Repository Universitas Pakuan

Detail Karya Ilmiah Dosen

Barahima Abbas1, Muhammad Dailami2, Florentina Heningtyas Listyorini1, Munarti3

Judul : Genetic Variations and Relationships of Papuaâ€™s Endemic Orchids Based on RAPD Markers

Abstrak :
Orchidaceae has known as an attractive flower and immense species. We have found a large
species of Orchidaceae grow naturally in Papua’s jungle, Indonesia territorial. This study
aims to reveal genetic variation and genetic relationships among endemic orchids in Papua
based on RAPD markers. The study included 26 accessions of Papua’s endemic orchids used
for genomic DNA extraction. Genomic DNAs were extracted by using DNA extraction kit
from Qiagen and genomic DNA amplification by using 10 decamer RAPD primers. DNA
fragments that were amplified by Polymerase Change Reaction (PCR) were visualized and
documented by using UV illumination apparatus. Genetically, endemic Orchids in Papua
were described high variation. Fragments amplification by using ten RAPD primers and
performed in the PCR tools resulted in 54 numbers of polymorphic fragments and no monomorphic
band. The number of polymorphic bands per primer ranged from 4 to 7 with
averaged 5.4 bands per assay unit. The genetic dissimilarities (GDs) among examined orchids
ranged from 0.10 to 0.94 based on Nei’s unbiased coefficients. Dendrogram construction
showed that Papua’s endemic orchid (PEO) samples different from another and separated
to form group by their own at the 0.40 coefficient value and at the 0.6 coefficient value
indicate that PEO sample is divided into nine groups i.e. samples at the genera level were
separated into their own groups.

Tahun : 2017 Media Publikasi : Jurnal Internasional

Kategori : Jurnal No/Vol/Tahun : 11 / 9 / 2017

ISSN/ISBN : ISSN Online 2150-4105

PTN/S : University of Papua (UNIPA), Manokwari, Indonesia, Pakuan University, Bogor, Indonesia Program Studi : PENDIDIKAN BIOLOGI

Bibliography :
1. Singh, M.K., Sherpa, A.R, Hallan, V. and Zaidi, A.A. (2007) A Potyvirus in Cymbidium spp. in Northern India.
Australasian Plant Disease Notes , 2, 11-13. https://doi.org/10.1071/DN07005
2. Meisel, J.E., Kaufmann, R.S. and Pupulin, F. (2014) Orchids of Tropical America: An Introduction and Guide.
Cornell University Press, Ithaca and London, 259 p. https://books.google.co.id/books?isbn=0801454921
3. Sutiyoso and Sarwono (2004) Orchids Care. Penebar Swadaya, Jakarta. (in Indonesian)
4. Abbas, B., Listyorini, F.H. and Amriati, B (2011) In vitro Seeds Germination and Plantlets Development of
Grammatophyllum scriptum Lindl. (Orchidaceae). African Journal of Plant Science , 2, 154-159.
5. Sapto, H.P. (2009) The Diversity of Orchid Archipelago and the Lack of Taxonomist. (Accessed 5/2’2010) (in
Indonesian)
6. Simardjo, M. (2009) Dewndrobium Species from Papua Have Been Used as a Parent for Breeding Activity (Indomesia
Language). Proceeding Efforts to Develop and Preserve the Natural Orchid of West Papua.
7. World Wildlife Fund (WWF) (2007) Bunga Rampai ALAMKU-Bird’s Head Seascape. 202 p.
http://birdsheadseascape.com/download/research/social%20Science%20and%20development/Bunga%20Rampai
%20ALAMKU%202007.pdf
8. Powel, W., Castillo, C.O., Chaluers, K.J., Provan, J. and Waugh, R. (1995) Polymerase Chain Reaction
Based-Assays for the Characterization of Plant Genetic Resources. Electrophoresis , 16, 1726-1730.
https://doi.org/10.1002/elps.11501601285
9. Colombo, C., Second, G., Valle, T.L. and Charrier, A. (1998) Genetic Diversity Characterization of Cassava Cultivars
(Manihot esculenta Cranz.) RAPD Markers. Genetics and Molecular Biology , 21, 69-84.
https://doi.org/10.1590/S1415-47571998000100018
10. Ferdinandez, Y.S.N., Somers, D.J. and Coulman, B.E. (2001) Estimation the Genetic Relationship of Hybrid
Bromegrass to Smooth Bromegrass and Medow Bromegrass Using RAPD Markers. Plant Breeding , 120,
149-153. https://doi.org/10.1046/j.1439-0523.2001.00555.x

