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Background: The insight concerning genetic diversity and relationship among the rice genotypes is a basic contribution to the crop improvement programs. The present field experiment was conducted to study the level of diversity present in 47 rice genotypes using both morphological and molecular analysis. Methods: The experiment was carried out at Agricultural Research Farm, Banaras Hindu University, Varanasi (U.P.), during Kharif-2019 with 47 rice genotypes. Mahalanobis’ D2 analysis was carried out to evaluate the morphological diversity present among the genotypes and 24 polymorphic SSR markers were used for molecular analysis using the NTSYSpc software. Result: Mahalanobis’ D2 grouped 47 rice genotypes into 6 clusters based on the inter-se genetic distance. The highest inter-cluster distance (1134.14) was observed between clusters II and IV indicating the genotypes present in these clusters to be highly divergent. Molecular diversity analysis grouped the 47 rice genotypes into 3 main clusters i.e., cluster I, cluster II and cluster III, which were further divided into sub-clusters. Polymorphic Information Content varied from 0.12 to 0.86, with an average of 0.465. The highest PIC value was observed for locus RM 507 (0.86). All the 24 primers showed polymorphism and the number of alleles was common for all i.e., 2. Together, the morphological and molecular diversity analysis revealed that Desi Dhan and IR 91143-AC 293-1, Desi Dhan and BD 105, IR 85850 and Lal Sundiya, Chauli and Swarna were the most diverse genotypes among the 47 rice genotypes included in the study.

Increasing trends in the occurrence of diabetes underline the need to develop low glycemic index (GI) rice with preferred grain quality. In the current study, a diverse set of 3 K sub-panel of rice consisting of 150 accessions was evaluated for resistant starch and predicted glycemic index, including nine other quality traits under transplanted situation. Significant variations were noticed among the accessions for the traits evaluated. Trait associations had shown that amylose content possess significant positive and negative association with resistant starch and predicted glycemic index. Genome-wide association studies with 500 K SNPs based on MLM model resulted in a total of 41 marker-trait associations (MTAs), which were further confirmed and validated with mrMLM multi-locus model. We have also determined the allelic effect of identified MTAs for 11 targeted traits and found favorable SNPs for 8 traits. A total of 11 genes were selected for haplo-pheno analysis to identify the superior haplotypes for the target traits where haplotypes ranges from 2 (Os10g0469000-GC) to 15 (Os06g18720-AC). Superior haplotypes for RS and PGI, the candidate gene Os06g11100 (H4-3.28% for high RS) and Os08g12590 (H13-62.52 as intermediate PGI). The identified superior donors possessing superior haplotype combinations may be utilized in Haplotype-based breeding to developing next-generation tailor-made high quality healthier rice varieties suiting consumer preference and market demand.