Background: Plant height (PH), spike length (SL) and spike compactness (SCN) are important agronomic traits in wheat due to their strong correlations with lodging and yield. Thus, dissection of their genetic basis is essential for the improvement of plant architecture and yield potential in wheat breeding. The objective of this study was to map quantitative trait loci (QTL) for PH, SL and SCN in a recombinant inbred line (RIL) population derived from the cross ‘PuBing3228 × Gao8901’ (PG-RIL) and to evaluate the potential values of these QTL to improve yield. Results: In the current study, Five, six and ten stable QTL for PH, SL, and SCN, respectively, were identified in at least two individual environments. Five major QTL QPh.cas-5A.3, QPh.cas-6A, QSl.cas-6B.2, QScn.cas-2B.2 and QScn.cas-6B explained 5.58–25.68% of the phenotypic variation. Notably, two, three and three novel stable QTL for PH, SL and SCN were identified in this study, which could provide further insights into the genetic factors that shape PH and spike morphology in wheat. Conditional QTL analysis revealed that QTL for SCN were mainly affected by SL. Moreover, a Kompetitive Allele Specific PCR (KASP) marker tightly linked to stable major QTL QPh.cas-5A.3 was developed and verified using the PG-RIL population and a natural population. Conclusions: Twenty-one stable QTL related to PH, SL, and SCN were identified. These stable QTL and the user-friendly marker KASP8750 will facilitate future studies involving positional cloning and marker-assisted selection in breeding.

Wheat-rye T1RS·1BL translocations have been widely used worldwide in wheat production for multiple disease resistance and superior yield traits. However, many T1RS·1BL translocations have successively lost their resistance to pathogens due to the coevolution of pathogen virulence with host resistance. Because of the extensive variation in rye (Secale cereale L.) as a naturally cross-pollinating relative of wheat, it still has promise to widen the variation of 1RS and to fully realize its application value in wheat improvement. In the present study, the wheat-rye breeding line R2207 was characterized by comprehensive analyses using genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization with multiple probes, multicolor GISH, and molecular marker analysis, and then was proven to be a cytogenetically stable wheat-rye T1RS·1BL translocation line. Based on the disease responses to different isolates of powdery mildew and genetic analysis, R2207 appears to possess a novel variation for resistance, which was confirmed to be located on the rye chromosome arm 1RS. Line R2207 also exhibited high levels of resistance to stripe rust at both seedling and adult stages, as well as enhanced agronomic performance, so it has been transferred into a large number of commercial cultivars using an efficient 1RS-specific kompetitive allele specific PCR marker for marker-assisted selection.

Summary: Rye (Secale cereale), a valuable relative of wheat, contains abundant powdery mildew resistance (Pm) genes. Using physical mapping, transcriptome sequencing, barley stripe mosaic virus‐induced gene silencing, ethyl methane sulfonate mutagenesis, and stable transformation, we isolated and validated two coiled‐coil, nucleotide‐binding site and leucine‐rich repeat (CC‐NBS‐LRR) alleles, PmTR1 and PmTR3, located on rye chromosome 6RS from different triticale lines. PmTR1 confers age‐related resistance starting from the three‐leaf stage, whereas its allele, PmTR3, confers typical all‐stage resistance, which may be associated with their differential gene expression patterns. Overexpression in Nicotiana benthamiana showed that the CC, CC‐NBS, and CC‐LRR fragments of PMTR1 induce cell death, whereas in PMTR3 the CC and full‐length fragments perform this function. Luciferase complementation imaging and pull‐down assays revealed distinct interaction activities between the CC and NBS fragments. Our study elucidates two novel rye‐derived Pm genes and their derivative germplasm resources and provides novel insights into the mechanism of age‐related resistance, which can aid the improvement of resistance against wheat powdery mildew.

Rye (Secale cereale L.), a close relative of wheat (Triticum aestivum L.), has significantly contributed to wheat breeding, exemplified by the global utilization of T1RS·1BL translocation lines. This highlights the strategic importance of integrating elite genes from related species into modern crop-breeding programs. This review explores the historical contributions of rye to wheat breeding and its potential in future applications. We delve into the impact of biotechnological approaches in unlocking the genetic repertoire of rye to bolster wheat improvement. Key strategies include goal-directed germplasm innovation, in-depth understanding of genetic basis, multi-omic big data and artificial intelligence (AI)-aided precision breeding, and strengthened global collaboration. These efforts are expected to maximize the potential of rye in sustainable wheat breeding.