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United States Department of Agriculture

Agricultural Research Service

Title: Single Nucleotide Polymorphisms and Indels for the Development of Integrated Physical and Genetic Maps of Maize

Authors
item Vroh, Bi - UNIV OF MISSOURI
item McMullen, Michael
item Schultz, Linda - UNIV OF MISSOURI
item Duru, Ngozi - UNIV OF MISSOURI
item Schroeder, Steven - UNIV OF MISSOURI
item Sanchez-Villeda, Hector - UNIV OF MISSOURI
item Schaeffer, Mary
item Gardiner, J - UNIV OF MISSOURI
item Useche, L - DUPONT, NEWARD, DE
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., MCMULLEN, M.D., SCHULTZ, L., DURU, N., SCHROEDER, S., SANCHEZ-VILLEDA, H., POLACCO, M.L., GARDINER, J., USECHE, L., COE JR, E.H. SINGLE NUCLEOTIDE POLYMORPHISMS AND INDELS FOR THE DEVELOPMENT OF INTEGRATED PHYSICAL AND GENETIC MAPS OF MAIZE. PLANT AND ANIMAL GENOME. 2003. Abstract p. 182.

Technical Abstract: Single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels) are becoming important genetic markers for major crop species. We amplified genomic regions corresponding to 678 unigenes across 12 maize inbred lines. The amplification products from 592 unigenes were sequenced (177,600 bp) across the 12 lines. Forty-six unigenes (8%) did not show any polymorphism. The remaining 546 loci contained 3024 sequence variants composed of 2448 (81%) SNPs, and 576 (19%) small InDels, an average of 5.5 variants per locus. Comparison of B73 and Mo17 sequences revealed 829 SNPs in 260 (44%) loci and 192 InDels in 150 (25%) loci. B73 and Mo17 are the parents of our high-resolution intermated B73 x Mo17 (IBM) mapping population that serves as the basis of the integrated genetic and physical map for maize. The unigenes have previously been assigned to maize bacterial artificial chromosomes (BAC) contigs by overgo hybridization (www.maizemap.org). Using 247 genetic markers restriction fragment length polymorphism and simple sequence repeats (RFLPs and SSRs) as a map framework, 226 unigenes (140 SNPs and 86 large InDels) were mapped on the IBM population. The resulting integrated map spans 5742 cM, and provides unambiguous anchoring of 123 BAC contigs to the integrated map. The developing integrated map of maize will be useful for map-based cloning, marker-assisted selection, and comparative genomics in grasses.

Last Modified: 12/19/2014
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