11. Cartea, M.E., Soengas, P., Picoaga, A. and Orda’s, A. (2005) Relationships among Brassica napus (L.)
Germplasm from Spain and Great Britain as Determined by RAPD Markers. Genetic Resources and Crop Evolution,
52, 655-662. https://doi.org/10.1007/s10722-003-6014-8
12. Venkatachalam, L., Sreedhar, R.V. and Bhagyalakshmi, N. (2007) Genetic Analyses of Micropropagated and
Regenerated Plantlets of Banana as Assessed by RAPD and ISSR Markers. In Vitro Cellular & Developmental
Biology , 43, 267-274.
13. Kishor, R., Devi, H.S. and Jeyaram, K. (2008) Molecular Characterization of Reciprocal Crosses of Aeridesvandarum
and Vanda stageana (Orchidaceae) at the Protocorm Stage. Plant Biotechnology Reports , 2, 145-152.
https://doi.org/10.1007/s11816-008-0053-8
14. Minoo, D., Jayakumar, V.N., Veena, S.S., Vimala, J., Basha, A. and Saji, K.V. (2008) Genetic Variations and Interrelationships
in Vanillaplanifolia and Few Related Species as Expressed by RAPD Polymorphism. Genetic
Resources and Crop Evolution, 55, 459-470. https://doi.org/10.1007/s10722-007-9252-3
15. Niknejad, A., Kadir, M.A., Kadzimin, S.B., Abdullah, N.A.P. and Sorkheh, K. (2009) Molecular Characterization
and Phylogenetic Relationships among and within Species of Phalaenopsis (Epindenroideae: Orchidaceae)
Based on RAPD Analyses. African Journal of Biotechnology , 8, 5225-5240.
16. Pfender, W.F., Saha, M.C., Johnson, E.A. and Slabaugh, M.B. (2011) Mapping with RAD (Restriction-Site Associated
DNA) Markersto Rapidly Identify QTL for Stem Rust Resistance in Loliumperenne. Theoretical and Applied
Genetics , 122, 1467-1480. https://doi.org/10.1007/s00122-011-1546-3
17. Zhao, M.Z., Zhang, Y.P., Wu, W.M., Wang, C., Qian, Y.M., Yang, G. and Fang, J.G. (2011) A New Strategy for
Complete Identification of 69 Grapevine Cultivars using Random Amplified Polymorphic DNA (RAPD) Markers.
African Journal of Plant Science , 5, 273-280.
18. Arias, A., Moreno, M.F., Tajes, J.F., Gaspar, M.B. and Jméndez, J.W. (2011) Strong Genetic Differentiation
among East Atlantic Populations of the Sword Razor Shell (Ensissiliqua ) Assessed with mtDNA and RAPD
Markers. Helgoland Marine Research, 65, 81-89. https://doi.org/10.1007/s10152-010-0203-6
19. Chase, M. and Hill, H. (1991) Silica Gel: An Ideal Material for Field Preservation of Leaf Samples. Taxon, 40,
215-220. https://doi.org/10.2307/1222975
20. Sneath, P.H. and Sokal, R.R. (1973) Numerical Taxonomy. Freeman, San Francisco, 573 p.
21. Rohlf, F.J. (1998) NTSYS-pc Numerical Taxonomy and Multivariate Analysis System. Version 2.02, Exter Sift
Ware, New York.
22. Miller, M.P. (1997) Tools for Population Genetic Analyses (TFPGA) Version 1.3. Departement of Biological
Sciences-Box 5640, Northern Arizona University.
23. Powel, W., Morgante, M., andre, C., Hanafey, M., Vogel, J., Tingey, S. and Rafalski, A. (1996) The Comparison
of RFLP, RAPD, AFLP, and SSR (Microsatellite) Markers for Germplasm Analysis. Molecular Breeding , 2,
225-238. https://doi.org/10.1007/BF00564200
24. Oliveira, L.V.R., Faria, R.T., Ruas, C.F., Ruas, P.M., Santos, M.O. and Cavarlho, V.P. (2010) Genetic Analysis of
