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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Molecular Diversity Preservation International (MDPI)
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3382826/ https://www.ncbi.nlm.nih.gov/pubmed/22754356 http://dx.doi.org/10.3390/ijms13056156 |
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author | Cheng, Acga Ismail, Ismanizan Osman, Mohamad Hashim, Habibuddin |
author_facet | Cheng, Acga Ismail, Ismanizan Osman, Mohamad Hashim, Habibuddin |
author_sort | Cheng, Acga |
collection | PubMed |
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 | Online Article Text |
id | pubmed-3382826 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Molecular Diversity Preservation International (MDPI) |
record_format | MEDLINE/PubMed |
spelling | pubmed-33828262012-06-29 Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties Cheng, Acga Ismail, Ismanizan Osman, Mohamad Hashim, Habibuddin Int J Mol Sci Article 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. Molecular Diversity Preservation International (MDPI) 2012-05-18 /pmc/articles/PMC3382826/ /pubmed/22754356 http://dx.doi.org/10.3390/ijms13056156 Text en © 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/). |
spellingShingle | Article Cheng, Acga Ismail, Ismanizan Osman, Mohamad Hashim, Habibuddin Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties |
title | 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_short | 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 |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3382826/ https://www.ncbi.nlm.nih.gov/pubmed/22754356 http://dx.doi.org/10.3390/ijms13056156 |
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