Search Results (223)

Maize (Zea mays L.), a vital crop for global food and economic security, faces intensifying biotic and abiotic stresses driven by climate change, including drought, heat, and erratic rainfall. This review synthesizes emerging biotechnology-driven strategies designed to enhance maize resilience under these shifting environmental conditions. We present an integrated framework that encompasses CRISPR/Cas9 and next-generation genome editing, Genomic Selection (GS), Environmental Genomic Selection (EGS), and multi-omics platforms—spanning transcriptomics, proteomics, metabolomics, and epigenomics. These approaches have significantly deepened our understanding of complex stress-adaptive traits and genotype-by-environment interactions, revealing precise targets for breeding climate-resilient cultivars. Furthermore, we highlight enabling technologies such as high-throughput phenotyping, artificial intelligence (AI), and nanoparticle-based gene delivery—including novel in planta and transformation-free protocols—that are accelerating translational breeding. Despite these technical breakthroughs, barriers such as genotype-dependent transformation efficiency, regulatory landscapes, and implementation costs in resource-limited settings remain. Bridging the gap between laboratory innovation and field deployment will require coordinated policy support and global collaboration. By integrating molecular breakthroughs with practical deployment strategies, this review offers a comprehensive roadmap for developing sustainable, climate-resilient maize varieties to meet future agricultural demands. Full article

The aim of this pilot study was to comprehensively evaluate the gut microbiota, mycobiome, and metabolomic profile of six 4-month-old crossbred pigs (A–F) originating from the same litter and from a specific breeding facility intended for preclinical transplantation experiments, in order to assess their physiological uniformity and identify potential health-related risks prior to inclusion in a kidney transplantation study. The results demonstrated an overall high degree of microbial and metabolic uniformity among the animals, confirming the stability and suitability of the selected breeding source for experimental purposes. At the same time, several individual differences of potential clinical relevance were observed. Animals A, E, and F exhibited signs of microbial and metabolic imbalance, including reduced diversity, increased oxidative activity, and the presence of potentially pathogenic taxa (Porphyromonadaceae bacterium DJF B175, Aspergillus). In contrast, animals B, C, and D showed a balanced metabolic and microbial profile without pathological deviations. The obtained results highlight the importance of preoperative assessment of the gut bacteriome, mycobiome, and metabolome when selecting animals for transplantation experiments. Such a selective screening approach may contribute to the early identification of physiological deviations, reduction of interindividual variability, and increased reliability and translational potential of preclinical studies. Full article

Agricultural systems face mounting pressures from climate change, as rising temperatures, elevated CO₂, and shifting precipitation patterns intensify plant disease outbreaks worldwide. Conventional strategies, such as breeding for resistance, pesticides, and even transgenic approaches, are proving too slow or unsustainable to meet these challenges. Synthetic biology offers a transformative paradigm for reprogramming plant immunity through genetic circuits, RNA-based defences, epigenome engineering, engineered microbiomes, and artificial intelligence (AI). We introduce the concept of synthetic immunity, a unifying framework that extends natural defence layers, PAMP-triggered immunity (PTI), and effector-triggered immunity (ETI). While pests and pathogens continue to undermine global crop productivity, synthetic immunity strategies such as CRISPR-based transcriptional activation, synthetic receptors, and RNA circuit-driven defences offer promising new avenues for enhancing plant resilience. We formalize synthetic immunity as an emerging, integrative concept that unites molecular engineering, regulatory rewiring, epigenetic programming, and microbiome modulation, with AI and computational modelling accelerating their design and climate-smart deployment. This review maps the landscape of synthetic immunity, highlights technological synergies, and outlines a translational roadmap from laboratory design to field application. Responsibly advanced, synthetic immunity represents not only a scientific frontier but also a sustainable foundation for climate-resilient agriculture. Full article

