A simplified low-cost and reliable plant genomic DNA extraction method for PCR-based genotyping and screening

Area of Science:

• Plant Genomics
• Molecular Biology
• Biotechnology

Background:

• Genomic DNA extraction is crucial for plant breeding and genetic research.
• Conventional methods (CTAB, commercial kits) are effective but labor-intensive, expensive, and generate plastic waste.
• Crude-extract methods are faster but often suffer from PCR inhibition.

Purpose of the Study:

• To develop a rapid, low-cost, high-throughput DNA extraction protocol for routine molecular applications.
• To overcome limitations of existing DNA extraction methods in plants.

Main Methods:

• A streamlined single-tube DNA extraction protocol was developed, minimizing supernatant transfers.
• The protocol was tested across multiple plant species including wheat, maize, Arabidopsis, and tomato.
• DNA yield and purity were assessed using NanoDrop and Qubit, and performance was validated in KASP assays.

Main Results:

• The single-tube method consistently yielded DNA suitable for PCR-based assays.
• Reduced handling errors, plastic consumption, and processing time were observed.
• Broad applicability was confirmed across diverse plant species and tissue types (freeze-dried, frozen, fresh).

Conclusions:

• The streamlined protocol offers a cost-effective, reliable, and scalable method for plant genomic DNA extraction.
• It is particularly valuable for high-throughput genotyping, marker development, and diversity analysis in breeding programs.
• The method is not suitable for applications demanding extremely high DNA purity, such as whole-genome resequencing.