Search Results (4,402)

The heat shock transcription factor (HSF) family is a core regulatory component for plants in response to adversity stress and plays a pivotal role in regulating plant reactions to abiotic stress. Lanzhou lily (Lilium davidii var. unicolor) is an economically and horticulturally important bulbous crop widely cultivated in Northwest China, and its growth and yield are severely threatened by high-temperature stress during the growing season. Although HSF genes have been extensively and thoroughly investigated in other plant species, their functional characterization in lilies remains elusive. In this study, a total of 41 LdHSF genes were identified from the genome of Lilium davidii var. unicolor using bioinformatics approaches. The proteins encoded by these genes exhibited considerable variations in the number of amino acids (aa), as well as distinct isoelectric points (pI) and instability indices. Phylogenetic analysis classified these 41 LdHSF genes into three subfamilies (A, B and C). Promoter analysis revealed that the promoters of most LdHSF genes were rich in light-responsive cis-elements. Meanwhile, the promoters of some genes were highly abundant in hormone-responsive cis-elements, whereas those of other genes were enriched in stress-responsive cis-elements. Gene expression heatmaps and transcriptomic data demonstrated that the expression patterns of LdHSF genes showed significant differences in various tissues and under heat treatment. Based on transcriptomic and RT-qPCR data, we further screened out LdHSF10 and LdHSF40 as the major genes responding to heat stress. Functional experiments verified that these two genes encoded nuclear-localized proteins with transcriptional activity. Collectively, these findings lay a solid foundation for elucidating the molecular mechanisms underlying the regulation of heat tolerance by HSF transcription factors (TFs) in lilies in future research. Full article

GDSL esterase/lipase (GELP) proteins constitute an evolutionarily conserved yet functionally diversified hydrolase family in land plants. They participate in cuticle and secondary cell wall biosynthesis, seed lipid remobilization, reproductive development, and hormone-mediated responses to biotic and abiotic stresses. Despite extensive genome-wide and comparative genomic studies that have categorized large GELPs across numerous crops and model species, only a fraction of members have been functionally characterized in plants, and their catalytic mechanisms and regulatory architectures remain poorly understood. Recent population genomics and cross-species orthogroup analyses in 46 angiosperms have uncovered substantial natural variation within GELP coding sequences and regulatory regions, providing a powerful framework to link allelic diversity to evolutionary trajectories and physiological functions. This review synthesizes current knowledge on GELP evolution, biochemical properties, and roles in development and stress adaptation, and critically evaluates how these insights can be translated into biotechnology and molecular breeding strategies. It highlights emerging resources and concepts from orthogroup-based classification and multi-species datasets that enable systematic discovery of GELP alleles affecting agronomic traits. It further outlines research exploiting GELPs in crop improvement, emphasizing the integration of reverse and forward genetics with multi-omics profiling, biochemical and structural characterization, and gene regulatory network reconstruction. Systematic assessment of the phenotypic impacts of single and combinatorial GELP perturbations on yield, quality, and stress resilience is proposed as a key step toward translating basic insights into breeding and engineering strategies. Full article

Starch synthesis is critical for crop yield and quality and is regulated and coordinated by a series of key enzymes encoded by starch synthesis-related genes (SSRGs). Although this process is well characterized in many crops, the genomic location and expression patterns of SSRGs in wheat remain unclear. Here, we performed a genome-wide analysis and identified 78 SSRGs in wheat, classified into the AGPase, SSS, GBSS, SBE, and DBE subfamilies. SSRGs within each subfamily showed conserved motifs and domain organization. RNA-seq analysis indicated that most SSRGs are expressed during early grain development. We further examined genetic variation in SSRGs across wheat and its progenitors using re-sequencing data. Diploid wheat showed greater genetic differentiation and diversity than tetraploid and hexaploid wheat. Five SSRGs exhibited significant haplotype differences between emmer wheat and common wheat; emmer wheat displayed diverse haplotypes, whereas common wheat showed a single dominant haplotype. Finally, starch characteristics differed between emmer wheat and common wheat in amylose content and thermodynamic properties, while viscosity, crystal structure, and morphology were largely similar. Overall, this study systematically characterizes SSRGs in wheat and provides insights for improving starch quality. Full article

