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Background  The adult plant stem rust resistance gene  Sr2  was introgressed into hexaploid wheat cultivar (cv) Marquis from tetraploid emmer wheat cv Yaroslav, to generate stem rust resistant cv Hope in the 1920s. Subsequently,  Sr2  has been widely deployed and has provided durable partial resistance to all known races of  Puccinia graminis  f. sp.  tritici . This report describes the physical map of the  Sr2 -carrying region on the short arm of chromosome 3B of cv Hope and compares the Hope haplotype with non- Sr2  wheat cv Chinese Spring.    Results   Sr2  was located to a region of 867 kb on chromosome 3B in Hope, which corresponded to a region of 567 kb in Chinese Spring. The Hope  Sr2  region carried 34 putative genes but only 17 were annotated in the comparable region of Chinese Spring. The two haplotypes differed by extensive DNA sequence polymorphisms between flanking markers as well as by a major insertion/deletion event including ten Germin-Like Protein (GLP) genes in Hope that were absent in Chinese Spring. Haplotype analysis of a limited number of wheat genotypes of interest showed that all wheat genotypes carrying  Sr2  possessed the GLP cluster; while, of those lacking  Sr2 , some, including Marquis, possessed the cluster, while some lacked it. Thus, this region represents a common presence-absence polymorphism in wheat, with presence of the cluster not correlated with presence of  Sr2 . Comparison of Hope and Marquis GLP genes on 3BS found no polymorphisms in the coding regions of the ten genes but several SNPs in the shared promoter of one divergently transcribed GLP gene pair and a single SNP downstream of the transcribed region of a second GLP.    Conclusion  Physical mapping and sequence comparison showed major haplotype divergence at the  Sr2  locus between Hope and Chinese Spring. Candidate genes within the  Sr2  region of Hope are being evaluated for the ability to confer stem rust resistance. Based on the detailed mapping and sequencing of the locus, we predict that  Sr2  does not belong to the NB-LRR gene family and is not related to previously cloned, race non-specific rust resistance genes  Lr34  and  Yr36 .    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-014-0379-z) contains supplementary material, which is available to authorized users.

Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus