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This research project is supported By National Science Foundation(NSF) DBI-0321711 .

Identifying Single Nucleotide Polymorphisms (SNPs) in B73 and Mo17 maize inbreds: A step-by-step approach Afriyie B. Dankwa 1 , Hsin Debbie Chen 2 , Josh Shendelman 2 and Patrick S. Schnable 2 . 1 Albany State University, Albany, GA 31705, 2 Iowa State University, Ames, IA 50011.

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This research project is supported By National Science Foundation(NSF) DBI-0321711 .

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  1. Identifying Single Nucleotide Polymorphisms (SNPs) in B73 and Mo17 maize inbreds: A step-by-step approach Afriyie B. Dankwa1, Hsin Debbie Chen 2, Josh Shendelman 2 and Patrick S. Schnable2. 1Albany State University, Albany, GA 31705, 2 Iowa State University, Ames, IA 50011 ALBANY STATE UNIVERSITY Introduction Results Figure 2. Picture of maize inbredlines Four primers pairs were designed using Primer3 software to flank putative SNPs. After sequencing we confirmed that all four putative SNPs are real. Sequence obtained for one putative SNP is illustrated in Figure 4. Summary Maize, also known as corn, is an economically important cereal grain that was domesticated in Mesoamerica. Maize is genetically diverse as illustrated in figure 1. Maize is often used as model research organism. In the light of that, this project seeks to use maize to identify Putative Single Nucleotide Polymorphism(SNP) in two Maize Inbreds--B73 and Mo17.(figure 2) The traditional method of sequencing DNA by utilizing the right primers and appropriate sequencer was used in investigating the presence of Single Nucleotide Polymorphism (SNP) in two maize inbreds. B73B73XMo17 Mo17 Materials and Methods Figure 3. Example of sequencing trace file Primers were designed for B73 and Mo17 based on Maize Assembled Genomic Island (MAGI) sequences. PCR were performed on Mo17 and B73 genomic DNA and the resulting PCR products were then sequenced using an ABI 3706X DNA sequencer. DNA sequences were analyzed using Sequencer software (Fig. 3). Figure 4. Example of confirmed SNP sequence Figure 1. Maize genetic diversity Conclusion and Discussion The sequencing results validate the existence of SNPs in the Mo17 and B73 alleles. These SNPs can serve as genetic markers for these inbred lines. Genetic markers can be used to study the relationship between an inherited disease and its genetic cause. Future Studies The next step is to genotype a population of Recombinant Inbred Lines (RIL) with iPLEX on the MassARRAY platform developed by SEQUENOM. Acknowledgements This research project is supported By National Science Foundation(NSF) DBI-0321711.

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