Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating disease that seriously threatens wheat yield and quality. To control this disease, host resistance is the most effective measure. Compared with the resistance genes from common wheat, alien resistance genes can better withstand infection of this highly variable pathogen. Development of elite alien germplasm resources with powdery mildew resistance and other key breeding traits is an attractive strategy in wheat breeding. In this study, three wheat-rye germplasm lines YT4-1, YT4-2, and YT4-3 were developed through hybridization between octoploid triticale and common wheat, out of which the lines YT4-1 and YT4-2 conferred adult-plant resistance (APR) to powdery mildew while the line YT4-3 was susceptible to powdery mildew during all of its growth stages. Using genomic in situ hybridization, multi-color fluorescence in situ hybridization, multi-color GISH, and molecular marker analysis, YT4-1, YT4-2, and YT4-3 were shown to be cytogenetically stable wheat-rye 6R addition and T1RS·1BL translocation line, 6RL ditelosomic addition and T1RS·1BL translocation line, and T1RS·1BL translocation line, respectively. Compared with previously reported wheat-rye derivative lines carrying chromosome 6R, YT4-1 and YT4-2 showed stable APR without undesirable pleiotropic effects on agronomic traits. Therefore, these novel wheat-rye 6R derivative lines are expected to be promising bridge resources in wheat disease breeding.

Agropyron cristatum (2n = 4x = 28, PPPP), which harbours many high-yield and disease-resistance genes, is a promising donor for wheat improvement. Narrow genetic diversity and the trade-off between grain weight and grain number have become bottlenecks for increasing grain yield in wheat. In this study, a novel translocation line, WAT650l, was derived from the chromosome 6P addition line 4844–12, which can simultaneously increase both grain number per spike (GNS) and thousand-grain weight (TGW). Cytological analysis and molecular marker analysis revealed that WAT650l was a 5BL·5BS-6PL (bin 12–17) translocation line. Assessment of agronomic traits and analysis of the BC₄F₂ and BC₅F₂ populations suggested that the 6PL terminal chromosome segment in WAT650l resulted in increased grain number per spike (average increased by 14.07 grains), thousand-grain weight (average increased by 4.31 g), flag leaf length, plant height, spikelet number per spike and kernel number per spikelet during the two growing seasons of 2020–2021 and 2021–2022. Additionally, the increased GNS locus and high-TGW locus of WAT650l were mapped to the bins 16–17 and 12–13, respectively, on chromosome 6PL by genetic population analysis of three translocation lines. In summary, we provide a valuable germplasm resource for broadening the genetic base of wheat and overcoming the negative relationship between GNS and TGW in wheat breeding.

Wide hybridization is a strategy for broadening the genetic basis of wheat. Because an efficient method for inducing wheat–alien chromosome translocations will allow producing useful germplasm, it is desirable to discover new genes that induce chromosomal variation. In this study, chromosome 5P from A. cristatum was shown to induce many types of chromosomal structural variation in a common wheat background, including nonhomoeologous chromosome translocations, as revealed by genomic in situ hybridization, fluorescence in situ hybridization, and DNA marker analysis. Aberrant meiosis was associated with chromosomal structural variation, and aberrant meiotic behavior was observed in wheat–A. cristatum 5P monosomic and disomic addition lines, suggesting that the effect of chromosome 5P was independent of the number of chromosome 5P copies. Chromosome 5P disturbed homologous chromosome pairing at pachytene stage in a common wheat background, resulting in a high frequency of univalent formation and reduced crossing over. Thirteen genes involved in DNA repair or chromatin remodeling, including RAD52-like and MSH6 genes, were differentially expressed (upregulated) in wheat–A. cristatum 5P addition lines according to transcriptome analysis, implicating chromosome 5P in the process of meiotic double-strand break repair. These findings provide a new, efficient tool for inducing wheat–alien chromosome translocations and producing new germplasm.

As an important wild relative of wheat, Agropyron cristatum has been successfully used for wheat improvement. Currently, a few useful agronomic traits of A. cristatum, such as high grain number per spike and resistance to diseases, have been transferred into common wheat. However, the effective detection of small A. cristatum segmental introgressions in common wheat is still difficult. The objective of this study was to identify A. cristatum-specific single nucleotide polymorphisms (SNPs) for the detection of small alien segments in wheat. The transcriptome sequences of A. cristatum were aligned against wheat coding DNA sequences (CDS) for SNP calling. As a result, we discovered a total of 167,613 putative SNPs specific to the P genome of A. cristatum compared with the common wheat genomes. Among 230 selected SNPs with functional annotations related to inflorescence development and stress resistance, 68 were validated as P genome-specific SNPs in multiple wheat backgrounds using Kompetitive Allele Specific PCR (KASP) assays. Among them, 55 SNPs were assigned to six homoeologous groups of the P genome using wheat-A. cristatum addition lines, and 6P-specific SNP markers were further physically mapped on different segments of chromosome 6P in 6P translocation lines. The P genome-specific SNPs were also validated by Sanger sequencing and used to detect the P chromatin in wheat-A. cristatum cryptic introgression lines. Two SNP markers (Unigene20217-182 and Unigene20307-1420) were detected in two wheat-A. cristatum introgression lines that showed enhanced grain number per spike and high resistance to powdery mildew. Together, the developed P genome-specific SNP markers will accelerate the detection of large numbers of wheat-A. cristatum derivatives and will be helpful for marker-assisted transfer of desirable traits from A. cristatum into adapted wheat cultivars in wheat breeding programs.