45. Phylogenetic relationship of Korean weedy rice based on RFLP analysis

Young-Chan Cho1 , Tae-Young Chung2 and Hak-Soo Suh3
1) Rice Breeding Division, Crop Experiment Station, RDA, Suweon 441-100, Rep. of Korea.
2) Agricultural Science and Technology Institute, RDA, Suweon 441-707, Rep. of Korea.
3) College of Natural Resources, Yeungnam University, Kyongsan 712-749, Rep. of Korea.

     Many weedy rices (Oryza sativa L., locally called "Aengmi" and "Sharei") were collected from farmers' fields in Korea (Suh et al. 1992a). In order to study their phylogenetic relationship 24 strains of weedy rice, one Chinese and one Indian red rice, Japonica cultivars Gihobyeo, Geumobyeo and Jodongji, Indica cultivar IR26, and Tongil (Indica/Japonica) cultivar Milyang 23 were analyszed by RFLP technique, and cluster analysis was applied to the RFLP data.
    Six restriction endonuclease enzymes, Dra I, Eco Rl, Eco RV, Hind III, Sca I, Xba I, were used for digestion of plant genomic DNA, and 40 genomic DNA clones (37 RG# clones mapped on RFLP linkage map, McCouch et al. 1988; 3 KR# clones of genomic


Fig. 1. Dendrogram showing the phylogenetic relationships among tewenty-four strains of Korean weedy rice, three Japonica cultivars, one Tongil (Indica/Japonica) cultivar, one Indica cultivar, and two strains of the foreign red rice based on cluster analysis of RFLPs. The numbers above dendrogram are the phylogenetic similarity coefficient scales according to Nei's formula (1987).
            (a)S; short grain types, (b) L: long grain types,
            (c)Japonica cultivars, (d) Tongil (Indica/Japonica) cultivar,
            (e) Indica cultivar.
DNA from Yeonkiaengmi 11, a Korean weedy rice of short grain type) were used for hybridization. The probes were labeled (non-radioactively) using a DIG-labeling kit (Boehringer Mannheim Biochemica) following the random hexamer priming method. Other methods for Southern analysis followed McCouch et al.(1988) and Ishii (1990). Each polymorphic fragment detected by Southern analysis was treated as a unit character: the presence or absence of a fragment was assigned a score of 1 or 0, respectively. The
phylogenetic similarity coefficients of the weedy strains and cultivars assayed were quantified according to Nei (1987, p. 108-1 10). The cluster analysis was performed using the unweighted pair-group method with arithmetic mean (UPGMA, Sokal and Michener 1958).
    Out of 83 clone-enzyme combinations used for Southern analysis, 37 combinations (37 clones with only an enzyme) showing polymorphisms were used for cluster analysis, and a total of 118 polymorphic fragments were detected. A dendrogram showing the phylogenetic relationship by the cluster analysis was constructed based on RFLP data (Fig. 1). Korean weedy rice could be classified into two main clusters. One cluster comprised the short-grain weedy strains including Japonica cultivars, and the other the long-grain weedy strains including Indica and Tongil cultivars. The phylogenetic similarity coefficient between the two main clusters was 0.44. The short-grain weedy rices were classified into three sub-clusters with a 0.88 phylogenetic similarity and appeared to be close to Japonica cultivars. The long grain weedy rice were classified into four sub-clusters with a 0.92 phylogenetic similarity. The phylogenetic similarity coefficient between the long grain weedy rices on the one hand and Tongil and Indica cultivars on the other was 0.72. The present RFLP results are consistent with the classification based on cross-affinity (Suh et al. 1992b) and isozymes (Suh and Morishima 1994).
    From the RFLP analysis, it was concluded that the short-grain strains of Korean weedy rice belonged to Japonica, while the long-grain strains were closer to Indica and Tongil than to Japonica rices.

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