Identification of dCAPS Markers that Discriminate A and B Cytoplasms in Banana (Musa spp.)

Abstract

A single nucleotide polymorphic sequence (SNP) in the trnL-F intergenic spacer region of chloroplast DNA that discriminate Musa acuminata (AA) cytoplasm from Musa balbisiana (BB) cytoplasm has been found. This mutation was initially amplified using a pair of universal primers and converted into dCAPS (derived cleaved amplified polymorphic sequence) markers. Using these markers in combination with flow cytometric analysis, ‘Pisang Klutuk’ (syn. ‘Pisang Awak’) was found to be a triploid ABB cultivar (not a wild BB accession as previously classified). A 15-bp long deletion was also found within the trnL-F spacer sequence of M. acuminata subspecies banksii. This mutation will be useful as a specific marker for the cytoplasm derived from this subspecies. These maternally inheritable chloroplast DNA mutations discovered in this study are vital for better understanding the origins of banana cytoplasm to clarify the lineage of banana cultivars and the contribution of wild progenitors to cultivated types.