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Leaf, spike, stem, and root morphologies are key factors that determine crop growth, development, and productivity. Multiple genes that control these morphological traits have been identified in Arabidopsis, rice, maize, and other plant species. However, little is known about the genomic regions and genes associated with morphological traits in wheat. Here, we identified the ethyl methanesulfonate-derived mutant wheat line M133 that displays multiple morphological changes that include upward-curled leaves, paired spikelets, dwarfism, and delayed heading. Using bulked segregant RNA sequencing (BSR-seq) and a high-resolution genetic map, we identified TraesCS1D02G155200 (HB-D2) as a potential candidate gene. HB-D2 encodes a class III homeodomain-leucine zipper (HD-ZIP III) transcription factor, and the mutation was located in the miRNA165/166 complementary site, resulting in a resistant allele designated rHb-D2. The relative expression of rHb2 in the mutant plants was significantly higher (P < 0.01) than in plants homozygous for the WT allele. Independent resistant mutations that disrupt the miRNA165/166 complementary sites in the A- (rHb-A2) and B-genome (rHb-B2) homoeologs showed similar phenotypic alterations, but the relative intensity of the effects was different. Transgenic plants expressing rHb-D2 gene driven by the maize UBIQUITIN (UBI) promoter showed similar phenotypes to the rHb-D2 mutant. These results confirmed that HB-D2 is the causal gene responsible for the mutant phenotypes. Finally, a survey of 1397 wheat accessions showed that the complementary sites for miRNA165/166 in all three HB2 homoeologs are highly conserved. Our results suggest that HB2 plays an important role in regulating growth and development in wheat.

Key message The stripe rust resistance gene Yr34 was transferred to polyploid wheat chromosome 5AL from T. monococcum and has been used for over two centuries.Wheat stripe (or yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is currently among the most damaging fungal diseases of wheat worldwide. In this study, we report that the stripe rust resistance gene Yr34 (synonym Yr48) is located within a distal segment of the cultivated Triticum monococcum subsp. monococcum chromosome 5AmL translocated to chromosome 5AL in polyploid wheat. The diploid wheat species Triticum monococcum (genome AmAm) is closely related to T. urartu (donor of the A genome to polyploid wheat) and has good levels of resistance against the stripe rust pathogen. When present in hexaploid wheat, the T. monococcum Yr34 resistance gene confers a moderate level of resistance against virulent Pst races present in California and the virulent Chinese race CYR34. In a survey of 1,442 common wheat genotypes, we identified 5AmL translocations of fourteen different lengths in 17.5% of the accessions, with higher frequencies in Europe than in other continents. The old European wheat variety "Mediterranean" was identified as a putative source of this translocation, suggesting that Yr34 has been used for over 200 years. Finally, we designed diagnostic CAPS and sequenced-based markers that will be useful to accelerate the deployment of Yr34 in wheat breeding programs to improve resistance to this devastating pathogen.

Wheat stem (or black) rust is one of the most devastating fungal diseases, threatening global wheat production. Identification, mapping, and deployment of effective resistance genes are critical to addressing this challenge. In this study, we mapped and characterized one stem rust resistance (Sr) gene from the tetraploid durum wheat variety Kronos (temporary designation SrKN). This gene was mapped on the long arm of chromosome 2B and confers resistance to multiple virulent Pgt races, such as TRTTF and BCCBC. Using a large mapping population (3,366 gametes), we mapped SrKN within a 0.29 cM region flanked by the sequenced-based markers pku4856F2R2 and pku4917F3R3, which corresponds to 5.6- and 7.2-Mb regions in the Svevo and Chinese Spring reference genomes, respectively. Both regions include a cluster of nucleotide binding leucine-repeat (NLR) genes that likely includes the candidate gene. An allelism test failed to detect recombination between SrKN and the previously mapped Sr9e gene. This result, together with the similar seedling resistance responses and resistance profiles, suggested that SrKN and Sr9e may represent the same gene. We introgressed SrKN into common wheat and developed completely linked markers to accelerate its deployment in the wheat breeding programs. SrKN can be a valuable component of transgenic cassettes or gene pyramids that includes multiple resistance genes to control this devastating disease.

Key message The stripe rust resistance gene Yr34 was transferred to polyploid wheat chromosome 5AL from T. monococcum and has been used for over two centuries.Wheat stripe (or yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is currently among the most damaging fungal diseases of wheat worldwide. In this study, we report that the stripe rust resistance gene Yr34 (synonym Yr48) is located within a distal segment of the cultivated Triticum monococcum subsp. monococcum chromosome 5A m L translocated to chromosome 5AL in polyploid wheat. The diploid wheat species Triticum monococcum (genome A m A m ) is closely related to T. urartu (donor of the A genome to polyploid wheat) and has good levels of resistance against the stripe rust pathogen. When present in hexaploid wheat, the T. monococcum Yr34 resistance gene confers a moderate level of resistance against virulent Pst races present in California and the virulent Chinese race CYR34. In a survey of 1,442 common wheat genotypes, we identified 5A m L translocations of fourteen different lengths in 17.5% of the accessions, with higher frequencies in Europe than in other continents. The old European wheat variety "Mediterranean" was identified as a putative source of this translocation, suggesting that Yr34 has been used for over 200 years. Finally, we designed diagnostic CAPS and sequenced-based markers that will be useful to accelerate the deployment of Yr34 in wheat breeding programs to improve resistance to this devastating pathogen.