A high-throughput and cost-efficient DNA extraction protocol for the tree fruit crops of apple, sweet cherry, and peach relying on silica beads during tissue sampling

2014 ◽  
Vol 34 (4) ◽  
pp. 2225-2228 ◽  
Author(s):  
Daniel A. Edge-Garza ◽  
Terrence V. Rowland ◽  
Stacey Haendiges ◽  
Cameron Peace
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Sweet Cherry ◽  
Tissue Sampling ◽  
Fruit Crops ◽  
Extraction Protocol ◽  
Tree Fruit ◽  
Silica Beads ◽  
Cost Efficient

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

2020 ◽  
Author(s):  
santiago vilanova ◽  
David Alonso ◽  
Pietro Gramazio ◽  
Mariola Plazas ◽  
Edgar Garcia Fortea ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Next Generation Sequencing ◽  
Dna Extraction ◽  
High Throughput ◽  
Extraction Method ◽  
High Quality ◽  
Extraction Protocol ◽  
Dna Extraction Method ◽  
Sequencing Platforms ◽  
Generation Sequencing

Abstract 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.

Earth Microbiome Project (EMP) high throughput (HTP) DNA extraction protocol v1 (protocols.io.pdmdi46)

protocols.io ◽  
2018 ◽  
Author(s):  
Lisa Marotz ◽  
Tara Schwartz ◽  
Luke Thompson ◽  
Greg Humphrey ◽  
Grant Gogul ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Extraction Protocol

Modified Rapid DNA Extraction Protocol for High Throughput Microsatellite Analysis in Wheat

Crop Science ◽  
2002 ◽  
Vol 42 (6) ◽  
pp. 2088-2091 ◽  
Author(s):  
Kristi L. Hill-Ambroz ◽  
Gina L. Brown-Guedira ◽  
John P. Fellers
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Microsatellite Analysis ◽  
Extraction Protocol

scholarly journals A high-throughput DNA extraction protocol for tropical molecular breeding programs

2003 ◽  
Vol 21 (4) ◽  
pp. 459-460 ◽  
Author(s):  
Emma S. Mace ◽  
Kutokshi K. Buhariwalla ◽  
Hutokshi K. Buhariwalla ◽  
Jonathan H. Crouch
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Molecular Breeding ◽  
Breeding Programs ◽  
Extraction Protocol

High-throughput genomic DNA extraction protocol from tilapia's fin tissue

Aquaculture ◽  
2006 ◽  
Vol 255 (1-4) ◽  
pp. 597-599 ◽  
Author(s):  
Noam Zilberman ◽  
Sharon Reikhav ◽  
Gideon Hulata ◽  
Micha Ron
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Genomic Dna ◽  
Genomic Dna Extraction ◽  
Extraction Protocol

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

2020 ◽  
Author(s):  
santiago vilanova ◽  
David Alonso ◽  
Pietro Gramazio ◽  
Mariola Plazas ◽  
Paola Ferrante ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Next Generation Sequencing ◽  
Dna Extraction ◽  
High Throughput ◽  
Extraction Method ◽  
High Quality ◽  
Extraction Protocol ◽  
Dna Extraction Method ◽  
Sequencing Platforms ◽  
Generation Sequencing

Abstract 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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