THE ABILITY OF matK AND trnL-trnL-trnF INTERGENIC SPACER TO DISCERN CERTAIN SPECIES ACCESSIONS OF THE FAMILIES SOLANACEAE AND FABACEAE

Abstract

Indonesia, as a mega-biodiversity country, has many kinds of tropical fruits. Solanaceae and Fabaceae families contain plant species that produce fruits and vegetables for human food, such as ‘rimbang’ (Solanum torvum), ‘terung asam’ (S. ferox), ‘kabau’ (Archidendron microcarpum), ‘jengkol’ (A. pauciflorum), and ‘petai’ (Parkia speciosa). This study aimed to determine the ability of DNA barcodes (matK and trnL-trnL-trnF intergenic spacer [IGS]) in distinguishing some of those tropical fruit plants. Plant materials came from Riau Province, Indonesia. Methods developed include total DNA extraction from fresh leaves and PCR using the primer pairs to amplify matK and trnL-trnL-trnF IGS. The PCR products underwent sequencing, with the DNA sequences analyzed using MEGA6. In this study, the obtained matK and trnL-trnL-trnF IGS sequences showed lengths ranging from 800 bp to 892 bp and 872 bp to 1113 bp, respectively. The matK and trnL-trnL-trnF IGS sequences of S. ferox, A. microcarpum, and A. pauciflorum provided the first sequences reported in those species. Several nucleotide variations in matK sequences emerged among the studied accessions caused by substitution mutation, including transversion and transition. No indel (insertion-deletion) mutation in the studied matK sequences occurred. Indel can also cause variations in trnL-trnL-trnF IGS sequences among the studied accessions aside from substitution mutation. For species S. torvum, S. ferox, and P. speciosa, there came about some decisive nucleotides based on the matK sequences. Moreover, for species S. torvum, S. ferox, A. microcarpum, A. pauciflorum, and P. speciose, there occurred few critical nucleotides based on trnL-trnL-trnF IGS. Also, there was a critical nucleotide for large-fruited ‘jengkol’ (one of the populations in A. pauciflorum) based on trnL-trnL-trnF IGS. However, both DNA barcodes could not differentiate the two types of S. ferox, i.e., ‘terung asam’ and ‘terung bulu.’ Both DNA barcodes showed to differentiate some species members of both families Solanaceae and Fabaceae into separate clusters. Moreover, compared with matK, the trnL-trnL-trnF IGS indicated uniqueness in discriminating populations within species.