Development of versatile gene-based SNP assays in maize (Zea mays L.)

A large number of maize single nucleotide polymorphism (SNP) candidate sequences have been generated and deposited in public databases. However, very little work has been done to date to comprehensively characterize those SNPs and identify a set of markers, which potentially would have high impact in molecular genetics research and breeding programs. Here we describe a multi-step process to identify highly polymorphic gene-based SNPs among ~130,000 public markers. A set of 695 highly polymorphic SNPs (minor allele frequency value >0.3), identified within exons, 5′ and 3′ untranslated regions of genes, were converted into four of the most popular high-throughput genotyping assays that include Illumina’s GoldenGate and Infinium chemistries, Life Technologies’ TaqMan assay and KBioSciences’ KASPar assay. The term “versatile” was applied to 162 gene-based SNPs that were successfully converted into all four chemistries and had perfect genotypic clustering patterns. This subset of discovered versatile SNP markers represents a universal tool for application in various molecular genetics and breeding projects in maize, where genotyping is based on one of the four above-mentioned chemistries. This study demonstrated that despite the availability of millions of discovered SNPs in maize, only a very small portion of those polymorphisms could be utilized for the development of robust, versatile assays, and has real practical value in marker-assisted selection.