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• Powdery mildew, a fungal disease caused by Blumeria graminis f. sp. tritici (Bgt), has a serious impact on wheat production. Loss of resistance in cultivars prompts a continuing search for new sources of resistance. • Wild emmer wheat (Triticum turgidum ssp. dicoccoides, WEW), the progenitor of both modern tetraploid and hexaploid wheats, harbors many powdery mildew resistance genes. We report here the positional cloning and functional characterization of Pm41, a powdery mildew resistance gene derived from WEW, which encodes a coiled-coil, nucleotide-binding site and leucine-rich repeat protein (CNL). Mutagenesis and stable genetic transformation confirmed the function of Pm41 against Bgt infection in wheat. • We demonstrated that Pm41 was present at a very low frequency (1.81%) only in southern WEW populations. It was absent in other WEW populations, domesticated emmer, durum, and common wheat, suggesting that the ancestral Pm41 was restricted to its place of origin and was not incorporated into domesticated wheat. • Our findings emphasize the importance of conservation and exploitation of the primary WEW gene pool, as a valuable resource for discovery of resistance genes for improvement of modern wheat cultivars.

KEY MESSAGE: By applying comparative genomics analyses, a high-density genetic linkage map narrowed the powdery mildew resistance gene Pm41 originating from wild emmer in a sub-centimorgan genetic interval. Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, results in large yield losses worldwide. A high-density genetic linkage map of the powdery mildew resistance gene Pm41, originating from wild emmer (Triticum turgidum var. dicoccoides) and previously mapped to the distal region of chromosome 3BL bin 0.63–1.00, was constructed using an F₅:₆ recombinant inbred line population derived from a cross of durum wheat cultivar Langdon and wild emmer accession IW2. By applying comparative genomics analyses, 19 polymorphic sequence-tagged site markers were developed and integrated into the Pm41 genetic linkage map. Ultimately, Pm41 was mapped in a 0.6 cM genetic interval flanked by markers XWGGC1505 and XWGGC1507, which correspond to 11.7, 19.2, and 24.9 kb orthologous genomic regions in Brachypodium, rice, and sorghum, respectively. The XWGGC1506 marker co-segregated with Pm41 and could be served as a starting point for chromosome landing and map-based cloning as well as marker-assisted selection of Pm41. Detailed comparative genomics analysis of the markers flanking the Pm41 locus in wheat and the putative orthologous genes in Brachypodium, rice, and sorghum suggests that the gene order is highly conserved between rice and sorghum. However, intra-chromosome inversions and re-arrangements are evident in the wheat and Brachypodium genomic regions, and gene duplications are also present in the orthologous genomic regions of Pm41 in wheat, indicating that the Brachypodium gene model can provide more useful information for wheat marker development.