Successful evaluation and screening of salt-tolerant wheat germplasm at different stages are of great importance for breeding resilient crops. In the present study, we tested 30 wheat entries out of 417 American accessions screened in a previous study. Fifteen physiological and biochemical indices were investigated at the seedling stage, and eight agronomic indices at the adult stage. Principal component analysis and correlation analysis found superoxide dismutase activity, soluble protein, and potassium levels to be related to high salt tolerance at the seedling stage. Hierarchical clustering analysis identified seven accessions exhibiting high salt tolerance at both the seedling and adult stages. A Random Forest model was constructed to predict salt-resilient entries at the seedling stage. Transcriptome and quantitative reverse-transcription PCR analyses comparing salt tolerant and sensitive accessions revealed that genes and signaling pathways related to the redox system, MAPK, and plant pathogen interactions contributed to salt resistance. Our results provide basic materials for the breeding of new salt-tolerant wheat varieties, indices to screen for salt-resilient cultivars, and insights into salt-tolerance mechanisms.

Tiller angle is a critical determinant of wheat plant architecture, which profoundly impacts yield potential. However, the regulatory mechanisms of tiller angle in wheat remain largely unexplored. To explore the underlying mechanisms, we identify two EMS-mutagenized wheat mutants tiller angle 1 (ta1) and ta2 with enlarged tiller angles. Molecular characterization reveals that TA1 and TA2 encode the DELLA protein Rht-A1 and TaLA1-D, respectively. Biochemical analyses demonstrate that the Rht-A1ta1 variant acquires enhanced protein stability, whereas TaLA1-Dta2 exhibits destabilization. We establish a mechanistic framework that Rht-A1 physically associates with TaPROG1 to synergistically repress TaLA1-D transcription. Moreover, we show that TaGSK3 directly interacts with and phosphorylates TaLA1-D to enhance its stability in reducing wheat tiller angles. Population genomic analyses uncover a significant selection for the elite TaLA1-DHap1 allele during modern wheat breeding, correlating with compact plant architecture and elevated thousand-grain weight. This study provides new insights into plant architecture regulation and target genes for improving yield potential in wheat.

Tiller number is a pivotal agronomic trait directly determining grain yield in wheat (Triticum aestivum L.). Although TN1 is a key positive regulator of tillering, its regulatory network remains incompletely characterized. In this study, we identify TaMYB72-B and TaGSK3 as convergent regulators of TN1 that together fine-tune tiller number. Promoter analysis established TaMYB72-B as an upstream transcriptional repressor of TN1, and its overexpression reduced tiller number, confirming that TaMYB72-B suppresses tillering through TN1. Independently, the kinase TaGSK3 physically interacts with and phosphorylates TN1, destabilizing the protein and accelerating its degradation; overexpression of TaGSK3 likewise reduced tiller number significantly. Together, these findings define a dual-layer regulatory mechanism in which transcriptional repression and post-translational modification converge on TN1 to precisely control tiller development. Haplotype analysis across global wheat germplasm identified TaMYB72-B Hap 1 as an elite haplotype associated with an optimal balance between reduced tiller number and increased grains per spike, a combination that has been preferentially selected during modern breeding. This study, therefore, uncovers a novel regulatory module governing wheat tillering and offers actionable genetic targets for molecular design breeding aimed at optimizing plant architecture and yield.

