Peduncle, the uppermost internode in cereals, connects the stem to the inflorescence and is critical for the transport of water, nutrients and photosynthetic assimilates. While peduncle length associates with plant height and its elongation is primarily regulated by phytohormones, we report a previously unrecognized mechanism involving the spatial distribution of silicon (Si). We identified a barley mutant, sheathed spike 2 (ss2), characterized by a specifically shortened peduncle that traps the spike within the flag leaf sheath. Positional cloning and analysis of allelic mutants revealed that the wild-type SS2 gene encodes a putative silicon efflux transporter. SS2 is expressed throughout the lifecycle, with higher transcriptional levels in the rachis and stem internodes, and its encoded protein localizes to the plasma membrane. We demonstrate that SS2 is required for polarized Si partitioning. Unlike wild-type plants, which ultimately deposit Si in spikes, the ss2 mutant exhibits an 8-fold increase in Si accumulation in the peduncle and a significant increase in the flag leaf. Hydroponic experiments without Si supply restored normal peduncle elongation in the ss2 mutant, demonstrating that local Si hyper-accumulation directly inhibits elongation. The conserved role of SS2 was supported by diversity analysis across barley and common wheat, as well as by the similar sheathed spike phenotype in tetraploid wheat lines carrying non-functional SS2 homologues. Collectively, our findings uncover an evolutionarily conserved, silicon-dependent mechanism that regulates peduncle elongation and spike emergence in Triticeae crops like barley and wheat.

Semidwarf varieties of wheat (Triticum aestivum L.) carrying Reduced height (Rht) genes revolutionized wheat production. Rht8, a widely deployed semidwarfing allele, encodes RNHL1 (ribonuclease H-Like 1); yet, the molecular mechanisms underlying its growth regulation remain unclear. Here, we uncover a liquid-liquid phase separation (LLPS)-mediated transcriptional pathway by which RNHL1 controls plant height. We show that RNHL1 forms nuclear biomolecular condensates via its intrinsically disordered regions (IDR1 and IDR3) and physically interacts with the ethylene signaling transcription factor TaEIL1 (ethylene insensitive3-like 1) to establish functional transcriptional hubs. These RNHL1-TaEIL1 condensates directly bind and repress the ethylene response factor gene TaERF1 (Ethylene response factor 1), and TaERF1 suppresses the gibberellin (GA) biosynthetic gene TaGA3ox2 (Gibberellin 3-beta dioxygenase 2). Genetic analyses demonstrate that both RNHL1 and TaEIL1 positively regulate plant height, with loss-of-function mutants exhibiting similar dwarf phenotypes and convergent transcriptomic profiles. Importantly, we establish TaERF1 as a direct repressor of TaGA3ox2, completing a regulatory cascade in which RNHL1-TaEIL1 condensates modulate GA-mediated internode elongation. Our findings reveal an integration point between ethylene and GA signaling orchestrated by RNHL1-TaEIL1 phase separation and highlight RNHL1's roles in nucleic acid metabolism and transcriptional regulation. This study provides fundamental insights into LLPS-mediated growth control in crops and identifies specific protein domains as potential targets for wheat improvement.

Global warming poses a substantial threat to crop productivity, yet the genetic basis of thermotolerance in wheat remains poorly understood. Here we cloned a heat stress tolerance (HST) gene, TaHST2, and revealed that it underwent functional silencing during wheat domestication. As a negative regulator of basal HST, TaHST2 was progressively suppressed through intronic sequence polymorphisms and epigenetic modifications, which might be an evolutionary consequence of hexaploidization. Haplotype analysis suggests strong artificial selection against TaHST2 expression, favouring improved thermotolerance in cultivated wheat. Further studies demonstrated that TaHST2 encodes a ubiquitin hydrolase that stabilizes HST repression proteins TaHSC701 and TaHSC702, thereby modulating heat response pathways. Our findings uncover a potential key genetic event in wheat evolution and offer new strategies for utilizing synthetic hexaploidy and octoploid wheat to breed heat-resilient varieties.

