Cost-effective and reliable genomic DNA extraction from plant seedlings for high-throughput genotyping in seed industries

Shyamkumar S Wanere; Archana P Phad; Rameshwar K Jagtap; Shuban K Rawal; Prashant S Pyati; Purushottam R Lomate

doi:10.1016/j.ab.2023.115245

Cost-effective and reliable genomic DNA extraction from plant seedlings for high-throughput genotyping in seed industries

Anal Biochem. 2023 Sep 1:676:115245. doi: 10.1016/j.ab.2023.115245. Epub 2023 Jul 8.

Authors

Shyamkumar S Wanere¹, Archana P Phad¹, Rameshwar K Jagtap¹, Shuban K Rawal¹, Prashant S Pyati², Purushottam R Lomate³

Affiliations

¹ Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India.
² Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India. Electronic address: prashant.pyati@ajeetseed.co.in.
³ Plant Biotechnology Research Center, Ajeet Seeds Private Limited, Gut No. 233, Chitegaon Tal., Paithan Dist., Aurangabad, 431105, MS, India. Electronic address: purushottam.lomate@ajeetseed.co.in.

PMID: 37429485
DOI: 10.1016/j.ab.2023.115245

Abstract

Genetic purity of seeds is one of the critical aspects in the seed industry. Molecular seed testing laboratories are utilizing PCR based diagnostic tools for genetic purity analysis. High quality DNA is an essential prerequisite for such analyses. Here, we demonstrate a robust and inexpensive DNA extraction method to isolate genomic DNA from variety of crops. Current method (M2) was compared with four commonly used DNA isolation methods for PCR-based genetic characterization and High Resolution Melt (HRM) based hybridity analysis of cotton, okra, tomato and maize using SSR markers. DNA extracted through current method showed excellent yield and quality as compared to other methods. High quality, PCR ready DNA was isolated within 30-50 min and displayed best results for genetic purity analysis using HRM. In contrast, several genomic DNA samples extracted using other methods were found unsuitable for HRM analysis. Our method can be a perfect choice in seed industry, where thousands of samples are processed every day. Notably, using our method single technician can extract DNA from 96 leaf samples within 30-50 min, at a cost of only $0.11/sample. Overall, current DNA extraction method is a reliable and cost-effective solution for large-scale genotyping experiments in the agricultural industry.

Keywords: Different plant families; Genetic purity; Genomic DNA extraction; High resolution melt analysis; PCR; SSR marker.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cost-Benefit Analysis
DNA, Plant / genetics
Genomics
Genotype
Genotyping Techniques* / methods
Seedlings*
Seeds / genetics

Substances

DNA, Plant