Journal of Applied Genetics最新文献

Europe is highly dependent on soybean meal imports and anticipates an increase of domestic plant protein production. Ongoing climate change resulted in northward shift of plant hardiness zones, enabling spring-sowing of freezing-sensitive crops, including soybean. However, it requires efficient reselection of germplasm adapted to relatively short growing season and long-day photoperiod. In the present study, a PCR array has been implemented, targeting early maturity (E1-E4, E7, E9, and E10), pod shattering (qPHD1), and growth determination (Dt1) genes. This array was optimized for routine screening of soybean diversity panel (204 accessions), subjected to the 2018-2020 survey of phenology, morphology, and yield-related traits in a potential cultivation region in Poland. High broad-sense heritability (0.84-0.88) was observed for plant height, thousand grain weight, maturity date, and the first pod height. Significant positive correlations were identified between the number of seeds and pods per plant, between these two traits and seed yield per plant as well as between flowering, maturity, plant height, and first pod height. PCR array genotyping revealed high genetic diversity, yielding 98 allelic combinations. The most remarkable correlations were identified between flowering and E7 or E1, between maturity and E4 or E7 and between plant height and Dt1 or E4. The study demonstrated high applicability of this PCR array for molecular selection of soybean towards adaptation to Central Europe, designating recessive qPHD1 and dominant Dt1, E3, and E4 alleles as major targets to align soybean growth season requirements with the length of the frost-free period, improve plant performance, and increase yield.

High-risk human papillomaviruses are well-established drivers of several cancer types including cervical, head and neck, penile as well as anal cancers. While the E6 and E7 viral oncoproteins have proven to be critical for malignant transformation, evidence is also beginning to emerge suggesting that both host pathways and additional viral genes may also be pivotal for malignant transformation. Here, we focus on the role of host APOBEC genes, which have an important role in molecular editing including in the response to the viral DNA and their role in HPV-driven carcinogenesis. Further, we also discuss data developed suggesting the existence of HPV-derived miRNAs in HPV + tumors and their potential role in regulating the host transcriptome. Collectively, while recent advances in these two areas have added complexity to the working model of papillomavirus-induced oncogenesis, these discoveries have also shed a light onto new areas of research that will be required to fully understand the process.

Strigolactones (SLs) are plant hormones that play a crucial role in regulating various aspects of plant architecture, such as shoot and root branching. However, the knowledge of SL-responsive genes and transcription factors (TFs) that control the shaping of plant architecture remains elusive. Here, transcriptomic analysis was conducted using the SL-insensitive barley mutant hvd14.d (carried mutation in SL receptor DWARF14, HvD14) and its wild-type (WT) to unravel the differences in gene expression separately in root and shoot tissues. This approach enabled us to select more than six thousand SL-dependent genes that were exclusive to each studied organ or not tissue-specific. The data obtained, along with in silico analyses, found several TFs that exhibited changed expression between the analyzed genotypes and that recognized binding sites in promoters of other identified differentially expressed genes (DEGs). In total, 28 TFs that recognize motifs over-represented in DEG promoters were identified. Moreover, nearly half of the identified TFs were connected in a single network of known and predicted interactions, highlighting the complexity and multidimensionality of SL-related signalling in barley. Finally, the SL control on the expression of one of the identified TFs in HvD14- and dose-dependent manners was proved. Obtained results bring us closer to understanding the signalling pathways regulating SL-dependent plant development.

Male infertility is a significant reproductive issue affecting a considerable number of couples worldwide. While there are various causes of male infertility, genetic factors play a crucial role in its development. We focused on identifying and analyzing the high-risk nsSNPs in DNAH1 and DNAH17 genes, which encode proteins involved in sperm motility. A total of 20 nsSNPs for DNAH1 and 10 nsSNPs for DNAH17 were analyzed using various bioinformatics tools including SIFT, PolyPhen-2, CADD, PhD-SNPg, VEST-4, and MutPred2. As a result, V1287G, L2071R, R2356W, R3169C, R3229C, E3284K, R4096L, R4133C, and A4174T in DNAH1 gene and C1803Y, C1829Y, R1903C, and L3595P in DNAH17 gene were identified as high-risk nsSNPs. These nsSNPs were predicted to decrease protein stability, and almost all were found in highly conserved amino acid positions. Additionally, 4 nsSNPs were observed to alter post-translational modification status. Furthermore, the interaction network analysis revealed that DNAH1 and DNAH17 interact with DNAH2, DNAH3, DNAH5, DNAH7, DNAH8, DNAI2, DNAL1, CFAP70, DNAI3, DNAI4, ODAD1, and DNAI7, demonstrating the importance of DNAH1 and DNAH17 proteins in the overall functioning of the sperm motility machinery. Taken together, these findings revealed the detrimental effects of identified high-risk nsSNPs on protein structure and function and highlighted their potential relevance to male infertility. Further studies are warranted to validate these findings and to elucidate the underlying mechanisms.

