Abstract
Oryza diploid species comprise AA, BB, CC, EE, FF, and GG genome groups. Cultivated rice, O. sativa L. of the AA genome, has two subspecies, indica and japonica. These two subspecies are differentiated in many characteristics, such as the number of nucleolar sites, annual-perennial habitat and polymorphism of plastid DNA. Although many researchers accept that japonica must originate from O. rufipogon, the evolutionary route of indica remains unclear. A 69-bp deletion in ORF100 is useful to discriminate between indica and japonica cultivars and between O. nivara and O. rufipogon; furthermore, PSID sequences of O. sativa–O. rufipogon complex contain hyper-variable sites consisting of C and A mononucleotide repeats, which are useful to classify wild accessions and cultivars into the six subtypes of 6C7A and 7C6A (japonica and O. rufipogon), 6C8A and 7C7A (O. nivara), 8C8A and 9C7A (indica). The 69-bp deletion is shared with O. nivara (6C8A, 7C7A) and indica (8C8A, 9C7A) but the 8C8A subtype is found only in indica. To elucidate variations of plastid DNA in the genus Oryza and cytoplasmic origin of indica, we compared two plastid sequences, ORF100 (676 bp) and PSBZ (629 bp), in 40 accessions of 14 Oryza diploid species. Sequence comparison showed that FF and GG genome species were distantly related to AA genome species. Both BB and CC genome species were related with AA genome species but were mutually differentiated. An evolutionary trace of ORF100 and PSBZ sequences indicated that O. barthii might have a consensus sequence among all AA genome species. Both O. longistaminata and O. glumaepatula were highly related with O. barthii; the O. sativa–O. rufipogon complex showed more various polymorphisms than other AA genome species. The results of this study show that 8C8A and 9C7A subtypes of plastids in indica cultivars are differentiated from 6C8A and 7C7A subtypes in O. nivara, despite sharing the same deletion in ORF100. In addition, 6C7A and 7C6A subtypes in japonica cultivars and O. rufipogon share identical sequences in PSBZ but differentiate at two SNP sites in ORF100.
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