A SCAR marker for detection of micropropagated banana dwarf off-types is chloroplast encoded

Dwarfs are the most common off-type regenerated from micropropagated bananas, particularly from the international banana of commerce, the Cavendish (AAA genome) types. A RAPD marker for dwarfism (Damasco et al. 1996, Plant Cell Reports 16:118) has been converted into a SCAR marker. This SCAR marker may be used as a robust means of identifying dwarf off-types both in vitro and at deflasking, which is normally not possible until 3-6 months post-deflasking. This marker is PCR-amplified in all "normal" Cavendish types but not in the dwarf-off-types. The 1625 bp fragment has been sequenced, with no strong homology to known sequences. Southern and PCR-based analysis of nuclear and chloroplast DNA has revealed that the fragment is on the chloroplast genome, with no homology to the nuclear genome. A rearrangement of the chloroplast genome is either induced by or selected for during tissue culture. RFLP analysis of chloroplast DNA has revealed that a single copy of the 1625 bp exists in the normal chloroplast genome, while there are 2 copies in the chloroplast genome of the dwarf off-types.