Theor Appl Genet DOI 10.1007/s00122-011-1664-y 123 ORIGINAL PAPER Association mapping and gene–gene interaction for stem rust resistance in CIMMYT spring wheat germplasm Long-Xi Yu · Aaron Lorenz · Jessica Rutkoski · Ravi P. Singh · Sridhar Bhavani · Julio Huerta-Espino · Mark E. Sorrells Received: 29 March 2011 / Accepted: 9 July 2011  Springer-Verlag 2011 Abstract The recent emergence of wheat stem rust Ug99 and evolution of new races within the lineage threatens glo- bal wheat production because they overcome widely deployed stem rust resistance (Sr) genes that had been eVective for many years. To identify loci conferring adult plant resistance to races of Ug99 in wheat, we employed an association mapping approach for 276 current spring wheat breeding lines from the International Maize and Wheat Improvement Center (CIMMYT). Breeding lines were gen- otyped with Diversity Array Technology (DArT) and microsatellite markers. Phenotypic data was collected on these lines for stem rust race Ug99 resistance at the adult plant stage in the stem rust resistance screening nursery in Njoro, Kenya in seasons 2008, 2009 and 2010. Fifteen marker loci were found to be signiWcantly associated with stem rust resistance. Several markers appeared to be linked to known Sr genes, while other signiWcant markers were located in chromosome regions where no Sr genes have been previously reported. Most of these new loci colocal- ized with QTLs identiWed recently in diVerent biparental populations. Using the same data and Q + K covariate matrices, we investigated the interactions among marker loci using linear regression models to calculate P values for pairwise marker interactions. Resistance marker loci including the Sr2 locus on 3BS and the wPt1859 locus on 7DL had signiWcant interaction eVects with other loci in the same chromosome arm and with markers on chromosome 6B. Other resistance marker loci had signiWcant pairwise interactions with markers on diVerent chromosomes. Based on these results, we propose that a complex network of gene–gene interactions is, in part, responsible for resistance to Ug99. Further investigation may provide insight for understanding mechanisms that contribute to this resistance gene network. Introduction Association mapping (AM) is one of several techniques to identify marker-trait associations and has been used exten- sively in human and animal genetic studies (DeWan et al. 2006; Karlsson et al. 2007). The principle of AM is based on linkage disequilibrium (LD), or non-random association of alleles at adjacent loci within a population. One impor- tant advantage of AM over traditional biparental QTL map- ping is that AM can be conducted directly on relevant breeding material, thus permitting direct inference from data analysis to the breeding program. Furthermore, pheno- typic variation is observed for most traits of interest and Communicated by B. Keller. Electronic supplementary material The online version of this article (doi:10.1007/s00122-011-1664-y) contains supplementary material, which is available to authorized users. L.-X. Yu · J. Rutkoski · M. E. Sorrells (&) Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY 14853, USA e-mail: mes12@cornell.edu A. Lorenz Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA R. P. Singh · S. Bhavani International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600 El Batan, Mexico J. Huerta-Espino Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230 Chapingo, Edo de México, Mexico