Simple Sequence Repeat (SSR) Marker-Based Parental Polymorphism Analysis between Improved Samba Mahsuri and Karuppunel for Grain Iron and Zinc Content in Rice (Oryza sativa L.)

Abstract

Aim: The present study aimed to assess parental polymorphism between two genetically contrasting rice genotypes using microsatellite (SSR) markers, with a focus on identifying markers associated with grain micronutrient traits, particularly iron and zinc content. Place and Duration of Study: The study was conducted at the Biotechnology Section, ICAR–Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, Telangana, India, during the period from August 2023 to September 2024. Methodology: Genomic DNA was extracted from young leaf tissues of two contrasting parents, Improved Samba Mahsuri and Karuppunel, using the standard CTAB method. A total of 1,318 SSR (RM) markers covering all 12 rice chromosomes were used for PCR amplification. Amplicons were resolved by agarose gel electrophoresis, and polymorphic markers were identified based on the allele position between the two genotypes. Results: Results revealed that out of 1,318 SSR markers screened, 171 markers (13.0%) exhibited clear polymorphism between the two genotypes. Chromosome-wise polymorphism ranged from 9.0% (chromosome 7) to 18.2% (chromosome 1). Notably, several of the polymorphic markers identified in this study have been previously reported to be associated with iron and zinc content in rice, indicating their relevance for future trait mapping and breeding efforts. Conclusion: The identified polymorphic SSR markers provide a valuable resource for the development of mapping populations and marker-assisted selection programs aimed at improving grain micronutrient content in rice. This study lays the foundation for future QTL mapping and biofortification efforts targeting iron and zinc efficiency in rice breeding.