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SNP Genotyping with Amplifluor-Like Method

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Plant Genotyping

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2638))

Abstract

For SNP genotyping, amplification of fluorescence (Amplifluor) is a popular and actively developing method in the plant sciences. The “Amplifluor-like” is a “home-made” modification of the original commercial Amplifluor method. Amplifluor-like genotyping requires two essential components: (1) two allele-specific forward primers targeting the SNP site with one common reverse primer; and (2) a universal part with two non-allele-specific molecular probes containing one of the two used fluorophores and a quencher. Allele discrimination is based on the fluorescence score, where the dominance of one dye over the other confirms the presence of each specific SNP allele. The Amplifluor-like method is similar to commercial KASP and original Amplifluor methods but is much cheaper because all components can be ordered as regular and modified oligos. The easily adaptable Amplifluor-like method can be modified by any researcher to make it suitable for available instruments, reagents and conditions in low-budget laboratories for SNP genotyping of any plant species with identified genetic polymorphism.

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Acknowledgments

This study was supported by Bolashak International Fellowships, Center for International Programs (GK and SK), and Research project AP14869777 (GK), Ministry of Education and Science, Kazakhstan. We want to thank Carly Schramm for critical comment of the chapter.

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Authors and Affiliations

  1. A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan

    Gulmira Khassanova & Maral Utebayev

  2. Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan

    Gulmira Khassanova

  3. Kazakh Research Institute of Agriculture and Plant Production, Almalybak, Almaty, Kazakhstan

    Sholpan Khalbayeva, Shynar Mazkirat & Kulpash Bulatova

  4. College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China

    Dauren Serikbay

  5. College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia

    Yuri Shavrukov

Authors
  1. Gulmira Khassanova
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  2. Sholpan Khalbayeva
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  3. Dauren Serikbay
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  4. Shynar Mazkirat
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  5. Kulpash Bulatova
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  6. Maral Utebayev
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  7. Yuri Shavrukov
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Correspondence to Yuri Shavrukov .

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Editors and Affiliations

  1. College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia

    Yuri Shavrukov

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Khassanova, G. et al. (2023). SNP Genotyping with Amplifluor-Like Method. In: Shavrukov, Y. (eds) Plant Genotyping. Methods in Molecular Biology, vol 2638. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3024-2_14

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  • DOI: https://doi.org/10.1007/978-1-0716-3024-2_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3023-5

  • Online ISBN: 978-1-0716-3024-2

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