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Originally published as Genetics Published Articles Ahead of Print on August 30, 2008.
Genetics, Vol. 180, 629-637, September 2008, Copyright © 2008
doi:10.1534/genetics.108.092239
Efficient Mapping of Plant Height Quantitative Trait Loci in a Sorghum Association Population With Introgressed Dwarfing Genes
Patrick J. Brown*,
,
William L. Rooney
,
Cleve Franks
and
Stephen Kresovich*,**,1
* Institute for Genomic Diversity, Department of Plant Biology, and ** Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843 and United States Department of Agriculture–Agricultural Research Service, Cropping Systems Research Laboratory, Lubbock, Texas 79415
1 Corresponding author: Institute for Genomic Diversity, 158 Biotechnology, Cornell University, Ithaca, NY 14853.
E-mail: sk20{at}cornell.edu
Of the four major dwarfing genes described in sorghum, only Dw3 has been cloned. We used association mapping to characterize the phenotypic effects of the dw3 mutation and to fine map a second, epistatic dwarfing QTL on sorghum chromosome 9 (Sb-HT9.1). Our panel of 378 sorghum inbreds includes 230 sorghum conversion (SC) lines, which are exotic lines that have been introgressed with dwarfing quantitative trait loci (QTL) from a common parent. The causal mutation in dw3 associates with reduced lower internode length and an elongation of the apex, consistent with its role as an auxin efflux carrier. Lines carrying the dw3 mutation display high haplotype homozygosity over several megabases in the Dw3 region, but most markers linked to Dw3 do not associate significantly with plant height due to allele sharing between Dw3 and dw3 individuals. Using markers with a high mutation rate and the dw3 mutation as an interaction term, significant trait associations were detected across a 7-Mb region around Sb-HT9.1, largely due to higher detection power in the SC lines. Conversely, the likely QTL interval for Sb-HT9.1 was reduced to 
100 kb, demonstrating that the unique structure of this association panel provides both power and resolution for a genomewide scan.
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