Development of SNP markers for marker-assisted breeding in Chinese cabbage using Fluidigm genotyping assays

Traditional breeding methods usually involve field tests carried out by experienced breeders. However, such methods are costly and time-consuming. Recently, with the development of Next-Generation Sequencing (NGS) technology, molecular markers are being utilized for selection processes in breeding. To implement a high-throughput system using molecular markers in Chinese cabbage (Brassica rapa subsp. pekinensis) breeding, we developed single nucleotide polymorphism (SNP) marker sets for background selection and testing F-1 purity using Fluidigm genotyping assays. SNPs were generated using NGS technology on 209 varieties of Chinese cabbage collected from around the world. Those with minor allele frequency >= 5% and polymorphism information content >= 0.3 were screened, and then based on the physical distribution among the 10 chromosomes, 177 SNPs were selected and synthesized for testing. To obtain marker sets with high selection efficiency, we tested 192 SNPs on 45 types of inbred lines and 29 types of F-1 hybrids. Among the 192 SNPs, we selected 96 markers sets for background selection and 24 marker sets for F-1 purity testing according to the following criteria; the genotype of the parents was homozygous, and the F-1 follows the parents' genotypes. These SNP sets are suitable for high-throughput systems using the 96.96 and 192.24 integrated fluidic circuit platforms of Fluidigm genotyping assays. These SNP marker sets are not only efficient for selecting of early fixed lines as background selection but are also useful for testing the purity of F-1 hybrids.