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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) · pp. 42–53

DOI
10.22146/jtbb.44047
ISSN
2540-9581, 2540-9573
Published
2019-08-12
Publisher
Universitas Gadjah Mada
Language
eng
License
creativecommons.org/licenses/by-sa/4.0

Abstract

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.

Keywords

Collaboration network of the authors

38 authors · 142 co-authorship links · 10 across different organisations

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  • Indonesian Institute of Sciences
  • National Research and Innovation Agency
  • University of Brawijaya
  • Affiliation unknown
  • Different organisations
  • Same organisation
  • Affiliation unknown
  • Thicker line = more joint articles · bigger circle = more articles
Show as table
Co-authorOrganisationJoint articles
Shofiyatul Mas’udahIndonesian Institute of Sciences3
Dewi Ayu LestariIndonesian Institute of Sciences3
Setyawan Agung DanartoIndonesian Institute of Sciences2
Janis DamaiyaniIndonesian Institute of Sciences2
Trimanto TrimantoAffiliation unknown2
Siti NurfadilahAffiliation unknown2
Suyono SuyonoAffiliation unknown2
Ruri Siti ResmisariAffiliation unknown2
Elok Rifqi FirdianaNational Research and Innovation Agency2
S. SundariAffiliation unknown2
TrimantoAffiliation unknown1
Sugeng BudihartaIndonesian Institute of Sciences1
TITUT YULISTYARINIIndonesian Institute of Sciences1
Rachmawan Adi LaksonoIndonesian Institute of Sciences1
Nurlaily LaviantiAffiliation unknown1
Bekti YunantoAffiliation unknown1
Fauziah FauziahAffiliation unknown1
Bagas PratesoAffiliation unknown1
Eriyanto YusnawanAffiliation unknown1
Ridesti RindyastutiAffiliation unknown1
Ilham Kurnia AbywijayaAffiliation unknown1
Ruth Feti RahayuniatiAffiliation unknown1
Siti SubandiyahAffiliation unknown1
Gebby Agnessya Esa OktaviaAffiliation unknown1
Kurniawan BudiartoAffiliation unknown1
Shofiyatul MasudahAffiliation unknown1
Ahmad Syahrian SiregarAffiliation unknown1
Syahran WaelAffiliation unknown1
Elga RenjanaIndonesian Institute of Sciences1
Linda Wige NingrumNational Research and Innovation Agency1
Apriyono RahadiantoroAffiliation unknown1
Fitriyah FitriyahAffiliation unknown1
Imey Tamara IndiviaAffiliation unknown1
Rodiyati AzrianingsihUniversity of Brawijaya1
Isna Arofatun NikmahAffiliation unknown1

Affiliations come from OpenAlex; journal OAI-PMH metadata carries none. Authors without an OpenAlex ID are matched by name, which can merge or split people.

Metadata source: OAI-PMH (metadata jurnal) https://jurnal.ugm.ac.id/jtbb/oai, first harvested 9 Nov 2026, last seen 9 Nov 2026.
Original metadata (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>https://journal.ugm.ac.id/jtbb/article/view/44047</dc:identifier>
	<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>
	<dc:rights xml:lang="en-US">http://creativecommons.org/licenses/by-sa/4.0</dc:rights>
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