Wheat production is increasingly threatened by biotic and abiotic stresses, with stripe rust, caused by Puccinia striiformis f. sp. tritici being among the most devastating diseases. To dissect stripe rust resistance mechanisms, 329 diverse wheat genotypes were evaluated across six distinct environments in India (three locations over two years). The panel exhibited wide variation for stripe rust resistance and was genotyped using a 35K SNP-array. Genome-wide association study (GWAS) revealed 49 significant marker-trait associations (MTAs), explaining 1.58% to 29.7% of phenotypic variation, with notable quantitative-trait locus (QTL) hotspots on chromosomes 2A, 3B and 4B. Several MTAs co-localized with known resistance loci, while AX-92621629 appeared novel, suggesting new genomic region contributing to adult plant resistance. Candidate genes near significant single-nucleotide polymorphisms (SNPs) were enriched for defense-related functions, including nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins, receptor-like kinases and transcription factors involved in defense signaling. To further investigate resistance mechanisms, metabolomic profiling, phytohormone and flavonoid dynamics were conducted on two contrasting wheat genotypes (resistant SKUA_415; susceptible SKUA_246) using untargeted Gas Chromatography-Mass Spectrometry (GC‒MS) and Liquid Chromatography-Mass Spectrometry (LC‒MS) approaches. Key defense-related metabolites, including myo-inositol, ketoglutaric acid, rutin and schaftoside and kaempferol derivatives were identified. These metabolites were downregulated in SKUA_246 following infection, while SKUA_415 showed up-regulation of defense phytohormones, anthocyanins and flavonoids. The two contrasting genotypes also exhibited clear allelic differentiation at key resistance-linked SNP loci, consistent with their divergent metabolomic responses. This study highlights identification of promising genes/QTLs/MTAs and metabolic markers for breeding next-generation stripe rust resistant wheat cultivars.

Type II ketosis in dairy cows is a common metabolic disorder characterized by hepatic lipid metabolism dysregulation. To investigate hepatic tissue heterogeneity and underlying molecular mechanisms in type II ketosis, this study utilized an integrated multi-omics and functional validation strategy. Serum (n = 20), plasma (n = 6), and liver tissue (n = 1 to 3) samples were obtained from Holstein cows in the early postpartum period (3 to 15 days), comparing ketotic and healthy groups. The experimental design combined plasma metabolomics (3 d postpartum, n = 6), cellular metabolomics (n = 6), single-nucleus RNA sequencing (snRNA-seq; 3 d postpartum, n = 1), bulk RNA-seq of hepatocytes (n = 6), and functional assays performed in primary bovine hepatocytes isolated from healthy donor livers (n = 3). This comprehensive framework enabled a systematic exploration of metabolic dysregulation, cellular diversity, and key disease-associated regulatory pathways. The study identified 15 potential biomarkers and extensive dysregulation of metabolic pathways. Liver tissues comprised 14 distinct cell types, with spatially heterogeneous hepatocyte subpopulations localized in periportal, midlobular, and central venous zones. Central venous hepatocytes were pivotal in lipid metabolism, whose reduction amplified interactions between hepatic stellate and endothelial cells, activating lipid-related pathways and driving disease progression. Critically, the ketone body-butyrate-HADHA axis was identified as a central pathogenic pathway. Silencing HADHA alleviated lipid metabolic dysfunction in hepatocytes induced by exogenous NEFA. Notably, HADHA exhibited dual regulatory roles in hepatic lipid metabolism under distinct pathological contexts. This study bridges hepatic cellular dynamics with systemic metabolic dysregulation, laying a theoretical foundation for mitigating lipid metabolism disorders in dairy cattle and informing translational applications in veterinary medicine.

