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Stem rust resistance genes Sr39 (RL6082) and Sr36 (Cook) were transferred from Aegilops speltoides and Triticum timopheevi to chromosome 2B of wheat. Both genes are located on large translocated segments. Genotypes carrying Sr36 and Sr39 produce infection types (ITs) 0; and 2, respectively, against avirulent pathotypes. This investigation was planned to study the genetic relationship between these genes with the aim of combining them in a single genotype. Seedling tests on RL6082/Cook F3 lines showed complete repulsion linkage [25 Sr39Sr39sr36sr36 (IT2-) : 53 Sr39sr39Sr36sr36 (IT2-, IT0;) : 13 sr39sr39Sr36Sr36 (IT 0;)], and preferential transmission of the Ae. speltoides segment over the T. timopheevi segment was evident from the segregation ratio. The Sr39-carrying translocation was shortened by Niu et al. (2011; Genetics 187: 1011-1021) and the genetic stock carrying the shortest segment was named RWG1. Based on the reported location of Sr39 in the smaller alien segment in RWG1, we predicted that it should recombine with Sr36. F3 lines derived RWG1/Cook were phenotyped for stem rust response at the two-leaf stage and again complete repulsion linkage between Sr39 and Sr36 was observed [23 Sr39Sr39sr36sr36 (IT2-) : 78 Sr39sr39Sr36sr36 (IT0;, IT2-) : 68 sr39sr39Sr36Sr36 (IT 0;)]. In contrast to the cross involving the large Sr39 translocation, preferential transmission of the T. timopheevi segment was observed. These results indicated that a genetic determinant of meiotic drive had been deleted in the shortened Ae. speltoides segment. Genotyping with the co-dominant STS marker rwgs28 matched the phenotypic classification of F3 families. Marker rwgs28 was diagnostic for the Ae. speltoides segment, but the rwgs28 allele amplified in Cook was not T. timopheevi-specific.