Allelic diversity among Basmati and non-Basmati long-grain indica rice varieties using microsatellite markers

Microsatellite or simple sequence repeat (SSR) marker analysis was carried out to assess allelic diversity and prepare a DNA fingerprint database of 24 rice genotypes including three premium traditional Basmati, 9 cross-bred Basmati, a local scented selection, eight indica and three japonica rice varieties. A total of 229 alleles were detected at the 50 SSR loci and 49 alleles were in fact present in only one of the 24 varieties. The size difference between the smallest and largest allele varied from 1 (RM333) to as high as 82 (RM206). Multiple alleles were observed at 13 loci. Polymorphism information content (PIC) values ranged between 0.0 (RM167) to 0.78 (RM170), with an average of 0.62 per marker. At 15 of the SSR loci, traditional and cross-bred Basmati rice varieties amplified different alleles than those in the indica and/or japonica rice varieties. A number of SSRs have been identified, which can be used to differentiate among the traditional Basmati varieties and between traditional Basmati and other cross-bred Basmati or long grain, non-Basmati rice varieties. Genetic relationships among rice genotypes as determined by UPGMA cluster analysis and three-dimensional scaling based on Principal Component Analysis showed that the three traditional Basmati rice varieties are closely related and have varying degree of similarity with other cross-bred Basmati rice varieties. Further implications of these results in genotype identification, monitoring purity and adulteration, and plant variety protection are discussed.