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Clustering Analysis and Genome Inference of Pisang Raja Local Cultivars (Musa spp.) from Java Island by Random Amplified Polymorphic DNA (RAPD) Marker

Journal of Tropical Biodiversity and Biotechnology · Vol. 4 No. 2 (2019) · hlm. 42–53

DOI
10.22146/jtbb.44047
ISSN
2540-9581, 2540-9573
Terbit
2019-08-12
Penerbit
Universitas Gadjah Mada
Bahasa
eng
Lisensi
creativecommons.org/licenses/by-sa/4.0

Abstrak

Pisang Raja is an important local banana cultivar in the economy and cultural life in Indonesia, especially at Java. There are many Pisang Raja cultivars found on Java Island with various local names in each region, resulted in problems on taxonomic identification and grouping. Conventional research for grouping banana cultivars is still using morphological characters but considered inaccurate because of its subjectivity. This study aims to analyze the genetic diversity, grouping, and genome estimation of 13 local cultivars of Pisang Raja based on molecular approach using RAPD markers (OPA primers 1-20). Clustering and Principal Coordinates Analysis were performed to the amplified products using Paleontological Statistics (PAST) application version 3.15. Results showed that there were 12 primers which successfully amplified and produced DNA polymorphic bands in Pisang Raja, specifically OPA 1, OPA 2, OPA 3, OPA 4, OPA 5, OPA 8, OPA 16, OPA 17, OPA 18, OPA 19, and OPA 20. Pisang Raja cultivars considered have high genetic diversity, indicated by high polymorphic bands (95.17%) and low similarity coefficient values (0.2-0.6). Clustering and PCo analysis resulted in 3 clusters following its genomic group consist of AAA, AAB and ABB genomes, with Pisang Raja Bali as an outgroup (ABB). However, the separation of each cluster for genome inference was unclear. Cluster 1 consists of Pisang Raja Madu (AAB) and Raja Sereh (AAB). Cluster 2 consists of AAA and AAB genomes; includes Pisang Raja Jambe (AAA), Raja Kriyak (AAA), Raja Kutuk (AAB), Raja Brentel (AAB), Raja Seribu (AAB), and Raja Lini (AAB). Cluster 3 consists of AAA and AAB genomes, includes Pisang Raja Kisto (AAA), Raja Delima (AAA), Raja Bandung (AAB) and Raja Gareng (AAB). While Pisang Monyet (AAw) and Klutuk Wulung (BBw) as wild relatives were nested in Cluster 2. There were some different results of genome estimation based on RAPD markers compared to morphological characterization, and other molecular techniques. The use of RAPD markers is quite efficient and effective for studying genetic diversity and identifying genomes in bananas.

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  • Indonesian Institute of Sciences
  • National Research and Innovation Agency
  • Universitas Islam Negeri Maulana Malik Ibrahim
  • University of Brawijaya
  • State University of Malang
  • Jenderal Soedirman University
  • Universitas Gadjah Mada
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Rekan penulisOrganisasiArtikel bersama
Shofiyatul Mas’udahIndonesian Institute of Sciences3
Setyawan Agung DanartoIndonesian Institute of Sciences2
Janis DamaiyaniIndonesian Institute of Sciences2
Siti NurfadilahIndonesian Institute of Sciences2
Ruri Siti ResmisariUniversitas Islam Negeri Maulana Malik Ibrahim2
Elok Rifqi FirdianaNational Research and Innovation Agency2
Dewi LestariNational Research and Innovation Agency2
Sundari SundariKhairun University2
TrimantoAfiliasi tidak diketahui1
Sugeng BudihartaIndonesian Institute of Sciences1
TITUT YULISTYARINIIndonesian Institute of Sciences1
Rachmawan Adi LaksonoIndonesian Institute of Sciences1
Nurlaily LaviantiAfiliasi tidak diketahui1
Bekti YunantoAfiliasi tidak diketahui1
Trimanto TrimantoAfiliasi tidak diketahui1
Fauziah FauziahIndonesian Institute of Sciences1
Dewi Ayu LestariIndonesian Institute of Sciences1
Suyono SuyonoUniversitas Islam Negeri Maulana Malik Ibrahim1
Bagas PratesoUniversitas Islam Negeri Maulana Malik Ibrahim1
Eriyanto YusnawanNational Research and Innovation Agency1
Ridesti RindyastutiIndonesian Institute of Sciences1
Ilham Kurnia AbywijayaIndonesian Institute of Sciences1
Ruth Feti RahayuniatiJenderal Soedirman University1
Siti SubandiyahUniversitas Gadjah Mada1
Shofiyatul MasudahAfiliasi tidak diketahui1
Gebby Agnessya Esa OktaviaIndonesian Institute of Sciences1
Kurniawan BudiartoNational Research and Innovation Agency1
Ahmad Syahrian SiregarNational Research and Innovation Agency1
Elga RenjanaNational Research and Innovation Agency1
Linda Wige NingrumNational Research and Innovation Agency1
Trimanto TrimantoIndonesian Institute of Sciences1
Apriyono RahadiantoroNational Research and Innovation Agency1
Suyono SuyonoUniversitas Islam Negeri Maulana Malik Ibrahim1
Imey Tamara IndiviaUniversitas Islam Negeri Maulana Malik Ibrahim1
Fitriyah FitriyahUniversitas Islam Negeri Maulana Malik Ibrahim1
Rodiyati AzrianingsihUniversity of Brawijaya1
Isna Arofatun NikmahUniversity of Brawijaya1