Plant architecture is a critical determinant of crop yield, in which plant height serves as a key morphological trait. In this study, we characterized a novel wheat mutant named AS34 carrying a pleiotrophic gene named semi-dwarf and dense-spike 1 (sdd1). AS34 has reduced height, shorter spikes and increased spikelet density. Genetic analysis demonstrated monogenic recessive inheritance of these coordinated traits, with a strong negative correlation between spike length and density. The mutant is insensitive to brassinosteroid (BR), shows a minimal response to applied 24-epibrassinolide and has altered expression of key genes in the BR pathway. AS34 also exhibits enhanced sensitivity to applied gibberellin (GA) and auxin compared with the wild type, suggesting that the phenotype involves modifications in multiple hormone signaling pathways. Transcriptome profiling identified 1869 differentially expressed genes, with upregulation of defense- and cell wall-related pathways and downregulation of sulfur metabolism processes. Sdd1 was localized to a 5.7 Mb interval on chromosome 3B (414.7‒420.4 Mb). Among 50 candidate genes located in the interval, TraesCS3B02G260400 was identified as a Sdd1 gene candidate following integrated fine gene mapping, resequencing, expression analysis, and mutant phenotype validation. This study provides new insights into the regulation of wheat architecture and identifies Sdd1 as a new gene resource for breeding for optimized plant architecture.

Wheat (Triticum aestivum L.) is one of the most important staple crops globally. Doubled haploid technology enables rapid development of pure lines and has been extended from maize to several other crop species. A key step in DH breeding is the identification of haploids from diploids, which requires accurate and convenient phenotypic markers. In this study, we generated two wheat haploid inducers carrying different markers by a one-step strategy. One harbored a dual fluorescent marker system consisting of eGFP and TagRFP, the other carried a RUBY reporter. Both markers enabled near 100% accuracy of haploid identification at the immature embryo, mature embryo, and germinating seedling stages. Moreover, both lines consistently exhibited a high and stable haploid induction rate (∼20%). This study not only provides efficient wheat haploid inducers but also establishes a convenient pipeline for developing haploid induction systems in other crop species.

Drought stress threatens global wheat productivity, yet the genetic and molecular mechanisms underlying drought resilience remain incompletely understood. Here we identify TaSCE1-A1, which encodes a SUMO-conjugating enzyme, as a positive regulator of drought resistance through genome-wide association studies. In arid regions, an evolutionary G-to-A transition in the promoter confers elevated TaSCE1-A1 expression through disruption of TaBPC1-mediated transcriptional repression. Prime-edited and near-isogenic lines harbouring elite alleles show improved drought resilience, confirming its functional significance. Moreover, TaSCE1-A1 mediates SUMOylation of TaBAP1/2, thereby enhancing its protein stability, which in turn modulates the ABA pathway to facilitate stomatal closure under drought conditions. Evolutionarily, this adaptive allele originated in tetraploid wheat and underwent positive selection during hexaploid wheat domestication. Our findings reveal a drought resistance pathway shaped by evolutionary selection, offering molecular targets for breeding drought-resilient wheat varieties.

Wheat (Triticum aestivum L.), one of the world's three major staple crops, continues to face challenges in yield enhancement to ensure food security. Photosynthesis, the most fundamental energy conversion process on Earth, provides the primary source of biomass formation in plants. The first “Green Revolution” in the mid-20th century employed dwarfing genes such as Rht-B1b or Rht-D1b, which reduced plant height by 30-50% and significantly enhanced lodging resistance. Combined with the widespread adoption of fertilizers and pesticides, these advancements led to substantial increases in global wheat yields. However, the yield benefits derived from dwarfing genes have since plateaued, creating a bottleneck for further improvement through height reduction while exacerbating environmental costs of fertilizer-intensive agriculture. With the FAO predicting a 60% increase in global wheat demand by 2050, there is an urgent need for innovative technological strategies to achieve a second leap in productivity. Improving photosynthesis, the core driver of biomass accumulation, offers a promising pathway to overcome current yield limitations. This review synthesizes recent advances in wheat photosynthesis research, focusing on the relationship between photosynthetic carbon assimilation and grain yield. It also identifies key scientific questions, outlines future research directions, and proposes technological strategies for enhancing wheat through photosynthetic optimization. Wheat breeding is now ushering in a second “Green Revolution” era, one powered by the efficient use of solar energy.

