Available TaqMan® assays
Comparison studies were performed to compare genotype calls between the TaqMan® Assays and KASP data previously generated. Using a selection of 20 markers across 10 different varieties, concordance was around 90% for genotypes in which both platforms were able to successfully make a call (see Table below). Interestingly TaqMan® Assays were able to make calls for certain SNP/sample combinations (white cells in the table below, e.g. BS00003717) which were not able to be obtained using the KASP chemistry. In addition, for non-concordant SNP calls, (pink cells in table, e.g. BS0009377) TaqMan® calls were confirmed using a real-time trace feature in Life Technologies’ ViiA 7™ instrument, although validation of which chemistry is actually making the right call could be performed using an independent platform such as sequencing.
The TaqMan® Assays include the core marker set of 960 SNPs which were selected to be evenly distributed (and where possible co-dominant and polymorphic) across the genome using the Avalon x Cadenza genetic map.
To order these TaqMan® Assays from Life Technologies and receive pricing and other important information for the wheat community please visit the Life Technologies web site or e-mail Agnese Winfield or telephone on (0044) 0145 4528326.
Comparison of TaqMan® and KASP data across 10 wheat varieties. For each variety, the KASP call is shown in the left-hand column and the corresponding TaqMan® call in the right column. Green cells indicate concordant calls, pink cells indicate discordant calls and white cells indicate a result in which only one platform was able to make a genotype call.
Maintained by Mark Winfield.