Genetics. Published Articles Ahead of Print: September 1, 2006, Copyright © 2006
doi:10.1534/genetics.106.060376


A more recent version of this article appeared on November 1, 2006.

REGULAR RESEARCH PAPERS

Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize that includes 1,329 novel PCR-based genic markers

Yan Fu 1, Tsui-Jung Wen 1, Yefim I. Ronin 2, Hsin D. Chen 1, Ling Guo 1, David I. Mester 2, Yongjie Yang 1, Michael Lee 1, Abraham B. Korol 2, Daniel A. Ashlock 3 and Patrick S. Schnable 1*

1 Iowa State University
2 University of Haifa
3 University of Guelph

* To whom correspondence should be addressed. E-mail: schnable{at}iastate.edu.

Submitted on July 6, 2006
Revised on August 21, 2006
Accepted on 21 August 2006


Abstract

A new genetic map of maize, ISU-IBM Map4, that integrates 2,029 existing markers with 1,329 new InDel Polymorphism (IDP) markers has been developed using Intermated Recombinant Inbred Lines (IRILs) from the Intermated B73xMo17 (IBM) population. The web site 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 QTLs and eQTLs, 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 QTLs 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.

Key Words: QTL mapping, gametic disequilibrium, genetic map, recombinant inbred lines, segregation distortion




This article has been cited by other articles:


Home page
 GeneticsHome page
J. Yu, J. B. Holland, M. D. McMullen, and E. S. Buckler
Genetic Design and Statistical Power of Nested Association Mapping in Maize
Genetics, January 1, 2008; 178(1): 539 - 551.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
F. I. E. Amarillo and H. W. Bass
A Transgenomic Cytogenetic Sorghum (Sorghum propinquum) Bacterial Artificial Chromosome Fluorescence in Situ Hybridization Map of Maize (Zea mays L.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion
Genetics, November 1, 2007; 177(3): 1509 - 1526.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
P. J. Balint-Kurti, J. C. Zwonitzer, R. J. Wisser, M. L. Carson, M. A. Oropeza-Rosas, J. B. Holland, and S. J. Szalma
Precise Mapping of Quantitative Trait Loci for Resistance to Southern Leaf Blight, Caused by Cochliobolus heterostrophus Race O, and Flowering Time Using Advanced Intercross Maize Lines
Genetics, May 1, 2007; 176(1): 645 - 657.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S. J. Emrich, L. Li, T.-J. Wen, M. D. Yandeau-Nelson, Y. Fu, L. Guo, H.-H. Chou, S. Aluru, D. A. Ashlock, and P. S. Schnable
Nearly Identical Paralogs: Implications for Maize (Zea mays L.) Genome Evolution
Genetics, January 1, 2007; 175(1): 429 - 439.
[Abstract] [Full Text] [PDF]