Gene origin, duplication, and loss are key drivers that shape genome evolution, phenotypic diversification, and plant adaptation. Nevertheless, the fine-scale evolutionary trajectories of genes within their local genomic contexts across diverse genera remain poorly characterized. Here, we developed an approach, GoldMiner, that uses homologous gene clusters (HOCs) as evolutionary units for investigating gene evolution and enables hierarchical alignment of pan-genomic HOCs across species and genera. We constructed a genus-level pangenomic map of half a million indexed HOCs across 248 diploid genomes from 25 Poaceae species. We found that most newborn HOCs were derived from existing homologous HOCs. The newborn HOCs in Triticeae were strongly associated with stress response and defense pathways. Two-thirds of Triticeae HOCs, including those containing NLR genes, underwent substantial expansions during evolution, contributing to disease resistance in wheat and barley. Genomic redundancy between wheat subgenomes drives HOC loss associated with genetic variation of wheat populations. We dissected seed storage protein (SSP) gene evolution at two scales: inter-HOC turnover, which governs the origin and amplification of distinct loci across Triticeae, and intra-HOC divergence, which drives functional diversification among paralogous copies. Finally, an interactive web platform, waGOLD (https://wheat.cau.edu.cn/TGT/waGOLD), was developed for the community to explore evolutionary trajectories of HOCs. Overall, we presented a digital atlas of gene evolution for Poaceae species as a resource that opens new avenues for fine-scale gene family evolution and provides a practical framework for constructing genus-level gene-based pangenomes.

The plasticity of crop development is crucial for survival and yield stability under adverse conditions. Saline-alkaline soil is a major environmental constraint limiting wheat productivity. Elucidating the regulatory basis of wheat developmental plasticity under salt stress is crucial for improving salt tolerance and yield stability. In this study, salt stress promotes the initiation of lateral root (LR) primordia while inhibiting LR emergence in wheat. Upon return to non-stress conditions, these primordia rapidly develop into LRs, enabling swift recovery and root system expansion. We identify glycogen synthase kinase 3 (TaGSK3) as a molecular switch that regulates this plastic response via brassinosteroid and auxin signaling pathways. By this mechanism, environmental signals are transduced into root development plasticity via TaGSK3 phosphorylation. This work provides new insights into how crops control developmental plasticity under stress.

