Journal of Applied Genetics最新文献

PJVK gene was recently shown to create hypervulnerability to sound in humans and was the first human gene implicated in non-syndromic hearing impairment due to neural defect. Targeted next-generation sequencing of over 150 known deafness genes was performed in the proband. Sanger sequencing was used to validate the PJVK variant and confirm familial segregation of the disease. A minigene-based assay has been performed to assess the impact of the variant on splicing. We identified a novel c.550-6A > G acceptor splice-site variant in the PJVK gene in the homozygous state in a Mauritanian child with severe to profound congenital deafness. The substitution was located in intron 4. The effect of the variation was demonstrated by a minigene assay which showed that the variation, an insertion of an additional 5 bp, created a new splice site resulting in the appearance of a premature stop codon (p.Phe184Tyrfs*26) and likely a truncated protein. This result constitutes a new splice-site variant report in the PJVK gene leading to DFNB59 type associated with autosomal recessive non-syndromic hearing impairment (ARNSHI).

This study evaluated the antagonistic capacity of eight Trichoderma isolates against two Fusarium proliferatum isolates that differed in their toxigenic potential. Using co-cultures on solid and liquid media, significant variability in antifungal efficacy was observed among Trichoderma species. T. atroviride and T. viridescens isolates demonstrated the highest antagonistic activity, with markedly stronger inhibition of the less toxigenic F. proliferatum isolate. Quantitative PCR analysis confirmed a reduction in Fusarium biomass, which closely correlated with decreased levels of fumonisins (FB1, FB2, FB3) and beauvericin, as determined by UHPLC-HRMS. Notably, the most effective Trichoderma isolates (AN153, AN215, AN523) consistently suppressed both fungal growth and mycotoxin biosynthesis. Although fumonisin levels were reduced in co-cultures, independent assays in FB1-supplemented liquid media indicated that Trichoderma did not directly degrade mycotoxin. The presence of selected secondary metabolites, including 6-pentyl-2H-pyrone and phenolic acids, was confirmed in co-culture extracts. These findings highlight the isolate-specific nature of Trichoderma-Fusarium interactions and emphasise the potential of selected Trichoderma isolates as biocontrol agents capable of simultaneously limiting pathogen growth and mycotoxin accumulation. Further mechanistic studies are warranted to identify the molecular basis of these antagonistic effects.

Recently, the knowledge of the genetic basis of fertility disorders has expanded enormously, mainly thanks to the use of next-generation sequencing (NGS). However, the genetic cause of infertility, in the majority of patients, is still undefined. The aim was to identify novel and recurrent pathogenic/likely pathogenic variants in patients with isolated infertility or puberty delay using a targeted NGS technique. We have enrolled 41 patients (36 males and 5 females) with infertility problems or delayed puberty. We included the patients with hypogonadotropic hypogonadism (n = 12), hypergonadotropic hypogonadism (n = 15), abnormal sperm parameters (n = 10), androgen insensitivity syndrome (n = 3) and 46,XY gonadal dysgenesis (n = 1). Genetic tests were performed using targeted NGS panel of 35 genes implicated in fertility. Pathogenic or likely pathogenic variants potentially explaining the clinical phenotype were identified in 12 of 41 patients (29%). These included 9 of 12 patients (75%) with hypogonadotropic hypogonadism, 2 of 3 patients (66%) with androgen insensitivity syndrome, and the single patient with 46,XY gonadal dysgenesis. Among the 18 identified variants, 4 were novel (FGF8:p.Ala147Thr; SEMA3A:p.Arg544Cys; FGFR1:p.Thr141IlefsTer10; NSMF: p.Tyr242Cys), while 14 were recurrent. Our study expands the knowledge of the genetic basis of the infertility disorders and highlights the importance of genetic testing for proper diagnosis making and genetic counselling.

Dominantly inherited GAA repeat expansions in the FGF14 gene have recently been identified as the cause of spinocerebellar ataxia 27B (SCA27B). Our study focused on a Polish patient case along with asymptomatic family members. Moreover, we systematically reviewed available case reports to better understand the SCA27B phenotype. Genetic tests for SCA27B were performed on genomic DNA isolated from blood. Long-range polymerase chain reaction (LR-PCR) followed by Nanopore sequencing was conducted to establish the number of GAA repeats. The available literature was systematically reviewed per the recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-analyses. The patient's genetic studies identified pure expansions of (GAA) 420/94 repeats in FGF14, confirming the SCA27B diagnosis. A systematic review of 815 cases provides further insight into the typical clinical presentation, with gait ataxia (95.96%) being the most prevalent symptom, followed by abnormal saccadic pursuits (80.69%), nystagmus (71.15%), diplopia (54.05%), and dysarthria (51.22%). Notably, 41.87% of cases exhibited episodic symptoms. The correlation between GAA repeat expansions and the pathogenesis of SCA27B requires further studies. The unique course of the disease with episodic symptoms may cause diagnostic difficulties. Due to its high prevalence in the European population, SCA27B should be considered when diagnosing the causes of late-onset cerebellar ataxia.

