Fei Li

Sorghum (Sorghum bicolor L.), the fifth-most important cereal crop globally, serves as a cornerstone crop for food security, forage production, and bioenergy feedstock on arid and semi-arid marginal lands, owing to its high water use efficiency derived from C4 photosynthesis and exceptional tolerance to abiotic stresses. Conventional sorghum breeding has long been constrained by insufficient genetic dissection of complex traits, the “black box” of genotype-to-phenotype mapping, and poorly understood genotype-by-environment interactions, resulting in stagnant genetic gain. In recent years, rapid advances in multi-omics technologies—including genomics, transcriptomics, epigenomics, single-cell omics, and microbiomics—have propelled sorghum research from single-gene mapping to systems-level dissection of regulatory networks, providing a novel paradigm for elucidating the molecular basis of agronomic traits across all molecular layers and breaking through the bottlenecks of conventional breeding. This review systematically synthesizes recent advances in sorghum multi-omics research, dissecting the molecular basis of key agronomic traits across distinct omics layers. We summarize the integrated multi-omics precision breeding technology system and elaborate on the practical applications of multi-omics approaches for four core breeding objectives: stress tolerance, yield, quality, and nutrient use efficiency. Finally, we discuss current challenges and future perspectives, aiming to provide a theoretical framework and technical reference for molecular design breeding in sorghum.

Background: Drought stress is a primary environmental constraint limiting crop growth and productivity. Current drought-related plant research predominantly focuses on whole-leaf analyses, neglecting the spatial heterogeneity of metabolites within leaf tissues. Methods: This study combined transcriptomic and metabolomic approaches to investigate spatially distinct metabolic responses in marginal versus central regions of Medicago lupulina L. leaves under PEG-simulated drought. Results: Findings demonstrated that TCA cycle metabolites exhibited relative stability between leaf margins and centers under drought conditions, suggesting preserved core metabolic functionality in central tissues to sustain stress tolerance. Additionally, shikimic acid displayed a significantly reduced regional gradient in stressed tissues (PEG Margin vs. PEG Center) compared to controls. Phenylalanine, tryptophan, liquiritigenin, isoliquiritigenin, coproporphyrin III, and coproporphyrinogen III itself exhibited significantly increased internal gradient differences in stressed groups compared to control groups. The coordinated upregulation of key biosynthetic genes (e.g., TAT, AST, FNS II) in both the marginal and central regions of stressed leaves indicates a metabolic shift toward the biosynthesis of downstream defensive flavonoids. These metabolites and genes accumulated preferentially in margin regions of stressed leaves, indicative of localized activation of defense-associated metabolic pathways. Conclusions: This study reveals a spatially partitioned metabolic response to drought stress in M. lupulina leaves, where defensive metabolism is preferentially enhanced at the leaf margins while core metabolic homeostasis is maintained. These findings provide new spatial insights into plant drought acclimation and identify potential targets for improving crop resilience through the fine-tuning of local metabolism.

Introduction: Codon usage bias (CUB) can influence host-microbe interactions and stress adaptation. In this study, we aimed to investigate how codon usage bias (CUB) similarity between Arabidopsis thaliana and Bacillus amyloliquefaciens influences their interaction and contributes to the adaptation of A. thaliana to high calcium stress.Methods: The CUB indices of both species were computed, and genes with high correlations were identified. The transcriptome sequencing data of gene expression in A. thaliana cultured under normal and high calcium conditions, with and without B. amyloliquefaciens treatment was used to analyze the expression of A. thaliana genes with CUB similar to that of B. amyloliquefaciens in relation with the adaptation of A. thaliana to high calcium stress and the interaction between both organisms.Results: We identified 19210 A. thaliana genes with CUB similar to B. amyloliquefaciens and 95 B. amyloliquefaciens-responsive and calcium-responsive genes in A. thaliana, which were involved in transport, carbohydrate metabolism, and response to chemical, and cellular homeostasis. Differential expression analysis showed a total of 733 A. thaliana genes with CUB similar to B. amyloliquefaciens to be dysregulated, among which 47 changed when A. thaliana was cultivated in the presence of the B. amyloliquefaciens LZ04 strain, 643 under high calcium condition and 43 with calcium treatment and the presence of the B. amyloliquefaciens LZO4 strain. The gene ontology (GO) biological processes termed among others of response to endogenous stimulus, response to oxygen containing compound, response to organic substance, response to abiotic and biotic stimuli, response to stress, and response to light stimulus, regulation of hormone levels, response to nutrient levels, post-embryonic plant morphogenesis, metabolic process, cell growth.Discussion: These findings highlight the importance of CUB in the interaction between A. thaliana and B. amyloliquefaciens as well as in the adaptation of A. thaliana to high calcium stress. They also show the underlying regulatory role of B. amyloliquefaciens, which could help develop new tactics for improving A. thaliana growth and yield in karst regions. A more elaborate analysis of the value of CUB in the interaction of these two organisms could assist in engineering host- sensitive micro-organism strains and enhance the microbial-based approaches for the improvement of A. thaliana growth and yield in such areas and for managing abiotic stress in crops.