Heterosis is an important approach to improving wheat yield and quality. Previously, five recurrent selection populations were established to broaden genetic diversity via a recurrent selection strategy using French wheat, Spelt wheat, spike-branched wheat, Tibetan semi-wild wheat and common wheat as distinct germplasm donors. The present study aimed to characterize and preliminary heterosis evaluate of these wheat recurrent selection populations after 20 cycles of recurrent selection, providing a reference for long-term recurrent selection to enhance inter-population genetic differentiation and heterosis potential. In this paper, 94 materials including recurrent selection lines and their donors, together with 120 common wheat cultivars/lines, were phenotyped for agronomic traits and genotyped with the wheat 90K SNP array to assess genotypic variation and genetic distance. Furthermore, 23 elite lines derived from different recurrent selection populations were used as parents in an incomplete NCII (inter-population crosses) and a full NCI(intra-population crosses) design to evaluate their genetic distance and the heterotic performance. The main results showed that significant phenotypic variation existed within each population, and its magnitude varied with traits and populations. Plant height (PH) and 1000-grain weight (TGW) showed evidence of convergent selection during population improvement, whereas spike length (SL) and mean grains per spike (GSN) displayed divergent selection, particularly within the four male parent populations (Set B). The SNP-based genetic distance and population differentiation patterns were basically consistent with the classification of exotic germplasm resources. The genetic differences of inter-populations were generally greater than those within PopulationI(Domestic wheat population). The general combining ability (GCA) differed across traits, while special combining ability (SCA) showed a significant correlation with parental phenotypic values. The proportion of crosses with positive mid-parent heterosis (MPH) ranged from 45.24% to 98.41%, varying with traits. Meanwhile, the percentage of crosses showing positive commercial heterosis (CH) was 58.73%–99.21%, which also differed across traits. Among all measured traits, TGW had the highest proportion of crosses with positive heterosis. MPH values within PopulationIwere less than that between PopulationI and other populations (Set B) in five traits (except GSN). Seven superior TGW crosses were identified, with CH exceeding 15% and specific combining ability (SCA) ranging from 1.56 to 13.06. A two-year field trial revealed that two of these crosses showed plot yield CH values of 4.81% and 8.54%, respectively. This study provides a reference for broadening genetic diversity for hybrid parents by recurrent selection using exotic germplasm resources, and preliminarily screened promising combinations, which provide an important reference for further investigations.

High temperature is a primary abiotic stress that severely constrains crop productivity. Deciphering the regulatory pathways underlying heat responses is essential for breeding heat-tolerant crops with stable yields. Although both epigenetic and epitranscriptomic regulations are involved in plant heat adaptation, their mechanistic interplay remains unclear. Here, integrated epigenomic (H3K9Ac/H3K14Ac) and transcriptomic profiling under heat stress identifies the mRNA m⁵C methyltransferase TaNSUN2 as a key regulator of thermotolerance in wheat. We demonstrate that TaNSUN2 is transcriptionally activated by the histone acetyltransferase TaHAG1, which deposits H3K9Ac at the TaNSUN2 promoter and transcription start site. This recruitment is facilitated by the transcription factors TaE2F1 and TaDP1, which interact with TaHAG1 to form a functional complex. Functional assays revealthat TaNSUN2 operates downstream of TaHAG1 and enhances thermotolerance through m⁵C‑dependent mRNA methylation and stabilization of transcripts involved in chloroplast organization. Furthermore, field trials show that TaNSUN2-overexpressing lines exhibit higher grain yield under normal conditions and reduced yield loss under heat stress. Our findings elucidate an integrated regulatory network linking histone acetylation to RNA m⁵C methylation in heat stress adaptation, providing promising targets for molecular breeding of heat‑resilient wheat. High temperature can severely constrain crop productivity. Here the authors show that the mRNA m⁵C methyltransferase TaNSUN2 regulates thermotolerance in wheat and show that TaNSUN2-overexpression can increase heat resilience.

As a cornerstone of global food security, wheat (Triticum aestivum) faces unprecedented pressure from a growing population and a changing climate. However, traditional breeding approaches are increasingly insufficient to address the genetic complexity required to achieve substantial gains in yield and resilience. This review highlights key advances in the generation of large-scale, standardized datasets through the integration of high-throughput genotyping and multidimensional phenotyping. We explore how multi-omics integration and knowledge graph-based frameworks transform heterogeneous data into actionable breeding knowledge. In addition, we examine the pivotal role of artificial intelligence (AI) and machine learning in enhancing predictive modeling, refining genomic selection, and enabling intelligent decision-making. These advances underpin the emerging paradigm of Breeding 5.0, which leverages data-driven innovation and closed-loop iterative cycles. Looking ahead, multimodal AI and personalized breeding strategies will be critical for developing sustainable systems capable of ensuring global food security under climate change.

