Stripe rust, caused by the fungus Puccinia striiformis f. s. tritici (Pst), is a destructive disease of wheat globally. A promising source for novel Pst resistance genes is wild emmer wheat (Triticum dicoccoides; WEW). Seven WEW R-genes, Yr15, YrH52, YrG303, Yr35, Yr36, YrSM139-1B, and YrTZ2, were characterized and mapped so far, but only Yr15 and Yr36 were positionally cloned. Both Yr15 and Yr36 confer broad-spectrum resistance to Pst, however, Yr36 encodes for START-Kinase protein domains1 while Yr15 has a kinase-pseudokinase domain structure, designated Wheat Tandem Kinase 1 (WTK1)2. Here, we elucidate the genetic relationships between Yr15, YrH52, and YrG303.

Comparative fine mapping of these genes revealed that the three of them occupy the same genetic position. Furthermore, Yr15 gene-specific markers showed the presence of WTK1 in the three WEW donor accessions (G25, H52 and G303). Sequencing of full-length WTK1 showed that all exons and introns (4657 bp) of this gene in G303 are identical to G25, while in H52 there is a small insertion of 6 bp (CATTGT) in the first intron. Sense and nonsense point mutations were identified for yr15, yrG303 and yrH52 susceptible mutants in the sequenced WTK1 locus validating that the resistance phenotypes of Yr15, YrG303, and YrH52 are all conferred by the functional WTK1 allele, designated as Wtk1.

Exon-intron comparisons of multiple WTK1 homoeologous and paralogous copies scattered along the allopolyploid wheat genomes enabled us to develop functional molecular markers (FMMs), which were used for population genetic study. The Wtk1 allele was found to be absent in a worldwide collection of 513 wheat cultivars, except for 32 introgression lines with Yr15 from WEW, as well as in 84% of the 382 tested WEW accessions collected across the Fertile Crescent. Yr15 was found to be distributed along a narrow axis from Mt. Carmel to Anti-Lebanon mountain ridge, mostly at elevation of above ~500 m, where the climatic conditions are favorable for disease development, therefore providing insights on gene flow and host-parasite co-evolution in WEW natural habitats. The worldwide absence of Wtk1 in cultivated wheat and in WEW natural populations from southeast Turkey, where wheat is believed to be domesticated, proposes that Yr15 was rather left behind, than lost during domestication. Our results highlight the importance of conservation of WEW populations in their natural habitats for discovery of novel R-genes and studies of host-parasite co-evolution. 1Fu et al. 2009; Science