DNA methylation constitutes a primary layer of epigenetic regulation in plants, operating across three sequence contexts (CG, CHG, and CHH) through distinct enzymatic pathways. Over the past fifteen years, accumulating evidence has shown that DNA methylation varies substantially among individuals and populations of wild plants, sometimes independently of underlying genetic polymorphism. This variation can influence gene expression, transposable element activity, and phenotypic traits relevant to ecological adaptation. Population epigenetics, the study of methylation variation at the population scale, has matured from initial surveys using methylation-sensitive amplified fragment length polymorphism (MS-AFLP) into a discipline increasingly reliant on reduced-representation bisulfite sequencing (epiGBS, bsRADseq), whole-genome bisulfite sequencing (WGBS), enzymatic methyl-seq (EM-seq), and direct long-read detection by nanopore sequencing. These methodological advances are opening population epigenetics to non-model organisms across the full breadth of the plant phylogeny, from angiosperms and gymnosperms to ferns and bryophytes. We cover (i) the molecular machinery underlying plant DNA methylation, including the debated status of N6-methyladenine (6mA); (ii) empirical evidence for natural epigenetic variation in plant populations, spanning clonal, invasive, and outcrossing species; (iii) the methodological toolkit available for population-scale methylation profiling, with emphasis on approaches suitable for non-model taxa; and (iv) the ecological and evolutionary significance of population epigenetic variation, including transgenerational inheritance, stress memory, epigenetic clocks, conservation applications, and the emerging integration of epigenetics into the extended evolutionary synthesis. We identify critical knowledge gaps, particularly the near-complete absence of population-level epigenetic data for bryophytes, ferns, and lycophytes, and outline priorities for future research. Full article

Ginseng Alternaria leaf and stem blight, caused by Alternaria panax, imposes substantial yield and economic losses to the ginseng cultivation industry. Current diagnostic methods for ginseng diseases primarily rely on pathogen isolation from infected tissues, a procedure that is laborious, time-consuming, and inherently low in sensitivity. This study has therefore developed a rapid, specific and sensitive SYBR Green-based quantitative real-time PCR (qPCR) assay for detecting A. panax in plants, seeds, and soil. The developed qPCR assay exhibited high sensitivity and repeatability, with a detection limit of 0.074 fg/μL of target amplicon DNA (0.619 ng/μL of genomic DNA) and a coefficient of variation below 2%. In artificially inoculated tissues (leaves, stems and seeds), Ct values decreased progressively with increasing incubation time, reflecting pathogen proliferation. Analysis of field-collected leaves and stems showed a strong overall correlation between Ct values and visual disease grades. Surveying of ginseng-growing areas revealed that A. panax was detected in asymptomatic leaves and stems at rates of 12.12% and 14.29%, respectively, and in 14.46% of soil samples and 23.73% of seed samples. This qPCR assay presented here provides a robust tool for forecasting early disease, tracking the primary inoculum of the pathogen and its transmission chains, and screening of both ginseng seed lots and candidate soils for ginseng Alternaria leaf and stem blight prior to planting. Full article

