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All Journal Pelita Perkebunan Biosaintifika: Journal of Biology & Biology Education
Su’udi, Mukhamad
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Agriculture, Biological Sciences & Forestry

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Characteristics of DNA Barcodes from Three Thrixspermum Orchids Based on ITS2 Regions Rohimah, Siti; Ratnasari, Tri; Su’udi, Mukhamad
Biosaintifika: Journal of Biology & Biology Education Vol 12, No 3 (2020): December 2020
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v12i3.23737

Abstract

Thrixspermum (T.) is one of the genus in Orchidaceae that has small flowers. Among species in this genus has a high homology and also has many synonyms. Identification using morphological characters can be constrained since Thrixspermum flowering time occurs in a very short period. This study aimed to conduct molecular-based identification of Thrixspermum orchids using DNA barcoding. This method applied molecular-based species identification technique using DNA sequences from genomic fragments that are considered fast, accurate, and consistent. The molecular markers used were Internal Transcribed Spacer 2 (ITS2), while the samples used were T. centipeda, T. lucidum, and T. angustifolium. BLAST results show that T. centipeda has a close relationship with T. centipeda from Malaysia (KX679332) with 99.79% percent identity, T. lucidum has a high homology with T. linusii (KX679333; 97.30%), while T. angustifolium has a high homology with T. triangulare (KX679348; 99.38%). There is a unique sequence that only T. lucidum and T. angustifolium have that distinguishes the two from other species. ITS2 can be recommended as a molecular marker for determining the Thrixspermum orchid barcode. The benefit obtained from this research is the DNA barcode sequences (ITS2) of Thrixspermum orchids would be very useful to enrich the plant barcodes database for further molecular taxonomy and biodiversity of orchid. 
Identification of cocoa (Theobroma cacao L.) genetic uniformity through RAPD molecular markers. Helia Dewi, Nur Afni; Pancaningtyas, Sulistyani; Su’udi, Mukhamad
Pelita Perkebunan (a Coffee and Cocoa Research Journal) Vol. 39 No. 3 (2023)
Publisher : Indonesian Coffee and Cocoa Research Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iccri.jur.pelitaperkebunan.v39i3.566

Abstract

Theobroma cacao L. has been propagated through either generative or vegetative techniques. One of the vegetative methods of propagating cocoa is somatic embryogenesis. Somatic embryogenesis has been employed by the Indonesian Coffee and Cocoa Research Institute for producing cocoa seedlings. Plant breeding activities are hampered by the significant level of plant heterogeneity among their progeny. Mislabelling of genetic impurities can be an issue. Molecular markers can be used to detect genetic variation at an early stage. The most common marker is the RAPD molecular marker. The study aims to determine the polymorphic RAPD primers in the analysis of genetic uniformity between mother plants and the seedlings derived from somatic embryogenesis (SE). The analyzed samples consisted of twelve individuals: six mother plants and six seedlings derived from SE. The results revealed that the percentage of polymorphic bands was 100% with band sizes ranging from 295-2785 bp for primer GY169 while for primer GY107 percentage of polymorphic bands was 80% with band sizes ranging from 345-1678 bp. Primer GY169 and primer GY107 can be amplified and used for cocoa similarity and heterogeneity.
Co-Authors Helia Dewi, Nur Afni Ratnasari, Tri Siti Rohimah Sulistyani Pancaningtyas