Journal of Applied Genetics最新文献

Resistance breeding is a widely promoted strategy for minimizing yield losses in wheat caused by various fungal diseases, including leaf rust (Puccinia triticina; Lr genes), Fusarium head blight (Fusarium spp.; Fhb), powdery mildew (Blumeria graminis; Pm), Septoria tritici blotch (Septoria tritici; Stb), eyespot (Oculimacula spp.; Pch-previously known as Pseudocercosporella herpotrichoides), stem rust (Puccinia graminis f. sp. tritici; Sr) and yellow rust (Puccinia striiformis; Yr). Understanding the prevalence of resistance genes in currently cultivated European varieties is crucial for their effective utilization in breeding programs. In this study, we developed 11 duplex and 13 triplex PCR assays for the simultaneous identification of diverse allelic combinations of disease resistance genes. Selected assays were used to analyze 70 European wheat varieties for the presence of 15 molecular markers associated with 12 resistance genes. The analyses identified diverse resistance gene combinations. The optimized multiplex PCR methods significantly reduce cost and time of analysis, making them valuable tools for marker-assisted selection (MAS) in wheat breeding programs.

Given the importance of epigenetic mechanisms in the downregulation of tumor suppressor genes and the activation of oncogenes, herein we focused on microRNA silencing as a cause of oncogene activation in laryngeal squamous cell carcinoma (LSCC). In our study, we aimed at identifying regulatory microRNA signatures in LSCC mRNA profiles from our previous analysis. By this approach, we identified 14 overexpressed genes that shared a common regulatory hsa-miR-299-5p signature in LSCC samples. Subsequent RT-qPCR analysis confirmed the downregulation of hsa-miR-299-5p as well as the overexpression of 3 out of 14 genes: PATZ1, PURB, and TFAM in both LSCC cell lines and tumor samples compared to non-cancerous controls. Further, we have demonstrated a direct interaction between hsa-miR-299-5p and TFAM 3'UTR using dual luciferase assay. Importantly, we have shown decreased TFAM protein level after mimicry of hsa-miR-299-5p expression in three LSCC cell lines. Moreover, cell lines with restored activity of hsa-miR-299-5p demonstrated reduced viability compared to cell lines treated with the negative control. In conclusion, we point to hsa-miR-299-5p as a tumor-suppressive microRNA with the potential to regulate TFAM and consequently influence cell viability.

Winter oilseed rape (Brassica napus), a crucial crop in temperate regions, is a key contributor to global vegetable oil production and an essential component of crop rotations due to its ability to improve soil structure and fertility. Enhancing its yield is vital for meeting the increasing demand for sustainable oil production, supporting food security, and optimizing biofuel production, while also ensuring the economic viability of agricultural systems in colder climates. The aim of the research was to determine association between SNP molecular markers and rapeseed yield. The plant material for this study consisted of 276 oilseed rape hybrids. The experiment was conducted in four localities: Borowo, Kończewice, Małyszyn, and Strzelce. The mean yield values ranged from 0.07 kg (for hybrid EH_20212 in Małyszyn) to 9.10 kg (for hybrid EH_20410 in Kończewice). The genotype matrix for 276 hybrids was constructed using marker data from the parental genotypes of inbred individuals (maternal and paternal lines). The matrix was coded as {- 1, 0, 1}, assuming an additive effect of the alleles. A total of 13,116 SNP markers were identified. For association mapping, 12,581 polymorphic markers were used. The results of the observation of the yield and sequencing were used for association mapping, which ultimately resulted in the selection of twenty-six molecular markers important (LOD > 5.0) simultaneously in all four localities.

High plant density assumes significance for higher yield per unit area. However, reports on breeding for ideal plant architecture (IPA) in maize are limited due to lack of comprehensive characterization of germplasm. Here, we assessed genetic variation and identified inbreds for 14 plant architectural traits among 48 subtropical maize inbreds through multi-location analysis. Wide genetic variation for (i) stalk-related traits, viz., plant height (100.5-209.8 cm), ear height (26.4-106.3 cm), internode number (3.8-10.9), and internode length (8.1-15 cm); (ii) leaf-related traits, viz., leaf length (39.7-77.1 cm), leaf width (5.2-10.5 cm), leaf area (158.6-568.4 cm²), leaf angle (18.4-84.6°), leaf orientation value (2.2-71.3), number of leaves above-ear (3.2-7.2), and husk number (5.7-14.4); and (iii) tassel-related traits, viz., tassel height (21.8-34.9 cm), number of tassel branches (3.9-16.6), and tassel branching angle (10.2-78.4°) were observed. All traits showed significant variation due to environment and genotype × environment interactions. Correlation analysis implied that narrow leaf angle would produce compact tassel as well (r = 0.53, p < 0.001). Internode number and leaf width (r = - 0.33, p = 0.031), number of leaves and leaf length (r = 0.42, p = 0.004), plant height and leaf length (r = 0.39, p = 0.005), and leaf length and tassel height (r = 0.44, p = 0.003) were also associated. HKI-1105, CML-568, BAUIM-4, and BAUIM-2 were the most stable and promising inbreds with IPA using three popular selection indices (AMMI-TGSI, WAASBY-I, and MTSI). These promising inbreds could serve as suitable donors for germplasm diversification, besides generating hybrid combinations for high plant density. This is the first comprehensive analysis to characterize sub-tropically adapted maize inbreds for plant architectural traits.

