Detection of DNA changes in somaclonal mutants of rice using SSR markers and transposon display

Somaclonal variation detected in plant tissues grown in vitro can be heritable, and thus provides an opportunity for plant breeders and geneticists to generate novel variants. However, incidence of somaclonal variation is problematic for plant transformation efforts and for micropropagation of true-to-type clones. The origin of somaclonal variation is still not well understood. In this study, 120 SSR markers, distributed across all 12 chromosomes of rice, have been used to analyze eight somaclonal mutants derived from seven different cultivars. Of these, 13 SSRs have detected polymorphisms between the bacterial blight resistant mutant HX-3 and its wild-type Minghui 63. While, ten SSRs have revealed differences between a purple sheath mutant, Z418, and the wild-type C418. None of the SSRs have been able to distinguish between tall and dwarf mutants, 02428h and A418, and their wild-type counterparts, respectively. Interestingly, six SSRs have identified differences in at least three mutant lines and their corresponding wild-type genotypes. These results have suggested that some SSR markers in the rice genome may detect higher numbers of polymorphisms than others. In addition, a transposon display (TD) of five active rice transposons, Tos17, Karma, mPing, nDart and dTok, has been conducted to evaluate DNA changes of eight mutants. Some mutant lines, such as HX-3 and Z418, have exhibited differences from their corresponding wild-type genotypes in TDs with two transposons. This has indicated that new insertions of transposons are involved in somaclonal variation derived from tissue culture. Taken together, these results suggest that multiple molecular mechanisms are responsible for somaclonal variation detected in tissue culture of rice.