Genetic variability and relationship of Banana cultivars (Musa L.) from East Java, Indonesia based on the internal transcribed spacer region nrDNA sequences

A genetic variability and relationship study subjected to 41 banana cultivars from East Java based on nrDNA sequences of the ITS region was conducted. It would be useful to consider the genomic identification, genetic conservation strategy, and for further banana improvement. ITSL and ITS4 primers were used to amplify the ITS region. Results show that the ITS region DNA sequences length of 41 banana cultivars examined varied from 631 bp to 651 bp. It showed high variability with conservation level G+C content of 62.79%. Total aligned and selected ITS region DNA sequences was 656 bp comprising 346 positions (52.74%) as conserved region, 223 positions (33.99%) as variable sites (polymorphic) and 87 positions (13.26%) alignment gaps. About 143 positions (64.13%) of the variable positions were potentially parsimony informative and 80 positions (35.87%) were singleton variables. The singletone variation sequences spesific to certain banana cultivars may be proposed as identification barcodes. The haplotype diversity was very rich (Hd=1.00), resulted 41 haplotypes with none of haplogroup. Haplotype distribution map revealed the lineage pattern of banana cultivars from East Java. They were presummably derived from common ancestors and the same population in East Java mainland which then experienced an evolution process, dispersed by human migration both in and out, and became isolated to the islands. Genetic relationship reconstruction using NJ algorithm resulted in a tree and classification better than MP algorithm. It was clustered according to its geomic group, into 3 main clades i.e. AA/AAA, AAB and ABB. The ITS region nrDNA sequences was proven powerful in classifying until cultivar level of bananas. All 41 banana cultivars examined are recommended for genetics conservation.