Donkeys (Equus asinus) are economically and ecologically important livestock species whose genetic potential remains underexplored. This review synthesizes recent advances in donkey genomics, tracing their evolutionary history while evaluating current applications in selective breeding, conservation genetics, and agricultural management. By integrating evidence from population genomics, functional genomics, and comparative evolutionary studies, we summarize major genomic discoveries and identify persistent knowledge gaps, with a focus on translating genomic information into practical breeding outcomes. High-quality reference genomes, population resequencing, and ancient DNA analyses have clarified the African origin, global dispersal history, and environmental adaptation of donkeys. Genome-wide approaches, including GWAS, QTL mapping, and multi-omics analyses, have further identified genes and regulatory pathways associated with thermotolerance, metabolism, reproduction, and milk production. Nevertheless, progress is still limited by small sample sizes, variable sequencing depth, and inconsistencies in phenotyping and bioinformatic pipelines, which constrain cross-population comparisons and practical applications. Addressing these challenges through standardized phenotyping, improved data integration, and collaborative research frameworks will lay the groundwork for effective conservation strategies and sustainable genomic breeding of global donkey populations. Full article

Metabolites, once viewed mainly as energy substrates or structural precursors, are now increasingly recognized as key extracellular signaling mediators that regulate diverse physiological processes. This review synthesizes and systematizes current knowledge on metabolite-mediated signaling through G-protein-coupled receptors (GPCRs) in teleosts and, importantly, highlights new conceptual links between specific metabolite–GPCR axes and key physiological functions relevant to aquaculture. By integrating evidence across metabolite–GPCRs axes, including succinate–SUCNR1, aromatic amino acids (tryptophan and phenylalanine)–GPR142, basic amino acids (L-arginine)–GPRC6A, and lactate–GPR81. We clarify how metabolite–receptor interactions have the potential to modulate glucose homeostasis, immune responses, energy metabolism, and stress coping. A major contribution of this review is illustrating how metabolites act not only as nutrients but also as extracellular signaling molecules governing core physiological processes via GPCRs. Particularly from an evolutionary perspective, compared with peptide-activated GPCRs, metabolite-sensing GPCRs are relatively conserved across different species, suggesting that relevant findings from biomedical research could be translated to aquaculture applications. Therefore, understanding GPCR-mediated metabolite sensing provides a molecular foundation for improving nutrient formulation, developing functional feeds, and designing selective breeding strategies in precision aquaculture. Full article

Enhancing photosynthetic efficiency represents a key approach for improving crop biomass, with its translation into higher grain yield being contingent upon the efficiency of photosynthate partitioning toward harvestable organs. The Rubisco small subunit (RbcS) gene family plays an essential role in this process by stabilizing and regulating Rubisco assembly and activity during photosynthesis. In this study, we identified 61 RbcS genes across B. napus, B. juncea, and B. carinata, and their diploid progenitors B. rapa, B. nigra, and B. oleracea by genome-wide screening and bioinformatic approaches. Phylogenetic relationships, gene structures, conserved domains, collinearity, cis-regulatory elements, expression profiles, and haplotype variations were systematically investigated, revealing the potential functional role significance and regulatory complexity of RbcS genes in photosynthesis. The results imply that the promoter type of this gene family may belong to light-inducible promoters. Furthermore, while a haplotype analysis provided valuable insights for selecting germplasm with potentially high photosynthetic efficiency, definitive confirmation of their effects requires functional validation. Collectively, our results establish a theoretical foundation for understanding the molecular mechanisms of BnRbcS genes and propose candidate genetic targets for further exploration to enhance photosynthetic performance in rapeseed breeding. Full article

Protein post-translational modifications (PTMs), as an important biological process of plants responding to environmental stimuli, can regulate the chemical decoration and properties of translated proteins by altering amino acid side chains or protein terminal structures, thereby affecting the synthesis, assembly, localization, function, and degradation of proteins. Notably, PTMs regulate protein function without changing protein expression levels. Two dozen types of PTMs have been identified. This review summarizes the molecular mechanisms of major types of PTMs, including phosphorylation, ubiquitination, SUMOylation, glycosylation, methylation, and acetylation, with a focus on their regulatory roles in plant responses to abiotic stresses. Under heat stress, phosphorylation activates transcription factors such as HSFA1 (heat shock transcription factor 1), while SUMOylation regulates the activity of HSFA1/HSFA2 in the heat stress signaling pathway. Upon cold stress, phosphorylation, ubiquitination, and S-acylation collectively regulate the expression of cold tolerance-related genes. The drought stress response relies on SnRK2s (Sucrose 321 non-Fermenting 1-related protein kinase 2s) -mediated phosphorylation, regulation of ARF7 (auxin response factor 7) by SUMOylation, and ubiquitination. In salt stress, the coupling of phosphorylation of SOS (salt overly sensitive) pathway-related proteins, ubiquitination, and phospholipid metabolism maintains ion homeostasis. Additionally, PTMs play a key role in ABA-mediated abiotic stress responses by regulating core components of signal transduction, such as PYR (pyrabactin resistance)/PYL (PYR1-LIKE)/RCAR (regulatory components of ABA receptor) receptors, PP2Cs (protein phosphatases type 2C), and SnRK2s. On the basis of the synthesis of the regulatory mechanisms of PTMs, we discuss how PTMs can be manipulated to breed abiotic stress resilient crops and the issues to be addressed to achieve the goal, such as crosstalk between PTMs, technical challenges in investigating PTMs and identifying PTM substrates. Full article

