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All Journal Biodiversitas Journal of Biological Diversity
Purnomo Purnomo
Laboratory of Plant Systematics, Faculty of Biology, Universitas Gadjah Mada. Jl. Teknika Selatan, Sekip Utara, Sleman 55281, Yogyakarta, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology

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Genetic variability of Indonesian eggplant (Solanum melongena) based on ISSR markers U.B. HUSNUDIN; B.S. DARYONO; Purnomo Purnomo
Biodiversitas Journal of Biological Diversity Vol. 20 No. 10 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d201038

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Abstract. Husnudin UB, Daryono BS, Purnomo. 2019. Genetic variability of Indonesian Eggplant (Solanum melongena) based on ISSR markers. Biodiversitas 20: 3049-3055. Eggplant (Solanum melongena L.) is one of important vegetable in Indonesia and this country has a variety of eggplant germplasm, whereas molecular data of Indonesian eggplant is limited. This study describes an analysis of genetic variation based on ISSR markers to determine the diversity and phenetic relationship of Indonesian eggplants. 23 samples were collected from the Indonesian Center for Agricultural Biotechnology Research and Development (ICABIOGRAD) and some commercial cultivars. Data were analyzed by ISSR analysis using UBC 809, UBC 880, UBC 888, UBC 892 and UBC 895 primers. Similarity index was counted by Jaccard Coefficient formula based on molecular scoring. Cluster analysis was conducted by Unweighted Pair Group Methods using Arithmetic averages (UPGMA) method to create a dendrogram with Multivariate Statistical Program (MVSP) v.3.1 software. The results showed that ISSR markers were effective in the estimation of the genetic variability of eggplant accessions characterized by different level of polymorphism. Five ISSR primers generated 40 polymorphic bands (64.5% of the total). The dendrogram divided 23 eggplant accessions into 2 main clusters and one accession ("terong jawa"/K18) located outside from the main cluster. Results suggested that all accessions were grouped randomly into some clusters not in accordance with the locations of sample collection.
Species diversity and phenetic relationship among accessions of api-api (Avicennia spp.) in Java based on morphological characters and ISSR markers fennalia putri sabdanawaty; Purnomo PURNOMO; Budi Setyadi Daryono
Biodiversitas Journal of Biological Diversity Vol. 22 No. 1 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220125

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Abstract. Sabdanawaty FP, Purnomo, Daryono BS. 2021. Species diversity and phenetic relationship among accessions of api-api (Avicennia spp.) in Java based on morphological characters and ISSR markers. Biodiversitas 22: 193-198. Api-api (Avicennia spp.) from mangrove groups is rich in economic and ecological benefits. Research on the potential of api-api has been extensively done, but no research is specifically focused on the identification of api-api. This study aims to identify species diversity and phenetic relationships of api-api in Java based on morphological and molecular characters. The morphological analysis was based on 35 characters and referred to the descriptor. The PCA analysis on the morphological characters of Avicennia spp. showed a high diversity. Morphological characters have a high effect on grouping patterns such as habitat, leaf shape, leaf tip, leaf base, and petal color. Molecular observations were done on the polymorphism of DNA bands. The ISSR primers used were ISSR02, ISSR04, and ISSR10. PCR amplification of DNA was separated and visualized using a doc gel electrophoresis. The results showed a high diversity based on the percentage of DNA polymorphism. The research resulted in three species of Avicennia spp. in Java, namely Avicennia officinalis, A. alba, and A. marina. Phenetic relationships between Avicennia spp. form was based on similarity in character, not based on the area of origin. The environmental conditions in this study slightly opposed the character of Avicennia spp., which presumably due to the similarity in various marine areas of Java such as temperature, pH, and the required salinity.
Genetic variability of Begonia longifolia Blume from Indonesia based on Nuclear DNA internal transcribed spacer (ITS) sequence data Wahyu Dewi Astuti Ningrum; Muhammad Bima Atmaja; Budi Setiadi Daryono; Purnomo PURNOMO
Biodiversitas Journal of Biological Diversity Vol. 21 No. 12 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d211239

Abstract

Abstract.Ningrum WDA, Atmaja MB, Daryono BS, Purnomo. 2020. Genetic variability of Begonia longifolia Blume from Indonesia based on Nuclear DNA internal transcribed spacer (ITS) sequence data. Biodiversitas 21: 5778-5785. Begonia longifolia Blume is a member of the Begoniaceae family which has the widest distribution in Asia including Indonesia. Diversity studies on B.longifolia from Indonesia were mainly based on morphological characters. The genetic diversity analysis of this pantropical species in Indonesia has never been reported yet. This research aimed to study genetic variability of B. longifolia in Indonesia based on nuclear DNA internal transcribed spacer (ITS) sequence data. Twelve living specimens were from Sumatra (Lampung), Java (Sukabumi, Purwokerto), Bali (Buleleng, Gianyar, Jembrana, Tabanan), and Lombok. The 831-839 length sequence was aligned using Mesquite software. Reconstruction of the phylogenetic tree was done by MEGA7 software using Neighbor-Joining method with Kimura-2-Parameter. The 827 fixed sites showed a genetic distance ranged from 0 to 1.6%. Among the 827 sites compared, 802 sites were invariable, 19 sites were variable (11 singleton variable sites and 8 parsimony informative sites) and 6 sites were gaps. The phylogenetic tree showed 1 clade and 6 sub-clades. Specimens from Sumatra and Java formed a single sub-clade, separate with five sub-clades from Bali. Specimen from Lombok belong to one of the sub-clades of the Bali specimens. All specimens can be divided into 2 groups: Sumatra-Java and Bali-Lombok group.
Co-Authors B.S. DARYONO Budi Setyadi Daryono Budi Setiadi Daryono fennalia putri sabdanawaty Muhammad Bima Atmaja U.B. HUSNUDIN Wahyu Dewi Astuti Ningrum