The MYC proto-oncogene encodes a basic helix-loop-helix leucine zipper (HLH-LZ) transcription factor, acting as a master regulator of genes involved in cellular proliferation, differentiation, and immune surveillance. Dysregulation of MYC is implicated in over 70% of human cancers, driving oncogenic processes through altered gene expression and disrupted cellular functions. Non-synonymous single nucleotide polymorphisms (nsSNPs) within coding regions can significantly impact protein structure and function, leading to abnormal cellular behaviours. This study employed 29 in silico tools to systematically evaluate the deleteriousness of nsSNPs within the MYC gene. These tools assessed the variants' effects on protein structure, disease association, functional domains, and post-translational modification sites. This study investigated if these variants may disrupt protein-protein interactions, critical for MYC's oncogenic roles and normal cellular functions. Our analysis identified 21 nsSNPs that were predicted to be deleterious and pathogenic. These variants correspond to residues D63H, D63Y, P74L, P75L, N375D, N375I, E378K, E378Q, E378A, E378G, E378V, R379P, R381K, R381T, R382W, L392P, R393C, R393H, R393P, L411H, and L411P. Stability assessments indicated that these variants could destabilise the MYC protein. None of the variants affected post-translational modifications. Protein-protein interaction and docking analysis revealed that variants within bHLH and LZ domains may disrupt MYC/MAX binding, potentially impacting MYC's oncogenic activity and transcriptional regulation. This computational assessment enhances our understanding of genetic variations within the MYC gene and prioritises candidate nsSNPs for experimental validation and therapeutic exploration.

Phosphorus (P) and water are essential for plant growth and development, exerting a significant influence on global crop production. The phosphate transporter (PHT) gene family plays a pivotal role in phosphate (Pi) uptake, transport, and homeostasis under diverse environmental conditions. In this study, we conducted a comprehensive genome-wide identification and characterization of the PHT gene family in Avena sativa. A total of 32 non-redundant AsPHT genes were identified in the OT3098 genome, classified into two subfamilies: AsPHT1 (21 genes) and AsPHO (11 genes). AsPHT1 proteins were predominantly hydrophobic with one or two exons, whereas AsPHO proteins were hydrophilic, exhibiting a more complex structure with 13-15 exons. Cis-regulatory element analysis revealed an abundance of hormone- and stress-responsive elements in the promoters of AsPHT genes, indicating their potential roles in adaptive responses to Pi and water deficiency. Gene expression profiling under low Pi and drought conditions demonstrated differential expression of 22 AsPHT genes in roots and leaves at the seedling stage, with distinct responses to the two stresses, highlighting the functional diversity of the AsPHT gene family. These findings provide valuable insights into the molecular mechanisms underlying Pi and water acquisition in oats and offer potential applications for developing varieties with enhanced Pi use efficiency and drought tolerance.

Accounting for genotype by environment interaction (GxE) and using genomic information may enhance the prediction accuracy $\left(\widehat{\text{ACC}}\right)$ of breeding values. Hence, the objective of this study was to evaluate the gain in $\widehat{\text{ACC}}$ using single-step genomic BLUP using high-density SNP chip (ssGBLUP_HD) or whole genome imputed sequence (ssGBLUP_SEQ) compared to pedigree BLUP in the presence of GxE. Phenotypic data for age at first calving (AFC), scrotal circumference (SC), post-weaning weight gain (PWG), and yearling weight (YW) were obtained from commercial breeding programs of Nellore cattle. There were 1,578,591 animals in the pedigree, from which 51,485 had genotypes with high-density SNP chip (HD) and whol- genome imputed sequence (WGS), totaling 460,578 and 2,437,948 SNPs, respectively, after quality control. Contemporary group effects, estimated with a regular animal model (without modeling GxE), were used to define the environmental gradients (EG) for the reaction norm model (RNM). Genetic sensitivity to environmental variation was assessed by fitting three different linear RNM: the first considering only pedigree (BLUP), the second also considering the genomic information from HD, and the third considering the genomic information from WGS. The validation was carried out for genotyped young bulls, with no progeny records in the reduced data and at least one in the complete data. Models were compared using prediction accuracy, dispersion, correlation between the breeding values from reduced data and complete data, and bias from the linear regression method. Re-ranking between animals and heterogeneity of genetic variance in different EG were observed, suggesting the presence of GxE. The results for the regression coefficients of the RNM showed, in general, that the inclusion of genomic information increased the $\widehat{\text{ACC}}$ for the RNM regression coefficients for all traits. For SC, PWG, and YW, the highest accuracies were obtained with ssGBLUP_SEQ. Conversely, AFC had higher accuracy with ssGBLUP_HD. In addition, the $\widehat{\text{ACC}}$ for genotyped young bulls increased as the EG increased. In conclusion, ssGBLUP_SEQ yielded higher $\widehat{\text{ACC}}$ and correlation and a lower bias than the BLUP across all EG, indicating that the implementation of genomic selection using the whole genome sequence and accounting for GxE benefits this Nellore beef cattle population.

