Advantages of Amplifluor-like SNP markers over KASP in plant genotyping

BMC Plant Biology

Methodology

Satyvaldy Jatayev¹  Dauren Serikbay¹  Askar Zhubatkanov¹  Gulmira Khasanova¹  Aibek Zhumalin¹  Arysgul Turbekova¹  Akhylbek Kurishbayev¹  Lyudmila Zotova¹  Makpal Botayeva¹  Peter Langridge²  Kathleen Soole³  Yuri Shavrukov⁴ 

[1] Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan;School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia;School of Biological Sciences, Flinders University, Bedford Park, SA, Australia;School of Biological Sciences, Flinders University, Bedford Park, SA, Australia;School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia;

关键词: Amplifluor;    Gene-specific primers;    KASP;    Single nucleotide polymorphism;    SNP markers;    Universal probes;   

DOI  :  10.1186/s12870-017-1197-x

来源: Springer

【 摘 要 】

BackgroundKASP (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.MethodsAmplifluor-like SNP and KASP analysis was carried out using published and own design of Universal probes (UPs) and Gene-specific primers (GSPs).ResultsAdvantages 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© The Author(s). 2017