Wheat (Triticum aestivum L.) yield and quality are critically influenced by starch and seed storage protein (SSP) content. In this study, we demonstrate that the transcriptional adapter ADA2 physically interacts with histone acetyltransferase GENERAL CONTROL NONDEREPRESSIBLE 5 (GCN5) and regulates starch synthesis and SSP content in wheat grains. In ada2 mutants, reduced H3K9ac enrichment was observed in the promoter regions of key starch synthesis genes and the SSP regulator NAC019 during endosperm development. This reduction leads to lower expression levels, resulting in decreased starch content, smaller grains, reduced yield, and poor gluten quality. We also found that ADA2 contains an intrinsically disordered region 2 (IDR2) that undergoes liquid-liquid phase separation (LLPS) and forms nuclear condensates. In vitro assays, the LLPS of ADA2 is affected by GCN5 through direct interaction with IDR2, and the ratio of their concentrations determines the behavior of phase-separated condensates and HAT activity. High levels of GCN5 can dissolve ADA2 aggregates, while excessive ADA2 recruits and sequesters GCN5 into co-aggregated droplets, with lower HAT activity. This potential dynamic regulatory mechanism may facilitate the efficient promotion of transcription by the ADA2-GCN5 complex in wheat. Finally, we identified an elite haplotype of ADA2-B Hap2, which is significantly associated with grain size and weight, highlighting its potential as a candidate gene for genetic improvement of wheat yield.

Summary statement Knockouts of cytokinin oxidase‐dehydrogenase (TaCKX2.2) homeologs increased grain number per spike, grain size, grain weight per spike, and final yield without negative impacts on other major agronomic traits, revealing a novel approach to improve grain yield by manipulating the TaCKX2.2 gene family in wheat.

Drought stress severely constrains wheat (Triticum aestivum L.) growth and productivity. Here, we identify the histone deacetylase TaHDA1 as a negative regulator of drought tolerance in wheat. We demonstrate that TaHDA1 interacts with and deacetylates the L-glutamate decarboxylase TaGAD1 at lysine 493, promoting its ubiquitination-dependent degradation and thereby suppressing γ-aminobutyric acid (GABA) accumulation. Loss of TaHDA1 function enhances TaGAD1 stability, increases GABA levels, and confers markedly improved drought tolerance, along with elevated grain GABA content. Integrated multi-omics analyses further reveal that TaHDA1 globally modulates H3K9 acetylation to orchestrate drought-responsive transcriptional programs. Notably, tahda1-ko mutants show a slight reduction in grain size under normal conditions, but maintain stable yield under drought stress. Our findings uncover a dual mechanism by which TaHDA1 integrates non-histone and histone deacetylation to balance growth and stress adaptation, providing a promising target for breeding drought-resilient and nutritionally enhanced wheat varieties.

Heat stress poses a severe threat to global crop yields and food security. Here, we demonstrate that TaSnRK1α1, the α-catalytic subunit of sucrose non-fermenting-1-related kinase 1, serves as a pivotal regulator that confers thermotolerance and enhances grain weight in wheat (Triticum aestivum L.). The findings reveal that TaMYB55 directly binds to the TaSnRK1α1 promoter to activate its expression, which positively contributes to heat tolerance in wheat. An A-to-G substitution in the TaSnRK1α1 promoter enhances the binding affinity of TaMYB55, which cosegregates with wheat thermotolerant phenotypes. In addition, we show that TaSnRK1α1 interacts with and phosphorylates the transcription factor TabZIP9, which subsequently promotes TabZIP9 degradation. Genetic analyses confirm that TaSnRK1α1 functions upstream of TabZIP9, and loss or gain-of-function of TabZIP9 significantly alters thermotolerance in wheat by modulating reactive oxygen species homeostasis and scavenging capacity. Together, our findings shed light on the importance of the TaMYB55-TaSnRK1α1-TabZIP9 signaling module in the regulation of heat tolerance, providing practical strategies for engineering climate-tolerant crops.

