Molecular character of ITS fragment of rDNA Dioscorea alata L. in Wakatobi archypelago Southeast Sulawesi

• Main Authors: Indrawati, Jamili, Saharuddin, Muzuni
• Format: Conference Proceeding
• Language: English
• Subjects: Algorithms; Amplification; Enzymes; Gene sequencing; Lobes; Nucleotides; Polymorphism; Similarity
• ISSN: 0094-243X; 1551-7616
• DOI: 10.1063/5.0138525

This study aims to determine the molecular character and phylogenetic relationship of Dioscorea alata L. from the Wakatobi archipelago. Young leaves of ‘manga daga’ from Wangi-wangi Island are delta-shaped, the leaf base lobes are wide, the tubers are white. While the young leaves of ‘santa tongke ungu’ from Binongko Island are heart-shaped, the leaf lobes are narrow, the tubers are dark purple. Them both were used as a sample of DNA isolation. Amplified ITS fragment of rDNA using Diosa-Forward and Diosa-Reverse as primers. Sequencing result from gene target in Diosa 2 dan 48, had shown sequence nucleotide’s were successfully amplified as much as 547bp. The Blastn at NCBI site showed both of samples had a closer similarity with fragment ITS 1, 5,8S rRNA and ITS 2 of rDNA Dioscorea alata Voucher GUH (KJ956698). Restriction enzyme site analyze with Restriction Mapper of Bioedit software 2.0 had results endonuclease restriction enzyme of ClaI can be used as molecular marker for detection polymorphism of Dioscorea alata L. Endonuclease restriction enzyme of ApaLI, BseYI, EcoRV, NaeI, NgoMIV and XhoI are molecular marker specific to contained analysis in Diosa 2 and 48. The phylogeny tree built by combining Clustal-X with Mega 7.0 uses the neighbor-joining algorithm with bootstrap values as much as 1000X viewed Diosa 2 and 48 have a similarity of 99,45% with value bootstrap 100%, and amounted of nucleotide difference as much as 3 nucleotides difference of 546 bp nucleotide are compared.