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Background DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor family has been reported in other species, no relevant studies have emerged in wheat. The aim of this study was to investigate the evolutionary and functional characteristics associated with plant growth and abiotic stress responses by genome-wide analysis of the wheat Dof transcription factor gene family. Results Using the recently released wheat genome database (IWGSC RefSeq v1.0), we identified 96 wheat Dof gene family members, which were phylogenetically clustered into five distinct subfamilies. Gene duplication analysis revealed a broad and heterogeneous distribution of TaDofs on the chromosome groups 1 to 7, and obvious tandem duplication genes were present on chromosomes 2 and 3.Members of the same gene subfamily had similar exon-intron structures, while members of different subfamilies had obvious differences. Functional divergence analysis indicated that type-II functional divergence played a major role in the differentiation of the TaDof gene family. Positive selection analysis revealed that the Dof gene family experienced different degrees of positive selection pressure during the process of evolution, and five significant positive selection sites (30A, 31 T, 33A, 102G and 104S) were identified. Additionally, nine groups of coevolving amino acid sites, which may play a key role in maintaining the structural and functional stability of Dof proteins, were identified. The results from the RNA-seq data and qRT-PCR analysis revealed that TaDof genes exhibited obvious expression preference or specificity in different organs and developmental stages, as well as in diverse abiotic stress responses. Most TaDof genes were significantly upregulated by heat, PEG and heavy metal stresses. Conclusions The genome-wide analysis and identification of wheat DOF transcription factor family and the discovery of important amino acid sites are expected to provide new insights into the structure, evolution and function of the plant Dof gene family.

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.

We investigated the functional properties of two 1S l -encoded high molecular weight glutenin subunits (HMW-GS), 1S l x2.3* and 1S l y16*, from Aegilops longissima L . , and developed single-nucleotide polymorphism (SNP)-based molecular markers. Two HMW-GS near-isogenic lines (NILs), HMW-NIL1 (1Ax1, 1S l x2.3* + 1S l y16*, and 1Dx2 + 1Dy12) and HMW-NIL2 (1Ax1, 1Bx17 + 1By18, and 1Dx2 + 1Dy12), were developed by crossing the ‘Chinese Spring’ (CS)- Ae. longissima 1S l /1B substitution line (CS-1S l /1B) with the spring wheat cultivar CB037A, and consecutive selfing combined with selection and identification. Quality analysis of the two NILs showed that the 1S l x2.3* + 1S l y16* subunits conferred better dough rheological properties and breadmaking quality than the 1Bx17 + 1By18 subunits; in particular, they significantly improved dough strength, loaf volume and texture, and final bread score. Allele-specific polymerase chain reaction markers for both genes were developed based on SNP variations and successfully amplified 290-bp and 283-bp specific fragments from the 1S l x2.3* and 1S l y16* genes, respectively. Both SNP-based molecular markers were further validated using 38 wheat varieties, two recombination inbred lines, and four F 2 generations and showed high specificity and accuracy. Thus, these markers can be used for molecular marker-assisted selection in the early generations of wheat quality improvement programs.

Diversity surveys of germplasm are important for gaining insight into the genomic basis for crop improvement; especially InDels, which are poorly understood in hexaploid common wheat. Here, we describe a map of 89,923 InDels from exome sequencing of 262 accessions of a Chinese wheat mini-core collection. Population structure analysis, principal component analysis and selective sweep analysis between landraces and cultivars were performed. Further genome-wide association study (GWAS) identified five QTL (Quantitative Trait Loci) that were associated with spike length, two of them, on chromosomes 2B and 6A, were detected in 10 phenotypic data sets. Assisted with RNA-seq data, we identified 14 and 21 genes, respectively that expressed in spike and rachis within the two QTL regions that can be further investigated for candidate genes discovery. Moreover, InDels were found to be associated with awn length on chromosomes 5A, 6B and 4A, which overlapped with previously reported genetic loci B1 (Tipped 1), B2 (Tipped 2) and Hd (Hooded). One of the genes TaAGL6 that was previously shown to affect floral organ development was found at the B2 locus to affect awn length development. Our study shows that trait-associated InDels may contribute to wheat improvement and may be valuable molecular markers for future wheat breeding