In contrast to many wheat ( Triticum aestivum )-based products that benefit from strong gluten development, cookies benefit from weaker gluten. However, the development of wheat varieties that produce flour optimal for cookie making remains limited. In this study, we identified the wheat mutant low gluten protein 2 ( lgp2 ), with reduced gluten content and a weakened gluten network, that significantly improved several aspects of cookie-making performance. The lgp2 phenotype is caused by a missense mutation in LGP2 that affects the signal peptide cleavage site of the encoded protein. Map-based cloning reveals that LGP2 encodes alpha-2-purothionin, a member of the thionin family of small proteins with potential antimicrobial activity. The lgp2 mutation leads to endoplasmic reticulum stress, abnormal protein body formation, and disrupted gluten development. Additionally, alpha-2-purothionin interacts with key seed storage proteins, contributing to gluten formation. Knockdown and overexpression studies confirmed that LGP2 affects gluten quantity and quality. Based on these findings, we propose dual genetic strategies targeting signal peptide processing and modulating LGP2 expression to fine-tune gluten properties for improved cookie quality. The lgp2 allele offers great potential for breeding low-gluten wheat varieties tailored for the production of cookies and other specialty food products.

Introduction of Reduced height (Rht) genes into modern wheat cultivars has resulted in 'Green Revolution' that skyrocketed wheat grain yields worldwide since the 1960s. These 'Green Revolution' cultivars show shorter plant height, but higher lodging resistance and harvest index. The identification and exploitation of novel Rht genes are of great significance for the development of high-yielding wheat cultivars. In this study, a semi-dwarf wheat mutant, d14078, with reduced plant height and grain size, was generated by ethyl methanesulfonate (EMS) mutagenesis. Here, through map-based cloning, we cloned the causal gene for the semi-dwarf phenotype of d14078 as TaWAK3-B that encodes a cell wall-associated receptor kinase 3. A single-base mutation occurred in the coding region of TaWAK3-B, resulting in an amino acid mutation from Glu to Lys (E938K) at residue 938, which reduces its stability and the formation of homodimers. The cytoskeletons were changed in both the d14078 and TaWAK3-B knockout mutants, as well as the TaWAK3-B overexpression of transgenic plants. Further investigation revealed that TaWAK3-B directly forms stable protein assembly with TaADF3-A (actin depolymerisation factor), TaKLCR1-A (kinesin light chain-related protein 1), and TaIQD2-D (IQ67-domain protein 2). These interactions and complex formations were significantly attenuated by the TaWAK3-BE938K mutation. Therefore, our findings clarify TaWAK3-B regulating the microfilament and microtubule formation that elucidate on the regulation of wheat stem development.

The florigen protein TaFT1 coordinately regulates heading time and spikelet number per spike (SNS), serving as a key yield determinant in wheat. However, how its stability is post-translationally controlled in the shoot apical meristem remains unclear. Here, we identify the F-box protein WHEAT ORTHOLOG OF APO1 (WAPO1), allelic to a major SNS quantitative trait locus (QSns.cau-7A), as a direct ubiquitin E3 ligase targeting TaFT1 for degradation. A crucial missense mutation (C47F) in the F-box domain of WAPO1 has a significant impact on the SNS. The elite allele WAPO-A1b (from large-spike germplasm AS420, encoding 47F) exhibits stronger binding affinity and ubiquitination activity toward TaFT1 compared with the allele WAPO-A1f (from cultivar Lunxuan987, encoding 47C). Enhanced degradation of TaFT1 by WAPO-A1b in the shoot apical meristem impairs the TaFT1-TaFDL transcriptional complex, thereby downregulating the floral identity gene VRN1/WAP1 and increasing SNS without delaying heading. Notably, the favourable WAPO-A1b allele has been positively selected in modern breeding, and its ectopic activation significantly boosts grain yield in field trials. Our work elucidates a post-translational pathway that fine-tunes spike architecture and highlights WAPO-A1b as a valuable genetic target for high-yield wheat breeding.