Genome identification of bananas (Musa L.) from East Java Indonesia assessed with PCR-RFLP of the internal transcribed spacers nuclear ribosomal DNA
Paper Details
Genome identification of bananas (Musa L.) from East Java Indonesia assessed with PCR-RFLP of the internal transcribed spacers nuclear ribosomal DNA
Abstract
East Java Province has high diversity of local banana cultivars with various local names and diverse morphological characteristics. The genome identification of those banana cultivars are needed to provide valid identity of the banana accessions to be used as basic data for in-situ and/or ex-situ banana conservation management and for further breeding banana material. Polymerase Chain Reaction – Restriction Fragment Length Polymorphism (PCR-RFLP) of the Internal Transcribed Spacer (ITS) region nuclear ribosomal Deoxyribo Nucleic Acid (nrDNA) using RsaI restriction endonuclease enzyme was conducted to 68 banana accessions collected from 17 Regencies in East Java Province. The RsaI digested fragments showed consistent polymorphic banding DNA patterns; in M. acuminata the wild species and cultivars produced two fragments of 530 bp and 120 bp whereas M. balbisiana species and its hybrid cultivars produced three fragments of 350 bp, 180 bp and 120 bp. From this study it was found that about 45 accessions were identified as M. acuminata species (AA/AAA genomes). It comprises of 3 wild species M. acuminata (AAw), 17 M. acuminata diploid cultivars (AA) and 25 M. acuminata triploid cultivars (AAA). Wild species M. balbisiana identified only one accession (BBw), and the hybrid cultivars comprises of 14 M acuminata × balbisiana (ABB) cultivars and 8 M. acuminata × balbisiana (AAB) cultivars. Clustering analysis result based on restriction fragment ITS region showed that BBw, ABB and AAB genome groups were close related and clustered as sister group whilst AA/AA genome group became the out-group with similarity coefficient between 0,635 to 1.00.
Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue MJ. 1995. The ITS region of nuclear ribosomal DNA: A valuable source of evidence on Angiosperm phylogeny. Annals of the Missouri Botanical Garden 82, 247-277.
Daniells J, Jenny C, Karamura D, Tomekpe K. 2001. Musalogue: a catalogue of Musa germplasm. Diversity in the genus Musa. Montpellier, France: International Network for the Improvement of Banana and Plantain/INIBAP., 1-4.
De Jesus ON, de Oliveira e Silva E, Amorim EP, Ferreira CF, de Campos JMS, de Gaspari Silva G, Figueira A. 2013. Genetic diversity and population structure of Musa accessions in ex-situ conservation. BMC Plant Biology 13, 41. http://www.biomedcentral.com/1471-2229/13/41.
De Langhe E, Vrydaghs L, de Maret P, Perrier X, Denham T. 2009. Why bananas matter: An introduction to the history of banana domestication. Ethnobotany Research and Applications 7, 165-177. http://www.ethnobotanyjournal.org/vol7/i1547-3465-07-165.pdf.
Doležel J, Doleželová M, Novak FJ. 1994. Flow cytometric estimation of nuclear DNA amount in diploid bananas (Musa acuminata and M. balbisiana). Biologia Plantarum 36(3), 351-357. http://dx.doi.org/10.1007/BF02920930.
Ekasari TWD, Retnoningsih A, Widianti T. 2012. Diversity analysis of banana cultivars using molecular marker PCR-RFLP of Internal Transcribed Spacer (ITS) ribosomal DNA. Journal Matematika dan Ilmu Pengetahuan Alam 35(1), 21-30.
Espino RRC, Jamaludin SH, Silayoi B, Nasution RE. 1992. Musa L. (edible cultivars). In: Verheij, E.W.M. and R.E. Coronel (Eds.). Plant Resources of South-East Asia No.2: Edible fruits and nuts. Bogor, Indonesia: Prosea Foundation, 225-233.
[FAO]. 2003. The world banana economy 1985-2002. Food Agriculture Organization. http://www.fao.org/docrep/007/y5102e/y5102e04.h tm#bm04.
Hapsari L, Masrum A. 2011. Diversity and characteristics of banana cultivar (Musa acuminata) diploid AA collection of Purwodadi Botanic Garden. In Poceeding of National Seminar 159th Anniversary of Cibodas Botanic Garden “Conservation of Tropical Plants: today and future challenge. Cibodas Botanic Garden – Indonesian Institute of Sciences, 225-229.
Hapsari L. 2013. Performance of seven accessions banana cultivars triploid Musa acuminata group (AAA) collection of Purwodadi Botanic Garden. In Proceeding of Humboldt Kolleg: Synergy, Networking and The Role of Fundamental Development in Asean in conjunction with: The International Conference on Natural Sciences (ICONS) 2011. Germany: Shaker Verlag Publisher, 283-287.
Hapsari L. 2014. Wild Musa species collection of Purwodadi Botanic Garden: Inventory and its morpho-taxonomic review. Journal of Tropical Life Scieces 4(1), 70-81.
Hapsari L, Masrum A, Lestari DA. 2015. Diversity of bananas (Musa spp.) in Madura Island, East Java: exploration and inventory. Journal of Biodiversity and Environmental Sciences 6(3), 256-264.
Hřibová E, Ćίžková J, Christelová P, Taudin S, de Langhe E, Doleźel J. 2011. The ITS1-5.8S-ITS2 sequence region in the Musaceae: structure, diversity and use in molecular phylogeny. PLoS ONE 6(3), e17863. http://dx.doi.org/10.1371/journal.pone.0017863.