To be useful for cereal breeding, cytoplasmic male sterility (CMS) should express the complete sterility of maternal lines and the full restoration of the male fertility of F₁ hybrids. The most reliable source of sterilizing cytoplasm for triticale is Triticum timopheevi; however, due to the low frequency of efficient non-restorer genotypes for this cytoplasm, new sources of CMS are needed. In this study, aside from T. timopheevi (T) cytoplasm, three alternative CMS sources were tested: Pampa (P) from Secale cereale L., Aegilops sharonensis (A), and Ae. ventricosa (V). The suitability of these cytoplasms for breeding was assessed based on the male fertility/sterility of F₁ hybrids obtained through the manual pollination of CMS maternal lines with 36 triticale cultivars and breeding strains. About half of the hybrids with each type of cytoplasm were fully fertile and produced more than 30 grains per bagged spike. The highest percentage was found in hybrids with P cytoplasm (58.33%) and the lowest in hybrids with A cytoplasm (44.44%). Male sterility was observed in hybrids with P cytoplasm (16.67%) and A cytoplasm (16.67%) but not in hybrids with T or V cytoplasm. In terms of practical aspects, male sterility systems with P or A cytoplasm exhibit similarity in their ability to restore male fertility that differ from the T and V cytoplasms. Although all studied cytoplasms exhibited some disadvantages for breeding purposes, none should be definitively classified as unacceptable for future breeding programs regarding the development of triticale hybrid cultivars.

Osteosarcoma is a primary malignant bone tumor that affects children and young adults. Understanding the molecular mechanisms underlying osteosarcoma is critical to develop effective treatments. This study aimed to identify core genes and explore the role of intercellular communication in osteosarcoma. We used GSE87437 and GSE152048 dataset to conduct a weighted correlation network analysis (WGCNA) and identify co-expression modules. The enriched biological processes and cellular components of the genes in the steelblue module were analyzed. Next, we explored the expression, diagnostic value, correlation, and association with immune infiltrate of CCSER1 and LOC101929154. Finally, we utilized CIBERSORT algorithm to predict the infiltrated immune cells in osteosarcoma tissues. Our results identified 44 co-expression modules, and the steelblue module was mainly associated with axon development, axonogenesis, and innervation. CCSER1 and LOC101929154 were significantly upregulated in osteosarcoma tissues with poor response to preoperative chemotherapy. Moreover, the expressions of CCSER1 and LOC101929154 were positively correlated. The area under the receiver operating characteristic curve of CCSER1 and LOC101929154 was 0.800 and 0.773, respectively. The expression of CCSER1 was negatively correlated with follicular helper T cells and positively correlated with M0 macrophages, while LOC101929154 was negatively correlated with activated mast cells. Besides, CD4 memory-activated T cells were observed at lower levels in patients who responded well to chemotherapy. Our study identified core genes CCSER1 and LOC101929154 and provided insight into the intercellular communication profile in osteosarcoma. Our results suggested that targeting CCSER1, LOC101929154, and CD4 memory-activated T cells may be a promising strategy for the treatment of osteosarcoma.

This study aims to harness bioinformatics to identify prognostic immune-related genes in clear cell renal cell carcinoma (ccRCC), focusing particularly on LILRB3. It evaluates LILRB3's expression in ccRCC, its association with patient prognosis, and its potential as a biomarker for predicting survival, thereby providing a preliminary basis for the diagnosis of ccRCC. Utilizing The Cancer Genome Atlas (TCGA) datasets and an immune gene set, we sought immune-related genes with elevated expression in ccRCC. Seventy-two normal tissue samples and 531 ccRCC samples were analyzed, and differential genes were identified with a screening criterion of fold change (FC) > 2 and P value < 0.01. Survival analysis and receiver operating characteristic (ROC) curve analysis were employed to discover genes of prognostic and diagnostic relevance to ccRCC. Pearson correlation analysis with a cutoff of |r|≥ 0.5, facilitated by cBioPortal, assessed genes co-expressed with LILRB3. The DAVID online tool conducted functional and pathway enrichment analyses for LILRB3-coexpressed genes. The TIMER and TCIA databases were utilized to explore LILRB3's influence on immune infiltration in the tumor microenvironment and its relation to key immunological checkpoints. Screening the TCGA database revealed 3719 up-regulated differential genes in ccRCC, with 355 overlapping immune-related genes. Survival analysis of these 355 genes revealed 100 with significant survival impact. ROC curve analysis pinpointed the top 10 genes, including LILRB3, with the highest diagnostic efficiency. LILRB3 emerged as an independent risk factor from the Cox risk regression model. GO and KEGG analyses linked LILRB3 to various biological processes, including chemokine signaling pathways, immunological response, antigen processing and presentation, inflammatory response, T cell co-stimulation, and signal transduction. LILRB3 significantly affected ccRCC immune infiltration and correlated positively with several immunological checkpoints, such as PD-1, LAG3, IDO1, PD-L1, CTLA4, TIM3, TIGIT, and VISTA. LILRB3 shows higher expression levels in ccRCC than in normal tissues and correlates with poor patient prognosis. Its impactful role in the immune infiltration of the RCC microenvironment suggests that LILRB3 could serve as a novel target for ccRCC treatment and prognosis, underlining its diagnostic and prognostic significance.

