Crop improvement, integral to global food security and environmental sustainability, has been significantly enhanced by molecular markers. Simple Sequence Repeats, or microsatellites, stand out as crucial markers due to their unique tandem repeat structure across genomes. These markers are pivotal in genetic diversity assessment, QTL mapping, and marker-assisted selection in crop breeding programs. Despite existing SSR extraction tools, challenges persist, including the need for language-specific expertise and limitations in handling complex genome data. To address these issues, we introduce SSRmine, a user-friendly Python-based tool designed for efficient SSR extraction from diverse sequence data. SSRmine employs a novel algorithm to analyze sequences systematically, extracting SSR markers of varying lengths. The presented tool's design ensures ease of use, platform independence, and adaptability, catering to researchers with varying computational expertise. The study results show that SSRmine significantly improves accessibility to SSR extraction, offering a robust solution for researchers involved in genetic variation studies. The tool's efficiency and versatility make it a valuable asset in advancing crop improvement strategies through precision breeding.

QTL mapping, Molecular marker, Simple Sequence Repeats

In the realm of genomic research, the extraction of SSR is a critical step, providing insights into genetic diversity, evolutionary dynamics, and potential applications in crop improvement. The detailed analysis emphasizes SSRMine's effectiveness in extracting SSR markers, positioning it as a robust tool for researchers exploring genomic repetitive elements in various crops. SSRMine emerges as a potent tool for researchers delving into the intricate world of genomic repetitive elements. Its consistent performance, versatility, and user-friendly design position it as a valuable asset in unravelling genetic mysteries and advancing our understanding of plant genomes. As genomic research continues to evolve, SSRMine stands as a testament to the power of innovative tools in propelling the field forward.

Shbana Begam, Samarth Godara, Ramcharan Bhattacharya, Rajender Parsad and Sudeep Marwaha (2023). SSRmine: Python-based Command-line Tool for Precise Genomic SSR Markers’ Extraction. Biological Forum – An International Journal, 15(12): 177-180.