Background/Objectives: Eleocharis ussuriensis Zinserl. is a perennial riparian sedge widely distributed in Northeast Asia and a dominant component of freshwater vegetation in South Korea. However, the intraspecific genetic structure of this species across contrasting hydrological habitats remains insufficiently understood. This study aimed to develop novel SSR markers from whole-genome data and investigate genetic variation and population structure among E. ussuriensis populations in South Korea. Methods: Twenty-one novel simple sequence repeat (SSR) markers were developed from whole-genome sequence data and applied to analyze genetic variation in 120 individuals from 6 populations. Genetic diversity, differentiation, and gene flow were estimated using allele-frequency-based metrics, and population genetic structure was further evaluated using spatial information derived from geographic coordinates. Results: A total of 201 alleles were detected, with a mean polymorphism information content (PIC) of 0.759, indicating high marker informativeness. Mean genetic diversity across populations showed observed heterozygosity (Ho = 0.360) and expected heterozygosity (He = 0.281), while multilocus genotype ratios (G/N) ranged from 0.30 to 1.00 among populations. Genetic differentiation was substantial (F_ST = 0.373–0.669; Jost’s D = 0.540–0.997). Mantel tests revealed that genetic differentiation was significantly correlated with geographic distance (r = 0.67, p < 0.001). Both allele-frequency-based and spatially explicit approaches suggested genetic structuring among populations. Conclusions: The results suggest spatial tendencies in genetic structure among populations, reflecting patterns of allele distribution across regions. These findings provide baseline information on genetic variation in E. ussuriensis and may contribute to a better understanding of its ecological dynamics. Full article

Teat number is an important economic trait in pigs because it affects sow reproductive performance and piglet nursing ability, yet its genetic basis and molecular regulatory mechanisms remain incompletely understood. In this study, a combined-population genome-wide association study was performed in Canadian and French Large White pigs to identify loci associated with teat number traits. A total of 4217 pigs were genotyped, and 2,244,684 autosomal single-nucleotide polymorphisms were retained after quality control and genotype imputation. Multiple association signals for total teat number were detected, with major peaks located on chromosomes 7 and 10. Among the positional candidate genes, PROX2 was prioritized for further validation, and genotype–phenotype association analysis showed that pigs with the CC genotype at the PROX2 polymorphic locus had significantly lower total teat number than those with the CT and TT genotypes. To investigate its biological role, PROX2 was silenced in porcine mammary epithelial cells. Transcriptome analysis identified 887 differentially expressed genes after PROX2 knockdown, and functional assays showed that PROX2 silencing inhibited cell proliferation, altered cell cycle progression, and affected the expression of proliferation- and development-related genes. These findings indicate that PROX2 is an important candidate gene associated with teat number variation in pigs. Full article

Pharmaceutical care provides the conceptual foundation for integrating pharmacogenetics into everyday pharmacy practice. Defined by Hepler and Strand as “the responsible provision of drug therapy for the purpose of achieving specific outcomes that improve a patient’s quality of life”, pharmaceutical care emphasizes a patient-centered approach in which the pharmacist collaborates with the patient, physician, and other healthcare professionals to design, implement, and monitor individualized therapeutic plans. In this context, pharmacogenetics can be regarded as an extension of pharmaceutical care: while the traditional model relies on monitoring patient outcomes and adherence, PGx adds a genetic dimension that allows treatment to be optimized from the very beginning. The pharmacist’s role therefore evolves from not only ensuring safe and effective use of medicines, but also interpreting genetic test results, supporting adherence to genetically guided therapy, and educating patients about the implications of their personal genetic profile. The introduction of pharmacogenetics testing as one of the potential services offered by community pharmacies is a promising proposition that may revolutionize the approach to drug therapy. Pharmacogenetics, a subset of pharmacogenomics, focuses on the study of DNA sequence variations that influence response to drugs. Thanks to advances in the field of genomics, it has become possible to study the genetic basis of variability in drug response. The identification of alleles responsible for the rapid or slow metabolism of xenobiotics has ushered in a new era in pharmacology. The aim of this interdisciplinary field, combining genetics and pharmacology, is to adapt treatment to a specific patient based on the analysis of their genome and gene polymorphism. Throughout the world, pharmacogenetics is gaining importance as a tool for personalizing medicine. In countries such as the United States, Canada, and the United Kingdom, programs integrating pharmacogenetics with healthcare are being developed. Clinical trials and the implementation of genetic tests into medical practice allow for better matching of medications and reducing the risk of side effects. Pharmacists will play a key role in integrating pharmacogenetics into healthcare. As specialists in the field of pharmacotherapy, they will support physicians in interpreting the results of genetic tests and adapting drug therapy to the individual needs of the patient. Additionally, pharmacists can educate patients and healthcare professionals about the benefits of pharmacogenetics and monitor the effects and safety of medications. Their involvement in the process of personalization of treatment may contribute to improving the effectiveness and safety of pharmacological therapies. Full article

