A total of 30 rice accessions were used for the experiment. Among these 26 were landraces and four were high yielding varieties. These accessions were grown in BRRI Farm (West bayd) in a complete randomized design (CRD) with three replications. Data on morphological characters viz. plant height (cm), days to maturity, number of total tillers/plant, number of effective tillers/plant, number of filled grains, number of spikelet/spike, panicle length, yield/plant (gm), 100 grain weight (gm), length of seed (mm), and seed length-breadth ratio recorded. Fresh, young and green leaf samples were collected from 25 day old seedlings and DNA was extracted according to CTAB protocol. A total of 27 SSR primers were used for analysis of genetic diversity covering all the 12 chromosomes. These primers were amplified by a thermal cycler (G-storm/Bio-red) with the following programs: 94°C for 5min (initial denaturation) followed by 35 cycles of 94°C for 30 seconds (denaturation), 55°C for 30 seconds (annealing), 72°C for 30 seconds (extension) with a final extension for 7 min at 72°C for RM5, RM452, RM564, RM565, RM124, RM273, RM413, RM178, RM133, RM11, RM118, RM284, RM205, RM171, RM474 and 94°C for 5 min (initial denaturation) followed by 35 cycles of 94°C for 1 minute (denaturation), 55°C for 1 minute (annealing), 72°C for 2 minutes (extension) with a final extension for 7min at 72°C for RM536, RM17, RM312, RM162, RM1287, RM174, RM585, RM25, RM152, RM1026, RM229, RM277 Primers. After amplification, PCR products electrophoresed using polyacrylamide gels (8%). 3μl of the amplification products were resolved by running the gel in 1xTBE buffer for 1 to 2 hrs (depending on the allele size) at 90 volts. The gels were stained in ethidium bromide and documented under ultraviolet light of gel documentation unit (Alfa-imager). The image of gel was saved as JPEG format and imported to Alpha-Ease FC 5.0 software (Alpha Innotech, USA). The allele size was measured compared to DNA ladder.
Morphological marker: The analysis of variance (ANOVA) was done using PROC ANOVA of the Statistical Analysis System (SAS 9.1) for all morphological quantitative characters. The t-test was performed for mean comparison when accession differences were significant. Relationship of 30 accessions was analyzed based on Euclidean coefficient by NTSYS-PC software, Version 2.1a. This similarity matrix was used to generate a dendrogram using the Unweighted Pair Group Method with Arithmetic Means (UPGMA) method of SHAN.
Molecular markers: Data from the primers were analyzed to obtain the information on genetic diversity of the rice accessions. The summary statistics including the number of alleles per locus, major allele frequency, gene diversity, Polymorphism Information Content (PIC) values were determined using Power Marker V3.25. The allele frequency data from Power Marker Version-3.25 was used to export the data in binary format (allele presence =1 and allele absence =0) for further analysis with NTSYS-PC Version 2.1a. NTSYS-PC data were further used to construct a UPGMA dendrogram showing the distance-based interrelationship among the accessions.