Search Results (1,555)

Saffron (Crocus sativus L.) is a vegetatively propagated crop of high economic and cultural value, potentially affected by viral infections that may impact its productivity. Despite Iran’s dominance in global saffron production, knowledge of its virome remains limited. In this study, we conducted the first nationwide virome survey of saffron in Iran employing a high-throughput sequencing (HTS) approach on pooled samples obtained from eleven provinces in Iran and one location in Afghanistan. Members of three virus families were detected—Potyviridae (Potyvirus), Solemoviridae (Polerovirus), and Geminiviridae (Mastrevirus)—as well as one satellite from the family Alphasatellitidae (Clecrusatellite). A novel Potyvirus, tentatively named saffron Iran virus (SaIRV) and detected in three provinces, shares less than 68% nucleotide identity with known Potyvirus species, thus meeting the ICTV criteria for designation as a new species. Genetic diversity analyses revealed substantial intrapopulation SNP variation but no clear geographical clustering. Among the two wild Crocus species sampled, only Crocus speciosus harbored turnip mosaic virus. Virome network and phylogenetic analyses confirmed widespread viral circulation likely driven by corm-mediated propagation. Our findings highlight the need for targeted certification programs and biological characterization of key viruses to mitigate potential impacts on saffron yield and quality. Full article

The increasing demand for food to meet the needs of the planet’s growing population requires, among other factors, greater and improved meat production. Meat quality is determined by key consumer-preferred traits, particularly tenderness, juiciness, and flavor. Recently, interest has grown in analyzing the genes associated with these phenotypic characteristics. Single-nucleotide polymorphisms (SNPs) are common genomic variations in cattle and represent the most widely used molecular markers. Research on SNP variation is now a major focus of genomic studies aimed at improving meat quality. Leptin levels reflect the amount of adipose tissue in meat, also known as marbling. Several SNPs in the leptin gene and its receptor have been linked to this meat quality trait. Similarly, SNPs in the calpain/calpastatin system play a significant role in postmortem muscle proteolysis and pork tenderness. This review examines these genetic variants as markers involved in the expression of phenotypic traits in meat products and explores their mechanisms of action. Additionally, it provides insights into the genetic variants associated with production-related characteristics. Full article

Microalgae, with their unparalleled capabilities for sunlight-driven growth, CO₂ fixation, and synthesis of diverse high-value compounds, represent sustainable cell factories for a circular bioeconomy. However, industrial deployment has been hindered by biological constraints and the inadequacy of conventional genetic tools. The advent of CRISPR-Cas systems initially provided precise gene editing via targeted DNA cleavage. This review argues that the true transformative potential lies in moving decisively beyond cutting to harness CRISPR as a versatile synthetic biology “Swiss Army Knife”. We synthesize the rapid evolution of CRISPR-derived tools—including transcriptional modulators (CRISPRa/i), epigenome editors, base/prime editors, multiplexed systems, and biosensor-integrated logic gates—and their revolutionary applications in microalgal engineering. These tools enable tunable gene expression, stable epigenetic reprogramming, DSB-free nucleotide-level precision editing, coordinated rewiring of complex metabolic networks, and dynamic, autonomous control in response to environmental cues. We critically evaluate their deployment to enhance photosynthesis, boost lipid/biofuel production, engineer high-value compound pathways (carotenoids, PUFAs, proteins), improve stress resilience, and optimize carbon utilization. Persistent challenges—species-specific tool optimization, delivery efficiency, genetic stability, scalability, and biosafety—are analyzed, alongside emerging solutions and future directions integrating AI, automation, and multi-omics. The strategic integration of this CRISPR toolkit unlocks the potential to engineer robust, high-productivity microalgal cell factories, finally realizing their promise as sustainable platforms for next-generation biomanufacturing. Full article

