2022
DOI: 10.3389/fpls.2021.747886
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Modified “Allele-Specific qPCR” Method for SNP Genotyping Based on FRET

Abstract: The proposed method is a modified and improved version of the existing “Allele-specific q-PCR” (ASQ) method for genotyping of single nucleotide polymorphism (SNP) based on fluorescence resonance energy transfer (FRET). This method is similar to frequently used techniques like Amplifluor and Kompetitive allele specific PCR (KASP), as well as others employing common universal probes (UPs) for SNP analyses. In the proposed ASQ method, the fluorophores and quencher are located in separate complementary oligonucleo… Show more

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Cited by 10 publications
(6 citation statements)
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“…The allele discrimination and genotyping results are clear using this ASQ method with medium throughput working effectively in 96-or 384-well microplates and qPCR instruments. Successful results for the ASQ method were recorded earlier in the genotyping of barley (Kalendar et al, 2022), sugar beet, and tomato (Amangeldiyeva et al, 2023).…”
Section: Discussionmentioning
confidence: 92%
See 1 more Smart Citation
“…The allele discrimination and genotyping results are clear using this ASQ method with medium throughput working effectively in 96-or 384-well microplates and qPCR instruments. Successful results for the ASQ method were recorded earlier in the genotyping of barley (Kalendar et al, 2022), sugar beet, and tomato (Amangeldiyeva et al, 2023).…”
Section: Discussionmentioning
confidence: 92%
“…In general, it is much faster to work with medium throughput methods, for example, based on fluorescence (Förster) resonance energy transfer (FRET). Recently, allele-specific qPCR (ASQ) methods for plant genotyping have been developed that are also suitable for chickpea (Kalendar et al, 2022;Amangeldiyeva et al, 2023). Microarray technology employing thousands of simultaneous reactions on a microchip represents the next generation of plant genotyping (Varshney et al, 2012), and diversity array technology (DArT) is also very powerful and popular for the identification of SNP and haplotypes (a group of closely located SNPs) in genetic regions of entire genomes (James et al, 2008;Deres and Feyissa, 2022), including chickpea (Roorkiwal et al, 2014;Thudi et al, 2014).…”
Section: Introductionmentioning
confidence: 99%
“…These results for SNP for genotyping of humans validated our conclusion that the proposed ASQ method is very accurate and effective for SNP genotyping; we expect similar results in other animal species. In addition, we developed ASQ sets and applied SNP genotyping in the barley genes HvSAP16 and HvSAP8 (controlling stress-associated proteins); these are validated examples and have been accepted for publication ( Baidyussen et al, 2021 ; Kalendar et al, 2022 ). Our tool and the ASQ method are suitable for two-, three-, or four-allelic uniplex reactions but can potentially be used for different SNPs in a multiplex format in a range of applications, including medical or forensic studies or other studies involving SNP genotyping.…”
Section: Resultsmentioning
confidence: 99%
“…These advancements have increased efficiency and reduced costs ( Elbaidouri et al., 2013 ; Mir and Varshney, 2012 ). With such NGS-based high-throughput technological developments, low-throughput molecular markers, such as Kompetitive allele-specific PCR (KASP) ( Makhoul et al., 2020 ), nevertheless remain indispensable for tracking specific genomic regions in molecular breeding programs when analyzing large numbers of samples ( Kalendar et al., 2022a ; Kalendar et al., 2022c ). Therefore, single nucleotide polymorphism (SNP) markers continue to be the most preferred marker systems for development of high-throughput genotypic platforms for genome-wide marker scanning.…”
Section: Prospects Challenges and Discussionmentioning
confidence: 99%