Abstract

Molecular characterization, evaluation of genetic diversity and assessment of relationship by simple sequence repeat (SSR) markers of 48 Bangladeshi Boro rice landraces was performed. Among the total 58 SSR markers, 55 markers has been distributing over 12 rice chromosomes showed clear polymorphic band patterns, and they were selected for genetic relationship assessment. A total of 228 alleles were detected with an average of 4.15 alleles per locus. The average values of gene diversity and polymorphic information content (PIC) were 0.39 and 0.36, respectively. Primer RM206 had the highest PIC value (0.78) and the highest number of alleles (10).Therefore, RM206 was detected for the highest level of polymorphism and RM206 is supposed to be the best marker for characterizing the 48 Boro rice landraces. The genetic distance-based results in the unrooted neighbor-joining (NJ) tree revealed four (4) major clusters (I,II,III and IV)and a model-based population structure analysis generated two clusters (A and B). Both neighbors joining tree analysis and the population structure analysis method showed the tested landraces as highly diverse in structure. The two and three dimensional graphical views of Principal Coordinate Analysis (PCoA) revealed that the landraces Mi-Pajang, Gopal Beshi, Borail, Madhabsail, Boro (sunga) and Jala Boro were found far away and distributed around the centroid of the cluster. This rice collection and information gained in this study will be useful for future rice breeding program.