Enhancing the specificity and applicability of PCR-based genome-walking methods is highly desirable. A new and universal genome-walking tool, called center degenerated walking-primer PCR (CDWP-PCR), is presented in this study. CDWP-PCR involves adopting a center degenerated walking primer (cdWP) in the secondary/tertiary round of amplification. This cdWP is generated by degenerating the seven central nucleotides of the normal walking primer (nWP) used in primary PCR to NNNNNNN (where N includes the bases A, T, C, and G). Clearly, a partially complementary structure is formed between the two primers. Accordingly, the primary CDWP-PCR non-target products defined by the nWP are diluted in secondary/tertiary CDWP-PCR, as these non-targets have difficulty in annealing with the cdWP; conversely, the primary target product can still be efficiently amplified. The working performance of the proposed CDWP-PCR is verified through cloning of the unknown flanks of three known genes. All the clear DNA bands in the tertiary CDWP-PCRs are confirmed to be correct, and the largest DNA band is 8.0 kb. Overall, CDWP-PCR can be considered as a reliable supplement to existing genome-walking methods. Full article

The yak (Bos grunniens) is a key species in high-altitude rangelands of Asia. Despite their ecological and economic importance, yak production faces persistent challenges, including low milk yields, vulnerability to climate changes, emerging diseases, and a lack of systematic breeding programs. This review presents the genomic, physiological, and environmental dimensions of yak biology and husbandry. Genes such as EPAS1, which encodes hypoxia-inducible transcription factors, underpin physiological adaptations, including enlarged cardiopulmonary structures, elevated erythrocyte concentrations, and specialized thermoregulatory mechanisms that enable their survival at elevations of 3000 m and above. Copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) present promising markers for improving milk and meat production, disease resistance, and metabolic efficiency. F1 and F2 generations of yak–cattle hybrids show superior growth and milk yields, but reproductive barriers, such as natural mating or artificial insemination, and environmental factors limit the success of these hybrids beyond second generation. Infectious diseases, such as bovine viral diarrhea and antimicrobial-resistant and biofilm-forming Enterococcus and E. coli, pose risks to herd health and food safety. Rising ambient temperatures, declining forage biomass, and increased disease prevalence due to climate changes risk yak economic performance and welfare. Addressing these challenges by nutritional, environmental, and genetic interventions will safeguard yak pastoralism. This review describes the genes associated with different yak traits and provides an overview of the genetic adaptations of yaks (Bos grunniens) to environmental stresses at high altitudes and emphasizes the need for conservation and improvement strategies for sustainable husbandry of these yaks. Full article

Background/Objectives: Campylobacteriosis in human populations is an ongoing issue in both developed and developing countries. Poultry production is recognized as a reservoir for antimicrobial resistance and main source of human Campylobacter infection. Methods: In this study, sixty-five Campylobacter isolates were cultured from fecal samples collected from 17 flocks of broiler chickens in Alberta, Canada over two years (2015–2016). Susceptibility assays and PCR assays were performed to characterize resistance phenotypes and resistance genes. Conjugation assays were used to examine the mobility of AMR phenotypes. Results: Campylobacter jejuni was the predominant species recovered during both years of sampling. There were no Campylobacter coli isolates found in 2015; however, approximately 33% (8/24) of isolates collected in 2016 were Campylobacter coli. The two most frequent antimicrobial resistance patterns in C. jejuni collected in 2015 were tetracycline (39%) and azithromycin/clindamycin/erythromycin/telithromycin resistance (29%). One isolate collected in 2015 has resistance pattern ciprofloxacin/nalidixic acid/tetracycline. The tetO gene was detected in all tetracycline resistant isolates from 2015. The cmeB gene was detected in all species isolates with resistance to azithromycin/clindamycin/erythromycin/telithromycin, and from two isolates with tetracycline resistance. Alignment of the nucleotide sequences of the cmeB gene from C. jejuni isolates with different resistance patterns revealed several single nucleotide polymorphisms. A variety of multi-drug resistance patterns were observed through conjugation experiments. Conclusions: These data suggest that poultry production may serve as a potential reservoir for and source of transmission of multi-drug resistant Campylobacter jejuni and supports the need for continued surveillance. Full article

