Rice Breeder's Chip: Development of SNP Marker Sets for Different Breeding Applications

Molecular markers have been useful in developing improved rice breeding lines and have reduced time in releasing new rice varieties. However, conventional marker platforms are still constrained with gel electrophoresis and manual scoring which are laborious and time-consuming. These constraints have been the bottleneck in marker-aided selection and other breeding applications. Consequently, single nucleotide polymorphism (SNP) markers are quickly replacing gel-based markers because of the availability of high-throughput, semi-automated platforms and accuracy of allele calling.  Our group is currently developing SNP marker sets that are customized for specific breeding applications and trait-specific breeding as part of a genotyping service. For population-specific genome-wide scans, surveys of informative SNP markers were based on previous SNP data from 384-plex Illumina, 44k and KBioscience KASPar SNP sets. On the other hand, gene-specific SNP markers were developed from published studies, PCR amplicon sequences, and physical marker positions. Fluidigm SNPtype assays were designed and synthesized for running on 96.96 and 192.24 Dynamic Array chips on the Fluidigm EP1 system. The 192.24 Dynamic Arrays have been useful for foreground selection of introgressed genes and screening of genotypes for gene pyramiding using gene-specific markers.  On the other hand, the 96.96 format is best for background selection, genetic diversity analysis and quality control. The cost-effectiveness and efficiency of this system reduces time in generating genotype data, which is critical to breeding programs. In addition, it requires less manual work while ensuring data quality. Thus, the deployment of these custom marker sets will accelerate molecular breeding activities.