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Development of New CAPS/dCAPS and SNAP Markers for Rice Eating Quality

HAYATI Journal of Biosciences · Vol. 20 No. 1 (2013)

DOI
10.4308/hjb.20.1.15
ISSN
2086-4094, 1978-3019
Published
2013-03-28
Publisher
Bogor Agricultural University, Indonesia
Language
eng

Abstract

Rice eating quality traits are very complex and essential to be evaluated not only through physicochemical analysis and sensory test but also by PCR-based marker approach. To date, simple markers based on single nucleotide polymorphism (SNP) discovery to evaluate eating quality of cooked rice are still limited. Thus, the aims of this study were to develop PCR-based markers, called SNAP (single nucleotide amplified polymorphism) as alternative markers of cleaved amplified polymorphic sequence/derived cleaved amplified polymorphic sequence (CAPS/dCAPS). Four primer pairs specific to targeted alleles (CAPS/dCAPS and SNAP) of four loci were successfully designed based on the discovered SNPs according to the eating quality-QTL and searching genomic database. The primer pairs were able to identify alleles corresponding loci among indica and japonica varieties with diverse palatability (overall eating quality). There was consistent allele pattern produced by SNAP and CAPS/dCAPS for the same base mutation. The SNAP marker for rice eating quality trait could be easily assayed by standard agarose gel electrophoresis, allowing to increase the advantage of genotyping methods. Moreover, the SNAP markers together with our previous developed markers which were recommended as applicable marker set for evaluation of rice eating quality, will facilitate as marker-assisted selection for rice breeding program.

Keywords

Collaboration network of the authors

40 authors · 96 co-authorship links · 8 across different organisations · showing the 40 most connected

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  • Universitas Pembangunan Nasional Veteran Yogyakarta
  • Jenderal Soedirman University
  • Universitas Amikom Yogyakarta
  • Affiliation unknown
  • Different organisations
  • Same organisation
  • Affiliation unknown
  • Thicker line = more joint articles · bigger circle = more articles
Show as table
Co-authorOrganisationJoint articles
Erisandi ArditamaAffiliation unknown4
Nur PrihatiningsihAffiliation unknown3
Yuyun FitrianaAffiliation unknown3
I Gede SwibawaAffiliation unknown3
Radix SuharjoAffiliation unknown3
Eko Teguh ParipurnoUniversitas Pembangunan Nasional Veteran Yogyakarta2
Yozi Aulia RahmanAffiliation unknown2
Ahmad Syahrul FauziAffiliation unknown2
M Fikri AmrullahAffiliation unknown2
Arvangga Oktadian KrisbiyantoroAffiliation unknown2
Moh Aris MunandarAffiliation unknown2
Tri Marhaeni Pudji AstutiAffiliation unknown2
Pradipta KurniasantiAffiliation unknown2
Martien Herna SusantiAffiliation unknown2
Sunarto SunartoAffiliation unknown2
Eko HandoyoAffiliation unknown2
Rerenstradika Tizar TerryanaAffiliation unknown2
Kristianto NugrohoAffiliation unknown2
Araz MeilinAffiliation unknown2
Yulia PujiastutiAffiliation unknown2
Jauharlina JauharlinaAffiliation unknown2
Tri AtmowidiAffiliation unknown2
RIKA RAFFIUDINAffiliation unknown2
Windra PriawandiputraAffiliation unknown2
Mahardika Gama PradanaAffiliation unknown2
Jasmi JasmiAffiliation unknown2
Heru Adi DjatmikoAffiliation unknown2
Devi Wening AstariUniversitas Amikom Yogyakarta1
Aqmarina Laili AsyrafiUniversitas Pembangunan Nasional Veteran Yogyakarta1
Hikmat SurbaktiAffiliation unknown1
Sri Isworo EdiningsihUniversitas Pembangunan Nasional Veteran Yogyakarta1
Lita Yulita FitriyaniUniversitas Pembangunan Nasional Veteran Yogyakarta1
Priyahita Garmadyuti SuryawijayaUniversitas Pembangunan Nasional Veteran Yogyakarta1
Vanissa Zera ArdiyantiUniversitas Pembangunan Nasional Veteran Yogyakarta1
Ari AsnaniJenderal Soedirman University1
Hartiwi DiastutiJenderal Soedirman University1
Lindha Riana WatiAffiliation unknown1
Ngabiyanto NgabiyantoAffiliation 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.ipb.ac.id/index.php/hayati/oai, first harvested 8 Nov 2026, last seen 8 Nov 2026.
Original metadata (oai_dc) 
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	<dc:title xml:lang="en">Development of New CAPS/dCAPS and SNAP Markers for Rice Eating Quality</dc:title>
	<dc:creator xml:lang="en">LESTARI, PUJI</dc:creator>
	<dc:creator xml:lang="en">KOH, HEE JONG</dc:creator>
	<dc:subject xml:lang="en">CAPS</dc:subject>
	<dc:subject xml:lang="en">dCAPS</dc:subject>
	<dc:subject xml:lang="en">SNAP</dc:subject>
	<dc:subject xml:lang="en">SNP</dc:subject>
	<dc:subject xml:lang="en">rice eating quality</dc:subject>
	<dc:description xml:lang="en"> Rice eating quality traits are very complex and essential to be evaluated not only through physicochemical analysis and sensory test but also by PCR-based marker approach. To date, simple markers based on single nucleotide polymorphism (SNP) discovery to evaluate eating quality of cooked rice are still limited. Thus, the aims of this study were to develop PCR-based markers, called SNAP (single nucleotide amplified polymorphism) as alternative markers of cleaved amplified polymorphic sequence/derived cleaved amplified polymorphic sequence (CAPS/dCAPS). Four primer pairs specific to targeted alleles (CAPS/dCAPS and SNAP) of four loci were successfully designed based on the discovered SNPs according to the eating quality-QTL and searching genomic database. The primer pairs were able to identify alleles corresponding loci among indica and japonica varieties with diverse palatability (overall eating quality). There was consistent allele pattern produced by SNAP and CAPS/dCAPS for the same base mutation. The SNAP marker for rice eating quality trait could be easily assayed by standard agarose gel electrophoresis, allowing to increase the advantage of genotyping methods. Moreover, the SNAP markers together with our previous developed markers which were recommended as applicable marker set for evaluation of rice eating quality, will facilitate as marker-assisted selection for rice breeding program.   </dc:description>
	<dc:publisher xml:lang="en">Bogor Agricultural University, Indonesia</dc:publisher>
	<dc:date>2013-03-28</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/6641</dc:identifier>
	<dc:identifier>10.4308/hjb.20.1.15</dc:identifier>
	<dc:source xml:lang="en">HAYATI Journal of Biosciences; Vol. 20 No. 1 (2013): March 2013; 15</dc:source>
	<dc:source>2086-4094</dc:source>
	<dc:source>1978-3019</dc:source>
	<dc:language>eng</dc:language>
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