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

• Published in: PloS one Vol. 14; no. 5; p. e0217222
• Main Authors: Ayalew, Habtamu, Tsang, Pak Wah, Chu, Chenggen, Wang, Junzhou, Liu, Shuyu, Chen, Caifu, Ma, Xue-Feng
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 22-05-2019; Public Library of Science (PLoS)
• Subjects: Agricultural production; Agronomy; Alleles; Amplification; Assaying; Biology and Life Sciences; Crop yields; Deoxyribonucleic acid; Design; DNA; Enzymes; Genes; Genes, Plant; Genetic aspects; Genetic improvement; Genetic polymorphisms; Genetic research; Genetic testing; Genomes; Genomics; Genotype; Genotyping; Marker-assisted selection; Physical Sciences; Platforms; Ploidies; Polymerase Chain Reaction - classification; Polymerase Chain Reaction - methods; Polymorphism; Polymorphism, Single Nucleotide; Quality control; R&D; Research & development; Research and Analysis Methods; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Technology; Triticum - genetics; Wheat; Amarillo Texas; California; United States > US; Texas; Oklahoma; Redwood City California
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0217222

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.