Species in the Genus Catasetum (Orchidaceae) using RAPD Markers. Brazilian Archives of Biology and Technology
, 53, 375-387. https://doi.org/10.1590/S1516-89132010000200017
25. Nei, M. (1978) Estimation of Average Heterozigosity and Genetic Distance from Small Number of Individuals.
Genetics , 89, 583-590.
26. Ding, G., Zhang, D., Ding, X., Zhou, Q., Zhang, W. and Li, X. (2008) Genetic Variation and Conservation of the
Endangered Chinese Endemic Herb Dendrobium officinale Based on SRAP Analysis. Plant Systematics and
Evolution, 276, 149-156. https://doi.org/10.1007/s00606-008-0068-1
27. Forrest, A.D., Hollingsworth, M.L., Hollingsworth, P.M., Sydes, C. and Bateman, R.M. (2004) Population Genetic Structure in European Populations of Spiranthes romanzoffiana Set in the Context of Other Genetic Studies
on Orchids. Heredity , 92, 218-227. https://doi.org/10.1038/sj.hdy.6800399
28. Aceto, S., Caputo, P., Cozzolino, S., Gaudio, L. and Moretti, A. (1999) Phylogeny and Evolution of Orchis and
Allied Genera Based on ITS DNA Variation: Morphological Gaps and Molecular Continuity. Molecular Phylogenetics
and Evolution, 13, 67-76. https://doi.org/10.1006/mpev.1999.0628
29. Yadav, K., Yadav, S.K., Yadav, A., Pandey, V.P. and Dwivedi, U.N. (2012) Genetic Diversity of Pigeonpea (Cajanus
cajan L. Millsp. Culviras and Its Wild Relatives using Randomly Amplified Polymorphic DNA (RAPD)
Markers. American Journal of Plant Science , 3, 322-330. https://doi.org/10.4236/ajps.2012.33038
30. Waitt, D.E. and Levin, D.A. (1998) Genetic and Phenotypic Correlations in Plants: A Botanical Test of Cheverud’s
Conjecture. Heredity , 80, 310-319. https://doi.org/10.1046/j.1365-2540.1998.00298.x
31. Moniruzzaman, M., Zaman, M.A., Hossain, M.E., Bhuiyan, M.M.H. and Rahman, M.Z. (2012) Genetic Variability
and Character Associated in Some Native Orchid Species (Dendrobium spp.). The Agriculturist , 10, 1-9.
32. Wahba, L.E., Hazlina, N., Fadelah, A. and Ratnam, W. (2014) Genetic Relatedness among Dendrobium (Orchidaceae
) Species and Hybrids using Morphological and AFLP Markers. Hort Science , 49, 524-530.
33. Giri, L., Jugran, A.K., Bahukhandi, A., Dhyani, P., Bhatt, I.D., Rawal, R.S., Nandi, S.K. and Dhar, U. (2017) Population
Genetic Structure an d Marker Trait Associations using Morphological, Phytochemical and Molecular
Parameters in Habenaria edgeworthii—A Threatened Medicinal Orchid of West Himalaya, India. Applied Biochemistry
and Biotechnology , 181, 267-282. https://doi.org/10.1007/s12010-016-2211-8
34. Abbas, B., Renwarin, Y., Bintoro, M.H., Sudarsono, S., Surahman, M. and Ehara, H. (2010) Genetic Diversity of
Sago Palm in Indonesia Based on Chloroplast DNA (cpDNA) Markers. Journal of Biological Diversity , 11,
112-117. https://doi.org/10.13057/biodiv/d110302
35. Abbas, B. and Ehara, H. (2012) Assessment Genetic Variation and Relationship of Sago Palm (Metroxylon sagu
Rottb.) in Indonesia Based on Specific Expression Gene (Wx Genes) Markers. African Journal of Plant Science ,
6, 314-320.

