Development and Validation of Gene-Based InDel Markers Specific to Indica-Japonica Subspecies for Matured Rice Seed Culturability

Callus induction is frequently employed in rice breeding to either regenerate entire plants from callus cultures or incorporate desired features through genetic alteration. Plant growth regulators, especially auxin, are known for its role in the embryogenic callus proliferation and plant growth. In the present study, the effect of 2, 4-D in callus induction and plant regeneration in 11 rice varieties of Manipur was evaluated. Experimental results revealed that the optimum level of 2,4-D for callus induction varies for different rice varieties. In most of the rice varieties, the optimum dose of callus induction was found to be 2 mg/L. However, 3mg/L concentration of 2,4-D was found to be the most efficient dose in Mani-10, Mani-12, and Mani-13, while a 4 mg/L concentration of 2,4-D was most efficient for callus induction in Mani-14. Using 23 indel markers and 13 SSR markers, genetic diversity and marker trait association were also examined in the 11 rice genotypes. The SSR profile clearly indicates significant heterogeneity among rice accessions and also revealed four sub-populations or groups. Among all the rice genotypes examined, Mani-4 and Ma-ni-5 exhibited the greatest similarity, potentially attributable to their shared lineage. Marker trait association study reveals that the markers RM21, RM411, RM569, RCu4, and RCu5, with R2 values of 0.517, 0.451, 0.451, 0.604, and 0.604, respectively, were found to have genetic correlations with 2,4-D growth hormone concentrations of 0.5 mg/L. This study’s findings will help to conserve rice germplasm and build high-yielding, sustainable rice breeding programs to assure global food security.