Highly efficient DNA extraction and purification from olive oil on a washable and reusable miniaturized device

Carvalho, Joana; Puertas, Gema; Gaspar, J.; Azinheiro, Sarah; Diéguez, Lorena; Garrido‐Maestu, Alejandro; Vázquez, Manuel; Barros‐Velázquez, Jorge; Cardoso, Susana; Prado, Marta

doi:10.1016/j.aca.2018.02.079

Cited by 24 publications

(18 citation statements)

References 32 publications

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“…Recently, Piarulli et al [121] compared four DNA isolation methods referenced in the literature and came up with a modified method based on the work of Consolandi et al [122] for the extraction of DNA from extra virgin olive oil in a much smaller time frame (4 h as compared with the 30 h reported) and involving low-cost options. A washable and reusable miniaturized device has been developed as well and tested for highly efficient DNA purification from olive oil, providing an increased surface-area-to-volume ratio when compared with other approaches, allowing highly efficient DNA purification and concentration from samples with minute DNA contents [123]. Molecular markers that amplify shorter fragments are supposed to work efficiently with low-quality or fragmented DNA isolated from oil, and SSRs and SNPs are the favored choice in such cases.…”

Section: Agri-food Traceability: Olive Oil and Table Olivesmentioning

confidence: 99%

Microsatellite Markers in Olives (Olea europaea L.): Utility in the Cataloging of Germplasm, Food Authenticity and Traceability Studies

Yadav

Carvalho

Trujillo

et al. 2021

Foods

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The olive fruit, a symbol of Mediterranean diets, is a rich source of antioxidants and oleic acid (55–83%). Olive genetic resources, including cultivated olives (cultivars), wild olives as well as related subspecies, are distributed widely across the Mediterranean region and other countries. Certain cultivars have a high commercial demand and economical value due to the differentiating organoleptic characteristics. This might result in economically motivated fraudulent practices and adulteration. Hence, tools to ensure the authenticity of constituent olive cultivars are crucial, and this can be achieved accurately through DNA-based methods. The present review outlines the applications of microsatellite markers, one of the most extensively used types of molecular markers in olive species, particularly referring to the use of these DNA-based markers in cataloging the vast olive germplasm, leading to identification and authentication of the cultivars. Emphasis has been given on the need to adopt a uniform platform where global molecular information pertaining to the details of available markers, cultivar-specific genotyping profiles (their synonyms or homonyms) and the comparative profiles of oil and reference leaf samples is accessible to researchers. The challenges of working with microsatellite markers and efforts underway, mainly advancements in genotyping methods which can be effectively incorporated in olive oil varietal testing, are also provided. Such efforts will pave the way for the development of more robust microsatellite marker-based olive agri-food authentication platforms.

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Section: Agri-food Traceability: Olive Oil and Table Olivesmentioning

confidence: 99%

Microsatellite Markers in Olives (Olea europaea L.): Utility in the Cataloging of Germplasm, Food Authenticity and Traceability Studies

Yadav

Carvalho

Trujillo

et al. 2021

Foods

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“…The precipitation method using CTAB allowed higher DNA extraction yields and higher purity ratios, however it is much more laborious and time consuming, and requires the use of hazardous reagents. Methods based on solid-phase extraction have shown its potential to be easily transferred into miniaturized devices, versus precipitation methods, making the integration with further DNA analysis steps easier ( Carvalho et al, 2018 ).…”

Section: Resultsmentioning

confidence: 99%

Evaluation of simple sequence repeats (SSR) and single nucleotide polymorphism (SNP)-based methods in olive varieties from the Northwest of Spain and potential for miniaturization

Carvalho

Yadav

Garrido‐Maestu

et al. 2021

Food Chemistry: Molecular Sciences

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“…Usually, commercial kits rely on the reversible interaction between DNA and a silica or silicate support, either in the form of a filter membrane or of silica-coated magnetic particles [17,18]. The adsorption of DNA to the silica surface is facilitated by buffers with low pH, high concentrations of chaotropic salts (such as guanidinium hydrochloride, guanidinium thiocyanate, or sodium iodide) and ethanol [19][20][21][22]. Under these conditions, the surface of the silica can interact with the negative surface of DNA via ionic interactions [23,24].…”

Section: Introductionmentioning

confidence: 99%

SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

et al. 2020

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Background: The use of sequencing and genotyping platforms has undergone dramatic improvements, enabling the generation of a wealth of genomic information. Despite this progress, the availability of high-quality genomic DNA (gDNA) in sufficient concentrations is often a main limitation, especially for third-generation sequencing platforms. A variety of DNA extraction methods and commercial kits are available. However, many of these are costly and frequently give either low yield or low-quality DNA, inappropriate for next generation sequencing (NGS) platforms. Here, we describe a fast and inexpensive DNA extraction method (SILEX) applicable to a wide range of plant species and tissues. Results: SILEX is a high-throughput DNA extraction protocol, based on the standard CTAB method with a DNA silica matrix recovery, which allows obtaining NGS-quality high molecular weight genomic plant DNA free of inhibitory compounds. SILEX was compared with a standard CTAB extraction protocol and a common commercial extraction kit in a variety of species, including recalcitrant ones, from different families. In comparison with the other methods, SILEX yielded DNA in higher concentrations and of higher quality. Manual extraction of 48 samples can be done in 96 min by one person at a cost of 0.12 €/sample of reagents and consumables. Hundreds of tomato gDNA samples obtained with either SILEX or the commercial kit were successfully genotyped with Single Primer Enrichment Technology (SPET) with the Illumina HiSeq 2500 platform. Furthermore, DNA extracted from Solanum elaeagnifolium using this protocol was assessed by Pulsed-field gel electrophoresis (PFGE), obtaining a suitable size ranges for most sequencing platforms that required high-molecular-weight DNA such as Nanopore or PacBio. Conclusions: A high-throughput, fast and inexpensive DNA extraction protocol was developed and validated for a wide variety of plants and tissues. SILEX offers an easy, scalable, efficient and inexpensive way to extract DNA for various next-generation sequencing applications including SPET and Nanopore among others.

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Highly efficient DNA extraction and purification from olive oil on a washable and reusable miniaturized device

Cited by 24 publications

References 32 publications

Microsatellite Markers in Olives (Olea europaea L.): Utility in the Cataloging of Germplasm, Food Authenticity and Traceability Studies

Microsatellite Markers in Olives (Olea europaea L.): Utility in the Cataloging of Germplasm, Food Authenticity and Traceability Studies

Evaluation of simple sequence repeats (SSR) and single nucleotide polymorphism (SNP)-based methods in olive varieties from the Northwest of Spain and potential for miniaturization

SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

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