SUMMARY
Background: Availability of related rice species is critical for rice breeding and improvement. Two distinct species
of domesticated rice exist in the genus Oryza: Oryza sativa (Asian rice) and Oryza glaberrima (African rice). New
rice for Africa (NERICA) is derived from interspecific crosses between these two species. Molecular profiling of
these germplasms is important for both genetics and breeding studies. We used 30 polymorphic SSR markers
to assess the genetic diversity and molecular fingerprints of 53 rice genotypes of O. sativa, O. glaberrima, and
NERICA.
Results: In total, 180 alleles were detected. Average polymorphism information content and Shannon's
information index were 0.638 and 1.390, respectively. Population structure and neighbor-joining phylogenetic
tree revealed that 53 genotypes grouped into three distinct subpopulations conforming to the original three
groups, except three varieties (IR66417, WAB450-4, MZCD74), and that NERICA showed a smaller genetic
distance from O. sativa genotypes (0.774) than from O. glaberrima genotypes (0.889). A molecular fingerprint
map of the 53 accessions was constructed with a novel encoding method based on the SSR polymorphic
alleles. Ten specific SSR markers displayed different allelic profiles between the O. glaberrima and O. sativa
genotypes.
Conclusions: Genetic diversity studies revealed that 50 rice types were clustered into different subpopulations
whereas three genotypes were admixtures. Molecular fingerprinting and 10 specific markers were obtained to
identify the 53 rice genotypes. These results can facilitate the potential utilization of sibling species in rice
breeding and molecular classification of O. sativa and O. glaberrima germplasms.