The core set of sequence-tagged microsatellite sites markers between halophytic wild rice Oryza coarctata and Oryza sativa complex

For breeding of salinity tolerant rice, halophytic species Oryza coarctata is considered as a valuable resource. Non-availability of molecular markers in the species is a major limitation and identification of markers applicable with wider gene pool will be resource-saving. Even after the recent advancement in high throughput genotyping techniques, sequence-tagged microsatellite sites (STMS) markers are considered as valuable resource for pre-breeding, especially when usable for a large number of species. Using a novel bioinformatics pipeline for cross transferable marker identification, whole genome sequences of nine Oryza species were surveyed with 23,499 STMS markers of rice. With this highly reproducible strategy, band sizes or polymorphism prediction among different species is possible before in-vitro validation. Only 359 STMS markers were cross-transferable to O. coarctata and 77 of those were common with O. sativa complex. These core markers were distributed over 11 chromosomes and nearly 76% were located within various genes of Oryza. The markers also showed unique genome specific polymorphism pattern with high levels of inter- and intraspecific variations in “AA” genome and complete absence of intra- or inter-population variations in O. coarctata (KKLL). The numbers of microsatellite motifs and the repeat numbers in different motifs were much lesser in O. coarctata leading to the exceptionally high level of polymorphism with all “AA” genome species. Two markers are also useful for species identification. The hyper-variable markers are effective resource for pre-breeding of O. sativa, O. glaberrima and new rice for Africa involving O. coarctata or any other species of O. sativa complex.