Cancer exhibits pronounced heterogeneity at both spatial and cellular levels, contributing to variability in therapeutic responses and the emergence of treatment resistance. This heterogeneity is underscored by the diverse genetic, epigenetic, and phenotypic variations found within tumor cell populations. Cancer stem cells (CSCs), although representing a minor fraction of tumor cells, possess the capacity to self-renew and differentiate, thereby driving the dynamic evolution of tumor heterogeneity. CSCs interact intricately with various elements of the tumor microenvironment (TME), further amplifying this heterogeneity. Recent advancements in organoid technology have facilitated the development of CSC-derived organoid models that more faithfully recapitulate the TME and intratumoral heterogeneity, which conventional 2D culture systems fail to replicate. These CSC-derived organoid systems not only preserve the structural and genomic characteristics of tumors, but they also enable the exploration and evaluation of therapeutic strategies that reflect tumor complexity. However, CSC-derived organoid systems face several challenges, such as the rarity of CSCs, lack of standardized culture conditions, absence of TME components, limited predictive accuracy, and insufficient modeling of tumor heterogeneity. This review discusses these limitations and explores potential solutions, including the use of artificial intelligence (AI) to enhance treatment predictability. These innovations may improve the utility of organoid models for therapeutic evaluation and for targeting tumor heterogeneity. Ultimately, CSC-derived organoids may serve as a valuable platform for advancing precision medicine and cancer research. Full article

Fruit anthocyanins are primary determinants of color, sensory quality, and nutritional value in grapes; however, their endogenous biosynthesis is governed by complex interactions among genetic, environmental, agronomic, and postharvest factors. This review elaborates recent advances in physiology and molecular biology to clarify the biosynthetic mechanisms in grapes, including the coordinated action of structural enzymes, MYB–bHLH–WD40 regulatory complexes, hormone-mediated signaling pathways, and vacuolar transport processes. Key environmental factors, such as temperature fluctuations, light exposure, water availability, and soil properties, regulate these networks, contributing to significant variation in pigmentation profiles across cultivars and growing regions. Strategic agronomic practices, including canopy management, regulated deficit irrigation, balanced nutrient management, and temperature-mitigation techniques, further influence pigmentation by modifying the microclimate of the fruit zone during development. Based on these mechanistic insights, this review evaluates targeted strategies for enhancing anthocyanin accumulation, highlighting recent progress in genetic improvement through CRISPR/Cas genome editing, transgenic approaches, and marker-assisted selection (MAS), which enable precise modulation of biosynthetic and regulatory genes. Complementary postharvest interventions, such as optimized cold storage, modified-atmosphere packaging, hormonal elicitors, and controlled oxidative technologies, provide additional opportunities to maintain or enhance pigment stability after harvest. Collectively, these advances establish a comprehensive framework linking molecular regulation with practical vineyard, breeding, and postharvest strategies, offering an integrated pathway to improve anthocyanin consistency, berry quality, and the phenolic characteristics of grape-derived products. Full article

The aim of this study was to identify SNPs in the cattle genome associated with estimated breeding values of feet (EBV_feet) in Holstein-Friesian (HF) cows in Hungary. Foot health is of major importance in dairy cattle industry whereas claw disorders are leading to lameness and thus result in low fertility rates and productivity. Genotyping was performed using the EuroG_MDv4 microarray platform. The final database comprised 2963 animals and 59,151 SNPs. EBV_feet values have been divided into high and low groups. All calculations regarding the genetic differentiation (genome-wide and locus-specific) between high- and low-value groups for EBV_feet, linear regression, and haplotype association tests have been performed with the SNP and Variation Suite software. Thirty-nine SNPs associated with EBV_feet were determined on BTAs 3, 7, 8, 15, 21, and X. The maximum values of the identified SNPs were 0.22 for F_{st_marker}, 23.1 for the −log10(p) of the linear regression, and 26.3 for the −log10(p) of the haplotype association tests on BTA 3. The closest genes to SNPs associated with estimated breeding values for feet (EBV_feet) are mainly associated with tissue structure, immune response, metabolism, growth, development, transport and signaling. Our results could add additional information to the genetic programs focusing on the improvement of foot health in HF cattle. Full article

