Originally published as Genetics Published Articles Ahead of Print on August 24, 2008.

Genetics, Vol. 180, 583-599, September 2008, Copyright © 2008
doi:10.1534/genetics.108.090118

Selection Mapping of Loci for Quantitative Disease Resistance in a Diverse Maize Population

Randall J. Wisser*,1, Seth C. Murray*, Judith M. Kolkman{dagger}, Hernán Ceballos{ddagger} and Rebecca J. Nelson*,{dagger},2

* Institute for Genomic Diversity, Department of Plant Breeding and Genetics and {dagger} Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853 and {ddagger} National University of Colombia, Valley of the Cauca, Colombia and International Center for Tropical Agriculture, Cali, Colombia

2 Corresponding author: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, 303A Plant Science, Ithaca, NY 14853.
E-mail: rjn7{at}cornell.edu

The selection response of a complex maize population improved primarily for quantitative disease resistance to northern leaf blight (NLB) and secondarily for common rust resistance and agronomic phenotypes was investigated at the molecular genetic level. A tiered marker analysis with 151 simple sequence repeat (SSR) markers in 90 individuals of the population indicated that on average six alleles per locus were available for selection. An improved test statistic for selection mapping was developed, in which quantitative trait loci (QTL) are identified through the analysis of allele-frequency shifts at mapped multiallelic loci over generations of selection. After correcting for the multiple tests performed, 25 SSR loci showed evidence of selection. Many of the putatively selected loci were unlinked and dispersed across the genome, which was consistent with the diffuse distribution of previously published QTL for NLB resistance. Compelling evidence for selection was found on maize chromosome 8, where several putatively selected loci colocalized with published NLB QTL and a race-specific resistance gene. Analysis of F2 populations derived from the selection mapping population suggested that multiple linked loci in this chromosomal segment were, in part, responsible for the selection response for quantitative resistance to NLB.