Originally published as Genetics Published Articles Ahead of Print on September 1, 2006.

Genetics, Vol. 174, 1671-1683, November 2006, Copyright © 2006
doi:10.1534/genetics.106.060376

Genetic Dissection of Intermated Recombinant Inbred Lines Using a New Genetic Map of Maize

Yan Fu^*,1, Tsui-Jung Wen, Yefim I. Ronin, Hsin D. Chen, Ling Guo, David I. Mester, Yongjie Yang^*, Michael Lee, Abraham B. Korol, Daniel A. Ashlock^** and Patrick S. Schnable^*,,,,2

^* Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa 50011, Department of Agronomy, Iowa State University, Ames, Iowa 50011, Institute of Evolution, University of Haifa, Haifa 31905, Israel, Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, Iowa 50011, ^** Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario N1G 2W1, Canada and Center for Plant Genomics, Iowa State University, Ames, Iowa 50011-3467

² Corresponding author: 2035B Roy J. Carver Co-Laboratory, Iowa State University, Ames, IA 50011-3650. 
E-mail: schnable{at}iastate.edu

A new genetic map of maize, ISU–IBM Map4, that integrates 2029 existing markers with 1329 new indel polymorphism (IDP) markers has been developed using intermated recombinant inbred lines (IRILs) from the intermated B73 x Mo17 (IBM) population. The website http://magi.plantgenomics.iastate.edu provides access to IDP primer sequences, sequences from which IDP primers were designed, optimized marker-specific PCR conditions, and polymorphism data for all IDP markers. This new gene-based genetic map will facilitate a wide variety of genetic and genomic research projects, including map-based genome sequencing and gene cloning. The mosaic structures of the genomes of 91 IRILs, an important resource for identifying and mapping QTL and eQTL, were defined. Analyses of segregation data associated with markers genotyped in three B73/Mo17-derived mapping populations (F₂, Syn5, and IBM) demonstrate that allele frequencies were significantly altered during the development of the IBM IRILs. The observations that two segregation distortion regions overlap with maize flowering-time QTL suggest that the altered allele frequencies were a consequence of inadvertent selection. Detection of two-locus gamete disequilibrium provides another means to extract functional genomic data from well-characterized plant RILs.

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