Advantages of Amplifluor-like SNP markers over KASP in plant genotyping
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Date
2017
Authors
Jatayev, S.
Kurishbayev, A.
Zotova, L.
Khasanova, G.
Serikbay, D.
Zhubatkanov, A.
Botayeva, M.
Zhumalin, A.
Turbekova, A.
Soole, K.
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Journal article
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BMC Plant Biology, 2017; 17(Suppl. 2):83-93
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Satyvaldy Jatayev, Akhylbek Kurishbayev, Lyudmila Zotova, Gulmira Khasanova, Dauren Serikbay, Askar Zhubatkanov, Makpal Botayeva, Aibek Zhumalin, Arysgul Turbekova, Kathleen Soole, Peter Langridge and Yuri Shavrukov
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Abstract
Background: KASP (KBioscience Competitive Allele Specific PCR) and Amplifluor (Amplification with fluorescence) SNP markers are two prominent technologies based upon a shared identical Allele-specific PCR platform. Methods: Amplifluor-like SNP and KASP analysis was carried out using published and own design of Universal probes (UPs) and Gene-specific primers (GSPs). Results: Advantages of the Amplifluor-like system over KASP include the significantly lower costs and much greater flexibility in the adjustment and development of ‘self-designed’ dual fluorescently-labelled UPs and regular GSPs. The presented results include optimisation of ‘tail’ length in UPs and GSPs, protocol adjustment, and the use of various fluorophores in different qPCR instruments. The compatibility of the KASP Master-mix in both original and Amplifluor-like systems has been demonstrated in the presented results, proving their similar principles. Results of SNP scoring with rare alleles in addition to more frequently occurring alleles are shown. Conclusions: The Amplifluor-like system produces SNP genotyping results with a level of sensitivity and accuracy comparable to KASP but at a significantly cheaper cost and with much greater flexibility for UPs with self-designed GSPs.
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© The Author(s). 2017. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.