Evaluation of Karyotype Diversity in Indian Traditional Aromatic Rice Cultivars Through EMA-based Non-Fluorescent Giemsa and Fluorescent DAPI Staining

Rice serves as a primary dietary source of nutrients and calories for over half of the global human population. With India being the world's second-largest producer and largest rice exporter, it boasts a vast collection of rice germplasm. Among these, traditional aromatic rice cultivars (TARCs) occupy a prominent position. Despite the challenges posed by the small size of chromosomes and procedural limitations, karyotype analysis of rice has not received adequate attention. However, such evaluation of karyotype diversity may enrich the global gene pool, which is a prerequisite for the success of new breeding programs. The enzymatic maceration and air drying (EMA) method, a fundamental technique in molecular cytogenetics, has rejuvenated plant chromosome research by providing a cytoplasm-free background. The objective of the present study was to document, decode, and conserve the untapped karyotypic diversity in TARCs of India. Karyotype diversity was evaluated in 22 populations of TARCs using the EMA-based chromosome preparation method, followed by staining with non-fluorescent Giemsa and DNA base-specific fluorescent dye DAPI (4’-6-diamidino-2-phenylindole) for the first time. Some unique and foundational highlighting features of this study include the diversity in staining pattern, total chromatin length, morphology of individual and landmark sat-bearing chromosomes in each cultivar, intraspecific sat-bearing chromosome number in several cultivars, the karyotype formula, and the effect of DAPI on sat-bearing chromosomes. The genomic diversity decoded and conserved in Indian rice for its adaptive potential is expected to be highly advantageous for global rice breeders and genome researchers in both conventional and new breeding initiatives.