Search Results (4,234)

Copy number variation (CNV) is a common source of genomic structural variation by altering the number of DNA fragments, which in turn affects phenotypic variation and gene expression levels. However, there have been no reports of CNV in Chinese jujube (Ziziphus jujuba Mill.). In this study, we identified 16,570 CNVs from “Yuhong” × “Jiaocheng 5” and 140 hybrid progeny materials, of which 3607 CNVs were deletion type and 12,963 CNVs were duplication type. The distribution of CNVs in the Chinese jujube genome was systematically described, and the CNV genetic map of the whole genome level of the Chinese jujube hybrid offspring was constructed. Based on the field investigations, 13 individuals with severe black spot disease and no disease were analyzed for trait association. A total of 1837 CNVs were detected at the significant level of association, of which 1371 were duplication type and 466 were deletion type. And the GO (Gene Ontology) annotation item identified a systemic acquired resistance (SAR), and eight genes related to disease resistance were screened by the annotation. After validation by qPCR, these results further support the potential role in regulating black spot disease resistance. The constructed genome-wide CNV map of the hybrid progeny of Chinese jujube provides a new way of thinking for understanding the genetic basis of phenotypic variation of complex traits in Chinese jujube. Full article

Camelina sativa is an oilseed crop that has shown strong promise as a biofuel feedstock. The profile of fatty acids greatly influences the oil quality; however, genetic mechanisms that determine the natural variation of fatty acid composition in camelina are not fully understood. A genome wide association study (GWAS) was performed to uncover genetic loci that may contribute to the contents of major fatty acids such as oleic and linolenic acids in camelina seed. Two approaches were taken to improve the GWAS efficiency. First, growing a diversity panel of 212 accessions in four locations and two nitrogen fertilization conditions revealed great variation in fatty acid contents in seeds. Second, using an improved reference genome, abundant markers, including 203,320 single nucleotide polymorphisms (SNPs) and 99,067 insertions/deletions (indels), were developed, which refined the population structure of the diversity panel. GWAS resulted in 118 genetic markers across 31 trait/treatment conditions. Closely linked markers were determined based on linkage decay and by comparing secondarily associated markers when highly associated ones were removed. Candidate genes were examined by comparing the pangenomes of 12 high-quality reference genomes. This study provides new resources to understand seed lipid metabolism and improve camelina oils through molecular breeding. Full article

A mutation detection strategy based on mismatch digestion was applied previously in barley seedlings carrying the chloroplast mutator (cpm) genotype through many generations. Sixty-one mutations were detected along with four large indels: a 15 bp insertion in the intergenic region between tRNA^His and rps19 genes, a 620 bp deletion in the psbA gene, a 79 bp deletion in the intergenic region between rpl33 and rps18 genes and a 45 bp deletion in the rps3 gene. The present investigation aims to understand the mechanisms producing the large indels and to better characterize the cpm mutagenic effect. Whole plastome sequencing revealed novel polymorphisms that were identified either in regions not previously examined or in regions that were explored but not detected through celery juice extract (CJE) digestion. The 620 bp deletion in the psbA gene was lethal when homoplastomic, whereas the 45 bp deletion in the rps3 gene did not affect the viability of the seedlings even in homoplastomy. The presence of direct repeats at the borders of large indels suggests that they could have originated by illegitimate recombination because of CPM protein malfunction. A truncated mismatch repair MSH1 protein identified in cpm seedlings suggests that CPM is involved in organellar genome stability maintenance. Full article