URL : http://www.scirp.org/journal/ns

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Detail Karya Ilmiah Dosen

Barahima Abbas1, Muhammad Dailami2, Florentina Heningtyas Listyorini1, Munarti3

Judul	:	Genetic Variations and Relationships of Papuaâ€™s Endemic Orchids Based on RAPD Markers
Abstrak	:	Orchidaceae has known as an attractive flower and immense species. We have found a large species of Orchidaceae grow naturally in Papua’s jungle, Indonesia territorial. This study aims to reveal genetic variation and genetic relationships among endemic orchids in Papua based on RAPD markers. The study included 26 accessions of Papua’s endemic orchids used for genomic DNA extraction. Genomic DNAs were extracted by using DNA extraction kit from Qiagen and genomic DNA amplification by using 10 decamer RAPD primers. DNA fragments that were amplified by Polymerase Change Reaction (PCR) were visualized and documented by using UV illumination apparatus. Genetically, endemic Orchids in Papua were described high variation. Fragments amplification by using ten RAPD primers and performed in the PCR tools resulted in 54 numbers of polymorphic fragments and no monomorphic band. The number of polymorphic bands per primer ranged from 4 to 7 with averaged 5.4 bands per assay unit. The genetic dissimilarities (GDs) among examined orchids ranged from 0.10 to 0.94 based on Nei’s unbiased coefficients. Dendrogram construction showed that Papua’s endemic orchid (PEO) samples different from another and separated to form group by their own at the 0.40 coefficient value and at the 0.6 coefficient value indicate that PEO sample is divided into nine groups i.e. samples at the genera level were separated into their own groups.
Tahun	:	2017	Media Publikasi	:	Jurnal Internasional
Kategori	:	Jurnal	No/Vol/Tahun	:	11 / 9 / 2017
ISSN/ISBN	:	ISSN Online 2150-4105
PTN/S	:	University of Papua (UNIPA), Manokwari, Indonesia, Pakuan University, Bogor, Indonesia	Program Studi	:	PENDIDIKAN BIOLOGI
Bibliography	:	1. Singh, M.K., Sherpa, A.R, Hallan, V. and Zaidi, A.A. (2007) A Potyvirus in Cymbidium spp. in Northern India. Australasian Plant Disease Notes , 2, 11-13. https://doi.org/10.1071/DN07005 2. Meisel, J.E., Kaufmann, R.S. and Pupulin, F. (2014) Orchids of Tropical America: An Introduction and Guide. Cornell University Press, Ithaca and London, 259 p. https://books.google.co.id/books?isbn=0801454921 3. Sutiyoso and Sarwono (2004) Orchids Care. Penebar Swadaya, Jakarta. (in Indonesian) 4. Abbas, B., Listyorini, F.H. and Amriati, B (2011) In vitro Seeds Germination and Plantlets Development of Grammatophyllum scriptum Lindl. (Orchidaceae). African Journal of Plant Science , 2, 154-159. 5. Sapto, H.P. (2009) The Diversity of Orchid Archipelago and the Lack of Taxonomist. (Accessed 5/2’2010) (in Indonesian) 6. Simardjo, M. (2009) Dewndrobium Species from Papua Have Been Used as a Parent for Breeding Activity (Indomesia Language). Proceeding Efforts to Develop and Preserve the Natural Orchid of West Papua. 7. World Wildlife Fund (WWF) (2007) Bunga Rampai ALAMKU-Bird’s Head Seascape. 