Soil salinity threatens agriculture worldwide. Nano-fertilizers offer a promising strategy to enhance tolerance to salinity and other stresses in crops, but their field performance is sometimes unpredictable, potentially due to complex interactions within the plant-microbe holobiont. Here, we designed chitosan-stabilized selenium nanoparticles (SeNPs@CS) as a novel nano-fertilizer. SeNPs@CS exhibited a uniform size (∼109.8 nm) and a positively charged surface (+14.7 mV), which confers good adhesion to plant tissues. Due to their good biocompatibility and small size, SeNPs@CS can be readily absorbed and utilized by plant leaves. When SeNPs@CS were combined with glutathione (GSH) to form a nanocomposite (SeG), they significantly promoted plant growth and enhanced salt tolerance in soybean (Glycine max). Multi-omics analyses revealed that SeG activates jasmonic acid (JA) pathways in the plant and remodels the root metabolic profile, leading to the enrichment of arbutin, a key signaling molecule, in the rhizosphere. This metabolic shift recruits and enriches beneficial salt-tolerant microbes, including Bacillus and Streptomyces, thereby establishing a protective microbiome. Treatment of plants with a synthetic microbial community (SynCom) composed of these elite strains, in combination with arbutin, reproduced the salt tolerance phenotype conferred by SeG treatment. Therefore, SeG improves salt tolerance in soybean via activation of the JA defense pathway and arbutin-driven recruitment of salt-tolerant rhizosphere microorganisms. Together, these two mechanisms enhance plant resilience under salt stress. This multi-kingdom synergistic mechanism for alleviating stress provides a new paradigm for developing smart agricultural inputs that target the plant holobiont to improve crop resilience.

Alternative splicing (AS) is a crucial post-transcriptional regulatory mechanism that enhances transcript and proteome diversity. However, AS in common wheat (Triticum aestivum) remains understudied due to the large and complex genome of this crop. Full-length transcriptome sequencing, which provides long, high-quality reads, offers a powerful tool for analyzing AS in wheat. In this study, we used the PacBio Sequel platform to sequence full-length transcripts from 5 wheat tissues (root, stem, leaf, spike, and grain) of the cultivar Aikang58 (AK58). We identified 560,631 isoforms from 86,073 genes, with 76.7% of genes producing multiple isoforms and 45.34% undergoing AS events (ASEs). Tissue-specific analysis revealed differences in the number and function of AS genes (ASGs), underscoring the potential role of AS in tissue differentiation. A comparison across the 3 wheat subgenomes showed similar numbers of ASGs and ASEs but distinct functional patterns, suggesting that AS is involved in subgenomic divergence. We also examined AS in genes linked to key agronomic traits, demonstrating association with trait regulation. These findings enhance our understanding of the adaptability and post-transcriptional gene regulation in wheat, offering insights for future research and breeding efforts.

Wheat grain weight and flour quality largely depend on starch biosynthesis, yet the mechanisms by which transcription factors coordinate this process remain poorly understood. In this study, using an integrative strategy that combines genome-wide association analysis with yeast two-hybrid library screening, we identify TaNF-YC10 , a Nuclear Factor Y transcription factor, as a positive regulator of starch accumulation in the wheat endosperm. Loss of TaNF-YC10 reduces starch content and alters starch granule size distribution, whereas overexpression enhances starch accumulation and increases grain weight. TaNF-YC10 binds and activates core starch biosynthetic-related genes, including AGPL1 , GBSS1 , YUC11 , and NF-YB7 , and forms higher-order transcriptional complexes with TaNF-YB1 and TabHLH95 to coordinate multiple regulatory pathways. TaNF-YC10-A1 - Hap2 is associated with higher starch content and thousand grain weight and has been selected during wheat breeding in China. Collectively, our findings establish TaNF-YC10 as a pivotal transcriptional hub in starch regulation and highlight its potential as a target for genetic improvement of grain yield in wheat.

Leaf width is an important component of plant architecture that strongly affects light capture during photosynthesis and thus grain yield, particularly under dense planting conditions. However, the genetic and molecular mechanisms regulating leaf width in wheat (Triticum aestivum L.) remain unclear. Here, we identified the narrow-leaf mutant nl1 with fewer small veins than the wild-type and isolated the narrow-leaf gene Narrow Leaf 1 (NL1) through a combination of map-based cloning and bulked segregant exome capture sequencing (BSE-seq). NL1 encodes CELL DIVISION CYCLE 48-like (CDC48-like). A single Ser-to-Phe amino acid substitution in this protein led to a narrow-leaf phenotype. Transcriptomic analysis and measurement of endogenous phytohormone levels in nl1 vs. the wild-type suggested that NL1 might regulate cell division and the cytokinin pathway to control leaf width. Haplotype analysis showed that Hap2 of NL1 has been selected during wheat breeding. These findings provide insights into the genetic and molecular mechanisms underlying the role of NL1 in regulating leaf width and point to the potential of Hap2 for improving wheat plant architecture.

