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Background  Research to identify and characterize stem rust resistance genes in common wheat,  Triticum aestivum , has been stimulated by the emergence of Ug99-lineage races of the wheat stem rust pathogen,  Puccinia graminis  f. sp.  tritici  ( Pgt ), in Eastern Africa. The Montenegrin spring wheat landrace PI 362698 was identified as a source of  Pgt  resistance. This accession exhibits resistance to multiple Ug99-lineage and North American  Pgt  races at seedling and adult-plant stages. A recombinant inbred population was developed by crossing the susceptible line LMPG-6 with a single plant selection of PI 362698. A genetic map was constructed using the Illumina iSelect 90 K wheat assay and the markers csLv34, NB-LRR3, and wMAS3 and quantitative trait locus (QTL) analysis was performed.    Results  QTL analysis identified five significant QTLs (α = 0.05) on chromosomes 2B, 3B, 6A, 6D, and 7A associated with wheat stem rust resistance. The QTL on chromosome 3B was identified using both field data from Kenya ( Pgt  Ug99-lineage races) and seedling data from  Pgt  race MCCF. This QTL potentially corresponds to  Sr12  or a new allele of  Sr12 . The multi-pathogen resistance gene  Sr57  located on chromosome 7D is present in PI 362698 according to the diagnostic markers csLv34 and wMAS3, however a significant QTL was not detected at this locus. The QTLs on chromosomes 2B, 6A, and 6D were identified during seedling trials and are thought to correspond to  Sr16 ,  Sr8a , and  Sr5 , respectively. The QTL identified on chromosome 7A was detected using MCCF seedling data and may be  Sr15  or a potentially novel allele of recently detected Ug99 resistance QTLs.    Conclusions  The combination of resistance QTLs found in PI 362698 is like the resistance gene combination present in the broadly resistant cultivar Thatcher. As such, PI 362698 may not be a landrace as previously thought. PI 362698 has been crossed with North Dakota wheat germplasm for future breeding efforts. Additional work is needed to fully understand why the combination of genes present in PI 362698 and ‘Thatcher’ provide such durable resistance.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4438-y) contains supplementary material, which is available to authorized users.

Dissection of the multigenic wheat stem rust resistance present in the Montenegrin spring wheat accession PI 362698