Identification of variety diagnostic molecular marker of high yielding rice varieties

Abstract

Twenty eight inter simple sequence repeat (ISSR) markers were used to determine the genotypic identification and phylogenetic relationship within 48 varieties of Indica rice including four aromatic rice grown in eastern part of India. Out of 44 upland and low land varieties, 39 varieties released by the Orissa University of Agriculture and Technology, Orissa and five released by the other National Institutes of India. A total of 28 ISSR primers were screened representing di- and tri- nucleotide repeats, out of which 12 ISSR markers were selected for varietal analysis as diagnostic markers. The number of bands per locus ranged from 4 to 8, with an average of 6. The results revealed that all the primers showed distinct polymorphism among the varieties indicating the robust nature of ISSR markers. Most of the primers showed highest polymorphic information content and resolving power. The cluster analysis indicates that all the rice genotypes are grouped into two classes in which aromatic rice varieties clustered separately from upland and lowland varieties. Principal component analysis showed the distinct differences among themselves. Based on this study, the larger range of similarity values using ISSR markers provides greater confidence for the assessment of genetic relationships among the varieties. The information obtained from the DNA profile helps to identify the variety diagnostic markers in 48 rice genotypes. This outcome of the investigation can be used in background selections during backcross breeding programs. © 2013 The Author(s).