4. Genetic diversity of Myanmar rice cultivars detected by DNA markers
  OHM MAR SAW1, K. DOI1, KHIN AYE2, K. IRIE3 and A. YOSHIMURA1

1) Plant Breeding Laboratory, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, 812-8581 Japan

2) Seed Bank, Central Agriculture Research Institute, Yezin, Myanmar

3) Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo 156-8502 Japan

Genetic diversity of Myanmar cultivated rice accessions was evaluated by DNA markers. The materials included 110 accessions from 6 different regions of Myanmar and 17 accessions previously analyzed (Doi et al. 2000). Twelve probe-enzyme combinations of restriction fragment length polymorphism (RFLP) markers (Saito et al. 1991) and 34 PCRbased polymorphic markers including 5 sequenced tagged site (STS) and 29 cleaved amplified polymorphic sequence (CAPS) markers (Rice Genome Research Program) were used.

The character was scored as 1 and 0 for the presence and absence of the fragment, respectively. The 1/0 matrix was used to calculate dissimilarity coefficients following Nei (1987). The resulting distance matrix was used to construct an unweighted pair-group method with arithmetic means (UPGMA) (Sokal and Michener 1958) phenogram using software package PHYLIP (Felsenstein 1993) to infer phylogenetic relationships. The stability of the nodes in the tree was tested by bootstrap analysis using the same software package.

All accessions except CR351 and CR378 could be distinguished from each other by at least one DNA marker. The dendrogram revealed 2 well distinguished groups, named groups I and II (Fig. 1). Group I seemed to correspond Japonica because it contained the accessions from Japan. It was further divided into the subgroups Ia and Ib. Most accessions in subgroup Ia are Japonica varieties originated in Japan, and all accessions contained in subgroup Ib are Myanmar cultivated rice accessions. Although Myanmar rice accessions were divided from other Japonica varieties, the genetic distance between the two subgroups was close and the group I is clearly differentiated from group II. Typical Indica accessions are contained in group II. It comprised smaller clusters (IIa, IIb and IIc) plus thirty five accessions which

formed no cluster (IId in Fig. 1). Some accessions within group II (designated as IIe in Fig. 1) are found to be somehow distant from clusters IIa, IIb, IIc and IId.

Bootstrap analysis was performed to determine the confidence levels of forks in the phenogram. In the resulting consensus tree only 6 forks had bootstrap values above 80% (Fig. 2). The grouping of the UPGMA tree and majority-rule consensus tree were in general comparable except subgroups IIa, IIb, IIc and IId. The composition of group I (subgroups Ia and Ib) and subgroup IIe were identical in the both phenograms. However, most of the forks in subgroups IIa, IIb, IIc and IId showed very low bootstrap values. The values of bootstrap analysis suggest that constituents of groups IIa, IIb, IIc and IId may not be significantly differentiated.

The information generated from this experiment would allow geneticists and breeders to select appropriate materials.

References

Doi, K., M. Nakano Nonomura, A.Yoshimura, N. Iwata and D.A. Vaughan, 2000. RFLP relationships of A- genome species in the genus Oryza. J. Fac. Agr., Kyushu Univ. 45(1): 83-98.

Felsenstein, J., 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.

Nei, M., 1987. Molecular Evolutionary Genetics. Columbia University Press, New York, USA.

Rice Genome Research Program. 332 PCR based genetic markers on rice chromosomes. http://rgp.dna.affrc.go.jp/publicdata/caps/index.html.

Saito, A., M. Yano, N. Kishimoto, M. Nakagahra, A. Yoshimura, K. Saito, S. Kuhara, Y. Ukai, M. Kawase, T. Nagamine, S. Yoshimura, O. Ideta, R. Ohsawa, Y. Hayano, N. Iwata and M. Sugiura, 1991. Linkage map of restriction fragment length polymorphism loci in rice. Jpn. J. Breed. 41: 665-670.

Sokal, K. K., C. D. Michener, 1958. A statistic method for evaluating systematic relationships. Univ. Kans. Bull. 38: 1409-1438.