Congenital ichthyoses, now grouped under the acronym EDD (Epidermal Differentiation Disorders), include nonsyndromic forms (nEDD) that may be caused by loss-of-function mutations in the CDSN gene encoding corneodesmosin (CDSN-nEDD, formerly Peeling skin syndrome type 1). It is characterized by skin peeling, inflammation, itching and food allergies, while no specific therapy is currently available. High levels of KLK5, the serine protease that initiates the desquamation cascade, are found in the epidermis of CDSN-nEDD patients. Thus, we hypothesized that KLK5 inhibition would alleviate the symptoms of CDSN-nEDD and could serve as a new pharmacological target. A human epidermal equivalent (HEE) model for CDSN-nEDD was developed using shRNA-mediated CDSN knockdown. This model was characterized and used to assess the role of KLK5 knockdown on CDSN-nEDD. Also, Klk5^−/− mice were crossed with Cdsn^epi−/− mice, the murine model of CDSN-nEDD, to examine in vivo the effect(s) of Klk5 deletion in CDSN-nEDD. Both models recapitulated the CDSN-nEDD desquamating phenotype. Elimination of KLK5 aggravated the CDSN-nEDD phenotype. Epidermal proteolysis was surprisingly elevated, while severe ultrastructural (corneo)desmosomal alterations increased epidermal barrier permeability and stratum corneum detachment was manifested. Based on these results, we concluded that targeting epidermal proteolysis with KLK5 ablation cannot compensate for the loss of corneodesmosin and rescue over-desquamation of the CDSN-nEDD. Possibly, in the absence of KLK5, other proteases take over which increases the severity of over-desquamation in CDSN-nEDD. The translational outcome is that over-desquamation may not always be rescued by eliminating epidermal proteolysis, but fine protease modulation is more likely required. Full article

Toxoplasma gondii is a globally prevalent parasite capable of establishing lifelong infections, which can have severe consequences in immunocompromised individuals and developing fetuses. GRAs are essential secretory effectors that facilitate nutrient acquisition, modulate host immune responses, and support intracellular survival. In this study, we characterized four putative GRAs (GRA85–88) that co-localize with GRA12 in both tachyzoite and bradyzoite stages. Using CRISPR-Cas9-mediated homologous recombination, we successfully generated knockout strains in both type I RH and type II Pru backgrounds. Phenotypic analysis revealed that GRA85, GRA87, and GRA88 were not individually required for parasite replication, invasion, or virulence. However, deletion of gra86 (PruΔgra86) resulted in a significant reduction in virulence and fewer brain cysts in chronically infected mice, although in vitro growth remained unaffected. Transcriptomic profiling of PruΔgra86 revealed downregulation of bradyzoite–related genes and upregulation of GRAs involved in host interaction. Additionally, in vitro differentiation assays showed impaired bradyzoite development in the absence of GRA86. These findings from murine models and in vitro phenotypic assays highlight GRA86 as a regulator of chronic infection and stage conversion, positioning it as an important player in T. gondii pathogenesis and a promising target for therapeutic intervention. Full article

Social interaction between the domesticated animal and the domesticator is one of the key features of the “domestication syndrome”. Recent research has identified genes in the WBSCR (Williams–Beuren syndrome control region) locus as significant contributors to social behavior in dogs. Large chromosomal deletions and duplications in the human WBSCR locus lead to the development of WBS (Williams–Beuren syndrome) and WBSCR duplication syndrome, respectively. Hypersociability is one of the key symptoms of WBS, while the duplication syndrome is manifested as an autism spectrum disorder (ASD). The data from both humans and dogs highlight the WBSCR locus as one of the key genetic determinants of social behavior in mammals. Several genes in the WBSCR are candidates for the regulation of social behavior in mammals including GTF2I, GTF2IRD, AUTS2 and GALNT17. Here, we discuss the role of WBSCR locus in the regulation of social behavior in mammals including the recent data that highlight the importance of 3D genome alterations in this genomic region for both domestication of animals and development of neurobehavioral disorders in humans. In addition, we bring attention to the role of the poorly characterized GALNT17 gene as a putative player in the development of ASD symptoms and in the regulation of social behavior in animals. We provide a brief summary of its known functions and propose the future research directions aimed at the elucidation of Galnt17 involvement in the regulation of central nervous system (CNS) functions. Full article

