Aili Li

Fusarium head blight (FHB) is a devastating fungal disease of wheat that causes severe yield loss and mycotoxin contamination. Wheat varieties offering higher grain yield while maintaining moderate resistance to FHB are highly desirable. Here, we report that microRNA168a (miR168a) acts as a key negative regulator of both FHB resistance and grain yield in wheat. Knockdown of miR168a via target mimicry (MIM168) enhanced resistance to FHB in transgenic plants, accompanied by increased H ₂ O ₂ accumulation and restricted fungal spread. MIM168 plants also exhibited higher grain yield with longer spikes and higher spikelet number per spike under uninfected field conditions. By contrast, miR168a overexpression (OE168) lines became more susceptible to FHB and displayed significantly reduced grain yield. We further identified TaAGO1b as a target of miR168a. Knockout of TaAGO1b using CRISPR/Cas9 ( ago1b ) recapitulated the FHB susceptibility and reduced spike length, demonstrating that miR168a and TaAGO1b work as a module. Moreover, miR168a positively regulates the miR156– TaSPL17 module, which is associated with spike development, and it also regulates miR444 in FHB infection, and that knockdown of miR444 via target mimicry (MIM444) enhances FHB resistance. Meanwhile, ago1b mutations upregulated miR156 and miR444. Thus, our data demonstrated that the miR168a– TaAGO1b module contributes to wheat spike architecture and FHB resistance via miR156 and miR444, providing a potential strategy for breeding high‐yielding and FHB‐resistant wheat varieties.

Powdery mildew, caused by the biotrophic fungus Blumeria graminis f. sp. tritici (Bgt), is one of the major pathogens that reduces wheat yield. Epigenetic regulation underlying wheat defense against Bgt infection, however, remains poorly characterized. Here, we conducted an integrative transcriptomic and histone H3 modification analysis on wheat leaves infected by mixed races of Bgt. RNA-seq revealed extensive transcriptional reprogramming in wheat leaves upon Bgt infection, with significant changes in a number of functional genes including those associated with histone modification. CUT&Tag analysis of two key activating histone marks, H3K4me3 and H3K36me3, showed an overall decrease in both modifications after infection. Nevertheless, H3K4me3 modification was notably increased in promoter regions, whereas H3K36me3 peaks were more enriched in the genic regions, indicating that Bgt infection induced a redistribution of these active histone marks. Integrative analysis revealed that only a subset of genes exhibited concordant changes between transcriptional levels and either H3K4me3 or H3K36me3 enrichment. Defense-related genes, including TaARF4, TaWRKY19, and TaCIPK19, were consistently down-regulated at both transcriptional and histone modification levels after Bgt infection, while TaCHIT8, TaPOD, and Calreticulin (TaCRT) were up-regulated. Consistently, virus-induced gene silencing (VIGS) of TaCIPK19, TaWRKY19, and TaARF4 enhanced resistance to Bgt, whereas silencing of TaCRT and TaCHIT8 increased susceptibility. Our integrative analysis shows that Bgt infection induces widespread transcriptional changes and alters the distribution of active histone marks, H3K4me3 and H3K36me3. Together, our results suggest that Bgt infection triggers coordinated epigenetic and transcriptional reprogramming, exemplified by defense-related genes such as TaCIPK19, TaWRKY19, and TaARF4, whose roles in wheat resistance was confirmed by VIGS assays.

The Glu-D1 locus of the Aegilops tauschii genome carries two high-molecular-weight glutenin genes, Dx and Dy, that are essential for viscoelastic properties of bread wheat dough, contributing to its success as a global staple crop. Here, we examined 48 Ae. tauschii high-quality genome assembles and identified a large dataset of Glu-D1, a locus that has remained recalcitrant to high-resolution analysis due to its genomic complexity. Phylogenetic analysis supported six major clades, slightly differing from the geography-based classification. Despite a short genomic distance, gene-based haplotype analysis detected possible ancestral recombination between Dx and Dy genes that were separated by distinctive repetitive sequences. Biochemically, glutenins of the same length can vary in isoelectric points, causing deviations in migration on traditional SDS-PAGE gels. Differential selection pressures were detected among clades and between Dx and Dy glutenin genes. Two clades, L2E-1 and L2W-2, with relatively lower coeliac motifs, were identified as the most probable ancestral contributors to bread wheat. Furthermore, key amino acids were identified as conceptually suitable for single-base editing to create novel elite alleles. Dissecting genomic diversity of the Glu-D1 loci deepens our understanding of the evolutionary trajectory of these long-studied seed storage proteins and offers new strategies for wheat grain-quality improvement.