Miscanthus lutarioriparius exhibits strong potential for cadmium (Cd) accumulation, making it a promising candidate for the phytoremediation of Cd-contaminated soils. However, its full remediation potential remains underexploited, highlighting the need for targeted genetic improvement This study presents a comprehensive genome-wide identification and systematic characterization of 20 Ml4CL (4-coumarate: CoA ligase genes) in the M. lutarioriparius. Results indicate that the Ml4CL gene family has undergone substantial evolutionary divergence and expansion. Phylogenetic classification is highly consistent with gene structures ad conserved motifs suggesting potential functional diversification. Promoter analysis revealed a complex cis-regulatory landscape enriched in n ABA- and light-responsive elements, frequently co-occuring with hormone-responsive elements associated with jasmonic acid (JA), gibberellins (GAs), salicylic acid (SA), and strigolactones (SLs) signaling. This pattern suggests that the Ml4CL family may function as an integrative regulatory node linking multiple stress and hormonal signaling pathways. Importantly, under Cd stress, Ml4CL genes exhibited diverse expression dynamics, including gene-specific repression and dose-dependent biphasic responses. Notably, Ml4CL4 showed strong repression, while other members displayed “induction-then-repression” or “repression-then-induction” patterns, suggesting a staged or hierarichical transcriptional response. These findings further suggest that Cd-responsive signaling networks may involve non-linear or threshold-dependent mechanismsthat activate distinct transcriptional programs depending on stress levels. Collectively, this study highlights the regulatory role of the Ml4CL family in plant adaptation to complex environments and identifies candidate dose-resonsive regulatory elements and key allelic variations. These findings provide valuable targets for molecular breeding and synthetic biology aimed at improving crop stress resilience. Full article

Grain number and size are important agronomic traits determining grain yield, and yield improvement depends on exploring functional variations of key regulatory genes. Mitogen-activated protein kinase 6 (MAPK6) plays a key role in crop development; however, its function and variation in wheat remain largely unclear. In this study, we aimed to characterize the function and haplotype variations of TaMAPK6-7A in wheat and develop functional molecular markers for marker assisted breeding. We identified three TaMAPK6 homoeologs on 7A, 7B, and 7D in wheat through bioinformatics analysis and revealed their evolutionary trajectory by phylogenetic analysis, with clear monocot-dicot lineage divergence and TaMAPK6 homoeolog clustering matching with hexaploid wheat’s allopolyploid origin. Spatiotemporal expression analysis showed that the TaMAPK6 homoeologs constitutively expressed in wheat tissues and were highly abundant in endosperm, spike, grain, and anther, with TaMAPK6-7A showing slightly higher transcript levels. In an ethyl methanesulfonate (EMS)-induced Jing411 mutant library, we identified a loss-of-function mutant of TaMAPK6-7A (J7633452), which exhibited severely reduced grain number per spike, impaired anther fertility, and increased grain size. Natural variation analysis of a large set of wheat accessions identified two major haplotypes of TaMAPK6-7A, with Type I was identical to the reference genome cultivar ‘Chinese Spring’, and Type II was consistent with the elite wheat cultivar ‘AK58’. We developed a PCR marker to accurately distinguish the two haplotypes and genotyped 192 wheat cultivars and elite breeding lines. Phenotypic evaluation indicated that Type II was an elite haplotype significantly associated with higher grain number per spike. This study characterizes TaMAPK6-7A as a key regulator of grain number per spike, providing a gene and molecular marker for marker-assisted breeding to improve grain yield. Full article

