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Diversity and Population Structure of Local Rice Varieties from Indonesia Revealed by SSR Markers

HAYATI Journal of Biosciences · Vol. 29 No. 6 (2022) · hlm. 749–761

DOI
10.4308/hjb.29.6.749-761
ISSN
2086-4094, 1978-3019
Terbit
2022-06-28
Penerbit
Bogor Agricultural University, Indonesia
Bahasa
eng

Abstrak

Indonesia's local rice varieties (Oryza sativa L.) have a wide range of diversity that can be valuable sources for crop improvement with molecular markers. This study investigated local rice varieties' genetic diversity and population structure using simple sequence repeat (SSR) markers. The SSR markers demonstrated their informativeness for genotypic characterization as represented by the gene diversity indices and polymorphic information content. The UPGMA dendrogram divided 63 varieties into two distinct clusters with different levels of sub-grouping and the tendency according to their origins, as supported by PCoA. In contrast, PCA of these varieties according to agro-morphological traits was scattered in all quadrants. Thus, DNA level variation analyzed by SSR seems to complement the phenotypic traits, which were not well structured and revealed significant genetic diversity among varieties, within, and among populations (P<0.01). The pattern of grouping structure analysis of total varieties into two subpopulations is similar to the dendrogram according to SSR markers but better resembles the pedigree information of the set local varieties. These findings have implied their importance in rice breeding for genetic improvement, maintenance, and management of local genetic resources in Indonesia.

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  • National Research and Innovation Agency
  • Indonesian Center for Agricultural Biotechnology and Genetic Resource Research and Development
  • IPB University
  • Indonesian Agency for Agricultural Research and Development
  • University of Brawijaya
  • Seoul National University
  • University of Bengkulu
  • Organisasi lain
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  • Organisasi berbeda
  • Organisasi sama
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Rekan penulisOrganisasiArtikel bersama
Ika RoostikaNational Research and Innovation Agency3
Mia KosmiatinNational Research and Innovation Agency2
Chaireni MartasariNational Research and Innovation Agency2
Hee‐Jong KohSeoul National University2
Kurniawan BudiartoNational Research and Innovation Agency2
Andari RisliawatiNational Research and Innovation Agency2
HS EdisonAfiliasi tidak diketahui2
Habib RijzaaniIndonesian Center for Agricultural Biotechnology and Genetic Resource Research and Development2
Eko SulistyonoIPB University1
Munif GhulamahdiIPB University1
Iskandar LubisIPB University1
Yartiwi YartiwiIPB University1
I Nyoman WidiartaNational Research and Innovation Agency1
Yusmani PrayogoNational Research and Innovation Agency1
Sempurna Br. GintingUniversity of Bengkulu1
Marida Santi Yudha Ika BayuNational Research and Innovation Agency1
Yuliantoro BaliadiNational Research and Innovation Agency1
Didik HarnowoNational Research and Innovation Agency1
Sri Wahyuni IndiatiNational Research and Innovation Agency1
Gatut Wahyu Anggoro SusantoNational Research and Innovation Agency1
Yadi SuryadiIndonesian Center for Agricultural Biotechnology and Genetic Resource Research and Development1
Trizelia TrizeliaAndalas University1
Sernan Entierro FortusKing Mongkut's Institute of Technology Ladkrabang1
Vibol PeuoNational University of Battambang1
Fajriyatus ShoidahAfiliasi tidak diketahui1
Dyah Retno WulandariNational Research and Innovation Agency1
Hadi Mokhamad YusufNational Research and Innovation Agency1
Muhammad Asya FadillahUniversity of Brawijaya1
Ali HusniNational Research and Innovation Agency1
Budi WaluyoUniversity of Brawijaya1

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Sumber metadata: OAI-PMH (metadata jurnal) http://journal.ipb.ac.id/index.php/hayati/oai, pertama di-harvest 8 Nov 2026, terakhir terlihat 8 Nov 2026.
Metadata asli (oai_dc) 
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	<dc:title xml:lang="en">Diversity and Population Structure of Local Rice Varieties from Indonesia Revealed by SSR Markers</dc:title>
	<dc:creator xml:lang="en">Terryana, Rerenstradika Tizar</dc:creator>
	<dc:creator xml:lang="en">Lestari, Puji</dc:creator>
	<dc:creator xml:lang="en">Arsana, I Gusti Komang Dana</dc:creator>
	<dc:creator xml:lang="en">Nugroho, Kristianto</dc:creator>
	<dc:creator xml:lang="en">Mejaya, I Made Jana</dc:creator>
	<dc:creator xml:lang="en">Sasmita, Priatna</dc:creator>
	<dc:creator xml:lang="en">Sastro, Yudi</dc:creator>
	<dc:creator xml:lang="en">Mulya, Karden</dc:creator>
	<dc:creator xml:lang="en">Utami, Dwinita Wikan</dc:creator>
	<dc:creator xml:lang="en">Mastur</dc:creator>
	<dc:description xml:lang="en">Indonesia's local rice varieties (Oryza sativa L.) have a wide range of diversity that can be valuable sources for crop improvement with molecular markers. This study investigated local rice varieties' genetic diversity and population structure using simple sequence repeat (SSR) markers. The SSR markers demonstrated their informativeness for genotypic characterization as represented by the gene diversity indices and polymorphic information content. The UPGMA dendrogram divided 63 varieties into two distinct clusters with different levels of sub-grouping and the tendency according to their origins, as supported by PCoA. In contrast, PCA of these varieties according to agro-morphological traits was scattered in all quadrants. Thus, DNA level variation analyzed by SSR seems to complement the phenotypic traits, which were not well structured and revealed significant genetic diversity among varieties, within, and among populations (P&amp;lt;0.01). The pattern of grouping structure analysis of total varieties into two subpopulations is similar to the dendrogram according to SSR markers but better resembles the pedigree information of the set local varieties. These findings have implied their importance in rice breeding for genetic improvement, maintenance, and management of local genetic resources in Indonesia.</dc:description>
	<dc:publisher xml:lang="en">Bogor Agricultural University, Indonesia</dc:publisher>
	<dc:date>2022-06-28</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:type xml:lang="en">Peer-reviewed Article</dc:type>
	<dc:format>application/pdf</dc:format>
	<dc:identifier>http://journal.ipb.ac.id/hayati/article/view/30716</dc:identifier>
	<dc:identifier>10.4308/hjb.29.6.749-761</dc:identifier>
	<dc:source xml:lang="en">HAYATI Journal of Biosciences; Vol. 29 No. 6 (2022): November 2022; 749-761</dc:source>
	<dc:source>2086-4094</dc:source>
	<dc:source>1978-3019</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>http://journal.ipb.ac.id/hayati/article/view/30716/23676</dc:relation>
	<dc:rights xml:lang="en">Copyright (c) 2022 Rerenstradika Tizar Terryana, Puji Lestari, I Gusti Komang Dana Arsana, Kristianto Nugroho, I Made Jana Mejaya, Priatna Sasmita, Yudi Sastro, Karden Mulya, Dwinita Wikan Utami, Mastur</dc:rights>
</oai_dc:dc>