In cooperation with Allen van Deynze (UC Davis) and Esther van der Knaap (OSU/OARDC) we are expanding our Single Nucleotide Polymorphisms (SNP) discovery to include sequence variation within the introns of Conserved Orthologous Set (COS) genes.  These COS intron (COSi) markers have a rate of polymorphism that is ~5 fold higher than the coding regions found in the EST databases.  Link to abstract of the USDA/NRI grant supporting this work.

Conservation of intron position between plant species allows us to predict intron position.  Primers based on EST sequences allow us to amplify and sequence introns in order to identify new SNPs.