Asian common wild rice (Oryza rufipogon) is a polycarpic perennial plant with a mixed inbreeder/outbreeder strategy. Seeds and clones are both reproductive components of the population. However, when collected in the flowering stage, the two differ substantially as to whether they have experienced natural selection directly or not. This study is aimed at evaluating mechanisms for the survival of a population by comparing genetic structure among subpopulations that are classified in terms of: (1) reproductive systems (clones or seeds); and also (2) location (fringe or inside). First, the genotypes determined at seven SSR (Simple Sequence Repeat) loci showed that parameters of observed heterozygosity (H O ) and outcrossing rate (t) were clearly higher in clones (H O ¼ 0.609, t ¼ 82.4%) than in seeds (H O ¼ 0.346, t ¼ 35.5%), although the two had approximately the same values for the number of alleles (A) and expected heterozygosity (H E ) (A ¼ 4.43 in both clones and seeds, H E ¼ 0.709, 0.692 in clones and seeds, respectively). This result indicates that the individuals showing 'heterosis', with high numbers of heterozygous loci and outcrossing rates, are more likely to survive in the natural habitat. Secondly, parameters of observed heterozygosity and outcrossing rates were lower for seeds from the fringe area (H O ¼ 0.238, t ¼ 24.6%) compared to seeds from the inside area (H O ¼ 0.443, t ¼ 60.7%), although values were similar in clones of both the fringe and inside areas. This result suggests that the 'edge effect' might be due mainly to the restriction of wind strength in fringe area of the forested swamp.

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A wild rice (BKK) strain showing sterile spikelet and big leaves inhabited at the basin of the Chao Phraya river of Bangkok city, Thailand. The BKK strain was found as a natural triploid and thus its origin has been interested long time. Three different-sized fragments were amplified in RNA polymerase I largest subunit (PolA1) gene, which is a single-copy nuclear gene per haploid genome. Short type (0.14 kb) intron 20 sequence of BKK strain was identical to that of O. rufipogon and O. sativa. Phylogenetic analysis showed that long type (1.5 kb and 1.8 kb) intron 20 sequences of BKK strain were closely related to that of O. longistaminata and O. officinalis, respectively. We analyzed protein tag (Ptag) sequence encoded by exons 19 to 21 of PolA1 gene. Determined three Ptag sequences of BKK strain were identical to that of O. rufipogon, O. longistaminata, and O. officinalis, respectively. Relative DNA content of nuclei in O. officinalis and BKK strain was 1.5 and 1.75 times than that in O. sativa, respectively. And BKK strain contained CentO-C1 repeats, which were unique to O. officinalis. These results indicated that BKK strain comprised three genomes of O. rufipogon, O. longistaminata, and O. officinalis.