Diversity analysis of indica rice accessions (Oryza sativa L.) using morphological and SSR markers

Morphological and molecular characterization of twenty six landraces rice and four high yielding rice accessions were studied to observe genetic diversity assessment and identification of superior genotypes for crop improvement program. Fourteen morphological and twenty seven DNA based molecular markers, simple sequence repeat (SSR), were used extensively to carry out this study. A wide range of morphological diversity was found among the rice accessions tested and it was grouped into 4 clusters based on morphological markers using Unweighted Pair Group Method with Arithmetic Means (UPGMA) cluster tree analysis at a cut-off similarity coefficient 0.98%. Landraces accession, Kaliboro, found significantly different in number total tiller, number effective tiller, and panicle length. On the other hand, high yielding rice varieties showed maximum number spikelet per spike in BR 11 and number grain filled in BRRI Dhan 34. Khirshapati, Tulshimala, Katijul and BR11 showed significant different in two or more morphological traits. Genetic diversity was also assessed using a set of 27 SSR markers which generated 321 polymorphic alleles. Polymorphism information content (PIC) values ranged between 0.6806 (RM 11) and 0.9416 (RM 474) with an average of 0.8414. Dendrogram was constructed based on the Nei’s genetic distance calculated from 27 SSR markers generated from the 30 rice accessions. Genetic similarity analysis using UPGMA, all 30 accessions were grouped into 6 clusters based on SSR markers’ data at a cut-off similarity coefficient 0.17%. This morphological and SSR marker based genetical diversity analysis could be useful for cultivar/accessions/ genotype identification and parental selection for breeding program.