Oryza nivara (Sharma et Shastry) the progenitor of O. sativa (L.) subspecies indica harbours rich genetic diversity as measured by SSR markers

Rice yield seems to have reached a plateau, probably as a consequence of narrow genetic base of modern varieties that are being used in the breeding programmes. Wild species, especially the closely related ones, could be a potential source for broadening the genetic base both for qualitative and quantitative traits, including productivity-related traits. Oryza nivara, the immediate progenitor of cultivated indica rice, is one such species that grows widely in South and South East Asia. A large number of accessions of this species are being preserved in vitro. However, for effective utilization of this germplasm a core collection needs to be identified for use in hybridization. A set of 127 0. nivara accessions and two cultivars were analysed for genetic variation using SSR markers. DNA of each of the 129 lines was amplified in vitro using 33 SSR markers and resolved in 2.5% high-resolution agarose gels. A total of 132 alleles, with an average of 3-7 alleles per accession, were amplified. PIC value of the primers varied from 0.41 to 0.80. The similarity coefficients based on Nei and Li's similarity coefficient ranged from 0.2 to 1.0, showing strikingly high level of genetic variation in the candidate germplasm. At 0.5% similarity, the 127 accessions formed 42 independent lineages. Based on genetic diversity, resistance to bacterial blight and other morphological traits in these accessions, a set of 13 accessions has been identified that are now being used for detection and transfer of novel QTL alleles for productivity traits into the 0. sativa background.