202 p. http://birdsheadseascape.com/download/research/social%20Science%20and%20development/Bunga%20Rampai %20ALAMKU%202007.pdf 8. Powel, W., Castillo, C.O., Chaluers, K.J., Provan, J. and Waugh, R. (1995) Polymerase Chain Reaction Based-Assays for the Characterization of Plant Genetic Resources. Electrophoresis , 16, 1726-1730. https://doi.org/10.1002/elps.11501601285 9. Colombo, C., Second, G., Valle, T.L. and Charrier, A. (1998) Genetic Diversity Characterization of Cassava Cultivars (Manihot esculenta Cranz.) RAPD Markers. Genetics and Molecular Biology , 21, 69-84. https://doi.org/10.1590/S1415-47571998000100018 10. Ferdinandez, Y.S.N., Somers, D.J. and Coulman, B.E. (2001) Estimation the Genetic Relationship of Hybrid Bromegrass to Smooth Bromegrass and Medow Bromegrass Using RAPD Markers. Plant Breeding , 120, 149-153. https://doi.org/10.1046/j.1439-0523.2001.00555.x 11. Cartea, M.E., Soengas, P., Picoaga, A. and Orda’s, A. (2005) Relationships among Brassica napus (L.) Germplasm from Spain and Great Britain as Determined by RAPD Markers. Genetic Resources and Crop Evolution, 52, 655-662. https://doi.org/10.1007/s10722-003-6014-8 12. Venkatachalam, L., Sreedhar, R.V. and Bhagyalakshmi, N. (2007) Genetic Analyses of Micropropagated and Regenerated Plantlets of Banana as Assessed by RAPD and ISSR Markers. In Vitro Cellular & Developmental Biology , 43, 267-274. 13. Kishor, R., Devi, H.S. and Jeyaram, K. (2008) Molecular Characterization of Reciprocal Crosses of Aeridesvandarum and Vanda stageana (Orchidaceae) at the Protocorm Stage. Plant Biotechnology Reports , 2, 145-152. https://doi.org/10.1007/s11816-008-0053-8 14. Minoo, D., Jayakumar, V.N., Veena, S.S., Vimala, J., Basha, A. and Saji, K.V. (2008) Genetic Variations and Interrelationships in Vanillaplanifolia and Few Related Species as Expressed by RAPD Polymorphism. Genetic Resources and Crop Evolution, 55, 459-470. https://doi.org/10.1007/s10722-007-9252-3 15. Niknejad, A., Kadir, M.A., Kadzimin, S.B., Abdullah, N.A.P. and Sorkheh, K. (2009) Molecular Characterization and Phylogenetic Relationships among and within Species of Phalaenopsis (Epindenroideae: Orchidaceae) Based on RAPD Analyses. African Journal of Biotechnology , 8, 5225-5240. 16. Pfender, W.F., Saha, M.C., Johnson, E.A. and Slabaugh, M.B. (2011) Mapping with RAD (Restriction-Site Associated DNA) Markersto Rapidly Identify QTL for Stem Rust Resistance in Loliumperenne. Theoretical and Applied Genetics , 122, 1467-1480. https://doi.org/10.1007/s00122-011-1546-3 17. Zhao, M.Z., Zhang, Y.P., Wu, W.M., Wang, C., Qian, Y.M., Yang, G. and Fang, J.G. (2011) A New Strategy for Complete Identification of 69 Grapevine Cultivars using Random Amplified Polymorphic DNA (RAPD) Markers. African Journal of Plant Science , 5, 273-280. 18. Arias, A., Moreno, M.F., Tajes, J.F., Gaspar, M.B. and Jméndez, J.W. (2011) Strong Genetic Differentiation among East Atlantic Populations of the Sword Razor Shell (Ensissiliqua ) Assessed with mtDNA and RAPD Markers. Helgoland Marine Research, 65, 81-89. https://doi.org/10.1007/s10152-010-0203-6 19. Chase, M. and Hill, H. (1991) Silica Gel: An Ideal Material for Field Preservation of Leaf Samples. Taxon, 40, 215-220. https://doi.org/10.2307/1222975 20. Sneath, P.H. and Sokal, R.R. (1973) Numerical Taxonomy. Freeman, San Francisco, 573 p. 21. Rohlf, F.J. (1998) NTSYS-pc Numerical Taxonomy and Multivariate Analysis System. Version 2.02, Exter Sift Ware, New York. 22. Miller, M.P. (1997) Tools for Population Genetic Analyses (TFPGA) Version 1.3. Departement of Biological Sciences-Box 5640, Northern Arizona University. 