f. sp. () causes wheat stem rust, a devastating fungal disease. The resistance gene confers immunity against this pathogen's most virulent races, including Ug99. We used comparative whole-genome sequencing of chemically mutagenized and natural isolates to identify a fungal gene named that is required for avirulence. The gene encodes a secreted protein capable of interacting with Sr35 and triggering the immune response. We show that the origin of isolates virulent on is associated with the nonfunctionalization of the gene by the insertion of a mobile element. The discovery of provides a new tool for surveillance, identification of host susceptibility targets, and characterization of the molecular determinants of immunity in wheat.

Background: Our understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. Using a differential nuclease sensitivity assay, we investigate the chromatin states of the coding and repetitive regions of the allopolyploid wheat genome. Results: Although open chromatin is found to be significantly enriched around genes, the majority of MNase-sensitive regions are located within transposable elements (TEs). Chromatin of the smaller D genome is more accessible than that of the larger A and B genomes. Chromatin states of different TEs vary among families and are influenced by the TEs' chromosomal position and proximity to genes. While the chromatin accessibility of genes is influenced by proximity to TEs, and not by their position on the chromosomes, we observe a negative chromatin accessibility gradient along the telomere-centromere axis in the intergenic regions, positively correlated with the distance between genes. Both gene expression levels and homoeologous gene expression bias are correlated with chromatin accessibility in promoter regions. The differential nuclease sensitivity assay accurately predicts previously detected centromere locations. SNPs located within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within more closed chromatin. Conclusions: Chromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes.