An exploratory study on allelic diversity among rice and its wild species as well as relatives with simple sequence repeat and inter simple sequence repeat markers

Abstract

Genomic information of crop plants is a pre-requisite for the enrichment and management of the crop’s genetic resources. Rice has a number of wild species and wild relatives, which harbour a good number of agronomically important genes that can be incorporated into the cultivated rice. In the present work, a wild rice (Oryza rufipogon Griff.) and a wild rice relative, Porteresia coarctata (Roxb.) Tateoka (syn. O. coarctata Roxb.), were genotyped with trait (osmotic stress tolerance) linked 29 SSR and 22 ISSR markers, distributed throughout the rice genome. For exploring the comparative allelic diversity (in the form of difference in mol wt of amplified products for a particular SSR or ISSR locus), two marker based panels were constructed considering cultivated rice (O. sativa L.) as the reference genotype. Among the studied SSR markers, the maximum allelic variation was found with RM10773, which showed the maximum difference (370.25 bp) between O. sativa and O. rufipogon, and also with RM10864 that showed a difference of 194.47 bp between O. sativa and P. coarctata. For ISSR loci, the maximum difference (300.73 bp) between O. sativa and O. rufipogon was shown by PR36, and the maximum difference (451.66 bp) between O. sativa and P. coartata was shown by PR29. The genotypic profiles prepared in the present investigation may be used for identification of the corresponding genotypes and in marker assisted hybridization programmes.