Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

Climate change will have numerous impacts on crop production worldwide necessitating a broadening of the germplasm base required to source and incorporate novel traits. Major variation exists in crop progenitor species for seasonal adaptation, photosynthetic characteristics, and root system architecture. Wheat is crucial for securing future food and nutrition security and its evolutionary history and progenitor diversity offer opportunities to mine favourable functional variation in the primary gene pool. Here we provide a review of the status of characterisation of wheat progenitor variation and the potential to use this knowledge to inform the use of variation in other cereal crops. Although significant knowledge of progenitor variation has been generated, we make recommendations for further work required to systematically characterise underlying genetics and physiological mechanisms and propose steps for effective use in breeding. This will enable targeted exploitation of useful variation, supported by the growing portfolio of genomics and accelerated breeding approaches. The knowledge and approaches generated are also likely to be useful across wider crop improvement.

Genome-wide introgression and substitution lines have been developed in many plant species, enhancing mapping precision, gene discovery and the identification and exploitation of variation from wild relatives. Created over multiple generations of crossing and/or backcrossing accompanied by marker-assisted selection, the resulting introgression lines are a fixed genetic resource. In this study we report the development of spring wheat chromosome segment substitution lines generated to systematically capture genetic variation from tetraploid ( Triticum turgidum ssp dicoccoides ) and diploid ( Aegilops tauschii ) progenitor species. Generated in a common genetic background over four generations of backcrossing, the material is a base resource for the mapping and characterisation of wheat progenitor variation. To facilitate further exploitation the final population was genetically characterised using a high- density genotyping array and a range of agronomic and grain traits assessed to demonstrate the the potential use of the populations for trait localisation in wheat.

Key message: Synthetic hexaploid wheat harbours STB resistance-associated loci with multi-isolate and isolate-specific effects, with partly independent genetic control of pycnidia suppression and necrosis. Septoria tritici blotch (STB), caused by Zymoseptoria tritici , is a major constraint on wheat production. Erosion of host resistance and declining fungicide efficacy highlight the need to exploit new resistance sources, including synthetic hexaploid wheat (SHW). We used a three-family nested association mapping (NAM) population derived from Niab SHW donors (SHW.035, SHW.054, and SHW.075) crossed with the UK variety Robigus to dissect the genetic basis of STB resistance under controlled conditions. Seedlings were challenged with five UK Z. tritici isolates differing in virulence, and disease progress was quantified separately as necrosis (AUDPC_N) and pycnidia coverage (AUDPC_P). Many SHW-derived lines showed strong suppression of pycnidia despite visible necrosis, consistent with partial genetic decoupling of pathogen reproduction and host tissue damage. GWAS identified a major multi-isolate association on chromosome 3D ( qSTB-3D.1 ), contributed by SHW.035 and detected in response to four of the five isolates, defining a 23.7 Mb candidate resistance-associated interval. This interval encompasses the Stb16q region but also contains other plausible resistance candidates, including a WAK close to the strongest association at 609.21 Mb; the causal basis therefore remains unresolved. Additional isolate-specific resistance-associated intervals were detected on chromosomes 1B, 2D, 3A, and 6D. In a BC ₂ F ₂ population derived from a resistant SHW.035-derived NAM line, pycnidia suppression segregated in a 3:1 ratio consistent with a single dominant factor, whereas necrosis showed more complex inheritance. These findings show that Niab SHWs are a valuable source of STB resistance and highlight the potential to select for reduced pathogen reproduction independently of visible leaf damage.

The outer epidermis of land plants secretes a cuticular layer, a hydrophobic diffusion barrier which minimises water loss into the atmosphere and protects from pests, ultraviolet light and organ fusion. Cuticles typically comprise a polyester cutin matrix embedded and overlaid with cuticular waxes, but their exact chemical make-up, structure and functions can vary widely depending on the tissue and species. Barley shows two such cuticular specialisations: (1) deposition of a thick β-diketone-rich wax bloom on multiple organs at reproductive stage, common in other Poeceae species and linked to yield; and, (2) secretion of a sticky layer on the grain fruit (caryopsis) pericarp cuticle which adheres to inner floral hulls, leading to barley’s distinctive ‘covered’ grain used in animal feed and malting. Two SHINE/WAX-INDUCER transcription factors in barley, HvWIN1 and NUD, promote the wax bloom and hull to caryopsis adhesion, respectively, yet little is understood about other genes involved. Leveraging near-isogenic lines of wax-deficient mutants, we identify the barley BODYGUARD1 ( HvBDG1 ) gene encoding an α/β-hydrolase essential for leaf cuticular integrity and wax bloom deposition. Modelling of functional and defective alleles suggests that HvBDG1 N-terminal region control of protein flexibility is important for HvBDG1 function. In addition to their role in controlling barley epicuticular wax deposition, we show that both HvBDG1 and HvWIN1 are essential for strong hull to caryopsis adhesion. Along with NUD, these gene products differentially contribute to ultrastructural changes on the pericarp associated with a cuticular building programme driven by NUD and HvWIN1 regulation of cuticle metabolism and transport and cell wall-related genes, and correlate with shifts in pericarp surface chemistry. We also show that the previously asserted ‘grain-specific’ role of NUD should be revised, as our findings reveal that it is essential for maintaining leaf cuticle integrity. Our analyses in barley suggest that NUD and HvWIN1 control cuticular specialisations and cuticle integrity in part via promotion of HvBDG1 expression, while HvWIN1 and NUD likely act independently from each other. Lastly, mining tetraploid wheat mutant populations followed by crossing to combine mutated homoeologues demonstrated that BDG1 and WIN1 orthologues also control wax bloom in wheat. Taken together, our work greatly expands the genetic networks and molecular activities important for cuticle development in cereals and the underlying mechanisms for both shared and species-specific cuticular specialisations.

Summary: Land plants secrete a protective outer cuticular layer with diverse functions. Barley ( Hordeum vulgare L.) develops two cuticular specialisations: the β‐diketone rich wax bloom on vegetative tissues and an adherent grain surface which sticks to the hulls, leading to barley's distinctive ‘covered’ grain phenotype. Two barley SHINE transcription factors, HvWIN1 and NUD, promote the wax bloom and covered grain phenotypes, respectively, yet we know little about other genes involved. We investigated a barley mutant showing defects in both cuticular specialisations to better understand the networks and processes underlying these traits. We identified the barley BODYGUARD1 ( HvBDG1 ) gene encoding an α/β hydrolase as crucial for leaf cuticular integrity and wax‐bloom deposition. Mining tetraploid wheat ( Triticum turgidum ssp. durum ) mutant populations demonstrated that BDG1 and WIN1 orthologues also control the wax bloom in wheat. We further reveal that NUD and HvWIN1 retain functional, independent overlap in leaf cuticle integrity and hull adhesion in barley, functions which involve upregulation of HvBDG1 and other direct or indirect targets, shared and distinct, depending on the stage and tissue. Our work greatly expands our knowledge of genetic and developmental mechanisms underlying shared and distinctive cuticular features in plants.