Tartary buckwheat is a nutritionally important crop of the Himalayas and is crucial for local economies and food security. However, key genes and superior alleles for high-altitude adaptability and yield remain poorly defined, constraining the breeding of high-altitude buckwheat varieties. Here, we generated a telomere-to-telomere reference genome and a 16-accession pangenome spanning Himalayan wild populations and globally distributed landraces. We identified 123,131 non-redundant structural variations in 16 accessions, including gene copy-number variations. The graph-based pangenome revealed FtRNH, a wild-specific gene that enhances high-altitude adaptability. We also identified a copy-number variation at the FtPLATZ locus and a 28-bp insertion in the FtPLATZ3 promoter that together contribute to seed-size variation across wild buckwheat and landraces. Leveraging these superior FtRNH and FtPLATZ alleles, we developed buckwheat lines with enhanced high-altitude adaptability and improved yields across sites. These findings establish a pangenome-guided strategy for recovering wild alleles and combining stress adaptation with yield improvement in crops.

Starch is the primary storage compound in wheat grains and is essential for both flour quality and grain weight. In this study, we identified TaMYB44, an R2R3-MYB transcription factor gene that controls starch content in wheat grains, through a genome-wide association study. The TaMYB44 homoeologs were predominantly expressed in developing grains, with peak levels observed 10 days after pollination. Functional analyses revealed that TaMYB44 acts as a negative regulator of starch synthesis in the endosperm, limiting grain size by repressing starch synthesis-related genes and modulating secondary metabolism. Knockout mutants of TaMYB44 exhibited significantly increased starch accumulation, larger grain size, and improved yield stability across diverse growing environments. Furthermore, we discovered that TaWDR1 interacts with TaMYB44, alleviating its repressive effects to restore starch synthesis and enhance grain weight. Notably, the functions of MYB44 appear to be partially conserved between wheat and rice, underscoring its potential as a target for genetic improvement. Our findings offer valuable insights into the transcriptional regulation of starch synthesis and provide genetic resources for enhancing grain yield in wheat and rice.

Colletotrichum graminicola can cause leaf spots and stalk rot in maize. The primary function of carbohydrate esterases (CEs) is to eliminate ester modifications from monosaccharides, oligosaccharides, and polysaccharides, thereby facilitating the hydrolysis of sugars. We identified 128 CE genes through whole-genome analysis and functional annotation of C. graminicola TZ–3 here. We further analyzed the physicochemical properties, subcellular localization, conserved motifs, gene structures, promoter regulatory elements of these 128 C. graminicola CE (CgCE) genes. Our results indicated that half of the CgCE proteins were located extracellularly. The CgCE proteins demonstrated diversity in both their structures and motifs. Furthermore, the CgCE gene family contained numerous conserved domains, suggesting potential functional diversity. Regulatory elements associated with various stresses and plant hormones were identified in this study. GO enrichment and expression pattern analysis indicated that the CgCE genes were involved in metabolic processes and might contribute to the establishment of fungal infections and lesion expansion. These results enhance our understanding of the CE family genes in C. graminicola and provide a foundation for further investigations into their roles in fungal pathogenesis.

