Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties

The polymorphisms of Waxy (Wx) microsatellite and G-T single-nucleotide polymorphism (SNP) in the Wx gene region were analyzed using simplified techniques in fifteen rice varieties. A rapid and reliable electrophoresis method, MetaPhor agarose gel electrophoresis (MAGE), was effectively employed as...

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Main Authors:	Cheng, Acga, Ismail, Ismanizan, Osman, Mohamad, Hashim, Habibuddin
Format:	Article
Language:	English
Published:	MDPI 2012
Subjects:	Q Science (General) QK Botany
Online Access:	http://irep.iium.edu.my/24393/ http://irep.iium.edu.my/24393/ http://irep.iium.edu.my/24393/ http://irep.iium.edu.my/24393/1/SIMPLE_AND_RAPID.pdf

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recordtype	eprints
spelling	iium-243932014-07-17T07:03:36Z http://irep.iium.edu.my/24393/ Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties Cheng, Acga Ismail, Ismanizan Osman, Mohamad Hashim, Habibuddin Q Science (General) QK Botany The polymorphisms of Waxy (Wx) microsatellite and G-T single-nucleotide polymorphism (SNP) in the Wx gene region were analyzed using simplified techniques in fifteen rice varieties. A rapid and reliable electrophoresis method, MetaPhor agarose gel electrophoresis (MAGE), was effectively employed as an alternative to polyacrylamide gel electrophoresis (PAGE) for separating Wx microsatellite alleles. The amplified products containing the Wx microsatellite ranged from 100 to 130 bp in length. Five Wx microsatellite alleles, namely (CT)10, (CT)11, (CT)16, (CT)17, and (CT)18 were identified. Of these, (CT)11 and (CT)17 were the predominant classes among the tested varieties. All varieties with an apparent amylose content higher than 24% were associated with the shorter repeat alleles; (CT)10 and (CT)11, while varieties with 24% or less amylose were associated with the longer repeat alleles. All varieties with intermediate and high amylose content had the sequence AGGTATA at the 5'-leader intron splice site, while varieties with low amylose content had the sequence AGTTATA. The G-T polymorphism was further verified by the PCR-AccI cleaved amplified polymorphic sequence (CAPS) method, in which only genotypes containing the AGGTATA sequence were cleaved by AccI. Hence, varieties with desirable amylose levels can be developed rapidly using the Wx microsatellite and G-T SNP, along with MAGE. MDPI 2012 Article PeerReviewed application/pdf en http://irep.iium.edu.my/24393/1/SIMPLE_AND_RAPID.pdf Cheng, Acga and Ismail, Ismanizan and Osman, Mohamad and Hashim, Habibuddin (2012) Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties. International Journal of Molecular Sciences, 13 (5). pp. 6156-6166. ISSN ISSN 1422-0067 http://www.mdpi.com/1422-0067/13/5/6156 10.3390/ijms13056156
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English
topic	Q Science (General) QK Botany
spellingShingle	Q Science (General) QK Botany Cheng, Acga Ismail, Ismanizan Osman, Mohamad Hashim, Habibuddin Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties
description	The polymorphisms of Waxy (Wx) microsatellite and G-T single-nucleotide polymorphism (SNP) in the Wx gene region were analyzed using simplified techniques in fifteen rice varieties. A rapid and reliable electrophoresis method, MetaPhor agarose gel electrophoresis (MAGE), was effectively employed as an alternative to polyacrylamide gel electrophoresis (PAGE) for separating Wx microsatellite alleles. The amplified products containing the Wx microsatellite ranged from 100 to 130 bp in length. Five Wx microsatellite alleles, namely (CT)10, (CT)11, (CT)16, (CT)17, and (CT)18 were identified. Of these, (CT)11 and (CT)17 were the predominant classes among the tested varieties. All varieties with an apparent amylose content higher than 24% were associated with the shorter repeat alleles; (CT)10 and (CT)11, while varieties with 24% or less amylose were associated with the longer repeat alleles. All varieties with intermediate and high amylose content had the sequence AGGTATA at the 5'-leader intron splice site, while varieties with low amylose content had the sequence AGTTATA. The G-T polymorphism was further verified by the PCR-AccI cleaved amplified polymorphic sequence (CAPS) method, in which only genotypes containing the AGGTATA sequence were cleaved by AccI. Hence, varieties with desirable amylose levels can be developed rapidly using the Wx microsatellite and G-T SNP, along with MAGE.
format	Article
author	Cheng, Acga Ismail, Ismanizan Osman, Mohamad Hashim, Habibuddin
author_facet	Cheng, Acga Ismail, Ismanizan Osman, Mohamad Hashim, Habibuddin
author_sort	Cheng, Acga
title	Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties
title_short	Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties
title_full	Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties
title_fullStr	Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties
title_full_unstemmed	Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties
title_sort	simple and rapid molecular techniques for identification of amylose levels in rice varieties
publisher	MDPI
publishDate	2012
url	http://irep.iium.edu.my/24393/ http://irep.iium.edu.my/24393/ http://irep.iium.edu.my/24393/ http://irep.iium.edu.my/24393/1/SIMPLE_AND_RAPID.pdf
first_indexed	2023-09-18T20:36:33Z
last_indexed	2023-09-18T20:36:33Z
_version_	1777409084310421504

Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties

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