Optimal spike architecture provides a favorable structure for grain development and yield improvement. However, the number of genes cloned to underlie wheat spike architecture is extremely limited. Here, we obtained a wheat dense spike mutant ( wds ) induced by 60 Co treatment of a common wheat landrace Huangfangzhu that exhibited significantly reduced spike and grain lengths. The shortened spike length was caused by longitudinal reduction in number and length of rachis cells. We adopted a multi-omics approach to identify the genomic locus underlying the wds mutant. We performed Exome Capture Sequencing (ECS) and identified two large deletion segments, named 6BL.1 at 334.8∼424.3 Mb and 6BL.2, 579.4∼717.8 Mb in the wds mutant. RNA-seq analysis confirmed that genes located in these regions lost their RNA expression. We then found that the 6BL.2 locus was overlapping with a known spike length QTL, qSL6B.2. Totally, 499 genes were located within the deleted region and two of them were found to be positively correlated with long spike accessions but not the ones with short spike. One of them, TraesCS6B01G334600 , a well-matched homolog of the rice OsBUL1 gene that works in the Brassinosteroids (BR) pathway, was identified to be involved in cell size and number regulation. Further transcriptome analysis of young spikes showed that hormone-related genes were enriched among differentially expressed genes, supporting TraesCS6B01G334600 as a candidate gene. Our work provides a strategy to rapid locate genetic loci with large genomic lesions in wheat and useful resources for future wheat study.

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.

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.

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.

Background: DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor family has been reported in other species, no relevant studies have emerged in wheat. The aim of this study was to investigate the evolutionary and functional characteristics associated with plant growth and abiotic stress responses by genome-wide analysis of the wheat Dof transcription factor gene family. Results: Using the recently released wheat genome database (IWGSC RefSeq v1.1), we identified 96 wheat Dof gene family members, which were phylogenetically clustered into five distinct subfamilies. Gene duplication analysis revealed a broad and heterogeneous distribution of TaDofs on the chromosome groups 1 to 7, and obvious tandem duplication genes were present on chromosomes 2 and 3.Members of the same gene subfamily had similar exon-intron structures, while members of different subfamilies had obvious differences. Functional divergence analysis indicated that type-II functional divergence played a major role in the differentiation of the TaDof gene family. Positive selection analysis revealed that the Dof gene family experienced different degrees of positive selection pressure during the process of evolution, and five significant positive selection sites (30A, 31T, 33A, 102G and 104S) were identified. Additionally, nine groups of coevolving amino acid sites, which may play a key role in maintaining the structural and functional stability of Dof proteins, were identified. The results from the RNA-seq data and qRT-PCR analysis revealed that TaDof genes exhibited obvious expression preference or specificity in different organs and developmental stages, as well as in diverse abiotic stress responses. Most TaDof genes were significantly upregulated by heat, PEG and heavy metal stresses. Conclusions: The genome-wide analysis and identification of wheat DOF transcription factor family and the discovery of important amino acid sites are expected to provide new insights into the structure, evolution and function of the plant Dof gene family.

Although the organic fraction of PM2.5 has been extensively studied, there is a considerable gap in understanding the organic fraction of coarse particles with diameters between 2.5 and 10 µm. We investigate the composition of coarse organic aerosol (OA) across rural, suburban, and urban areas of Switzerland. Using Aerosol Mass Spectrometer analyses of water-soluble OA extracted from collected filter samples (one entire year, 441 samples per size fraction), we identified two distinct classes of coarse OA. The first class, which constitutes 41–81% of coarse organic carbon (OC), is associated with primary biological organic carbon (PBOC). PBOC is characterized by specific marker ions (e.g., C2H5O2+) and exhibits pronounced seasonal variation, with peak concentrations observed in the summer. This seasonal trend correlates with that of molecular markers such as arabitol and mannitol, as well as the fraction of biological particles determined by automated scanning electron microscopy coupled to energy dispersive X-ray spectroscopy of individual particles. The second class, contributing 7.9–17.8% to OCcoarse, is denoted as sulfur-containing organic carbon (SCOC) due to the presence of sulfur-containing ions such as CH3SO2+. Elevated concentrations of SCOC in urban environments near roadways suggest a strong influence from non-exhaust traffic emissions and resuspended dust. While the overall variation in coarse OC between rural and urban areas is approximately 10%, PBOC concentrations are 1.4 times higher in rural areas, whereas SCOC concentrations are 1.5 times higher in urban settings. Overall, our study shows that although OCcoarse concentrations in Switzerland are relatively consistent across site types, major water-soluble sources, particle properties and composition vary considerably geographically and seasonally.