Cloning of genome-specific repetitive DNA sequences in wild rice (O. rufipogon Griff.), and the development of Ty3-gypsy retrotransposon-based SSAP marker for distinguishing rice (O. sativa L.) indica and japonica subspecies

In the rice genome, insertions and eliminations of transposable elements have generated numerous transposon insertion polymorphisms (TIPs). Common wild rice (O. rufipogon Griff.), the ancestor of Asian cultivated rice (O. sativa L.), carries abundant genetic variations. To find subspecies-specific (SS) markers that can distinguish O. sativa ssp. indica and ssp. japonica, some long terminal repeat (LTR) sequences (sc1-14) of AA genome-specific RIRE retrotransposon were isolated from O. rufipogon genome. Sequences sc1 and sc12 were successfully utilized to develop the SS marker system based on retrotransposon inserted position polymorphisms. Twenty-two SS markers (ssi1-9, ssj1-13) were developed, where ssi1-9 are the indica-specific types, and ssj1-13 the japonica-specific types. The average accuracy of these markers in distinguishing the two subspecies is over 85%. SS marker ssj-10 can distinguish the two subspecies at 100% accuracy. Principal component analysis (PCA) showed that these markers could successfully distinguish indica from japonica varieties, regardless of their geographical origin.