Assessment of genetic diversity of rainfed lowland rice genotypes using microsatellite markers

Genetic diversity in rainfed lowland rice genotypes constituting landraces, high yielding varieties and improved lines was assessed using microsatellite markers distributed over 12 chromosomes of rice. A total of 143 alleles were amplified, of which 136 were polymorphic. The polymorphism information content (PIC) and discriminating power of microsatellite markers ranged between 0 and 0.91 with an average of 0.66 per locus. Genetic similarities among genotypes varied from 0.37 to 0.89 with an average of 0.6. The UPGMA cluster analysis grouped the rice genotypes into two major clusters at 50% level of genetic similarity. All the genotypes studied could be uniquely distinguished from each other at probability of 2.2 x 10(-13) of identical match by chance. The high level of genetic variability was detected among the lowland rice genotypes which would enable for selection of diverse donors in the development high yielding rice varieties suitable for rainfed lowland ecosystem. Seven genotype with specific unique alleles were identified, which can be used as molecular tags. A basic molecular database was created for rainfed lowland genotypes which will be useful for future reference and to protect this unique rice under IPR regime.