High-Throughput SNP Genotyping Platform for Marker-Assisted Breeding in Soybean

Single nucleotide polymorphism (SNP) markers have been widely utilized for genetic mapping and molecular breeding in several crop plants, including soybean.  For the past few years, we have been using the SimpleProbe SNP genotyping method for our marker-assisted selection (MAS) program.  However, low throughput, time consumption, and cost-effectiveness draw our concerns while adapting this method for marker-assisted backcrossing (MABC) and genomic selection (GS).  A new platform, using SNPType Assays developed by Fluidigm, provided a remarkable alternative approach for high-sample throughput and flexible SNP genotyping applications.  An initial study of a subset of selected SNP markers associated with quantitative trait loci (QTL) for different traits of interest in soybean was conducted using the Fluidigm EP1 system.  Preliminary results showed that the SNPType assays for 96.96 or 48.48 Fluidigm chips produced high-quality, reproducible data.  With the highest rates of allele call and concordance, the SNPType assays successfully confirmed and validated all SNP markers studied.  The study allows us to develop high-throughput and flexible SNP panels that will be efficiently employed for our MABC and GS programs in soybean.