KASP Markers for Maize

Maize data were taken with permission from Ed Buckler’s Lab (esb33@cornell.edu). The map is an integration of both Pioneer Hybrid Maize (PHM) and Panzea (PZA) data sets, located at http://www.panzea.org/.

How PZA Markers were generated: A maize association panel with 277 inbred lines of diverse origins recognised by plant breeders were assembled. SNP discovery was performed using a diverse set of 14 maize inbreds and 16 teosinte (Zea mays ssp. Parviglumis) inbreds. SNPs were designed from 413 randomly selected genes out of the ~10,000 maize ESTs in the MMP-Dupont set. SNP assay development and scoring was performed by Gennaissance Pharmaceutical using the Sequenom MassARRAY System (Yu et al., 2006). For details refer to:  Yu, J, et al. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature 38(2): 203-208.

How PHMSNP markers were generated: Nested primer pairs were designed to target high quality ESTs of 24 diverse Pioneer-proprietary inbreds. Amplification products were sequenced, the sequences were aligned and SNPs and indels were identified using software tools proprietary to Myriad. From this procedure, 1088 sequence loci were selected that had high quality sequence and showed a match by BLASTIN. Sequences were examined for 60 public inbreds of diverse origins. Based on consensus sequences for the 1088 loci, SNP and indel frequencies were estimated. SNP loci were further selected for marker development which resulted in 640 SNPs. These SNPs (plus additional 895 ‘PZA’) were validated on the Illumina GoldenGate Platform. For details refer to: Jones E, et al. 2009. Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L) germplasm. Mol Breeding 24: 165-176.