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United States Department of Agriculture

Agricultural Research Service

Title: Bioinformatic Resources for Snp and Indel Discovery in the Maize Mapping Project

Authors
item Vroh, Bi - UNIV OF MISSOURI
item Sanchez-Villeda, Hector - UNIV OF MISSOURI
item Schroeder, Steve - UNIV OF MISSOURI
item McMullen, Michael
item Fang, Zhiwei - UNIV OF MISSOURI
item Schaeffer, Mary
item Gardiner, Jack - UNIV OF MISSOURI
item Davis, Georgia - UNIV OF MISSOURI
item Cone, Karen - UNIV OF MISSOURI
item Coe Jr, Edward

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: January 12, 2003
Publication Date: January 12, 2003
Citation: VROH, B.I., SANCHEZ-VILLEDA, H., SCHROEDER, S., MCMULLEN, M.D., FANG, Z., POLACCO, M.L., GARDINER, J., DAVIS, G., CONE, K., COE JR, E.H. BIOINFORMATIC RESOURCES FOR SNP AND INDEL DISCOVERY IN THE MAIZE MAPPING PROJECT. PLANT AND ANIMAL GENOME ABSTRACTS. 2003. Abstract p. 183.

Technical Abstract: The objective of our single nucleotide polymorphism (SNP) project is to anchor maize unigenes to the intermated B73 x Mo17 (IBM) genetic map. Starting with maize unigene sequences, primers were designed with Primer3 to give a polymerase chain reactor (PCR) products of ~300 bases. The PCR products from 12 maize inbred lines were sequenced in both directions on an ABI 3700 Sequencer. Sequences were automatically processed using a combination of Phred, Phrap, and PERL scripts. Sequences from the 12 inbred lines were aligned with the ClustalW program, and the alignments were imported into GeneDoc for automated detection of variants. Haplotypes are generated per loci, using SNP Detector. For SNP genotyping, we used multiplex primer extension assays. We imported GeneScan files and custom modified templates from Genotyper to the Maize Mapping Project laboratory information mapping system (LIMS) for automated genoype scoring and tracking. The LIMS consists of a relational database working with Visual Basic and PERL programs. Visual Basic scripts accept color of SNP peaks, and SNP primer length to read the genotype profile and generate genotype segregation files. Genotypes for InDels are visually scored from gels and entered into LIMS for verification of data, and for generation of Mapmaker files. The options for generating the Mapmaker file include specifying the number and the type of markers (SNPs and/or InDels), as well as the template of the mapping population. Using these bioinformatic tools, we have mapped over 200 unigenes, and expect to anchor another 1000 unigenes to the IBM genetic map. The bioinformatic procedures for sequence analysis and genotyping are presented.

Last Modified: 4/18/2014
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