Renal phosphate transporters NaPi-IIa (SLC34A1) and NaPi-IIc (SLC34A3) play a crucial role in phosphate reabsorption in the proximal tubule. Biallelic loss-of-function variants in SLC34A1 and SLC34A3 cause two rare phosphate-wasting tubulopathies: idiopathic infantile hypercalcemia (IIH) and hereditary hypophosphatemic rickets with hypercalciuria, respectively. The phenotypes associated with these diseases are highly variable and sometimes overlap. Here, we report a rare case of a six-month-old girl of consanguineous parents with symptoms related to these diseases, including failure to thrive, nephrocalcinosis, hypercalcemia, hypophosphatemia with low TRP, elevated levels of 1,25-(OH)₂D₃, and suppressed PTH. An exome sequencing analysis was carried out to determine the genetic variants associated with her disease. Bioinformatics tools were used to assess variant pathogenicity. We identify a novel homozygous mutation in the SLC34A1 gene, c.1361C>T; p.(T454M), and a previously described heterozygous SLC34A3 101 bp deletion. Mutation p.(T454M) affects transmembrane domain 5 of the NaPi-IIa protein, which is involved in substrate binding, probably impairing phosphate transport. Our results suggest the diagnosis of IIH type 2 in our patient and highlight the importance of exome analysis in diagnosing these tubulopathies. We suggest that the coexistent heterozygous SLC34A3 deletion could increase the risk of renal calcifications and the severity of other symptoms. Full article

Rice lipoxygenase 3 (OsLOX3) is a lipid hydroperoxidase found in rice embryos. Previous studies have reported that OsLOX3 is associated with seed quality and stress resistance, however, its relationship with grain shape and weight remains unknown. In this study, the first exon of OsLOX3 gene was edited in the indica rice variety GDR998 using CRISPR/Cas9 technology. Two homozygous mutants, Oslox3-1 (single-base deletion) and Oslox3-2 (single-base insertion) were identified among eight positive mutant plants from the T2 generation. The agronomic evaluation of genotypic OsLOX3 mutants showed significant increase in grain length, grain length-to-width ratio, 1000-grain weight, plant height, panicle length, and yield per plant compared with the wild type GDR998. The number of effective panicles and total grains per panicle did not significantly change. Further germination tests of seeds after three years of natural aging revealed that, compared with the control GDR998, the germination percentages of the mutants Oslox3-1 and Oslox3-2 increased significantly by 41.1% and 45.6%, respectively. These findings indicate that the knockout of OsLOX3 simultaneously improve grain weight and seed vigor, providing valuable germplasm resources for rice breeding targeting high-yield, improved seed longevity and rice quality. Full article

Hearing loss is a genetically heterogeneous sensory defect for which biallelic pathogenic variants in the GJB2 gene are a frequent cause. Here, we report a novel intragenic large deletion in GJB2 in a Mayan family with several members affected by congenital non-syndromic hearing loss. The analysis of the GJB2 gene in the proband was performed through Sanger sequencing. A novel homozygous 1259 bp deletion in GJB2 was identified, starting at nucleotide 248 of the coding region and ending at nucleotide 825 of the 3′-UTR (g.20188077_20189335del). Bioinformatic tools were used to predict the structural impact of the variant. This deletion would result in a truncated protein of 86 amino acids, p.(Phe83Cysfs*5), disrupting several critical domains of the connexin-26 protein. We developed an endpoint-PCR assay to test for the deletion. It was present homozygously in all affected siblings and was absent in 153 ethnically matched controls with normal hearing. Both parents and two unaffected siblings were heterozygous carriers, consistent with an autosomal recessive inheritance pattern. The identification of this novel large deletion expands the spectrum of GJB2 pathogenic variants causing non-syndromic hearing loss, and it is of concern to GJB2 screening methods that rely primarily on Sanger sequencing for its coding region. Full article

Fusarium crown rot, a widespread and destructive disease affecting cereal crops (particularly wheat and barley), is primarily caused by the soil-borne fungal pathogen Fusarium pseudograminearum. Secondary metabolites (SMs) play a crucial role in colonization and host tissue invasion by pathogenic fungi. In this study, we investigated the functional role of FpTox2, a secondary metabolite-related gene in F. pseudograminearum. An FpTox2 deletion mutant exhibited significantly reduced radial growth compared to wild-type F. pseudograminearum. Notably, the mutant strain completely lost conidiation capacity under induced conditions. Furthermore, although it showed decreased sensitivity to the cell membrane inhibitor sodium dodecyl sulfate (SDS), the mutant demonstrated enhanced susceptibility to NaCl, a metal ion stressor. Most importantly, the pathogen’s virulence was markedly attenuated in wheat stem base infections following FpTox2 deletion, and we demonstrated that FpTox2 regulates pathogen virulence by influencing deoxynivalenol production. In conclusion, FpTox2 is crucial for vegetative growth, asexual development, abiotic stress responses, and full virulence in F. pseudograminearum. Full article

