Comparative Analysis of DNA Extraction Approaches to Verify Hybrid Purity and Genetic Relationships in Maize

Moch Rosyadi Adnan (Politeknik Negeri Jember)
Elly Daru Ika Wilujeng (Politeknik Negeri Jember)
Mahindra Dewi Nur Aisyah (Politeknik Negeri Jember)
Trisnani Alif (Politeknik Negeri Jember)
Dewi Puspa Arisandi (Politeknik Negeri Jember)
Nur Aini Alfiah (Politeknik Negeri Jember)
Mochamat Bintoro (Politeknik Negeri Jember)
Leli Kurniasari (Politeknik Negeri Jember)
Hari Prasetyo (Politeknik Negeri Jember)
Rahmat Ali Syaban (Politeknik Negeri Jember)

Futures in Agro-Food Economics and Logistics Analytics Journal
Vol. 2 No. 2 (2026): June

Genetic purity in hybrid maize is essential to ensure the stable combination of parental genetic materials, which underpins heterosis and on-field hybrid performance. Conventional field-based tests for assessing hybrid purity are labor-intensive, time-consuming, and less efficient compared to molecular marker-based approaches. Alternatively, DNA-based markers such as simple sequence repeats (SSRs) provide a feasible alternative. DNA-based markers assay requires the DNA extraction method that produces sufficient amount and quality of DNA. Therefore, this study compared three extraction methods—SDS-based, CTAB-based, and a commercial DNA extraction kit—using leaf tissue from maize seedlings as the DNA source. The extracted DNA samples were assessed for yield, quality, and suitability for SSR-based polymerase chain reaction (PCR) assays. Results demonstrated that all three methods successfully produced DNA of adequate quality and quantity for SSR-PCR analysis. These findings confirm the applicability of multiple extraction techniques for molecular based hybrid purity testing. The study contributes practical guidance for optimizing DNA extraction in maize, supporting the broader adoption of molecular markers in hybrid breeding programs.