Banana is Malaysia’s second most cultivated fruit, with 50% of the cultivation focusing on Berangan and Cavendish types. Bananas have been identified as one of the important fruits in the National Agrofood Policy (2011-2020) due to their demand in the domestic and export markets. Thus, FGV is committed to achieving a 50% market share of local banana production through tissue culture propagation techniques. This technique enables the mass production of banana planting material in a short period. However, one downside of this technique is the random occurrence of somaclonal variation, which has been reported for various crops. FGV’s clonal propagation aims to produce true-to-type banana planting materials, therefore, somaclonal variants are undesired. Hence, we aimed to establish a marker-based screening method for early detection and elimination of Berangan somaclonal variants prior to field planting. Berangan leaf samples with and without somaclonal variation were collected from different sites. The samples’ DNA was extracted using an in-house cetyltrimethylammonium bromide (CTAB) extraction method and screened using 145 Random Amplified Polymorphic DNA (RAPD) markers. RAPD markers that could distinguish somaclonal variation in the Berangan samples were developed into Sequence Characterized Amplified Region (SCAR) markers for routine screening. The SCAR markers were validated for their ability to reproduce the specific bands from the RAPD results. Of the 145 RAPD markers, three markers do not produce any bands, 47 RAPD markers produce monomorphic bands and 95 RAPD markers produce polymorphic bands. Three out of the 95 polymorphic RAPD markers were able to selectively distinguish the somaclonal variation in samples from similar sources. The three RAPD markers were developed into SCAR markers, and they successfully reproduced the specific bands from their respective RAPD results. Hence, the developed SCAR markers will be utilized for the early detection and elimination of Berangan somaclonal variants from selected sources.
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