The genus Trichoderma plays a pivotal role in sustainable agriculture through its multifaceted contributions to plant health and productivity. This review explores Trichoderma’s biological functions, including its roles as a biocontrol agent, plant growth promoter, and stress resilience enhancer. By producing various enzymes, secondary metabolites, and volatile organic compounds, Trichoderma effectively suppresses plant pathogens, promotes root development, and primes plant immune responses. This review details the evolutionary adaptations of Trichoderma, which has transitioned from saprotrophism to mycoparasitism and established beneficial symbiotic relationships with plants. It also highlights the ecological versatility of Trichoderma in colonizing plant roots and improving soil health, while emphasizing its role in mitigating both biotic and abiotic stressors. With increasing recognition as a biostimulant and biocontrol agent, Trichoderma has become a key player in reducing chemical inputs and advancing eco-friendly farming practices. This review addresses challenges such as strain selection, formulation stability, and regulatory hurdles and concludes by advocating for continued research to optimize Trichoderma’s applications in addressing climate change, enhancing food security, and promoting a sustainable agricultural future.

This review highlights the emerging role of cross-kingdom RNA interference in plant–microbe interactions, particularly the transfer of sRNAs from microbes to plants and vice versa, emphasizing the importance of this mechanism in both mutualistic and pathogenic contexts. As plants adapted to terrestrial life, they formed symbiotic relationships with microbes, essential for nutrient uptake and defense. Emerging evidence underscores sRNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs), as critical regulators of gene expression and immune responses in plant–microbe interactions. In mutualistic symbioses, such as mycorrhizal fungi and nitrogen-fixing bacteria associations, sRNAs are hypothesized to regulate nutrient exchange and symbiotic stability. In pathogenic scenarios, microbes utilize sRNAs to undermine plant defenses, while plants employ strategies like host-induced gene silencing (HIGS) to counteract these threats. We further explore the emerging role of extracellular vesicles (EVs) in sRNA transport, which is critical for facilitating interspecies communication in both pathogenic and mutualistic contexts. Although the potential of ckRNAi in mutualistic interactions is promising, the review highlights the need for further experimental validation to establish its true significance in these relationships. By synthesizing current research, this review highlights the intricate molecular dialogues mediated by sRNAs in plant–microbe interactions and identifies critical gaps, proposing future research directions aimed at harnessing these mechanisms for agricultural advancements.

Recent advancements in the field of plant–pathogen interactions have spotlighted the role of extracellular vesicles (EVs) as pivotal mediators of cross-kingdom communication, offering new vistas for enhancing crop protection strategies. EVs are instrumental in the transport of small regulatory RNAs (sRNAs) and other bioactive molecules across species boundaries, thus playing a critical role in the molecular warfare between plants and pathogens. This review elucidates the sophisticated mechanisms by which plants utilize EVs to dispatch sRNAs that silence pathogenic genes, fortifying defenses against microbial threats. Highlighting both eukaryotic and prokaryotic systems, this review delves into the biogenesis, isolation, and functional roles of EVs, illustrating their importance not only in fundamental biological processes but also in potential therapeutic applications. Recent studies have illuminated the significant role of EVs in facilitating communication between plants and pathogens, highlighting their potential in host-defense mechanisms. However, despite these advancements, challenges remain in the efficient isolation and characterization of plant-derived EVs. Overcoming these challenges is critical for fully harnessing their potential in developing next-generation crop protection strategies. This review proposes innovative strategies for utilizing RNA-based interventions delivered via EVs to bolster plant resilience against diseases. By integrating the latest scientific findings with practical applications in agriculture, this review aims to enhance the connection between fundamental plant biology and the development of innovative crop management technologies.

