3. Microsatellites as diagnostic markers for differentiating Indica and Japonica subspecies of Asian rice (Oryza sativa L.)

Directorate of Rice Research, Rajendranagar, Hyderabad, 500030 India

Sub specific classification of Asian rice (Oryza sativa L.) into indica and japonica has always been a subject of interest althrough for rice breeders and geneticists. The two subspecies differing in a large array of morphological and physiological characteristics can be differentiated using isozyme and DNA markers (Oka, 1988; Glaszmann, 1987; Zhang et al. 1992; Ni et al. 2002). From practical standpoint, it is desirable to have markers that would enable easy identification of two subspecies. Keeping this in view, the present study was undertaken with six genotypes each of indica (IR8, T(N)1, IR36, IR20, Jaya and Khodawkmali) and japonica (Yamadanshiki, Hinohikari, Koshihikari, Taichung 65, Moroberekan and Azucena) using 375 microsatellite primers covering the entire genome. PCR conditions and profile were according to Temnykh et al. (2000). The PCR products were analyzed on 3% agarose and stained with ethidium bromide.

Only 36 of the 375 microsatellite primers tested, gave clear polymorphism between the two sets of genotypes and those, which could differentiate the two sets of genotypes, were only chosen. Allele sizes were found to be sufficiently different to suggest that they could be assessed on 3% agarose and used as diagnostic markers for routine and easy identification of the subspecies (Table 1). Their distribution covering the entire genome suggests that the subspecific differentiation was a result possibly of accumulative process at multiple independent loci (Li et al. 1998). The 36 polymorphic markers did not show any association with the nature of microsatellite motif and subspecies differentiation. While 118 primers gave monomorphic pattern, 122 showed polymorphism in both the groups. 69 primers showed polymorphism only in indica and 30 primers only in japonica. Indica genotypes revealed more genetic

variation than japonica rices in conformity with earlier reports. The primer RM455 only was found to be associated with Est-9 isozyme allele, which was earlier reported to differentiate the two subspecies of O.sativa.


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