Background: Pancreas and pancreas–kidney transplantation are well-established therapeutic options for patients with type 1 diabetes mellitus (T1DM) and end-stage kidney disease (ESKD), offering the potential to restore endogenous insulin production and kidney function. It improves metabolic control, quality of life, and long-term survival. While surgical techniques and immunosuppressive strategies have advanced considerably, graft rejection and limited long-term graft survival remain significant clinical challenges. Method: To better understand these risks, the genetic and immunological factors that influence transplant outcomes are examined. Beyond traditional human leukocyte antigen (HLA) matching, non-HLA genetic variants such as gene deletions and single-nucleotide polymorphisms (SNPs) have emerged as contributors to alloimmune activation and graft failure. Result: Polymorphisms in cytokine genes, minor histocompatibility antigens, and immune-regulatory pathways have been implicated in transplant outcomes. However, the integration of such genomic data into clinical practice remains limited due to underexplored gene targets, variability in study results, and the lack of large, diverse, and well-characterized patient cohorts. Initiatives like the International Genetics & Translational Research in Transplantation Network (iGeneTRAiN) are addressing these limitations by aggregating genome-wide data from thousands of transplant donors and recipients across multiple centers. These large-scale collaborative efforts aim to identify clinically actionable genetic markers and support the development of personalized immunosuppressive strategies. Conclusions: Overall, genetic testing and genomics hold great promise in advancing precision medicine in pancreas and pancreas–kidney transplantation. Full article

Corn smut, caused by Ustilago maydis, significantly threatens maize production. This study evaluated 199 maize inbred lines at the seedling stage under greenhouse conditions for resistance to U. maydis, identifying 39 highly resistant lines. A genome-wide association study (GWAS) using the mrMLM model detected 19 significant single-nucleotide polymorphism (SNP) loci. Based on a linkage disequilibrium (LD) decay distance of 260 kb, 226 candidate genes were identified. Utilizing the significant loci chr1_244281660 and chr5_220156746, two kompetitive allele-specific PCR (KASP) markers were successfully developed. A PCR-based sequence-specific oligonucleotide probe hybridization technique applied to the 199 experimental lines and 60 validation lines confirmed polymorphism for both markers, with selection efficiencies of 48.12% and 43.33%, respectively. The tested materials were derived from foundational inbred lines of domestic and foreign origin. Analysis of 39 highly resistant lines showed that the advantageous alleles carrying thymine/cytosine (T/C) predominated at frequencies of 94.87% and 53.84%, respectively. The genotype TTCC conferred high resistance, while CCTT was highly susceptible. The resistance exhibited high heritability and significant gene-by-environment interaction. This work systematically dissects the genetic basis of common smut resistance in maize, identifies favorable alleles, and provides a novel KASP marker-based strategy for developing disease-resistant germplasm. Full article

Alzheimer’s disease (AD) and ischemic stroke (IS) are prevalent neurological disorders that frequently co-occur in the same individuals. Recent studies have demonstrated that AD and IS share several common risk factors and pathogenic elements, including an overlapping genomic architecture. However, the relationship between IS risk gene polymorphisms and AD has been less extensively studied. We aimed at determining whether IS risk gene polymorphisms were associated with the risk of AD and the severity of AD in AD patients. We utilized data of AD patients and normal controls (NCs) sourced from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. IS risk single nucleotide polymorphisms (SNPs) were identified through the most recent and largest IS genome-wide association study (GWAS) meta-analysis. Subsequently, we conducted SNP-based association analysis of IS-risk SNPs with the risk of AD, along with amyloid, tau, and neuroimaging for AD. The generalized multifactor dimensionality reduction (GMDR) model was used to assess the interactions among IS-risk SNPs and apolipoprotein E (ApoE) ε4. Protein–protein interactions (PPIs) of the IS-risk genes product and APOE were explored using the STRING database. Seven IS-risk SNPs were involved in the study. Five SNPs were found to be associated with at least one measurement of cerebrospinal fluid (CSF) levels of amyloid-beta 1–42 (Aβ₄₂), total tau (t-tau), and phosphorylated tau 181 (p-tau₁₈₁), as well as the volumes of the hippocampus, whole brain, entorhinal cortex, and mid-temporal regions. After multiple testing corrections, we found that T allele of rs1487504 contributed to an increased risk of AD in non-ApoE ε4 carriers. The combination of rs1487504 and ApoE ε4 emerged as the optimal two-factor model, and its interaction was significantly related to the risk of AD. Additionally, C allele of rs880315 was significantly associated with elevated levels of CSF Aβ₄₂ in AD patients, and A allele of rs10774625 was significantly related to a reduction in the volume of the entorhinal cortex in AD patients. This study found that IS risk SNPs were associated with both the risk of AD and AD major indicators in the ADNI cohort. These findings elucidated the role of IS in AD from a genetic perspective and provided an innovative approach to predict AD through IS-risk SNPs. Full article

