Genetic variability of porang populations (Amorphophallus muelleri) in West Java and Central Java based on trnL intron sequences
Paper Details
Genetic variability of porang populations (Amorphophallus muelleri) in West Java and Central Java based on trnL intron sequences
Abstract
Porang (A. muelleri) is herbaceous plant which is included in the family of Araceae. Previous studies showed morphological and genetic variation in A. muelleri. The suitable molecular marker used to indicate genetic variation is trnL intron. It is based on, trnL intron is non-coding regions of chloroplast genome which evolved more rapidly than coding region. The present study is aimed to find out genetic variability and phylogenetic relationship among A. muelleri populations in Central Java and West Java which is based on trnL intron sequences. Porang samples are obtained from central Java (Karangtengah, Wonogiri, Grobogan and Brebes) and West Java (Cisompet Garut). trnL sequences were analyzed by maximum parsimony and neighbor joining method. trnL intron has singletone variation as many as 13 sites, i.e on the order of squences: 49, 109, 144, 145, 159, 253, 297, 298, 300, 302, 379, 461, 463. In addition, trnL intron has 9 parsimony informative sites, i.e on the order of squences: 160, 184, 299, 409, 452, 454, 513, 527, 534. The highest number of haplotypes came from Grobogan populations with values diversity of haplotype is 1, while the least number of haplotypes came from Karangtengah and Wonogiri populations with diversity of haplotype is 0.000. phylogenetic tree shows the clustering of populations into three clade, first clade is A. variabilis and second clade are A. ochroleucus, A. longituberosus and A. sumawongii as outgroup and thirth clade divided into two subclade porang are clustered based on their population in Central Java and West Java
Asins MJ, Herrero R, Navarro L. 1995. Factors affecting citrus tree isozyme gene expression. Theor. Appl. Genet 90, 892-898.
Besendahl Q, Lee J, Palmer D, Bhattacharya D. 2000. The cyanobacterial origin and vertical transmission of theplastid tRNALEU group-I intron. Current Genetics 37, 12–23.
Ermiati dan MP, Laksmanahardja. 1996. Manfaat iles-iles (Amorphophallus spp.) sebagai bahan baku makanan dan industri. Jurnal Litbang Pertanian 15, 74-80.
Grob GBJ, Gravendeel B, Eurlings MCM, Hetterscheid WLA. 2004. Phylogeny of the Tribe Thomsonieae (Araceae) Based on Chloroplast matK and trnL Intron Sequences. Systematic Botany 27, 453-467
Hetterscheid WLA, Ittenbach S. 1996. Everything you always wanted to know about Amorphophallus but were afraid to stick your nose into. Aroideana 19, 7-129.
Jansen PCM, van der Wilk C, Hetterscheid WLA. 1996. Amorphophallus Blume exDecaisne. In Flach, M. and F. Rumawas (eds.). PROSEA: Plant Resources of South- East Asia No 9. Plant Yielding Non-seed Carbohydrates. Leiden: Backhuys Publishers, 134-135
Jones CJ, Edwards KJ, Castagiole S, Winfield MO, Sala F, van del Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettsshneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, J. J., R. Linacero, Vasquez A, Karp A. 1997. A reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Molecular Breeding 3, 382-390.
Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. UK: Oxford University Press, 203-204
Kojoma M, Kurihara K, Yamada K, Sekita S, Satake M, Iida O. 2002. Genetic identification of cinnamon (Cinnamomum spp.) based on the trnL-trnF chloroplast DNA. Planta Med 68, 94–96.
Kim CS, Lee CH, Shin S, Chung YS, Hyung NI. 1997. A simple and rapid method for isolation of high quality tress and conifers genomic DNA from fruit using PVP. Nucleid acid research 25, 1085-108.
Nei M. 1987. Molecular Evolutionary Genetics. Columbia University Press. NewYork.
Page RDM, Holmes EC. 1998. Molecular Evolution: A Phylogenetic Approach. USA: Blackwell Science Pub, 107-108
Poerba, Yuyu S, Diyah M. 2008. Genetic diversity based on Random Amplified Polymorphic DNA (RAPD) markers in Amorphophallus muelleri Blume in Java. Technology 9, 245-249.
Provan J, Powell W, Hollingsworth PM. 2001. Choloroplast microsatellites: new tools for studies in plant ecology and evolution. TREE 16, 142 – 147.
Rosidiani, Erta P. 2011. Genetic variation in some populations of Porang in eastern Java Based on Intron trnL. Magister Tesis, Biology Departement, Brawijaya University, Indonesia, 55-56
Sankaran NP, Chander D, Nedunchezhiyan M, Santhosh dan, Ngachan SV. 2008. Morphological and Proximate Composition of Amorphophallus muelleri Blume. Journal of Root Crops 34, 79-81
Sambrook J, Fritsch E, Maniatis T. 1989. Molecular Cloning a Laboratory Manual. Ed ke-2. New York: Cold Spring Harbor Laboratory.
Sedayu A, Marcel CM, Barbara G, dan Wilbert LA. 2010. Morphological character evolution of Amorphophallus (Araceae) based on a combined phyligenetic analysis of trnL, rbcl idan LEAFY second intron sequences. Botanical Studies (2010) 51: 473-390 Sumarwoto. 2004. Pengaruh Pemberian Kapur dan Ukuran Bulbil Terhadap Pertumbuhan Iles-iles (Amorphophallus muelleri Blume) pada Tanah Ber-AL Tinggi. Ilmu Pertanian 11, 45-53
Simon D, Fewer D, Friedl T, Bhattacharya D. 2003. Phylogeny and self splicing ability of the plastid tRNA-Leu group I intron. Journal of Molecular Evolution 57, 710–720.
Simpson MG. 2006. Plant Systematic.. San Diego: California: Elsevier Academic Press, 453-454 Sumarwoto. 2005. Iles-iles (Amorphophallus muelleri Blume); Deskripsi dan Sifat-sifat Lainnya. Biodiversitas 3, 185-190
Taberlet PL, Gielly G, Pautou J. 1991.Universal primer for amplification of three non-coding region of chloroplast DNA. Plant Molecular Biology 17, 1105-1109
Taberlet P, Eric C, Fran CP, Ludovic G, Christian M, Alice V, Thierry V, Gerard C, Christian B, dan Eske W. 2007. Power and limitations of the chloroplast trnL (UAA)intron for plant DNA barcoding. Nucleic Acids Research 35 (3).
Tsai L, Yung-Chien Y, Hsing-M, Jenn-Che W, Adrian L, James CL. 2006. Species identification using sequences of the trnL intron and the trnL-trnF IGS of chloroplast genome among popular plants in Taiwan. Forensic Science Internationa 164, 193–200.
Yingzhi LC, Yunziang T, Nengguo dan DX. 2007. Phylogenetic Analisys of Mandarin Landraces, Wild Mandarin, and Related Species in China Using Nuclear LEAFY second Intron and Plastid trnL-trnF Sequence. J. AMER. SOC. HORT.SCI 132, 796-806
Yuzammi. 2000. A Taxonomid Revision Of The Terestrial and Aquatic Aroid (Araceae) in Java. Thesis, School of Biological Science, Faculty of Life Science, University of New South Wales, 75-77
Didik Wahyudi, Rodiyati Azrianingsih, Retno Mastuti, 2013. Genetic variability of porang populations (Amorphophallus muelleri) in West Java and Central Java based on trnL intron sequences. J. Biodiv. Environ. Sci., 3(9), 31-41.
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