Conventional alligator farming, characterized by reliance on chilled fish meat, faces significant challenges, including risks of bacterial contamination and nutritional imbalances. These issues heighten increasing disease susceptibility and threaten industry sustainability, underscoring the critical need for developing nutrient-dense, low-pathogenicity compound feeds. This study conducted a comparative analysis of newborn Siamese crocodiles fed either chilled fish meat or compound feed formulation. Intestinal microbial samples from both cohorts underwent 16S rRNA gene high-throughput sequencing to evaluate differences in microbial composition, diversity, and predicted functionality. The compound feed, specifically formulated for this investigation, possessed the following nutritional composition: crude protein 52.42%; digestible crude protein/digestible energy 16 mg/kcal; crude fat 12.31%; ash 17.42%; crude fiber 0.45%; starch 7.69%; digestible energy 3450 kcal/kg; lysine 3.66%; threonine 1.92%; methionine 1.27%; arginine 3.07%; total essential amino acids 22.97%; calcium 2.51%; total phosphorus 1.8%; available phosphorus 0.98%. Bioinformatics analysis revealed that the compound feed group exhibited numerically higher richness and alpha diversity indices within the intestinal microbiota compared to the chilled fish group. The microbial communities in both groups were dominated by the phyla Proteobacteria, Bacteroidetes, Fusobacteriota, and Firmicutes, collectively representing over 50% of the relative abundance. Functional prediction indicated that the compound feed group possessed the highest relative abundance in metabolic pathways associated with cofactor and vitamin metabolism, carbohydrate metabolism, amino acid metabolism, terpenoid and polyketide metabolism, lipid metabolism, and replication and repair. In contrast, the chilled fish group exhibited significant functional alterations in glycan biosynthesis and metabolism, translation, nucleotide metabolism, transcription, and biosynthesis of other secondary metabolites. Histomorphological analysis demonstrated greater villus height and crypt depth in the compound diet group compared to chilled fish group, although no significant differences were observed in crypt depth or the villus-to-crypt depth ratio. Collectively, these findings indicate that the compound feed enhances intestinal microbial diversity and optimizes its functional structure. Furthermore, while no statistically significant difference in small intestinal villus height was detected, the results suggest a potential positive influence on intestinal development. This investigation provides a scientific foundation for compound feed development, supporting sustainable breeding practices for Siamese crocodiles. Full article

Egg quality is a critical economic trait in poultry production, influencing consumer preference and production efficiency. The genetic and epigenetic regulation of egg quality involves complex biological pathways across various traits such as shell quality, albumen composition, and yolk biochemistry. This review synthesizes recent advances in the genetic, molecular, and epigenetic mechanisms that determine poultry egg quality. Specifically, it focuses on external traits such as eggshell strength, color, and thickness, and internal traits including albumen height, yolk composition, and the Haugh unit. Through genome-wide association studies (GWAS), quantitative trait loci (QTL) mapping, whole-genome sequencing (WGS), and multi-omics approaches, key candidate genes such as OC-116, CALB1, CA2 (shell formation), OVAL, SPINK5, SERPINB14 (albumen quality), and FGF9, PIAS1, NOX5 (lipid metabolism) have been identified. These genes play a pivotal role in shell biomineralization, albumen protein regulation, and yolk lipid transport. This review also explores the heritability of these traits, emphasizing the challenges posed by polygenic architecture and the influence of environmental factors. Furthermore, it addresses the dynamic spatiotemporal regulation of egg quality traits, including epigenetic layers such as DNA methylation, histone modifications, RNA methylation, and post-translational protein modifications. This paper highlights the application of these findings to breeding programs via genomic selection, marker-assisted breeding, and epigenetic engineering approaches. Future directions for precision breeding and the development of functional eggs with enhanced quality are also discussed. Full article

