Wheat stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a devastating disease threaten food security in China and worldwide. Epidemics of wheat stripe rust have been under control through applying resistant cultivars and crop protection approaches. However, due to climate change, innovation of cropping system, improvement of breeding technology, yield level enhancement of wheat cultivars, variation in structure and frequency of virulence genes in Pst populations in the new era, the current status of stripe rust resistance genes in wheat breeding programs need to be evaluated. The results could provide useful information for applying stripe rust resistance genes to develop new wheat cultivars with broad-spectrum and durable rust resistance. After multiple year’s stripe rust resistance survey, genetic analysis, molecular tagging and mining of stripe rust resistance genes in wheat cultivars and advanced breeding lines, the current status of major stripe rust resistance genes utilization was reviewed. We summarized the present situations of major stripe rust resistance gene discovery and germplasm innovation, the most frequently used stripe rust resistance genes, new strategy for pyramiding adult plant partial resistance and all stage resistance, and molecular marker assisted selection for developing wheat cultivars with broad spectrum and durable resistance in China. This review also proposes the major research areas in wheat stripe rust resistance breeding in the new era.

Plant height, spike, leaf, stem and grain morphologies are key components of plant architecture and related to wheat yield. A wheat (Triticum aestivum L.) mutant, wpa1, displaying temperature-dependent pleiotropic developmental anomalies, was isolated. The WPA1 gene, encoding a von Willebrand factor type A (vWA) domain protein, was located on chromosome arm 7DS and isolated by map-based cloning. The functionality of WPA1 was validated by multiple independent EMS-induced mutants and gene editing. Phylogenetic analysis revealed that WPA1 is monocotyledon-specific in higher plants. The identification of WPA1 provides opportunity to study the temperature regulated wheat development and grain yield.

Puccinia striiformis Westend. f. sp. tritici (Pst) pathotype CYR34 is widely virulent and prevalent in China. Here, we report identification of a strpie rust resistance (Yr) gene, designated Yr041133, in winter wheat line 041133. This line produced a hypersensitive reaction to CYR34 and conferred resistance to 13 other pathotypes. Resistance to CYR34 in line 041133 was controlled by a single dominant gene. Bulked segregant RNA sequencing (BSR-Seq) was performed on a pair of RNA bulks generated by pooling resistant and susceptible recombinant inbred lines. Yr041133 was mapped to a 1.7 cM genetic interval on the chromosome arm 7BL that corresponded to a 0.8 Mb physical interval (608.9–609.7 Mb) in the Chinese Spring reference genome. Based on its unique physical location Yr041133 differred from the other Yr genes on this chromosome arm.

Reduced plant height is one of the most important traits related to lodging resistance and crop yield. The use of reduced height genes has been one of the main features in breeding modern high-yielding wheat varieties with less lodging. A spontaneous dwarf mutant DD399 was identified in a high yielding, gibberellic acid (GA)-insensitive, lodging-resistant variety Nongda 399 (ND399). Significant differences in upper internode lengths between mutant DD399 and wild type ND399 were caused by reduced cell elongation. The plant height of ND399 × DD399 F₁ hybrids was intermediate between the parents, indicating incomplete dominance or a dose–response effect of a reduced height gene. Plant height showed continuous distribution in the F₂ population, and segregation distortion was observed among the 2292 F_2:3 progenies. The reduced height mutation was characterized by Illumina 90 K iSelect SNP genotyping and bulked segregant RNA-Seq (BSR-Seq) analysis of the segregating population. A concentrated cluster of polymorphic SNPs associated with the reduced height phenotype was detected in the distal region of chromosome arm 2BL. Co-segregation of reduced height phenotype with the clustered markers revealed a 36 Mb terminal deletion of chromosome 2BL in mutant DD399.

Stripe rust and powdery mildew are both devastating diseases for durum and common wheat. Pyramiding of genes conferring resistance to one or more diseases in a single cultivar is an important breeding approach to provide broader spectra of resistances in wheat improvement. A new powdery mildew resistance gene originating from wild emmer (Triticum turgidum var. dicoccoides) backcrossed into common wheat (T. aestivum) line WE35 was identified. It conferred an intermediate level of resistance to Blumeria graminis f. sp. tritici isolate E09 at the seedling stage and a high level of resistance at the adult plant stage. Genetic analysis showed that the powdery mildew resistance in WE35 was controlled by a dominant gene designated Pm64. Bulked segregant analysis (BSA) and molecular mapping indicated that Pm64 was located in chromosome bin 2BL4-0.50–0.89. Polymorphic markers were developed from the corresponding genomic regions of Chinese Spring wheat and wild emmer accession Zavitan to delimit Pm64 to a 0.55 cM genetic interval between markers WGGBH1364 and WGGBH612, corresponding to a 15 Mb genomic region on Chinese Spring and Zavitan 2BL, respectively. The genetic linkage map of Pm64 is critical for fine mapping and cloning. Pm64 was completely linked in repulsion with stripe rust resistance gene Yr5. Analysis of a larger segregating population might identify a recombinant line with both genes as a valuable resource in breeding for resistance to powdery mildew and stripe rust.