The Q gene is a key domestication gene in wheat (Triticum aestivum) that regulates free-threshing habit, spike morphology, height, and other critical agronomic traits. However, the precise molecular mechanisms underlying its function remain unclear. In this study, we identified a Q allele with a missense mutation (G to A) in the fifth exon of the Q gene, resulting in reduced plant height and spike length. Further investigation revealed that this mutation causes a Gly-229-Ser amino acid substitution, which enhances Q protein stability. Furthermore, we discovered that Q directly binds to the promoter region of Gibberellin 3-oxidase 2 gene (TaGA3ox2) and represses its expression. Moreover, Q interacts with both REDUCED HEIGHT1 (RHT1) and GIBBERELLIN INSENSITIVE 2 (TaGID2), which may disrupt GID2-triggered RHT1 degradation. Collectively, these findings reveal the dual roles of Q in regulating both GA biosynthesis and signaling, providing insights into the molecular mechanisms through which Q modulates plant height and spike length in wheat.

SKP1 constitutes the Skp1-Cullin-F-box ubiquitin E3 ligase (SCF), which plays a role in plant growth and development and biotic and abiotic stress in ubiquitination. However, the response of the SKP1-like gene family to abiotic and biotic stresses in cotton has not been well characterized. In this study, a total of 72 SKP1-like genes with the conserved domain of SKP1 were identified in four Gossypium species. Synteny and collinearity analyses revealed that segmental duplication played a major role in the expansion of the cotton SKP1-like gene family. All SKP1-like proteins were classified into three different subfamilies via phylogenetic analysis. Furthermore, we focused on a comprehensive analysis of SKP1-like genes in G. hirsutum. The cis-acting elements in the promoter site of the GhSKP1-like genes predict their involvement in multiple hormonal and defense stress responses. The expression patterns results indicated that 16 GhSKP1-like genes were expressed in response to biotic or abiotic stresses. To further validate the role of the GhSKP1-like genes in salt stress, four GhSKP1-like genes were randomly selected for gene silencing via VIGS. The results showed that the silencing of GhSKP1-like_7A resulted in the inhibition of plant growth under salt stress, suggesting that GhSKP1-like_7A was involved in the response to salt stress. In addition, yeast two-hybrid results revealed that GhSKP1-like proteins have different abilities to interact with F-box proteins. These results provide valuable information for elucidating the evolutionary relationships of the SKP1-like gene family and aiding further studies on the function of SKP1-like genes in cotton.

Wide hybridization is crucial for broadening the genetic basis of common wheat. Agropyron cristatum (2n = 4x = 28, PPPP), a wild relative of wheat, harbors numerous favorable genes for genetic improvement. The variability related to the expression of alien genes in different wheat backgrounds is a crucial factor that limits the effective utilization of these genes. In this study, the introduction of chromosome 6P from A. cristatum into different wheat backgrounds resulted in different leaf colors: green in plants with the Fukuho background and yellow‒green in plants with the Jimai 22 background. Genetic analysis suggested that yellow‒green leaves were caused by gene interactions between chromosome 6P and genes from the Jimai 22 background, which negatively affected agronomic traits. To determine the locus on chromosome 6P responsible for yellow‒green leaves, six wheat–A. cristatum deletion lines and five wheat–A. cristatum translocation lines were crossed with Jimai 22 to produce F1 progeny for leaf color investigation. We found that the F1 progeny carrying the short arm of chromosome 6P (6PS) presented yellow–green leaves, and the relevant locus was ultimately mapped to 6PS (0.81-1.00). A total of 50 A. cristatum genes related to chlorophyll catabolite reductase and chloroplast development were annotated within this interval. A locus on chromosome 6P of A. cristatum that caused a yellow–green leaf in the Jimai 22 background was mapped to chromosome 6PS (0.81-1.00). This study provides valuable germplasm for the study of leaf color and guidance for the use of valuable genes on A. cristatum chromosome 6P.