The pine wood nematode (PWN) Bursaphelenchus xylophilus is a highly destructive forest quarantine pest and causal agent of pine wilt disease. The molecular response mechanism of Larix kaempferi (Japanese larch) to B. xylophilus infection remains unclear. This study aims to reveal the dynamic patterns of its defense response and screen key genes through time series transcriptomics. We found larch trees can proactively adjust their defense strategies to deal with the invasion of B. xylophilus. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, plant hormone signal transduction, MAPK signal pathway, and genes related to phenylpropane biosynthesis were more important. Through weighted gene coexpression network analysis (WGCNA), we identified two core modules that were rich in terpenoids, genes related to phenylpropane metabolism and cell wall strengthening, hormone signaling and defense regulation, and cytoskeleton and transport. Ultimately, we identified 20 core genes that were associated with several resistance-related processes, including the biosynthesis of resistance metabolites, post-translational regulation of protein homeostasis and defense signals, and transcriptional and translational reprogramming of gene expression. This study systematically depicted for the first time the continuous transcriptional regulatory network of L. kaempferi in response to pine wood nematodes. The key genes discovered provide important targets for subsequent functional verification and resistance breeding. Full article

Seed biochemical composition critically influences the quality and industrial value of oilseed rape (Brassica napus L.). Understanding the genetic basis of seed oil, protein, and fiber content is essential for breeding improved cultivars. Here we conducted a genome-wide association study (GWAS) on 350 diverse winter oilseed rape lines over three years, using near-infrared reflectance spectroscopy (NIRS) to measure seed traits and SNP genotyping for association mapping. We identified numerous SNP markers significantly associated with seed oil, protein, acid detergent fiber (ADF), and neutral detergent fiber (NDF) content. From 18,566 detected SNPs, 3782 met stringent criteria and were used for association mapping, resulting in 3189 significant associations across three years. The highest number of associations was observed for protein (3480), followed by NDF (3662), ADF (3422), and oil (2046). Individual markers explained up to 35% of phenotypic variation, indicating strong genetic control of these traits. Gene ontology enrichment analyses linked candidate genes to key metabolic and regulatory pathways influencing these traits: protein biosynthesis and post-translational modification, lipid metabolism regulated by phosphorylation, and transcriptional control of cell wall polysaccharide synthesis. These findings provide valuable molecular markers that can be validated for further use in marker-assisted selection, supporting the development of rapeseed cultivars with optimized seed quality for food, feed, and industrial applications. Full article

Myxomatous mitral valve disease (MMVD) is the most prevalent cardiac disorder in small and toy breed dogs, with the Cavalier King Charles Spaniel (CKCS) showing exceptionally high predisposition and early onset of the disease. MMVD is characterized by progressive mitral valve degeneration, volume overload, and eventual development of congestive heart failure (CHF). Given the strong hereditary component in CKCS, considerable research has focused on elucidating the genetic basis of MMVD in this breed. This review article summarizes the current state of knowledge on the phenotypic features, inheritance, and candidate loci potentially responsible for early onset and severe course of the disease. The pathogenesis of the disease, its classification, and the effects of breeding programs aimed at reducing the occurrence of MMVD have been described. Key findings include associations between MMVD severity and polymorphisms in genes such as NEBL, ACE, CDK6, HEPACAM2, COL5A1, and FAH, as well as evidence implicating dysregulated TGF-β signaling, serotonin signaling, and extracellular matrix remodeling pathways. The current state of knowledge on the role of miRNA in the pathogenesis of MMVD was also summarized. Despite these findings, no specific high-penetrating mutation has been identified. MMVD is a complex, polygenic condition shaped by regulatory variants and breed-specific genetic bottlenecks. Comparative studies underscore the translational relevance of canine MMVD to human mitral valve disease, while genomic insights may be basis for the future selective breeding strategies and therapeutic approaches. Further large-scale, integrative studies combining genomics, transcriptomics, and functional validation are needed to clarify disease mechanisms and support targeted treatment in CKCS as well as the development of new breeding strategies and programs. Full article

