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GENETIC DIVERSITY AND TRAIT ASSOCIATION ANALYSIS OF INDONESIAN RICE (Oryza sativa L.) GERMPLASM USING SSR MARKERS

BIOTROPIA · Vol. 23 No. 2 (2017) · pp. 107–117

DOI
10.11598/btb.2016.23.2.489
ISSN
1907-770X, 0215-6334
Published
2017-01-06
Publisher
SEAMEO BIOTROP
Language
en
License
creativecommons.org/licenses/by-nc-nd/4.0

Abstract

Generating a new crop variety with certain desirable traits requires germplasm collection with wide genetic diversity to facilitate accelerated development of improved cultivars. This study was conducted to characterize genetic diversity of Indonesian rice accessions using SSR markers and their agro-morphological characters to allow the identification of Marker Trait Association (MTA). A survey of genetic diversity among 72 traditional landraces of 15 provinces in Indonesia and 24 improved varieties was conducted using four multiplex panels of 14 fluorescent-labeled SSR markers and 22 agro-morphological characters. A total of 140 alleles with an average of 10 alleles per locus and Polymorphism Information Content (PIC) values at 0.73. The population structure identified five subgroups. A total of 4 highly significant MTA were identified. One character with highly significant MTA was number of panicle associated with RM277. Based on SSR marker, RM105 had two MTAs for auricle color and ligule shape. After validation, these MTAs may be deployed to improve rice productivity.

Keywords

Collaboration network of the authors

40 authors · 68 co-authorship links · showing the 40 most connected

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  • State University of Semarang
  • Affiliation unknown
  • Different organisations
  • Same organisation
  • Affiliation unknown
  • Thicker line = more joint articles · bigger circle = more articles
Show as table
Co-authorOrganisationJoint articles
Amin RetnoningsihAffiliation unknown2
Noor Aini HabibahAffiliation unknown2
Dheny PrasetyaAffiliation unknown2
Mahlil MahlilAffiliation unknown2
Siti MaisarahAffiliation unknown2
Bonjok IstiajiAffiliation unknown2
Nitri MiroseaAffiliation unknown1
Tuti DharmawatiAffiliation unknown1
ABDUL KARIMAffiliation unknown1
Abdul Wahid WahabAffiliation unknown1
Krispinus Kedati PukanState University of Semarang1
Junica FitrianaAffiliation unknown1
Nidaul KhoiriahAffiliation unknown1
Enni Suwarsi RahayuAffiliation unknown1
Agung SuwarnoAffiliation unknown1
Noor Aini HabibahAffiliation unknown1
Nana Kariada Tri MartutiState University of Semarang1
Ananto AjiAffiliation unknown1
Lutfian NazarAffiliation unknown1
Ahmad NurkhinAffiliation unknown1
Gisna AuliyaAffiliation unknown1
SajidinAffiliation unknown1
Firli NurainiAffiliation unknown1
Kuntoro BudiyantoAffiliation unknown1
Euis Komariah SiswatiAffiliation unknown1
Tyas Agung PribadiAffiliation unknown1
Andreas Junaedi Raja Guk GukAffiliation unknown1
Tri Lestari HandayaniAffiliation unknown1
Mualimin -Affiliation unknown1
Priyantini WidiyaningrumAffiliation unknown1
Indriastuti IndriastutiAffiliation unknown1
Bambang PriyonoState University of Semarang1
Fatkhurrohman FatkhurrohmanAffiliation unknown1
Aprilianingtyas AnggraeniAffiliation unknown1
Ning SetiatiAffiliation unknown1
Kurnia Nor LitasariAffiliation unknown1
Naila Rofi’atiAffiliation 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) http://journal.biotrop.org/index.php/biotropia/oai, first harvested 8 Nov 2026, last seen 8 Nov 2026.
Original metadata (oai_dc) 
<oai_dc:dc xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/  http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
	<dc:title xml:lang="en">GENETIC DIVERSITY AND TRAIT ASSOCIATION ANALYSIS OF INDONESIAN RICE (Oryza sativa L.) GERMPLASM USING SSR MARKERS</dc:title>
	<dc:creator xml:lang="en">Fatimah, Fatimah</dc:creator>
	<dc:creator xml:lang="en">Herlina, Lina</dc:creator>
	<dc:creator xml:lang="en">Silitonga, Tiur Sudiaty</dc:creator>
	<dc:subject xml:lang="en">Genetic diversity</dc:subject>
	<dc:subject xml:lang="en">Indonesian rice</dc:subject>
	<dc:subject xml:lang="en">Marker-Trait Association</dc:subject>
	<dc:subject xml:lang="en">SSR</dc:subject>
	<dc:description xml:lang="en">Generating a new crop variety with certain desirable traits requires germplasm collection with wide genetic diversity to facilitate accelerated development of improved cultivars. This study was conducted to characterize genetic diversity of Indonesian rice accessions using SSR markers and their agro-morphological characters to allow the identification of Marker Trait Association (MTA). A survey of genetic diversity among 72 traditional landraces of 15 provinces in Indonesia and 24 improved varieties was conducted using four multiplex panels of 14 fluorescent-labeled SSR markers and 22 agro-morphological characters. A total of 140 alleles with an average of 10 alleles per locus and Polymorphism Information Content (PIC) values at 0.73. The population structure identified five subgroups. A total of 4 highly significant MTA were identified. One character with highly significant MTA was number of panicle associated with RM277. Based on SSR marker, RM105 had two MTAs for auricle color and ligule shape. After validation, these MTAs may be deployed to improve rice productivity.</dc:description>
	<dc:publisher xml:lang="en">SEAMEO BIOTROP</dc:publisher>
	<dc:date>2017-01-06</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://journal.biotrop.org/index.php/biotropia/article/view/489</dc:identifier>
	<dc:identifier>10.11598/btb.2016.23.2.489</dc:identifier>
	<dc:source xml:lang="en">BIOTROPIA; Vol. 23 No. 2 (2016): BIOTROPIA Vol. 23 No. 2 December 2016; 107 - 117</dc:source>
	<dc:source>1907-770X</dc:source>
	<dc:source>0215-6334</dc:source>
	<dc:source>10.11598/btb.2016.23.2.</dc:source>
	<dc:language>en</dc:language>
	<dc:relation>https://journal.biotrop.org/index.php/biotropia/article/view/489/306</dc:relation>
	<dc:rights xml:lang="en">Copyright (c) 2017 BIOTROPIA - The Southeast Asian Journal of Tropical Biology</dc:rights>
	<dc:rights xml:lang="en">http://creativecommons.org/licenses/by-nc-nd/4.0</dc:rights>
</oai_dc:dc>