield was determined using the Nanodrop DNA quantification technique. Results: The optimal sodium chloride salt concentration for DNA extraction from banana fruits was 4mM and the amount of DNA extracted increased as the temperature decreased. The highest yield was obtained between 4 0C to 0 0C. Conclusion: We report for the first time a protocol with an optimal salt concentration (NaCl, 4mM) for quality DNA yield from banana fruits. A critical consideration is required to establish an optimal range of moderate temperatures and DNA concentrations for better quality and desired yields. There may not be a universal protocol for DNA extraction from all plant materials.

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Workflow for development of CAPS markers with one type of restriction enzyme to identify citrus cultivars

Nishimura,

Okuma,

Kaneyoshi

et al. 2024

Tree Genetics & Genomes

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Given the ease of propagating fruit tree species through cloning, the economic viability of their breeding programs hinges on protecting breeders' rights. This necessitates the development of highly accurate DNA markers for cultivar identification. Here, we present a methodology for the rapid design of cleaved amplified polymorphic sequence (CAPS) markers to discriminate newly bred Japanese citrus cultivars from genetically related cultivars. We first compared the performance of ddRAD-seq and MIG-seq in citrus germplasm. The ddRAD-seq libraries generated using EcoRI and HindIII restriction enzymes yielded the highest number of polymorphisms. Subsequently, ddRAD-seq with EcoRI and HindIII was employed to analyze 29 citrus cultivars and thus identify 331,801 genome-wide polymorphisms. A semi-automated bioinformatics pipeline was then utilized to identify candidate CAPS markers, resulting in the discovery of 14,072 potential markers. Of these candidates, 52 were chosen for validation based on their recognition by the PstI restriction enzyme. This evaluation resulted in the development of 11 highly discriminative CAPS markers. Remarkably, a combination of only six such markers was sufficient to differentiate newly bred cultivars from their genetically related parents. The single restriction enzyme employed for these markers facilitates straightforward multiplexing. Finally, a combination of one multiplex marker testing two loci and four singleplex markers was successfully selected that completely discriminated the cultivars other than the bud sports used in this study. The pipeline established here extends beyond citrus and has the potential to simplify marker development and cultivar protection in various plant species.

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Determining the optimal method for DNA isolation from fruit jams

Cited by 7 publications

References 28 publications

cor1 Gene: A Suitable Marker for Identification of Opium Poppy (Papaver somniferum L.)

cor1 Gene: A Suitable Marker for Identification of Opium Poppy (Papaver somniferum L.)

Protocol Optimization of DNA Extraction from Banana Fruits

Workflow for development of CAPS markers with one type of restriction enzyme to identify citrus cultivars

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