Infertility presents a substantial challenge for women of reproductive age, exerting profound effects on both individual well-being and healthcare systems. Despite its critical role in folate and homocysteine pathways, the influence of methylenetetrahydrofolate reductase (MTHFR) on the success of assisted reproductive techniques (ART) remains insufficiently understood. This knowledge gap impedes the development of personalized therapeutic strategies. Our study seeks to elucidate the relationship between MTHFR and ART outcomes, exploring potential mediators to enhance treatment efficacy. A cohort of 311 women with infertility was recruited for our study. Multivariate linear models were utilized to evaluate the relationship between the MTHFR 677T allele (a missense mutation resulting in an alanine to valine substitution) and the efficacy of ART, including both treatment outcomes and the number of ART cycles required. Sequential mediation analysis was conducted to elucidate the potential mediators influencing ART efficacy. The MTHFR 677T allele carried by infertile women was associated with a 17-51% reduction in ART efficacy (P < 0.05). This encompassed poorer overall ART outcomes, such as clinical pregnancy and live birth rates, as well as an increased number of ART cycles. Sequential mediation analysis suggested that anti-Müllerian hormone (AMH) and age may act as mediators modulating the impact of the MTHFR 677T allele on ART treatment efficacy. This study has unveiled the intricate connection between MTHFR 677T allele and ART treatment efficacy in infertile women, shedding light on the mediating role of AMH and age.

Endometrial cancer (EC) is the second most frequent gynecological malignancy and the sixth most common women's cancer worldwide. EC incidence rate is increasing rapidly. Apart from the classical, we should consider angiogenesis and hypoxia-related genes as a reason for EC manifestation and progression. We compared the patterns of HIF1A, EPAS1, and VEGFA (genes of interest - GOIs) mRNA expression in 92 cases. HIF1A and VEGFA levels were higher in EC patients than in controls. VEGFA differed significantly between controls and both tumor grades G2 and G3, and we observed a positive correlation for HIF1A and VEGFA with EC grading. VEGFA levels were significantly higher in post-menopausal compared to pre-menopausal patients. All GOIs demonstrated strong correlations in pre-menopausal cases and weak correlations in post-menopausal cases. A positive correlation was observed in pre-menopausal controls for all GOIs and in post-menopausal patients for only EPAS1 and VEGFA. HIF1A and EPAS1 positively correlated with VEGFA in post-menopausal EC cases. Multiple linear regression analyses revealed that menopause, body mass index (BMI), and HIF1A expression are significant stimulating factors for EC occurrence. HIF1A levels were higher in EC patients after BMI and comorbidity number adjustment. The gene-to-gene relation could be seen as either a diagnostic or a therapeutic target in EC. Physicians should inform patients about modifiable risk factors such as BMI. Second, more attention should be paid to diagnosing patients with comorbidities in older age and after menopause. These factors should be considered in designing angiogenesis and hypoxia-related gene-targeting therapies.

Chromosome number abnormalities is one of the hallmarks of cancer. DNA copy number alterations (CNA) are studied using various genome-wide methods. In our study, we investigated CNA in human pituitary tumors using three platforms CytoSNP-850 K microarrays, low-pass whole-genome sequencing (average × 7 coverage, LPWGS), and Infinium Methylation EPIC array. Virtual karyotypes based on each dataset were generated using open-source software packages for each sample. Concordant CNA profiles were found for most of tumor. Surprisingly, substantial discrepancies between results from SNP arrays and LPWGS/EPIC arrays were identified in 20% of tumors, for which discrimination of true karyotype was required. B-allelic frequency data from SNP arrays was crucial to adjust normal ploidy level as ultimately verified with FISH. The discrepancy between virtual karyotypes was more pronounced the more CNAs were found. When CNAs covered around half of genome, the level of normal/diploid copy number was incorrectly set with methods, based solely on signal intensity/read-counts coverage. To conclude, CNA analyses with methods such as LPWGS and methylation arrays in highly aneuploid tumors are prone to a bias from improper normal ploidy level setting. These methods are commonly used therefore, we aimed to aware the scientific community about this underestimated methodological problem.