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.

BackgroundOryza sativa L. contains two cultivated subspecies, indica and japonica, which are considered to be derived from wild rice relative, O. rufipogon. Although domestication cinario of O. sativa has been extensively studied, it is still inconclusive and contradictory. Moreover, it remains to be revealed why O. rufipogon had acquired wide range of genetic diversity to fit various habitat and life cycle of plant from annual to perennial.ResultsAlthough O. rufipogon distributes in southeast Asia from Indonesia to India, perennial wild rice strains were distributed in deep-water area of the Mekong Delta in Southern Vietnam. Some of wild rice strains collected in Dong Thap were heterologous in the length of intron 20 sequence of single-copy nuclear PolA1 gene, encoding for the largest subunit of RNA polymerase I. Thus, these wild rice strains were probably considered as interspecific hybrids, because the S-type (0.14 kb) intron 20 was found in O. rufipogon, O. glumaepatula, and O. barthii while L-type (1.5 kb) was shared by O. longistaminata and O. meridionalis. Therefore, we identified two wild rice strains that contained homologous L-type intron 20 of PolA1 gene in the CLRRI collection. These two strains, named as MD1 and MD2, had fertile spikelet with long anthers which were typical feature of African O. longistaminata. In addition, MD1 strain and O. longistaminata shared the same protein tag (Ptag) sequence, which was different to that of O. rufipogon and O. sativa. Interestingly, MD1 strain contained plastid DNA with a 69-bp deletion in ORF100 which was shared with indica and annual O. rufipogon, but not with japonica and perennial O. rufipogon. ConclusionWe have identified that MD strains found in the Mekong Delta were probably O. longistaminata-like cryptic species and contributed to enlarge genetic diversity of O. rufipogon, and is probably involved in the origin of O. rufipogon indica ancestor of as the maternal lineage.