Genome-wide development of novel miRNA-based microsatellite markers of rice (Oryza sativa) for genotyping applications

Rice (Oryza sativa L.) plays a crucial role in assuring food security to the world’s population and is recognized as a superior model plant of monocot crops. Molecular markers, especially co-dominant markers such as simple sequence repeats (SSRs), play an important role in marker-assisted breeding of rice. Although a large number of SSRs are available, most of them are either from protein-coding regions or untranslated regions of the rice genome. SSRs from non-coding regions of the rice genome are almost undiscovered, but discovery of new SSR markers remains a challenge for molecular breeders. The development of novel markers from the conserved regions of different genomes will thus be useful for studying the genetic diversity of closely related species or self-pollinated species. In the present study, a genome-wide investigation yielded a total of 129 SSR markers from the conserved microRNA (miRNA) genes of rice, and 20 of them with repeat numbers ≥7, from all the 12 chromosomes, were validated among 24 diverse rice genotypes. The highest number of repeat motifs corresponded to di-nucleotides, while the tetra-nucleotides were repeated the lowest number of times. Our results therefore show that the number of repeats is inversely related to the length of repeat. The genetic diversity was found to be higher among the exotic material than the Indian landraces, as indicated by their polymorphic information content values of 0.31 and 0.29, respectively. The results hence showed that the miRNA-based microsatellite marker system is a very proficient, novel and breeder-friendly source for genetic diversity analysis or genotyping of rice. The present study is the first report on genome-wide identification and characterization of rice miRNA-SSRs.