This review presents soybean responses to drought, heat, and salinity within a signal–transcript–chromatin framework. In this framework, calcium/reactive oxygen species and abscisic acid cues converge on abscisic acid-responsive element binding factor (ABF/AREB), dehydration-responsive element binding protein (DREB), NAC, and heat shock factor (HSF) families. These processes are modulated by locus-specific chromatin and non-coding RNA layers. Base-resolved methylomes reveal a high level of CG methylation in the gene body, strong CHG methylation in heterochromatin, and dynamic CHH ‘islands’ at the borders of transposable elements. CHH methylation increases over that of transposable elements during seed development, and GmDMEa editing is associated with seed size. Chromatin studies in soybean and model species implicate the reconfiguration of salt-responsive histone H3 lysine 27 trimethylation (H3K27me3) in G. max and heat-linked H2A.Z dynamics at thermoresponsive promoters characterized in Arabidopsis and other plants, suggesting that a conserved chromatin layer likely operates in soybean. miR169–NF-YA, miR398–Cu/Zn Superoxide Dismutases(CSD)/copper chaperone of CSD(CCS), miR393–transporter inhibitor response1/auxin signaling F-box (TIR1/AFB), and miR396–growth regulating factors (GRF) operate across leaves, roots, and nodules. Overexpression of lncRNA77580 enhances drought tolerance, but with context-dependent trade-offs under salinity. Single-nucleus and spatial atlases anchor these circuits in cell types and microenvironments relevant to stress and symbiosis. We present translational routes, sentinel epimarkers (bisulfite amplicons, CUT&Tag), haplotype-by-epigenotype prediction, and precise cis-regulatory editing to accelerate marker development, genomic prediction and the breeding of resilient soybean varieties with stable yields. Full article

Legumes are important food crops and play a central role in sustainable agriculture through their ability to form symbiosis with rhizobia, soil bacteria that fix atmospheric nitrogen. Recent advances in single-cell and spatial transcriptomics, along with single-cell epigenomics, have enabled high-resolution analysis of gene expression dynamics and the prediction of cell-type-specific regulatory networks. In this review, we highlight recent progress in the use of single-cell omics in legumes, with a particular focus on how genes functioning in distinct cell types contribute to plant development, responses to pathogens, stress-induced plasticity, and the establishment of root nodule symbioses. Case studies in Medicago truncatula, Lotus japonicus, Glycine max, and Arachis hypogaea illustrate the shift from bulk to single-cell multi-omics. We conclude by outlining current limitations and future directions for building integrated legume cell atlases that will support translational research and crop improvement. Full article

(1) Background: Compound leaf morphogenesis in alfalfa (Medicago sativa), a key trait determining yield and agronomic value, is governed by complex molecular mechanisms. (2) Methods: This study systematically investigates the transcriptomic profiles of space-induced alfalfa mutants exhibiting diverse compound leaf numbers through RNA sequencing and Short Time-series Expression Miner (STEM)-based data analysis. (3) Results: Our findings reveal that transcriptional regulators, phosphorylation-related protein kinases, and glycoside hydrolases collectively modulate this trait. Specifically, GRAS and WRKY transcription factors show positive correlations with increased leaflet numbers, highlighting their roles in promoting leaflet initiation. Conversely, transcript levels of serine-threonine/tyrosine-protein kinases are inversely related to leaflet number, suggesting their involvement in suppressing excessive leaflet formation via post-translational modifications. Notably, glycoside hydrolases exhibit suppressed expression in mutants with higher leaflet numbers compared to wild-type plants, implying a regulatory role in balancing cell wall plasticity during morphogenesis. (4) Conclusions: These results provide critical insights into the interplay between transcriptional control, phosphorylation dynamics, and cell wall remodeling in shaping compound leaf architecture. Furthermore, the identified genes and pathways offer novel molecular targets for breeding strategies aimed at optimizing multi-leaflet alfalfa varieties, with potential applications in agricultural productivity and functional genomics. Full article