Durum wheat, the world’s second most cultivated wheat species, is a staple crop, critical for global food security, including in Ethiopia where it serves as a center of diversity. However, climate change and genetic erosion threaten its genetic resources, necessitating genomic studies to support conservation and breeding efforts. This study characterized genome-wide diversity, population structure (STRUCTURE, principal coordinate analysis (PCoA), neighbor-joining trees, analysis of molecular variance (AMOVA)), and selection signatures (F_ST, Hardy–Weinberg deviations) in Ethiopian durum wheat by analyzing 376 genotypes (148 accessions) using an Illumina Infinium 25K single nucleotide polymorphism (SNP) array. A set of 7842 high-quality SNPs enabled the assessments, comparing landraces with cultivars and breeding populations. Results revealed moderate genetic diversity (mean polymorphism information content (PIC) = 0.17; gene diversity = 0.20) and identified 26 loci under selection, associated with key traits like grain yield, stress tolerance, and disease resistance. AMOVA revealed 80.1% variation among accessions, with no significant differentiation by altitude, region, or spike density. Landraces formed distinct clusters, harboring unique alleles, while admixture suggested gene flow via informal seed exchange. The findings highlight Ethiopia’s rich durum wheat diversity, emphasizing landraces as reservoirs of adaptive alleles for breeding. This study provides genomic insights to guide conservation and the development of climate-resilient cultivars, supporting sustainable wheat production globally. Full article

The root of Plumbago indica L. is commercially available in herbal markets in both crude and powdered forms. P. indica root is a key ingredient in numerous polyherbal formulations. However, P. indica has two closely related species, P. zeylanica L. and P. auriculata Lam. Since only P. indica is traditionally used in Thai polyherbal products, adulteration with other species could potentially compromise the therapeutic efficacy and overall effectiveness of these formulations. To address this issue, a MassARRAY iPLEX assay was developed to accurately identify and differentiate P. indica from its closely related species. Five single nucleotide polymorphism (SNP) sites—positions 18, 112, 577, 623, and 652—within the internal transcribed spacer (ITS) region were selected as genetic markers for species identification. The assay demonstrated high accuracy in identifying P. indica and was capable of detecting the species at DNA concentrations as low as 0.01 ng/µL. Additionally, the assay successfully identified P. zeylanica in commercial crude drug samples, highlighting potential instances of adulteration. Furthermore, it was able to distinguish P. indica in mixed samples containing P. indica, along with either P. zeylanica or P. auriculata. The developed MassARRAY iPLEX assay proves to be a reliable and effective molecular tool for authenticating P. indica raw materials. Its application holds significant potential for ensuring the integrity of herbal products by preventing misidentification and adulteration. Full article

A novel barna-like virus was found to be associated with field-collected Afrina sporoboliae plant-parasitic nematodes. The positive-sense, single-stranded RNA genome of this virus, named Afrina barna-like virus (AfBLV), comprises 4020 nucleotides encoding four open reading frames (ORFs). ORF 1 encodes a protein product spanning a transmembrane, a peptidase, and VPg domains, whereas an overlapping ORF 2 encodes an RNA-dependent RNA polymerase (RdRP). ORF2 may be expressed via a −1 translational frameshift. In phylogenetic reconstructions, the RdRP of AfBLV was placed inside a separate clade of barna and barna-like viruses related to but distinct from the genera in the Solemoviridae and Alvernaviridae families, within the overall lineage of Sobelivirales. ORF 3 of AfBLV encodes a protein product of 206 amino acids (aa) long with homology to a putative protein encoded by a similarly positioned gene of an uncharacterized virus sequence identified previously as Barnaviridae sp. ORF 4 encodes a 161 aa protein with no significant similarities to sequences in the GenBank databases. AfBLV is the first barnavirus found in a nematode. Sequence comparisons of the AfBLV genome and genomes of other barna-like viruses suggested that a recombination event was involved in the evolution of AfBLV. Analyses of the phylogeny of RdRPs and genome organizations of barna-like and solemo-like viruses support the re-classification of Barnavirus and Dinornavirus genera as members of the Solemoviridae family. Full article