Many studies have attempted to explore the changes in the structure and function of symbiotic microbiomes, as well as the underlying genetic mechanism during crop domestication. However, most of these studies have focused on crop root microbiomes, while those on leaf and fruit are rare. In this study, we generated a comprehensive dataset including the metagenomic (leaf) and metatranscriptomic (fruit pericarp in the orange stage) data of hundreds of germplasms from three tomato clades: Solanum pimpinellifolium (PIM), cherry tomato (S. lycopersicum var. cerasiforme) (CER), and S. lycopersicum group (BIG). We investigated the effect of domestication and improvement processes on the structure of the symbiotic microbiome of tomato leaf and fruit pericarp, as well as its genetic basis. We were able to obtain the composition of the symbiotic microbiome of tomato leaf and fruit pericarp, based on which the tomato clade (PIM, CER, or BIG) was predicted with high accuracy through machine learning methods. In the processes of tomato domestication and improvement, changes were observed in the relative abundance of specific bacterial taxa, Bacillus for example, in the tomato leaf and fruit pericarp symbiotic microbiomes, as well as in the function of these symbiotic microbiomes. In addition, SNP loci that were significantly associated with microbial species that are characteristic of tomato leaf were identified. Our results show that domestication and genetic improvement processes alter the symbiotic microbiome structure and function of tomato leaf and fruit pericarp. We propose that leaf and fruit microbiomes are more suitable for revealing changes in symbiotic microbiomes during the domestication process and the underlying genetic basis for these changes due to the exclusion of the influence of environmental factors such as soil types on the microbiome structure.

Introduction: Transmembrane 9 superfamily (TM9SF) proteins play significant roles in plant physiology. However, these proteins are poorly characterized in wheat (Triticum aestivum). The present study aimed at the genome-wide analysis of putative wheat TM9SF (TraesTM9SF) proteins and their potential involvement in response to nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatments.Methods: TraesTM9SF genes were retrieved from the wheat genome, and their physiochemical properties, alignment, phylogenetic, motif structure, cis-regulatory element, synteny, protein-protein interaction (PPI), and transcription factor (TF) prediction analyses were performed. Transcriptome sequencing and quantitative real-time polymerase reaction (qRT-PCR) were performed to detect gene expression in roots under single or combined treatments with nitrogen limitation and B. amyloliquefaciens PDR1.Results and discussion: Forty-seven TraesTM9SF genes were identified in the wheat genome, highlighting the significance of these genes in wheat. TraesTM9SF genes were absent on some wheat chromosomes and were unevenly distributed on the other chromosomes, indicating that potential regulatory functions and evolutionary events may have shaped the TraesTM9SF gene family. Fifty-four cis-regulatory elements, including light-response, hormone response, biotic/abiotic stress, and development cis-regulatory elements, were present in the TraesTM9SF promoter regions. No duplication of TraesTM9SF genes in the wheat genome was recorded, and 177 TFs were predicted to target the 47 TraesTM9SF genes in a complex regulatory network. These findings offer valued data for predicting the putative functions of uncharacterized TM9SF genes. Moreover, transcriptome analysis and validation by qRT-PCR indicated that the TraesTM9SF genes are expressed in the root system of wheat and are potentially involved in the response of this plant to single or combined treatments with nitrogen limitation and B. amyloliquefaciens PDR1, suggesting their functional roles in plant growth, development, and stress responses.Conclusion: These findings may be vital in further investigation of the function and biological applications of TM9SF genes in wheat.

Tobacco is one of the vital economic crops in China. Nevertheless, tobacco diseases cause substantial economic losses each year. Tobacco target spot is a fungal disease which commonly found on the ...

The rhizosphere microbiome can regulate various plant biological activities; however, the composition of the rhizosphere microbiome is easily affected by the growing environment and plant genotype. To further explore the differences and the interaction mechanisms between the rhizosphere microbiome of different wheat cultivars planted in northern China, we systematically compared the rhizosphere microbiome of major wheat cultivars Jimai22 and Xiaoyan22 planted in the field in Jinan and Qingdao, Shandong Province. The rhizosphere microbiome data were obtained from Jimai22 and Xiaoyan22 at the three‐leaf stage by 16S rRNA gene amplicon sequencing and were compared based on diversity analysis, principal coordinates’ analysis, machine learning methods such as random forest, and network analysis. The results showed that the plant growing environment and genotype significantly affected the community structure of the wheat rhizosphere microbiome. Operational taxonomic units belonged to Actinobacteria, Bacteroidetes, Firmicutes, Acidobacteria, and Proteobacteria were differentially enriched between the two wheat genotypes. Moreover, random forest model could accurately (accuracy rate 96.4%) predict wheat genotype across locations based on differences in rhizosphere microbiome of Jimai22 and Xiaoyan22. The findings of this study provide supporting data and a theoretical basis for in‐depth understanding of the composition of the rhizosphere microbiome of wheat planted in northern China, which can be applied to improve wheat breeding from the perspective of root microbe–plant interaction.