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Sumber metadata: OAI-PMH (metadata jurnal) https://jurnal.ugm.ac.id/jtbb/oai, pertama di-harvest 9 Nov 2026, terakhir terlihat 9 Nov 2026.
Metadata asli (oai_dc) 
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	<dc:title xml:lang="en-US">Clustering Analysis and Genome Inference of Pisang Raja Local Cultivars (Musa spp.) from Java Island by Random Amplified Polymorphic DNA (RAPD) Marker</dc:title>
	<dc:creator>Probojati, Rasyadan Taufiq</dc:creator>
	<dc:creator>Wahyudi, Didik</dc:creator>
	<dc:creator>Hapsari, Lia</dc:creator>
	<dc:subject xml:lang="en-US">clustering analysis, genetic diversity genome inference, Java Island, Pisang Raja, RAPD</dc:subject>
	<dc:description xml:lang="en-US">Pisang Raja is an important local banana cultivar in the economy and cultural life in Indonesia, especially at Java. There are many Pisang Raja cultivars found on Java Island with various local names in each region, resulted in problems on taxonomic identification and grouping. Conventional research for grouping banana cultivars is still using morphological characters but considered inaccurate because of its subjectivity. This study aims to analyze the genetic diversity, grouping, and genome estimation of 13 local cultivars of Pisang Raja based on molecular approach using RAPD markers (OPA primers 1-20). Clustering and Principal Coordinates Analysis were performed to the amplified products using Paleontological Statistics (PAST) application version 3.15. Results showed that there were 12 primers which successfully amplified and produced DNA polymorphic bands in Pisang Raja, specifically OPA 1, OPA 2, OPA 3, OPA 4, OPA 5, OPA 8, OPA 16, OPA 17, OPA 18, OPA 19, and OPA 20. Pisang Raja cultivars considered have high genetic diversity, indicated by high polymorphic bands (95.17%) and low similarity coefficient values (0.2-0.6). Clustering and PCo analysis resulted in 3 clusters following its genomic group consist of AAA, AAB and ABB genomes, with Pisang Raja Bali as an outgroup (ABB). However, the separation of each cluster for genome inference was unclear. Cluster 1 consists of Pisang Raja Madu (AAB) and Raja Sereh (AAB). Cluster 2 consists of AAA and AAB genomes; includes Pisang Raja Jambe (AAA), Raja Kriyak (AAA), Raja Kutuk (AAB), Raja Brentel (AAB), Raja Seribu (AAB), and Raja Lini (AAB). Cluster 3 consists of AAA and AAB genomes, includes Pisang Raja Kisto (AAA), Raja Delima (AAA), Raja Bandung (AAB) and Raja Gareng (AAB). While Pisang Monyet (AAw) and Klutuk Wulung (BBw) as wild relatives were nested in Cluster 2. There were some different results of genome estimation based on RAPD markers compared to morphological characterization, and other molecular techniques. The use of RAPD markers is quite efficient and effective for studying genetic diversity and identifying genomes in bananas.</dc:description>
	<dc:publisher xml:lang="en-US">Universitas Gadjah Mada</dc:publisher>
	<dc:contributor xml:lang="en-US"></dc:contributor>
	<dc:date>2019-08-12</dc:date>
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	<dc:identifier>10.22146/jtbb.44047</dc:identifier>
	<dc:source xml:lang="en-US">Journal of Tropical Biodiversity and Biotechnology; Vol 4, No 2 (2019): August; 42-53</dc:source>
	<dc:source>2540-9581</dc:source>
	<dc:source>2540-9573</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://journal.ugm.ac.id/jtbb/article/view/44047/24920</dc:relation>
	<dc:relation>https://journal.ugm.ac.id/jtbb/article/downloadSuppFile/44047/7427</dc:relation>
	<dc:rights xml:lang="en-US">Copyright (c) 2019 Journal of Tropical Biodiversity and Biotechnology</dc:rights>
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