ABSTRACT Gut microbiota crucially affects metabolism and health. Hycleus cichorii Linnaeus has been listed as a medicinal insect in the Pharmacopeia of the People's Republic of China due to the presence of cantharidin, which has a curative effect on many cancers and skin diseases. In order to analyze the effects of dietary habits and gender on the diversity and composition of gut microbiota in H. cichorii and provide a basis for an artificial diet, in this study, the full‐length 16S rRNA sequencing technology was used to analyze the gut microbiota of 35 H. cichorii adults, including wild female adults (WFA), wild male adults (WMA), female adults fed with luffa flowers (LFA), male adults fed with luffa flowers (LMA), female adults fed with artificial diet (AFA), and male adults fed with artificial diet (AMA). The results displayed that the major bacterial phyla present in the gut microbiota of the H. cichorii were Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, Teneriicutes, and Actinobacteria. The major bacterial genera were Lactococcus, Lactobacillus, Enterococcus, Ralstonia, Sebaldella, Dysgonomonas, Spiroplasma, Weissella, Klebsiella, and Serratia. Food habits had a significant effect on the diversity and composition of gut microbiota in H. cichorii, whereas gender did not exhibit a remarkable impact on the diversity and composition of gut microbiota. The artificially fed group of H. cichorii had more beneficial microorganisms in the intestine and higher food utilization efficiency. These results provide a basis for subsequent examination of gut microbiota in H. cichorii or other Coleoptera insects, as well as the artificial rearing of blister beetles.

Diaphorina citri Kuwayama (1908), the Asian citrus psyllid (ACP), is a major pest of citrus crops, responsible for transmitting the bacterium that causes Huanglongbing (HLB), a disease devastating to citrus industries worldwide. Despite extensive research on its population genetics in other regions, the genetic structure of D. citri in Sichuan Province, China, remains poorly understood, complicating the development of effective pest management strategies. This study aims to fill this gap by investigating the genetic diversity and population structure of D. citri using genome-wide single nucleotide polymorphisms (SNPs). Three natural populations of D. citri from southeastern Sichuan were sequenced, revealing a total of 7,010,305 SNPs and relatively low genetic differentiation among populations. Phylogenetic analysis identified two primary genetic groups with limited gene flow, supported by principal component analysis (PCA) and Admixture analysis. The populations exhibited high genetic diversity, with notable variations in nucleotide diversity and inbreeding coefficients. Functional enrichment analysis highlighted genes involved in cellular processes and stress response, which may contribute to local adaptation. These findings provide valuable insights into the evolutionary dynamics of D. citri and suggest that genetic diversity and selective pressures play a key role in its adaptability. The results underscore the importance of considering genetic variation in the development of targeted and sustainable pest management strategies in southeastern China.

l-isoleucine, a value-added branched-chain amino acid, has been widely used in the food, feed, and pharmaceutical industries. However, the production efficiency of l-isoleucine is relatively low due to the complex and inefficient biosynthetic network of the canonical threonine pathway. Here, we report the exploitation of a concise citramalate pathway for the development of an efficient l-isoleucine producer. First, chassis strain and key genes were screened for establishment of the citramalate pathway. Subsequently, a citramalate importer was identified and applied to enhance citramalate's utilization efficiency. Finally, a plasmid-free high-l-isoleucine producer was developed by enhancement of l-isoleucine efflux, optimization of rate-limiting gene expression, and introduction of a nonoxidative glycolysis pathway. Fed-batch fermentation of the final strain in a 10-L bioreactor produced 56.6 g/L l-isoleucine with a productivity of 1.66 g/L/h, which is the highest l-isoleucine titer and productivity reported. This study paves the way for construction of efficient microbial cell factories for production of l-isoleucine and related derivatives based on the citramalate pathway.

Fagopyrum tibeticum is a small woody shrub, which was initially classified under the genus Parapteropyrum (Polygonaceae) as Parapteryrum tibeticum. However, recent molecular evidences has shown that it should belong to Fagopyrum. By integrating cytological, morphological, and molecular biology evidences, we compare F. tibetium with the other Fagopyrum species, once again proving that F. tibeticum should belong to the Fagopyrum genus. Moreover, F. tibeticum is the only existing hexaploid species in the genus Fagopyrum. The speciation of F. tibeticum may be related to the uplift of the Qinghai Tibet Plateau and the distinctive climate environment.