Hsiao C, Chatterton NJ, Asay KH, Jensen KB. 1994. Phylogenetic relationships of ten grass species: An assessment of phylogenetic utility of the Internal Transcribed Spacer region in the nuclear ribosomal DNA in monocots. Genome 37, 112–120.
Irishs BM, Crespo A, Goenaga R, Niedz R, Ayala Silua T. 2009. Ploidy level and genomic composition of Musa spp. accessions at the USDA-ARS Tropical Agriculture Research Station. The Journal of Agriculture University of Puerto Rico 93(1.2), 1-21.
Jingyi W, Xueting C, Zilong M, Yaoting W. 2013. Analysis of nuclear ribosomal ITS sequences in Musa (Musaceae). Chinese Agricultural Bulletin 29(25), 6-11.
Li LF, Häkkinen M, Yuan YM, Hao G, Ge XJ. 2010. Molecular phylogeny and systematics of the banana family (Musaceae) inferred from multiple nuclear and chloroplast DNA fragments, with a special reference to the genus Musa. Molecular Phylogeny and Evolution 57, 1–10. http://dx.doi.org/10.1016/j.ympev.2010.06.021.
Li LF, Wang HY, Zhang C, Wang XF, Shi FX, Chen WN, Ge XJ. 2013. Origins and domestication of cultivated banana inferred from chloroplast and nuclear genes. PLoS ONE 8(11), e80502. http://dx.doi.org/10.1371/journal.pone.0080502.
Liu AZ, Kress WJ, Li DZ. 2010. Phylogenetic analyses of the banana family (Musaceae) based on nuclear ribosomal (ITS) and chloroplast (trnL-F) evidence. Taxon 59(1), 20-28.
Megia R. 2005. Musa as genomic model. Hayati 12(4), 167-170.
Nwakanma C, Pillay M, Okoli BE, Tenkuano A. 2003. PCR-RFLP of the ribosom DNA Internal Transcribed Spacer (ITS) provide markers for the A and B genomes in Musa L. Theory of Application Genetics 108, 154-159. http://dx.doi.org/10.1007/s00122-003-1402-1.
Pachuau L, Atom AD, Thangjam. 2014. Genome classification of Musa cultivars from Northeast India as revealed by ITS and IRAP markers. Journal Application of Biochemistry and Biotechnology 172, 3939-3948. http://dx.doi.org/10.1007/s12010-014-0827-0.
Rao NK. 2004. Plant genetic resources: Advancing conservation and use through biotechnology. African Journal of Biotechnology 3(2), 136-145.
Ravishankar KV, Ajitha-Kumar R, Mathiazhagan M, Ambika DMS. 2011. Apomictic seed development in Ensete superbum induced by pollen of wild banana sp. Musa balbisiana. Current Science 101(4), 493-495.
Sharma AK, Sharma A. 1980. Staining. In: Sharma AK and A Sharma (eds). Chromosome techniques, theory and practice Third Edition. London, UK: Butterworth and Co. Publishers Ltd., 91-139.
Simmonds NW, Shepherd K. 1955. The taxonomy and origins of the cultivated banana. Journal of Linnean Society (Botany) 55, 302-312. http://dx.doi.org/10.1111/j.10958339.1955.tb00015.x.
Simmonds NW. 1959. Bananas. New York, USA: Longman Inc., 45-65.
Singh HP, Uma S, Sathiamoorthy S. 2001. A tentative key for identification and classification of Indian bananas. Tiruchirapalli, India: National Research Centre for Banana (NRCB), 7-16.
Sulistyaningsih LD, Megia R, Widjaja EA. 2014. Phylogenetical study of wild banana species (Musa L.) in Sulawesi inferred from Internal Transcribed Spacer region of nuclear ribosomal DNA sequences. Biotropia 21(1), 13-24. http://dx.doi.org/10.11598/btb.2014.21.1.2.
Tarigan H. 2007. Increasing the value added of the bananas agro-industry development in Lumajang. In Proceeding of Perfomance and Prospect of Agriculture Development in Indonesia 4, 128-134
Valmayor RV, Jamaluddin SH, Silayoi B, Kusumo S, Danh LD, Pascua OC, Espino RRC. 2000. Banana Cultivar Names and Synonyms in Southeast Asia. Los Banos, Laguna, Philipines: International Network for the Improvement of Banana and Plantain Asia and the Pasific Office., 1-24. http://kukr.lib.ku.ac.th/fulltext_kukr/ku0222075c.pdf.
White TJ, Bruns TD, Lee SB, Taylor JW. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M.A., D.H. Gelfrand, J.I. Snisky and T.J. White (Eds.). PCR protocols: A guide to methods and applications. New York, USA: Academic Press., 315-322.
Lia Hapsari, Didik Wahyudi, Rodiyati Azrianingsih, Estri Laras Arumingtyas (2015), Genome identification of bananas (Musa L.) from East Java Indonesia assessed with PCR-RFLP of the internal transcribed spacers nuclear ribosomal DNA; IJB, V7, N3, September, P42-52
https://innspub.net/genome-identification-of-bananas-musa-l-from-east-java-indonesia-assessed-with-pcr-rflp-of-the-internal-transcribed-spacers-nuclear-ribosomal-dna/
Copyright © 2015
By Authors and International
Network for Natural Sciences
(INNSPUB) https://innspub.net
This article is published under the terms of the
Creative Commons Attribution License 4.0