Leaf senescence is normally the last stage of plant development. Early senescence of functional leaves significantly reduces the photosynthetic time and efficiency, seriously affecting grain yield and quality in wheat. Discovering genes responsible for early leaf senescence (els) are necessary for developing novel germplasms and cultivars with delayed leaf-senescence through molecular manipulation and marker assisted selection. In this study, we identified an early leaf senescence line M114 in a derivative of a wheat breeding population. Genetic analysis indicated that early leaf senescence in M114 is controlled by a single recessive gene, provisionally designated els1. By applying bulked segregant analysis and RNA-Seq (BSR-Seq), seven polymorphic markers linked to els1 were developed and the gene was located on chromosome arm 2BS in a 1.5cM genetic interval between markers WGGB303 and WGGB305. A co-segregating marker, WGGB302, provide a starting point for fine mapping and map-based cloning of els1.

Stripe rust (yellow rust), caused by Puccinia striiformis f. sp. tritici (PST), is one of the most devastating fungal diseases in common wheat (Triticum aestivum L.) in China and worldwide. Resistance breeding is the most effective strategy to control diseases in crop plants. Chinese wheat lines Mengmai 58 and Huaiyang 1 are highly resistant to PST race CYR34 (V26) at the adult plant stage. To genetically map the underlying resistance genes we developed segregating populations by crossing Mengmai 58 and Huaiyang 1 with the susceptible cultivar Nongda 399. The stripe rust resistances in Mengmai 58 and Huaiyang 1 were both controlled by single dominant genes, provisionally designated YrMM58 and YrHY1, respectively. Bulked segregant RNA-Seq (BSR-Seq) analysis showed that YrMM58 and YrHY1 were located in the same distal ~16Mb region on chromosome 2AS. Comparative genomics analysis with the physical map of Aegilops tauschii proved useful for developing additional markers to saturate the genetic linkage map. YrMM58 and YrHY1 were mapped to the distal end of chromosome arm 2AS, with the closest marker WGGB148 being 7.7cM and 3.8cM from the resistance gene, which was considered to be Yr17. These markers can be used in marker-assisted selection.

Barley stripe mosaic virus (BSMV) is the type member of the genus Hordeivirus. Brachypodium distachyon line Bd3-1 shows resistance to the BSMV ND18 strain, but is susceptible to an ND18 double mutant (β _NDTGB1_{R390K, T392K}) in which lysine is substituted for an arginine at position 390 and for threonine at position 392 of the triple gene block 1 (TGB1) protein. In order to understand differences in gene expression following infection with ND18 and double mutant ND18, Bd3-1 seedlings were subjected to RNA-seq analyses at 1, 6, and 14days post inoculation (dpi). The results revealed that basal immunity genes involved in cellulose synthesis and pathogenesis-related protein biosynthesis were enhanced in incompatible interactions between Bd3-1 and ND18. Most of the differentially expressed transcripts are related to trehalose biosynthesis, ethylene, jasmonic acid metabolism, protein phosphorylation, protein ubiquitination, transcriptional regulation, and transport process, as well as pathogenesis-related protein biosynthesis. In compatible interactions between Bd3-1 and ND18 mutant, Bd3-1 developed weak basal resistance responses to the virus. Many genes involved in cellulose biosynthesis, protein amino acid phosphorylation, protein biosynthesis, protein glycosylation, glycolysis and cellular macromolecular complex assembly that may be related to virus replication, assembly and movement were up-regulated. Some genes involved in oxidative stress responses were also up-regulated at 14dpi. BSMV ND18 mutant infection suppressed expression of genes functioning in regulation of transcription, protein kinase, cellular nitrogen compound biosynthetic process and photosynthesis. Differential expression patterns between compatible and incompatible interactions in Bd3-1 to the two BSMV strains provide important clues for understanding mechanism of resistance to BMSV in the model plant Brachypodium.