SSR Markers in Rice (Oryza sativa L.) Genotyping: A Review of Applications and Advances

Rice (Oryza sativa L.) is the staple food for more than half of the world’s population. Genotyping of rice varieties is crucial for germplasm characterization, varietal identification, and crop improvement. Simple Sequence Repeats (SSRs) or microsatellites are PCR-based, co-dominant, and highly polymorphic markers that have become indispensable tools in rice genetics and breeding. This review highlights the use of SSR markers in rice, presenting their applications in genetic diversity, QTL mapping, and marker-assisted selection. We compile nucleotide sequences and primer details for ten widely used SSR markers and describe differences in DNA band sizes among popular rice varieties. The comparative advantages of SSRs over other molecular markers are also discussed, along with future prospects integrating SSRs with next-generation sequencing and genome editing approaches. SSR markers remain a cost-effective and efficient tool to accelerate rice breeding and ensure food security.