S.J. KWON, S.N. Ahn, H.C. HONG, H.C. CH0I and H.P. MooN

    Rice Breeding Division, National Crop Experiment Station, RDA, Suwon 441-100, Korea

     Cultivated rice consists of two subspecies, indica and japonica and has many ecotypes adapted to various environmental conditions. The extent of genetic diversity of these two rice groups have been studied based on morphological and physiological characters (Morishima and Oka 1981), and isozyme analysis (Glaszmann 1987) and DNA markers (Wang and Tanksley 1992). Although numerous studies have been conducted to assess the genetic diversity in Oryza sativa, attempts to identify molecular markers differentiating the two rice groups are limited.

     This study was carried out to evaluate the nuclear DNA diversity of 165 Korean bred rice cultivars and to identify markers for subspecies differentiation using simple sequence repeats (SSRs) and randomly amplified polymorphic DNA (RAPDs) markers. These include 42 Tongil-type (indica/japonica) and 123 japonica cultivars. Also three indica cultivars (IR36, IR66 and IR72) were included as a control. Forty-two markers generated a total of 214 informative alleles for cultivar differentiation. Nei’s (1987) genetic distances were calculated between the 168 cultivars. The cluster analysis based on the genetic distances clearly classified 168 cultivars into two major groups,japonica vs indica and Tongil-type (data not shown). Hereafter in this study, Tongil-type cultivars will be considered indica.

     The majority of the polymorphic bands amplified by 24 RAPDs primers were shared by two subspecies. However bands generated by 12 primers were present exclusively or in high frequency in only one of the two subspecies (Table 1 and Fig. 1A). Four primers produced bands completely differentiating two subspecies. OPP-Ol produced a band that appeared only injaponica but not in indica cultivars whereas OPA-07 and OPP-16 gave a band unique to indica cultivars. Among the five subspecies-specific bands produced by OPU-06, one completely discriminated two subspecies. The subspecies-specificities of the other four bands were not complete. The other eight primers produced bands unique to indica orjaponica subspecies except for a few cultivars. Three primers gave three indica-specific bands and four primers gave four japonica-specific bands (Fig. 1A). A putative codominant band pattern was observed by OPT-07 with one band specific to indica and the other to japonica cultivars. Thus, their subspecies-specificities were not complete. The distinctive pattern between the two groups in terms of the length difference of the PCR-amplified products was detected for eight out of 18 microsatellite loci (Table 1). It can be seen from Table 1 that the length differences were detected for some loci within both japonica and indica. At two loci, CT469 and CT522, the two varietal groups were completely differentiated. Eleven out of 13 alleles generated by CT522 were present only injaponica and the other two were present in indica group. CT469 amplified two alleles injaponica and four alleles in indica. The subspecies-specificities at the other six loci were not complete. Among six alleles amplified by CT206, two were shared by japonica cultivars and four were found in only indica cultivars except for Nonganbyeo (Fig. 1B). There were five cases where japonica-specific bands occurred in indica cultivars. Also four cases of japonica cultivars having indica-specific alleles were observed.