23. Powel, W., Morgante, M., andre, C., Hanafey, M., Vogel, J., Tingey, S. and Rafalski, A. (1996) The Comparison of RFLP, RAPD, AFLP, and SSR (Microsatellite) Markers for Germplasm Analysis. Molecular Breeding , 2, 225-238. https://doi.org/10.1007/BF00564200 24. Oliveira, L.V.R., Faria, R.T., Ruas, C.F., Ruas, P.M., Santos, M.O. and Cavarlho, V.P. (2010) Genetic Analysis of Species in the Genus Catasetum (Orchidaceae) using RAPD Markers. Brazilian Archives of Biology and Technology , 53, 375-387. https://doi.org/10.1590/S1516-89132010000200017 25. Nei, M. (1978) Estimation of Average Heterozigosity and Genetic Distance from Small Number of Individuals. Genetics , 89, 583-590. 26. Ding, G., Zhang, D., Ding, X., Zhou, Q., Zhang, W. and Li, X. (2008) Genetic Variation and Conservation of the Endangered Chinese Endemic Herb Dendrobium officinale Based on SRAP Analysis. Plant Systematics and Evolution, 276, 149-156. https://doi.org/10.1007/s00606-008-0068-1 27. Forrest, A.D., Hollingsworth, M.L., Hollingsworth, P.M., Sydes, C. and Bateman, R.M. (2004) Population Genetic Structure in European Populations of Spiranthes romanzoffiana Set in the Context of Other Genetic Studies on Orchids. Heredity , 92, 218-227. https://doi.org/10.1038/sj.hdy.6800399 28. Aceto, S., Caputo, P., Cozzolino, S., Gaudio, L. and Moretti, A. (1999) Phylogeny and Evolution of Orchis and Allied Genera Based on ITS DNA Variation: Morphological Gaps and Molecular Continuity. Molecular Phylogenetics and Evolution, 13, 67-76. https://doi.org/10.1006/mpev.1999.0628 29. Yadav, K., Yadav, S.K., Yadav, A., Pandey, V.P. and Dwivedi, U.N. (2012) Genetic Diversity of Pigeonpea (Cajanus cajan L. Millsp. Culviras and Its Wild Relatives using Randomly Amplified Polymorphic DNA (RAPD) Markers. American Journal of Plant Science , 3, 322-330. https://doi.org/10.4236/ajps.2012.33038 30. Waitt, D.E. and Levin, D.A. (1998) Genetic and Phenotypic Correlations in Plants: A Botanical Test of Cheverud’s Conjecture. Heredity , 80, 310-319. https://doi.org/10.1046/j.1365-2540.1998.00298.x 31. Moniruzzaman, M., Zaman, M.A., Hossain, M.E., Bhuiyan, M.M.H. and Rahman, M.Z. (2012) Genetic Variability and Character Associated in Some Native Orchid Species (Dendrobium spp.). The Agriculturist , 10, 1-9. 32. Wahba, L.E., Hazlina, N., Fadelah, A. and Ratnam, W. (2014) Genetic Relatedness among Dendrobium (Orchidaceae ) Species and Hybrids using Morphological and AFLP Markers. Hort Science , 49, 524-530. 33. Giri, L., Jugran, A.K., Bahukhandi, A., Dhyani, P., Bhatt, I.D., Rawal, R.S., Nandi, S.K. and Dhar, U. (2017) Population Genetic Structure an d Marker Trait Associations using Morphological, Phytochemical and Molecular Parameters in Habenaria edgeworthii—A Threatened Medicinal Orchid of West Himalaya, India. Applied Biochemistry and Biotechnology , 181, 267-282. https://doi.org/10.1007/s12010-016-2211-8 34. Abbas, B., Renwarin, Y., Bintoro, M.H., Sudarsono, S., Surahman, M. and Ehara, H. (2010) Genetic Diversity of Sago Palm in Indonesia Based on Chloroplast DNA (cpDNA) Markers. Journal of Biological Diversity , 11, 112-117. https://doi.org/10.13057/biodiv/d110302 35. Abbas, B. and Ehara, H. (2012) Assessment Genetic Variation and Relationship of Sago Palm (Metroxylon sagu Rottb.) in Indonesia Based on Specific Expression Gene (Wx Genes) Markers. African Journal of Plant Science , 6, 314-320.
URL	:	http://www.scirp.org/journal/ns