Sex determination is a fundamental biological process governing animal reproduction. Although substantial progress has been made in elucidating its genetic basis, the genetic architecture underlying complex sex determination systems remains poorly understood. In this study, we identify sex-associated insertion–deletion (indel) variants, screen candidate genes, and compare sex-associated variation across populations with different genetic backgrounds in the Fujian oyster (Magallana angulata). Based on whole-genome resequencing data of a culture strain (designated FL), a total of 299,774 high-quality indels were identified. By integrating genome-wide association analysis (GWAS), fixation index (F_ST) analysis, and sex-biased genotype frequency comparisons, 77 overlapping sex-associated indels were identified, predominantly clustered within a 1.8 Mb (8.3–10.1 Mb) region on chromosome 9. Principal component analysis (PCA) based on the sex-associated markers and their subsets consistently separated male and female individuals in the FL strain. For two representative sex-associated indels, PCR-based genotyping methods were developed and validated. Functional annotation identified putative candidate genes for sex determination, including PKD1L1, 5-HTRL, SCP, and CCKRa. Comparative analysis of variants within PKD1L1 across wild, farmed, and selectively bred populations revealed a progressive enrichment of male-linked alleles in domesticated and selectively bred groups, particularly in male individuals. This study provides direct evidence that sex in the Fujian oyster is genetically determined and reveals that domestication and artificial selection may drive the emergence of major sex-determining loci, offering important insights into the genetic basis of sex determination in the Fujian oyster, and establishing a theoretical and practical foundation for molecular marker-assisted breeding of monosex lines for this species. Full article

Fusarium verticillioides, an important global pathogenic fungus, compromises crop quality and yield by infecting maize, sugarcane, and some Solanaceae, endangering food security through contaminated grains and cereals with the fumonisin B1 (FB1) toxin. While Con7 has been reported as a transcription factor involved in the sporulation and pathogenicity of some pathogenic fungi, the function of FvCon7 and its regulatory genes in F. verticillioides remains uncharacterized. Gene deletion mutants of ΔFvcon7 were constructed through homologous recombination, which exhibited defects in vegetative growth, survival, sporophore development, conidiation, conidial germination, and carbon metabolism. Carbon metabolism defects led to a significant accumulation of glycogen granules in hypha and lipid bodies in conidia. Additionally, ΔFvcon7 displayed impaired cell wall structure and integrity, along with an altered expression of genes encoding cell wall-degrading enzymes (such as chitinase), as detected by qRT-PCR. Moreover, Fvcon7 also plays a role in the pathogenicity of maize and sugarcane through different splicing, defective conidia, reduced survival viability, differential expression of secreted proteins, and deficiencies in antioxidant stress capacity. Furthermore, using yeast one-hybrid (Y1H) assays, FvCon7 was found for the first time to directly regulate the expression of FvFUMs by binding to the CCAAT box within the promoters of six key FvFUMs, thereby affecting FB1 production. Overall, FvCon7 functions as a global transcription factor regulating multiple phenotypes. This study provides a theoretical basis for elucidating the mechanism of transcription factor FvCon7 regulating toxin production and pathogenesis in F. verticillioides. Full article

Ganoderic acid (GA) is a key bioactive component with pharmacological properties that is found in Ganoderma lingzhi, a renowned medicinal mushroom. Currently, the regulatory mechanisms underlying GA biosynthesis in G. lingzhi remain to be further elucidated. In this study, blue light induction was found to significantly enhance the GA content in G. lingzhi. To explore the regulatory mechanism of GA biosynthesis in response to blue light, the blue light receptor WC-2 was identified, and its regulatory role was characterized. The deletion of wc-2 resulted in a significant reduction in both GA content and the accumulation of intermediates compared to the wild-type control strain, largely due to the strong downregulation of key GA biosynthetic genes. Additionally, decreased asexual spore production and reduced expression of sporulation-specific genes were observed with the deletion of wc-2. The overexpression of wc-2 led to greatly enhanced GA accumulation. Under blue light induction, the maximum contents of GA-Mk, GA-T, GA-S, and GA-Me were 2.27-, 2.51-, 2.49-, and 2.08-fold higher, respectively, compared to the control kept in darkness. These results demonstrate that the blue light receptor WC-2 functions as a positive regulator of GA biosynthesis in G. lingzhi, influencing the expression of genes involved in GA biosynthesis and asexual spore production, thereby advancing our understanding of the intricate regulatory network of GA biosynthesis. Full article