H5 subtype avian influenza virus (AIV) can infect both chickens and ducks, leading to substantial economic losses. Nevertheless, certain strains cause silent infections in ducks. In this study, a goose-origin clade 2.3.4.4h H5N6 AIV was isolated, which caused high mortality in mixed-gender white leghorn chickens but no deaths in mixed-gender mallard ducks. After independent serial in vitro passage in duck embryo fibroblasts (DEFs) and in vivo passage in specific-pathogen-free (SPF) ducks, the DEF-passage 10 (P10) virus induced markedly higher mortality rates and viral loads in SPF ducks compared to the DEF-P1 virus and the original parental virus prior to passage. Similarly, the in vivo-passaged P3 and P4 viruses exhibited significantly higher mortality rates than the P1 virus in SPF ducks, with 100% mortality and markedly increased viral titers in the organs. A whole-genome SNP analysis identified seven high-frequency mutations in the M1, NA and NS1 proteins. The NS1-F161L substitution virus exhibited significantly increased mortality rates, viral loads in multiple tissues, and a robustly induced innate immune response in ducks. Furthermore, dynamic evolutionary variations in the NS1 protein among global H5 avian influenza viruses revealed that the NS1-F161L substitution became dominant in clade 2.3.4.4b viruses in 2021 and subsequent years. Collectively, our findings demonstrate that host-driven adaptation can rapidly increase the pathogenicity of H5N6 AIVs in ducks and identify NS1-F161L as a critical virulence marker. These results offer novel insights relevant to the molecular surveillance, virulence prediction, and risk assessment of circulating H5 AIVs in waterfowl. Full article

Background: Cellular senescence is a key regulatory mechanism in tumor initiation and progression, influencing cancer development through modulation of the cell cycle, the immune microenvironment, and inflammatory responses. However, the molecular characteristics and potential clinical value of senescence-related genes in lung adenocarcinoma (LUAD) have not been systematically elucidated. This study aimed to comprehensively characterize the expression patterns, molecular subtypes, and prognostic significance of cellular senescence-related genes in LUAD, and to identify key regulatory determinants. Methods: Transcriptomic data of cellular senescence-related genes were obtained from The Cancer Genome Atlas (TCGA) cohort, and integrated analyses were performed to characterize their mutational landscape, copy number variations, and differential expression profiles. Senescence-related molecular subtypes were established using consensus clustering, followed by gene set variation analysis (GSVA) for pathway enrichment and immune infiltration analyses. A prognostic risk model was subsequently constructed using LASSO-penalized Cox regression, and its predictive performance was systematically evaluated. Candidate key regulators were further prioritized through bioinformatic screening, identifying FOLR1 as a hub gene. The biological function of FOLR1 was validated by qRT–PCR, Western blotting, assessment in clinical specimens, and a subcutaneous xenograft tumor model in mice. Results: Cellular senescence-related genes in LUAD exhibited a high frequency of somatic mutations and copy number alterations, accompanied by marked transcriptional dysregulation. Based on the expression profiles of these genes, LUAD patients could be stratified into three distinct molecular subtypes with significantly different clinical outcomes. These subtypes displayed pronounced heterogeneity in pathway enrichment patterns and immune cell infiltration. The subsequently developed prognostic signature demonstrated robust predictive performance in both the training and validation cohorts. Functional assays showed that FOLR1 was significantly downregulated in LUAD tissues and cell lines; FOLR1 knockdown promoted tumor cell proliferation, whereas restoration of its expression or pharmacological intervention markedly suppressed tumor progression. Consistently, in vivo xenograft experiments further corroborated the tumor-suppressive role of FOLR1 in lung adenocarcinoma. Conclusions: This study systematically delineated the molecular landscape of cellular senescence-related genes in LUAD and elucidated their associations with the tumor immune microenvironment and patient prognosis. Moreover, FOLR1 was identified as a potential tumor suppressor and therapeutic target. These findings provide a theoretical basis for senescence-informed molecular stratification and the development of precision treatment strategies in lung adenocarcinoma. Full article