Journal of Applied Genetics最新文献

Alternative splicing (AS) produces various forms of mRNAs and protein isoforms and contributes to biodiversity. However, different mRNAs might have identical CDS and encode the same protein sequence. It is unclear why organisms need these distinct mRNAs if they encode the same protein? We propose two complementary hypotheses, namely adaptive hypothesis and error hypothesis, and tested these ideas using genomes of four representative organisms, human, mouse, fruitfly, and Arabidopsis. We found that only the fruitfly meets most predictions made by the adaptive hypothesis, while the other species generally align with the error hypothesis. Fruitfly exhibits a surprisingly high fraction (> 70%) of protein-coding genes (PCGs) having multiple mRNAs encoding identical proteins. These mRNAs have long CDS, variable UTR lengths, and highly conserved protein sequences. In contrast, opposite or insignificant trends are observed in human, mouse, and Arabidopsis. While molecular errors are common in cell systems, in species like the fruitfly with large effective population size, the strong natural selection might maintain those mRNAs with potentially adaptive regulatory roles. Although encoding identical proteins, different mRNAs can be regulated in a condition-specific manner, facilitating adaptive evolution. Our work provides novel perspectives in genomics and evolutionary biology.

The genetic structure and variability of sea trout populations in the southern Baltic Sea were shaped during the last glaciation, in parallel with the evolution of the Baltic Sea. However, human activities-particularly hydrotechnical development and the introduction of non-local genetic lines-have altered and partially reduced the original genetic diversity. In the present study, the authors describe the historical changes that have occurred and present the current level of genetic variability within Polish sea trout populations. A total of 575 sea trout from nine river populations and three hatchery broodstocks were genotyped at 13 microsatellite loci. The global F_ST obtained via AMOVA was moderate, at 0.041. The highest pairwise F_ST values were observed between the Rutki and Aquamar broodstocks and all other populations. The lowest and statistically non-significant pairwise differences were detected between the Rega and Ina river populations, as well as between the Słupia and Łupawa. Genetic structure analysis revealed geographic differentiation, identifying either four or seven distinct clusters. Additionally, neighbour-joining clustering showed that the examined populations and stocks were divided into two main subgroups: one consisting of samples related to the Vistula origin, and the other comprising clearly separated Pomeranian populations. This paper discusses the emergence of new genetic variability driven by microevolutionary processes and presents a revised approach for sea trout population management.

Essential thrombocythemia and primary myelofibrosis belong to the group of BCR::ABL1-negative myeloproliferative neoplasms. The presence of mutations in the JAK2, CALR, and MPL genes is essential for the diagnosis of myeloproliferative neoplasms. These mutations are called "driver" mutations. However, not only leading mutations have been identified in patients with MPN, but also more than half of individuals with essential thrombocythemia and more than 80% of patients with myelofibrosis have additional mutations. One technique that makes it possible to find prognostic, predictive, and diagnostic indicators is next-generation sequencing. Coexisting mutations are associated with reduced response to therapy, shortened overall survival, and a higher risk of transformation to acute myeloid leukemia or myelofibrosis. The study group consisted of 42 patients with the diagnosis of BCR::ABL1-negative MPN and the presence of a mutation in the CALR gene. The research material was archival, and DNA was obtained from patients' peripheral blood. Forty genes (17 genes, 23 hotspots) were sequenced using the commercial kit AmpliSeq for Illumina Myeloid Panel applying the targeted next-generation sequencing approach. For the study, the Illumina MiniSeq platform was used. The analysis of the obtained genetic results was carried out using bioinformatics tools and genetic databases. We studied 42 CALR-positive ET (n = 28) and MF (n = 14) patients with NGS panel testing. The median age at diagnosis of the entire patient series was 58 years. Additional mutations were detected in 48% of patients in the whole cohort. The most frequently mutated genes in the study population were ASXL1, TET2, and DNMT3A, which are largely associated with epigenetic regulatory mechanisms. NGS panel studies represent a breakthrough in the diagnostic and prognostic evaluation of MPNs with CALR mutations. The ability to perform such a comprehensive study provides valuable information on the biology of the disease and the selection of the appropriate treatment regimen. The use of new technologies shows that not only driver mutations have clinical significance for the patient. NGS has the potential to increase the precision and effectiveness of diagnosis and prognosis.

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.