Cereals are crucial sources of food for human and animal populations worldwide. Their grain and fodder primarily serve as sources of energy and nutrition. Cereal production is hampered because of the prevalent abiotic stress worldwide. Abiotic stresses such as drought, salinity, extreme temperatures, and heavy metal toxicity significantly reduce global cereal crop production. Previously, traditional breeding and transgenic technology have been promising and potent approaches used to mitigate unfavourable abiotic stresses, enhancing crop production to some extent. The recent advent of more potent genome-editing technologies, particularly Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), has revolutionized the pace of crop improvement programs. Genome-editing technology using engineered nucleases offers significant opportunities for crop improvement. Genome editing tools include Meganucleases, Zinc Finger Nucleases (ZFN), Transcription activator-like effector nucleases (TALENs), and CRISPR/CRISPR-associated protein (Cas). Among all genome-editing tools, CRISPR/Cas9 has been widely used to improve crop cultivars due to its specificity, simplicity, robustness, and flexibility. Recent progress in genome-editing technology have improved various plant traits in cereals. Among these traits, cereal genotypes have shown substantial advances in the last decade, particularly in enhanced tolerance to abiotic stress, enabled by genome-editing tools. This review summarizes the recently developed cereal cultivars for abiotic stress tolerance that employ different genome-editing technologies, including the most recent additions, prime editing and base editing. These improved cereal cultivars perform better and maintain higher yields under adverse abiotic stresses.

Intrahepatic cholangiocarcinoma (iCCA) is a highly malignant liver cancer with limited treatment options. Recent evidence implicates lactate metabolism as playing a crucial role in tumor progression, but its precise contribution in iCCA remains unclear. In this study, lactate metabolism-related genes (LMRGs) in iCCA were identified through analyses of bulk and single-cell RNA sequencing data, diagnostic models were developed using machine learning algorithms, and the functional significance of candidate genes was validated through a combination of in vitro and in vivo experiments. 38 differentially expressed LMRGs were identified, and two genes, HMGCL and PCK1, were selected as robust diagnostic biomarkers. A nomogram incorporating both markers achieved excellent diagnostic performance (AUC = 0.999). Single-cell analyses revealed cell-type-specific expression and extensive intercellular communication involving these genes. Functional studies demonstrated that PCK1 acts as a tumor suppressor, concurrently reducing lactate accumulation, downregulating protein lactylation, and inhibiting the PI3K-AKT signaling pathway. Overexpressing PCK1 significantly impaired iCCA cell proliferation, migration, and invasion. These results indicate PCK1 is a key lactate metabolism-related tumor suppressor in iCCA. PCK1 exerts its anti-tumor effects by coordinately suppressing lactate accumulation and inhibiting the PI3K-AKT signaling pathway, positioning it as a promising diagnostic biomarker and therapeutic target for iCCA.

Central airway stenosis, arising from both benign and malignant etiologies, remains challenging to treat effectively. Elucidating the underlying molecular mechanisms is therefore essential.We integrated single-cell RNA sequencing with bulk transcriptomic data to identify key mechanisms in airway stenosis. Findings were subsequently validated using molecular biology assays.Fibroblasts were identified as key contributors to fibrotic remodeling in stenotic airways. Four genes-FAM118A, RCN3, PCSK7, and REEP3-were found to promote airway stenosis. Elevated immune activity was observed in stenotic tissues and showed a positive correlation with the expression of these genes. Mechanistically, these genes facilitate stenosis by activating KRAS→PI3K-AKT pathway, leading to upregulation of fibroblast activation markers. The expression of these genes is transcriptionally regulated by TBX20. Specifically, the ILF3-AS1/miR-212-5p axis regulates FAM118A, PCSK7, and REEP3, but not RCN3.This studyaims to provide insights into the pathological mechanisms underlying airway stenosis, with all findings experimentally validated through integrated molecular and cellular approaches.