Background and Clinical Significance: Arterial and venous thromboses are typically distinct clinical entities, each governed by unique pathophysiological mechanisms. The concurrent manifestation of both, particularly in the setting of massive pulmonary embolism (PE), is exceptionally rare and poses significant diagnostic and therapeutic challenges. Case Presentation: This report describes a 61-year-old male with well-controlled hypertension and type 2 diabetes who developed extensive thromboses involving deep vein thrombosis (DVT) of the right popliteal vein, arterial thrombosis of the left iliac artery, and massive PE. The patient was initially managed conservatively, in accordance with the European Society of Cardiology (ESC) 2019 Guidelines for Acute PE, using unfractionated heparin (UFH), low-molecular-weight heparin, a direct oral anticoagulant (DOAC), and adjunctive therapy. This approach was chosen due to the absence of hemodynamic instability. However, given failed percutaneous revascularization and persistent arterial occlusion, surgical thromboendarterectomy (TEA) was ultimately required. Post hoc genetic testing was prompted by the complex presentation in the absence of classical provoking factors—such as trauma, surgery, malignancy, or antiphospholipid syndrome—consistent with recommendations for selective thrombophilia testing in atypical or severe cases. The analysis revealed four thrombophilia-associated polymorphisms: heterozygous Factor V Leiden (FVL; R506Q genotype), Plasminogen Activator Inhibitor-1 (PAI-1; 4G/5G genotype), Methylenetetrahydrofolate reductase (MTHFR; c.677C > T genotype), and homozygous Angiotensin-Converting Enzyme Insertion/Deletion (ACE I/D; DD genotype). Conclusions: While each variant has been individually associated with thrombotic risk, their co-occurrence in a single patient with simultaneous arterial and venous thromboses has not, to our knowledge, been previously documented. This case underscores the potential for gene–gene interactions to amplify thrombotic risk, even in the presence of variants traditionally considered to confer only modest to moderate risk. It highlights the need for a multidisciplinary approach and raises questions regarding pharmacogenetics, anticoagulation, and future research into cumulative genetic risk in complex thrombotic phenotypes. Full article

The global impact of COVID-19 was staggering, with millions of cases and related mortality reported worldwide. Genetic variations play a significant role in determining an individual’s susceptibility to SARS-CoV-2 infection and progress to severe disease. This pilot study provides an experimental approach using WES to identify certain rare and novel genetic variants that might affect an individual’s susceptibility to the risk of SARS-CoV-2 infection, offering an initial exploration of these genetic variants. In the study cohort with 16 patients, the mortality rate was higher in male patients due to severe disease. There was a substantial burden of comorbidity, including hypertension, ischemic heart disease, and T2DM, conditions which independently increase the risk of adverse outcomes in COVID-19 patients. A total of 4478 variants were identified, distributed across 322 genes within the cohort. The majority of these variants were missense substitutions along with frameshift variants, inframe insertions/deletions (indels), and nonsense variants. The variants were further categorized by types to include single-nucleotide polymorphisms (SNPs), deletions (DEL), and insertions (INS). The gene with the highest number of variants was HLA-DRB1, followed by HLA-B, ABO, HPS4, and SP110 displaying both common polymorphisms and rare variants. Moreover, the HLA-B gene exhibited the highest number of rare candidate variants, followed by AK2, IRF7, KMT2D, TAP1, and HLA-DRB1. Several genes harbored multiple novel variants, including TAP1, AK2, G6PC3, HLA-B, IL12RB2, and ITGB2. The frequencies of the identified variants were found to be either zero or extremely low (below 1% threshold) in the Middle Eastern or in the overall combined population, suggesting that these are indeed rare and do not represent common indigenous polymorphisms. Functional enrichment analysis of the constructed protein–protein interaction network in our preliminary findings revealed that the identified genes are primarily enriched in pathways associated with immune deficiency and DNA repair. This initial exploration of genetic variants in COVID-19 susceptibility provides a foundation for future large-scale studies. Full article