Summary: Wheat domestication gene Q controls threshability and also pleiotropically affects plant morphogenesis. However, its specific roles in modulating plant architecture and the underlying mechanisms remain unclear. We dissected Q effects on plant architecture using transgenic overexpression and knockout assays. The analyses of micromorphological and dynamic imaging, physiological productivity, multi‐omics, and molecular interaction were performed to dissect the underlying regulatory mechanism. Allelic variation and genetic effect assays were employed to identify desirable haplotypes. The domesticated Q allele 5AQ in wild‐type lines optimized plant architecture and endowed yield gain by modulating cell size of stem internodes and flag leaves, tiller initiation and outgrowth, and photosynthetic capacity. Q regulated many homologs of previously reported functional genes controlling plant architecture, multiple hormone homeostasis, and cell wall components. Q upregulated plant architecture regulators TaARF12‐2B and TaARF12‐2D by binding to the promoters. However, Q and the TaARF12 genes antagonistically modulate plant architecture. The favorable haplotypes of TaARF12‐2B and the functional variation site were identified, and their origin, spread, and distribution were also traced. These findings specify the Q function in controlling plant architecture and yield formation, broaden insights into the underlying mechanism, and provide new molecular tools for wheat improvement.

JASMONATE-ZIM DOMAIN (JAZ) repressor proteins work as co-receptors in the jasmonic acid (JA) signalling pathway and are essential for plant development and environmental adaptation. Despite wheat being one of the main staple food crops, until recently, comprehensive analysis of its JAZ gene family has been limited due to the lack of complete and high-quality reference genomes. Here, using the latest reference genome, we identified 17 JAZ genes in the wheat D-genome donor Aegilops tauschii. Then, 54 TaJAZs were identified in common wheat. A systematic examination of the gene structures, conserved protein domains, and phylogenetic relationships of this gene family was performed. Five new JAZ genes were identified as being derived from tandem duplication after wheat divergence from other species. We integrated RNA-seq data and yield QTL information and found that tandemly duplicated TaJAZ genes were prone to association with spike-related traits. Moreover, 12 TaJAZ genes were located within breeding selection sweeps, including 9 tandemly duplicated ones. Haplotype variation analysis of selected JAZ genes showed significant association of TaJAZ7A and TaJAZ13A with thousand-grain weight. Our work provides a clearer picture of wheat JAZ gene evolution and puts forward the possibility of using these genes for wheat yield improvement.

Summary: Plant breeding is constrained by trade‐offs among different agronomic traits by the pleiotropic nature of many genes. Genes that contribute to two or more favourable traits with no penalty on yield are rarely reported, especially in wheat. Here, we describe the editing of a wheat auxin response factor TaARF12 by using CRISPR/Cas9 that rendered shorter plant height with larger spikes. Changes in plant architecture enhanced grain number per spike up to 14.7% with significantly higher thousand‐grain weight and up to 11.1% of yield increase under field trials. Weighted Gene Co‐Expression Network Analysis (WGCNA) of spatial–temporal transcriptome profiles revealed two hub genes: RhtL1, a DELLA domain‐free Rht‐1 paralog, which was up‐regulated in peduncle, and TaNGR5, an organ size regulator that was up‐regulated in rachis, in taarf12 plants. The up‐regulation of RhtL1 in peduncle suggested the repression of GA signalling, whereas up‐regulation of TaNGR5 in spike may promote GA response, a working model supported by differential expression patterns of GA biogenesis genes in the two tissues. Thus, TaARF12 complemented plant height reduction with larger spikes that gave higher grain yield. Manipulation of TaARF12 may represent a new strategy in trait pyramiding for yield improvement in wheat.