Zinc (Zn) and Iron (Fe) are essential trace elements for human health, yet deficiencies in both are widespread worldwide. As a major staple crop, wheat is an important dietary source of Zn and Fe. However, the concentrations of Zn and Fe in common wheat grains are generally low, making it necessary to enhance the nutritional value of wheat. This study first elaborated that both elements are absorbed by wheat via "Strategy II", which relies on phytosiderophores (such as mugineic acids) and related transporter proteins (e.g., YSL and ZIP families). Nicotianamine (NA) plays a key chelating role in the long-distance transport of Zn and Fe. Therefore, we further analyzed the NAS gene family in wheat, which showed high genetic diversity, unique gene structures, distinct evolutionary features, and was subject to purifying selection. Expression profiling revealed that NAS genes were tissue-specific and responsive to various stress conditions. The overexpression of TaNAS4-A in rice, as well as the silencing of TaNAS4-A in wheat using BSMV-VIGS, confirmed the role of TaNAS4-A in enhancing NAS enzyme catalytic efficiency, promoting phytosiderophore secretion, and increasing the accumulation of Zn and Fe in grains. Additionally, this study suggested that NAS genes may confer other functions, such as stress resistance, which deserve further investigation. This research provides a theoretical basis for Zn and Fe biofortification in wheat.

WRKYs represent a large family of plant transcription factors characterized by a highly conserved WRKY domain. WRKY transcription factors are important for plant growth, development, and responses to environmental stresses. However, this family has not been previously identified in Sesuvium portulacastrum, a typical halophyte that grows in saline soils and coastal marshlands and contributes to the stability of coastal ecosystems. Here, we identified 68 SpWRKYs from S. portulacastrum and classified them into six subclades. These genes were unevenly distributed across twenty-two chromosomes and exhibited both intra- and interspecific expansion based on segmental duplication events, orthologous gene pairs, and duplication relationships. All SpWRKY proteins contained at least one conserved WRKY domain, and their promoters contain 33 cis-elements involving abiotic stress signaling, developmental regulation, phytohormone responses, light responsiveness, and tissue-specific expression. Transcriptome analysis under cadmium, copper, and salt stress showed that many SpWRKYs were stress-responsive. Among them, SpWRKY40 and SpWRKY51 showed 3.8-fold and 4.2-fold induction in roots under cadmium treatment, which was further confirmed by quantitative real-time PCR. Subcellular localization and transient expression in tobacco, together with yeast one-hybrid experiments, demonstrated that SpWRKY40 and SpWRKY51 function as transcription activators. They bind specifically to the GTCAA and TTGACC cis-elements. Our study provides a detailed overview of the SpWRKY family and functional insights into SpWRKY40 and SpWRKY51 as transcription activators. The findings offer valuable candidate genes for future applications in improving cadmium stress tolerance in S. portulacastrum and related crop species.

Peroxidases (PRXs) are involved in diverse physiological processes, including cell elongation and lignification. However, studies on PRX genes and their tissue specificity in Medicago truncatula remain limited. In this study, 117 MtPRX genes were identified through bioinformatic analysis and classified into five distinct groups. Segmental duplications were identified as the major driving force for MtPRX expansion. Evolutionary analysis revealed closer phylogenetic relationships between MtPRX and GmPRX in soybean. Expression of MtPRXs were detected in roots, stems, leaves, flowers, seeds, and leaf buds, with members exhibiting distinct tissue-specific expression patterns. Tnt1 insertion mutants of the tissue-specific gene MtPRX76, designated mtprx76-1 and mtprx76-2, showed significantly reduced gene expression levels and decreased lignin content. Transcriptome analysis identified 3015 and 3564 differentially expressed genes (DEGs) in mtprx76-1 and mtprx76-2, respectively. GO and KEGG enrichment analyses revealed that the phenylpropanoid biosynthesis pathway was the most significantly enriched. Furthermore, transcriptional levels of 14 key regulatory genes involved in lignin biosynthesis were significantly downregulated in both mutant lines. These results demonstrate that MtPRX76 functions as a positive regulator influencing lignin biosynthesis. This study systematically characterizes the member features, sequence structures, evolutionary relationships, and tissue-specific expression patterns of the MtPRX gene family, and tissue specific expression patterns, while functionally validating MtPRX76. These findings establish a theoretical basis for understanding Class III PRX gene functions and breeding low lignin germplasm in alfalfa.