In the last decades, the rate of stillbirths in the Icelandic Dairy Cattle population has increased. Some of these stillbirths may be caused by recessive lethal mutations segregating in the population. These alleles can be identified by detecting homozygous haplotype deficiency (HHD) in genotyped animals. The aim of this study was to find genomic regions affecting stillbirth and fertility in the Icelandic Dairy Cattle population. We analysed genotypes from 20,557 animals with 35,481 autosomal markers. We identified HHD segments and estimated their effects on stillbirths and insemination failure, measured as non-return rates. We conducted genome-wide association studies (GWAS) for stillbirth and five fertility traits: interval from first to last inseminations, conception rate, number of inseminations, calving interval and infertility. While no GWAS association reached the genome-wide significance threshold, some of the top signals co-located with HHD haplotypes. A total of 19 haplotypes significantly either decreased fertility, or increased incidence of stillbirths, or both. Two HHD regions on BTA13: 43,577,221-59,026,521 and BTA8: 83,276,598-84,472,391 were associated with both lower fertility and higher incidence of stillbirths. We found no evidence of large structural variations in or around the HHD regions, suggesting that these signals are likely due to single loss-of-function mutation or small structural variations. Further research should focus on exploring these regions using whole genome sequence data.

Leaf rust, caused by Puccinia triticina, is a major wheat disease that impacts yield and quality. This study aimed to identify genetic loci associated with seedling resistance to leaf rust in European winter wheat cultivars. A genome-wide association study was conducted on a panel of 181 wheat genotypes, including 143 modern cultivars and 38 lines with known leaf rust resistance genes. Pathogen evaluation involved 18 P. triticina isolates, which revealed diverse virulence levels and allowed resistant cultivars to be identified. The study identified 88 marker-trait associations clustered into 23 quantitative trait loci (QTL) across 13 chromosomes. Three QTL-QLr.ihar-1B.1, QLr.ihar-3D.1, and QLr.ihar-4 A.1-correspond to the major resistance genes Lr26, Lr24, and Lr28. Several QTL appear novel, with six (QLr.ihar-2B.2, QLr.ihar-3 A.1, QLr.ihar-3B.2, QLr.ihar-7 A.1, QLr.ihar-7D.1, and QLr.ihar-7D.2) explaining over 20% of phenotypic variance that could be considered for breeding purposes. Among 113 resistant cultivars, only 23 QTL were present in 51 genotypes, suggesting that resistance in the remaining 62 cultivars is under control of unidentified loci. The findings highlight the complex and diverse resistance patterns in European wheat, offering significant insights for breeding programs targeting enhanced leaf rust resistance.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 is a powerful tool for gene editing and the regulation of gene expression. It enables the introduction of targeted mutations, thereby facilitating functional studies of specific genes in various cellular processes. In this study, we aimed to generate a deletion in the promoter region of the CEBPB gene, which encodes a transcription factor involved in adipogenesis, and to evaluate the impact of this modification on the adipogenic differentiation potential of porcine mesenchymal stem cells (MSCs). A 575-bp deletion was introduced in the target region, resulting in the generation of both homozygous and heterozygous mutant cells. Adipogenic differentiation was assessed by quantifying transcript levels of adipocyte marker genes (GATA2, CEBPA, PPARG, and FABP4) at days 0, 4, 6, 8, and 10 of the differentiation process. Disruption of CEBPB expression led to the downregulation of these adipogenic markers, indicating impaired adipocyte differentiation. Additionally, to assess the proliferative capacity of the edited cells, the expression levels of proliferation-associated genes (CCND1, MCM2, and PCNA) were measured. A reduction in their transcript levels was observed in both homozygous and heterozygous mutant cells. These findings indicate that both homozygous and heterozygous deletions in the CEBPB promoter completely block adipogenesis and alter MSC proliferation, highlighting the pivotal role of CEBPB not only in adipogenic differentiation but also in the regulation of cell proliferation in porcine mesenchymal stem cells. These results provide new insights into the molecular mechanisms underlying adipose tissue development and have implications for pig breeding strategies aimed at optimizing carcass composition, as well as for biomedical research focused on adipose tissue biology.

