Molecular Profiling of Major Indian Rice Cultivars Using a Set of Eight Hypervariable Microsatellite Markers

Abstract

India bred high yielding rice varieties have enriched to a great extent the global rice germplasm since the mid-sixties. Systematic research efforts for development of cultivar-specific DNA fingerprints of major Indian rice cultivars, however, have not received due attention. The present investigation was aimed at development of DNA fingerprints for 90 high yielding rice varieties using hypervariable microsatellite (hvRM) markers. A panel of eight markers, viz. RM11313, RM13584, RM15004, RM5844, RM22250, RM22565, RM24260 and RM8207 was chosen from 52 polymorphic markers based on their highly polymorphic nature, SSR repeat type and number and ability to distinguish genotypes, in order to develop DNA fingerprints of 90 varieties. The remaining high polymorphic hvRM markers could be of immense value in future to distinguish new cultivars, in case they could not be distinguished by the 8 marker panel. Four of the 8 markers, viz. RM22250, RM13584, RM24260 and RM5844 were located in expressed genes and could be of value in DUS (Distinctness, Uniformity and Stability) testing. Thus we suggested, that this set of 8 loci could be used as standard for DNA fingerprinting of Indian rice cultivars.

Review of methods for the detection and quantification of adulteration of rice: Basmati as a case study

“…Earlier, Archak et al (2007) developed cultivarspecific allele profiles using 8 microsatellite markers viz., RM1, RM55, RM44, RM72, RM348, RM241, RM202 and RM171 to differentiate the traditional basmati, evolved basmati and non-basmati varieties. Very recently, Vemireddy et al (2014) developed DNA barcodes/fingerprints for 90 high yielding rice varieties using a panel of eight hypervariable microsatellite (hvRM) markers viz., RM11313, RM13584, RM15004, RM5844, RM22250, RM22565, RM24260 and RM8207 and validated in survey samples of Sona Mahsuri variety.…”

Houba retrotransposon-based molecular markers: a tool for variation analysis in rice

“…Molecular markers are useful tools for identification of genetic variation among cultivars. There are many studies for cultivar-specific DNA fingerprint analyses in rice that are performed with molecular markers such as microsatellite, SSR, ISSR, and RAPD (Muhammad et al, 2009;Zhu et al, 2012;Subudhi et al, 2013;Ashu and Sengar, 2015;Vemireddy et al, 2015). SSR, RAPD, and ISSR PCR-based marker systems were used in 30 rice varieties to generate a DNA fingerprint database (Ashu and Sengar, 2015).…”

DNA Fingerprinting and Genetic Diversity Analysis of some Egyptian Rice Genotypes

“…In today's high-throughput setting, the cost of materials and consumables for PCR testing has dropped significantly, making it economically feasible and cheap A set of multiple assays was developed for all 15 rice genotypes, each with five markers (RM307, RM317, RM470, RM412 and RM242). Similar multiplex assays were previously established by Vemireddy et al, (2014) and used to identify and quantify adulteration in Basmati rice. Details (identity code, code key and DNA barcode) of the multiplex assay are given in Figure 4 and Tables 4 and 5.…”