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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
Terbit
2013-03-28
Penerbit
Bogor Agricultural University, Indonesia
Bahasa
eng

Abstrak

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.

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  • Universitas Pembangunan Nasional Veteran Yogyakarta
  • Jenderal Soedirman University
  • Universitas Amikom Yogyakarta
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Rekan penulisOrganisasiArtikel bersama
Erisandi ArditamaAfiliasi tidak diketahui5
Eko Teguh ParipurnoUniversitas Pembangunan Nasional Veteran Yogyakarta3
Nur PrihatiningsihAfiliasi tidak diketahui3
Yuyun FitrianaAfiliasi tidak diketahui3
I Gede SwibawaAfiliasi tidak diketahui3
Radix SuharjoAfiliasi tidak diketahui3
Ari AsnaniJenderal Soedirman University2
Hartiwi DiastutiJenderal Soedirman University2
Yozi Aulia RahmanAfiliasi tidak diketahui2
Ahmad Syahrul FauziAfiliasi tidak diketahui2
M Fikri AmrullahAfiliasi tidak diketahui2
Arvangga Oktadian KrisbiyantoroAfiliasi tidak diketahui2
Moh Aris MunandarAfiliasi tidak diketahui2
Aprila NiravitaAfiliasi tidak diketahui2
Tri Marhaeni Pudji AstutiAfiliasi tidak diketahui2
Eta Yuni LestariAfiliasi tidak diketahui2
Pradipta KurniasantiAfiliasi tidak diketahui2
Martien Herna SusantiAfiliasi tidak diketahui2
Sunarto SunartoAfiliasi tidak diketahui2
Eko HandoyoAfiliasi tidak diketahui2
Rerenstradika Tizar TerryanaAfiliasi tidak diketahui2
Kristianto NugrohoAfiliasi tidak diketahui2
Dwinita Wikan UtamiAfiliasi tidak diketahui2
Araz MeilinAfiliasi tidak diketahui2
Yulia PujiastutiAfiliasi tidak diketahui2
Jauharlina JauharlinaAfiliasi tidak diketahui2
Tri AtmowidiAfiliasi tidak diketahui2
RIKA RAFFIUDINAfiliasi tidak diketahui2
Windra PriawandiputraAfiliasi tidak diketahui2
Mahardika Gama PradanaAfiliasi tidak diketahui2
Jasmi JasmiAfiliasi tidak diketahui2
Heru Adi DjatmikoAfiliasi tidak diketahui2
Devi Wening AstariUniversitas Amikom Yogyakarta1
Aqmarina Laili AsyrafiUniversitas Pembangunan Nasional Veteran Yogyakarta1
Hikmat SurbaktiAfiliasi tidak diketahui1
Sri Isworo EdiningsihUniversitas Pembangunan Nasional Veteran Yogyakarta1
Lita Yulita FitriyaniUniversitas Pembangunan Nasional Veteran Yogyakarta1
Priyahita Garmadyuti SuryawijayaUniversitas Pembangunan Nasional Veteran Yogyakarta1

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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">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>
	<dc:relation>http://journal.ipb.ac.id/hayati/article/view/6641/6641</dc:relation>
</oai_dc:dc>