ARS | Publication request: SINGLE NUCLEOTIDE POLYMORPHISM DISCOVERY AND MAPPING IN MAIZE

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: March 14, 2002
Publication Date: March 14, 2002
Citation: I VROH, B., MCMULLEN, M.D., SCHROEDER, S., SANCHEZ-VILLEDA, H., HOUCHINS, K.E., FANG, Z., POLACCO, M.L., GARDINER, J., MORGANTE, M., COE JR, E.H. SINGLE NUCLEOTIDE POLYMORPHISM DISCOVERY AND MAPPING IN MAIZE. MAIZE GENETICS CONFERENCE. 2002. ABSTRACT. P. 83.

Technical Abstract: There is increased interest in using single nucleotide polymorphism (SNPs) for detecting genes linked to economically important traits in plants. Single nucleotide polymorphisms are biallelic markers that have the potential for inexpensive genotyping using high-throughput methods. The present study is aimed at developing SNP markers to integrate the genetic and the physical maps of maize. Two hundred unigenes from the "Cornsensus" set served as templates for this preliminary study. Primers were designed to amplify approximately 300 bp from each unigene. The amplification products were sequenced with forward and reverse primers in 12 lines including B73 and Mo17 (the parents of the IBM intermated B73 x Mo17 mapping population). Sequence quality was assessed using modified Phred and Phrap software. Primer sequences were trimmed with PERL scripts before aligning with the Clustal software. Only one locus was monomorphic. Sequence comparisons of 178 loci, consisting of 62,300 bp, contained a total of 1288 variants; 58% SNPs and 42% indels. This is an average of 7.2 variants per locus. The frequency of SNPs and indels is 1 in 84 bp and 1 in 115 bp, respectively. Seventy-five loci contained SNPs between B73 and Mo17. The SNPs between B73 and MO17 were validated and used in multiplexed primer extension reactions on the IBM population. The scoring of the SNP mapping data was automated and integrated to a Laboratory Information System Management (LIMS) for mapping and for submission to MaizeDB. The pipeline of SNP production and mapping will be presented. This work was funded by NSF Plant Genome Grant DBI 9872655.