Key message

The diploid wheat recessive stem rust resistance gene SrTm4 was fine-mapped to a 754-kb region on chromosome arm 2A^mL and potential candidate genes were identified. Race Ug99 of Puccinia graminis f. sp. tritici (Pgt), the causal agent of wheat stem (or black) rust is one of the most serious threats to global wheat production. The identification, mapping, and deployment of effective stem rust resistance (Sr) genes are critical to reduce this threat. In this study, we generated SrTm4 monogenic lines and found that this gene confers resistance to North American and Chinese Pgt races. Using a large mapping population (9522 gametes), we mapped SrTm4 within a 0.06 cM interval flanked by marker loci CS4211 and 130K1519, which corresponds to a 1.0-Mb region in the Chinese Spring reference genome v2.1. A physical map of the SrTm4 region was constructed with 11 overlapping BACs from the resistant Triticum monococcum PI 306540. Comparison of the 754-kb physical map with the genomic sequence of Chinese Spring and a discontinuous BAC sequence of DV92 revealed a 593-kb chromosomal inversion in PI 306540. Within the candidate region, we identified an L-type lectin-domain containing receptor kinase (LLK1), which was disrupted by the proximal inversion breakpoint, as a potential candidate gene. Two diagnostic dominant markers were developed to detect the inversion breakpoints. In a survey of T. monococcum accessions, we identified 10 domesticated T. monococcum subsp. monococcum genotypes, mainly from the Balkans, carrying the inversion and showing similar mesothetic resistant infection types against Pgt races. The high-density map and tightly linked molecular markers developed in this study are useful tools to accelerate the deployment of SrTm4-mediated resistance in wheat breeding programs.

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.

Leaf rust, caused by Puccinia triticina Eriksson (Pt), is one of the most severe foliar diseases of wheat. Breeding for leaf rust resistance is a practical and sustainable method to control this devastating disease. Here, we report the identification of Lr47, a broadly effective leaf rust resistance gene introgressed into wheat from Aegilops speltoides. Lr47 encodes a coiled-coil nucleotide-binding leucine-rich repeat protein that is both necessary and sufficient to confer Pt resistance, as demonstrated by loss-of-function mutations and transgenic complementation. Lr47 introgression lines with no or reduced linkage drag are generated using the Pairing homoeologous1 mutation, and a diagnostic molecular marker for Lr47 is developed. The coiled-coil domain of the Lr47 protein is unable to induce cell death, nor does it have self-protein interaction. The cloning of Lr47 expands the number of leaf rust resistance genes that can be incorporated into multigene transgenic cassettes to control this devastating disease.