Buckwheat is an underutilized crop with high nutritional values and antioxidant properties. The study was conducted with an aim to assess the genetic variability of 37 Fagopyrum esculentum Moench. and 67 Fagopyrum tataricum Gaertn. accessions using agro-morphological, biochemical, and microsatellite markers. For yield per plant, accessions, namely, IC24297, IC26591, and IC13413, with superior performances were identified. Based on correlations and regression-based path analysis, the key component traits, namely, number of seeds per plant, 100-seed weight, leaf blade width, seed width, and cyme length, were identified. Among F. esculentum group, EC18771, IC107238, and IC107265 had the highest carbohydrate, protein, and the lowest phytic acid, respectively. Likewise, IC24297, EC18769, and IC26596, with the highest carbohydrate, protein, and lowest phytic acid content, respectively, were identified under the F. tataricum group. By analyzing 65 SSR markers, an average of 2.63 alleles per locus was detected, with an average PIC value of 0.431. The observed heterozygosity for the polymorphic markers varied from 0.019 (Fagopyrum tataricum) to 0.462 (Fagopyrum esculentum), with an average of 0.099, showing the lower level of expected heterozygosity in tartary buckwheat accessions. Based on Nei's genetic distances, the buckwheat accessions were grouped into three clusters. Clusters I and III included the tartary accessions, while Cluster II encompassed both species. The AMOVA, conducted by categorizing the accessions into 25 subpopulations, indicated that 80% of the observed variation was due to differences among individuals, whereas 19% was due to within individuals. Based on additive main effects and multiplicative interaction (AMMI) and multi-trait stability index (MTSI) analyses, accessions, namely, IC13141, IC49667, IC26587, IC107983, and IC107981, have been identified as the best accessions, exhibiting high mean yield and stability across all three environments, and could be utilized in augmenting the buckwheat cultivation.

Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling regulates immune responses and tumorigenesis. Variations in NF-κB pathway genes may alter susceptibility to acute lymphoblastic leukemia (ALL). To evaluate associations between selected NFKB1 and NFKBIA polymorphisms and ALL risk in a Saudi population. We genotyped NFKB1 (rs93059, rs1287, rs1801) and NFKBIA (rs1050851, rs1957106, rs3138054) in 150 ALL patients and 115 matched controls using TaqMan® assays. Associations were assessed under multiple genetic models, and odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. The NFKB1 rs93059 A allele was associated with reduced ALL risk (OR = 0.68; 95% CI: 0.48-0.97; p = 0.03), with the AA genotype showing protection in codominant (p = 0.03) and recessive (p = 0.02) models. For NFKB1 rs1287, the AA genotype increased risk (OR = 2.75; 95% CI: 1.14-6.62; p = 0.02) in the codominant model. The NFKB1 rs1801 C allele was enriched in patients (OR = 1.54; 95% CI: 1.04-2.23; p = 0.01). No significant associations were observed for NFKBIA variants after multiple-testing correction. NFKB1 rs93059 and rs1801 may influence ALL susceptibility in the Saudi population, underscoring the potential contribution of NF-κB pathway variants to leukemia risk. Functional analyses are warranted to clarify underlying mechanisms.

Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality globally. COPD, within its context of disease etiology, is characterized by chronic inflammation of the lungs. It is distinguished by the aberrant production of oxidants, inflammatory cytokines, dysregulated immune cell activity, and remodeling of the airways. In this study, we analyzed the polymorphic association of antioxidants (GSTM1/T1) and inflammation-related genes (CXCL8, IL-33, and IL-6) with COPD. A case-control study was conducted with 227 subjects (116 healthy controls and 111 COPD cases). GSTM1/T1 genes were amplified by multiplex PCR' and inflammatory genes (CXCL8, IL-33, and IL-6) were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. GSTM1/T1 gene deletion rates in the COPD group were significantly higher than those in the control group (GSTM1: OR = 11.85, CI = 4.033-34.79, P < 0.0001; GSTT1: OR = 2.303, CI = 1.206-4.399, P = 0.0113). In addition, our research revealed a significant association between the combined GSTM1/T1 null genotype and increased susceptibility to COPD (OR = 18.66, CI = 2.345-148.5, P = 0.0003). A significantly increased frequency of the "CC" genotype of the CXCL8 (rs2227532) gene variant (OR = 7.50, CI = 2.429-23.16, P < 0.0001) was observed in COPD patients compared to the control group. However, there was no significant association of the IL-33 (rs7044343) polymorphism between healthy controls and COPD patients. The IL-6 (rs2069860) gene variant was found to be monomorphic. As a result of the investigation, it was concluded that individuals with the null genotype of GSTM1/T1 combined and the presence of the CXCL8 (rs2227532) gene variant have a higher likelihood of developing COPD.