Comparison of TaqMan, KASP and rhAmp SNP genotyping platforms in hexaploid wheat

PLoS One. 2019 May 22;14(5):e0217222. doi: 10.1371/journal.pone.0217222. eCollection 2019.

Abstract

Advances in high-throughput genotyping enable the generation of genome-scale data much more easily and at lower cost than ever before. However, small-scale and cost-effective high-throughput single-nucleotide polymorphism (SNP) genotyping technologies are still under development. In this study, we compared the performances of TaqMan, KASP and rhAmp SNP genotyping platforms in terms of their assay design flexibility, assay design success rate, allele call rate and quality, ease of experiment run and cost per sample. Fifty SNP markers linked to genes governing various agronomic traits of wheat were chosen to design SNP assays. Design success rates were 39/50, 49/50, and 49/50 for TaqMan, KASP, and rhAmp, respectively, and 30 SNP assays were manufactured for genotyping comparisons across the three platforms. rhAmp showed 97% of samples amplified while TaqMan and KASP showed 93% and 93.5% of amplifications, respectively. Allele call quality of rhAmp was 97%, while it was 98% for both TaqMan and KASP. rhAmp and KASP showed significantly better (p < 0.001) allele discrimination than TaqMan; however, TaqMan showed the most compact cluster. Based on the current market, rhAmp was the least expensive technology followed by KASP. In conclusion, rhAmp provides a reliable and cost-effective option for targeted genotyping and marker-assisted selection in crop genetic improvement.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Genes, Plant*
  • Genotype
  • Ploidies*
  • Polymerase Chain Reaction / classification*
  • Polymerase Chain Reaction / methods*
  • Polymorphism, Single Nucleotide*
  • Triticum / genetics*

Grants and funding

The Integrated DNA Technologies provided support in the form of research materials for rhAmp SNP genotyping platform and salaries for authors PWT, JW and CC. In addition, the Samuel Roberts Noble Foundation provided support for this study. The funders did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.