Leymus chinensis (Trin.) Tzvel., a vital native forage grass in northern China for ecological restoration and livestock production, faces severe yield losses and grassland degradation due to rust (Puccinia spp.) infection. Current control strategies, reliant on chemical interventions, are limited by evolving resistance risks and environmental concerns, while rust-resistant breeding remains hindered by insufficient molecular insights. To address this, we systematically evaluated rust resistance in 24 L. chinensis germplasms from diverse geographic origins, identifying six highly resistant (HR) and five extremely susceptible (ES) genotypes. Integrating transcriptomics and metabolomics, we dissected molecular responses to Puccinia infection, focusing on contrasting HR (Lc71) and ES (Lc5) germplasms at 48 h post-inoculation. Transcriptomic analysis revealed 1012 differentially expressed genes (DEGs: 247 upregulated, 765 downregulated), with enrichment in cell wall biosynthesis and photosynthesis pathways but suppression of flavonoid synthesis. Metabolomic profiling identified 287 differentially accumulated metabolites (DAMs: 133 upregulated, 188 downregulated), showing significant downregulation of pterocarpans and flavonoids in HR germplasms, alongside upregulated cutin synthesis-related metabolites. Multi-omics integration uncovered 79 co-enriched pathways, pinpointing critical regulatory networks: (1) In the nucleotide metabolism pathway, genes Lc5Ns011910, Lc1Xm057211, and Lc4Xm043884 exhibited negative cor-relations with metabolites Deoxycytidine and Cytosine. (2) In flavonoid biosynthesis, Lc2Xm054924, Lc4Xm044161, novel.8850, Lc2Ns006303, and Lc7Ns021884 were linked to naringenin and naringenin-7-O-glucoside accumulation. These candidate genes likely orchestrate rust resistance mechanisms in L. chinensis. Our findings advance the molecular understanding of rust resistance and provide actionable targets for breeding resilient germplasms. Full article

Temperature is the most critical factor in fish preservation. Superchilled storage represents a novel technology that effectively retards quality deterioration in aquatic products. This study investigated the flavor variation patterns and deterioration mechanisms in 16 northern pike (Esox lucius) samples during superchilled storage (−3 °C) based on analysis using gas chromatography-ion mobility spectrometry (GC-IMS) and ultra-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS). The results indicate that GC-MS analysis identified 25 key volatile flavor compounds. These comprised seven ketones, thirteen alcohols, aldehydes including 2-methylbutanal, esters such as 2-heptyl acetate and methyl butyrate, as well as nitrogen-containing compounds, exemplified by pyrazines and indole. Non-targeted metabolomics further revealed four pivotal metabolic pathways, glycerophospholipid metabolism, purine metabolism, the pentose phosphate pathway, and arginine biosynthesis. These metabolic pathways were found to regulate flavor changes through modulation of lipid oxidation, nucleotide degradation, and amino acid metabolism. Notably, the arginine biosynthesis pathway exhibited significant correlations with the development of characteristic cold-storage off-flavors, mediated by glutamate accumulation and fumarate depletion. This investigation provided a theoretical foundation for optimizing preservation strategies in cold-water fish species at the molecular level. Full article

Hyaluronic acid (HA) is a linear heteropolysaccharide that naturally occurs in vertebrates. Thanks to its unique physico-chemical properties, it is involved in many key processes in living organisms. These biological activities provide the basis for its broad applications in cosmetics, medicine, and the food industry. The molecular weight of HA might vary significantly, as it can be less than 10 kDa or reach more than 6000 kDa. There is a strong correlation between variations in its molecular weight and bioactivities, as well as with various pathological processes. Consequently, monodispersity is a crucial requirement for HA production, together with purity and safety. Common industrial approaches, such as extraction from animal sources and microbial fermentation, have limits in fulfilling these requests. Research and protein engineering with hyaluronic acid synthases can provide a strong tool for the production of monodisperse HA. One-pot multi-enzyme reactions that include in situ nucleotide phosphate regeneration systems might represent the future of HA production. In this review, we explore the current knowledge about HA, its production, hyaluronic synthases, the most recent stage of in vitro enzymatic synthesis research, and one-pot approaches. Full article