Identification of microsatellite markers for differentiating some Basmati and non-Basmati rice varieties

519-526Microsatellite marker (SSR) analysis was used to differentiate premium traditional Basmati rice varieties from other cheaper cross-bred Basmati/long-grain rice varieties and monitor the cases of adulteration in milled rice samples. Thirteen rice cultivars (4 commercial traditional Basmati, 6 cross-bred Basmati and 3 non-Basmati varieties) were evaluated for allelic diversity using 35 SSR markers. A total of 123 alleles (79-345 bp) were detected; 25 of these were present in Basmati rice varieties only. Polymorphism information content (PIC) value, which is indicative of level of polymorphism, varied from 0.0 (RM167) to 0.858 (RM252), with an average value of 0.447. SSR analysis generated polymorphism sufficient to differentiate all the 13 rice genotypes. Of the 35 markers, 16 showed amplification of a different allele in one or more of the traditional/cross-bred Basmati rice varieties than in IR36 (indica) and Azucena (japonica). Some SSRs (RM60, RM84, RM252, RM171, and RM257) were found unique among the closely related traditional Basmati rice varieties. Traditional Basmati rice varieties could be differentiated from one or more of the cross-bred Basmati rice varieties by allelic polymorphism at 27 of the 35 SSR loci; the most useful markers being RM171, RM1, RM44, RM110, RM229, RM234, RM242, and RM255. Rice varieties were clustered in three groups (indica, japonica, Basmati groups), which correspond well to their known pedigree data. This paper provides effective means to the Basmati traders for varietal differentiation and monitoring adulteration cases using milled rice samples