Waxy maize grains rich in amylopectin have emerged as a popular food and industrial raw materials. Here, a set of waxy inbreds having recessive waxy1 (wx1) gene derived through marker-assisted selection (MAS), and their original versions were evaluated for germination, seed vigour index-I and vigour index-II, electrical conductivity (EC) and enzymatic activities viz., dehydrogenase (DH), esterase (EST), peroxidase (POX), superoxide dismutase (SOD) and α-amylase (AMY). Waxy inbreds under study possessed average 97.8% amylopectin compared to 72.4% in original inbreds. Waxy versions showed 15.2% more test weight, 4.3% increase in germination, 22.7% higher seed vigour index-I and 28.3% higher seed vigour index-II, respectively, over the original inbreds. Further, activity of DH, EST, POX, SOD and AMY of MAS-derived waxy inbreds was more than that of original inbreds, whereas EC was less in improved inbreds compared to originals. Amylopectin exhibited strong positive correlations (r = 0.69 to 0.97**) with seed germination, vigour index-I and -II, DH, SOD, POX, EST and AMY activity. However, amylopectin showed negative correlation of - 0.82** with EC. Seed germination and seed vigour indices were also positively correlated with all enzymatic activities (r = 0.58 to 0.92**). The analysis revealed that waxy inbreds possess better seed vigour and enzymatic activities over traditional inbreds. This is the first report of synergistic effects of wx1 gene on seed germination, vigour and enzymatic activities in maize endosperm.

Sweet corn has emerged as a favorite food item worldwide owing to its kernel sweetness. However, traditional sweet corn cultivars are poor in provitamin-A (proA) and essential amino acids, viz., lysine and tryptophan. So far, no sweet corn hybrid with high nutritional qualities has been commercialized elsewhere. Here, we analyzed accumulation of provitamin-A (proA), lysine, and tryptophan in a set of mutant versions of (i) crtRB1-, (ii) o2-, and (iii) crtRB1 + o2-based sweet corn inbreds and hybrids with (iv) traditional sweet corn (wild-type: O2 + CrtRB1). The crtRB1- and crtRB1 + o2-based genotypes possessed significantly higher proA (17.31 ppm) over traditional sweet corn (2.83 ppm), while o2- and crtRB1 + o2-based genotypes possessed significantly higher lysine (0.345%) and tryptophan (0.080%) over traditional sweet corn (lysine 0.169%, tryptophan 0.036%). Late sowing favored high kernel lysine, proA, and green cob yield among hybrids. Sweetness (17.87%) among the improved inbreds and hybrids was comparable to the original sweetcorn genotypes (17.84%). Among the four genotypic classes, crtRB1 + o2-based improved genotypes showed stronger association among traits over genotypes with o2 and crtRB1 genes alone. Significant association was observed among (i) proA and BC (r = 0.99), (ii) proA and BCX (r = 0.93), (iii) lysine and tryptophan (r = 0.99), and (iv) green cob yield with fodder yield (r = 0.73) in sweet corn hybrids. The study demonstrated that combining crtRB1 and o2 genes did not pose any negative impact on nutritional, yield, and agronomic performance. Sweet corn with crtRB1 + o2 assumes significance for alleviating malnutrition through sustainable and cost-effective approach.

Neoadjuvant chemotherapy is the foundation treatment for triple-negative breast cancer (TNBC) and frequently results in pathological complete response (pCR). However, there are large differences in clinical response and survival after neoadjuvant chemotherapy of TNBC patients. The aim was to identify genes whose expression significantly associates with the efficacy of neoadjuvant chemotherapy in patients with TNBC. Transcriptomes of 46 formalin-fixed paraffin-embedded (FFPE) tumor samples from TNBC patients were analyzed by RNA-seq by comparing 26 TNBCs with pCR versus 20 TNBCs with pathological partial remission (pPR). Subsequently, we narrowed down the list of genes to those that strongly correlated with drug sensitivity of 63 breast cancer cell lines based on Dependency Map Consortium data re-analysis. Furthermore, the list of genes was limited to those presenting specific expression in breast tumor cells as revealed in three large published single-cell RNA-seq breast cancer datasets. Finally, we analyzed which of the selected genes were significantly associated with overall survival (OS) in TNBC TCGA dataset. A total of 105 genes were significantly differentially expressed in comparison between pPR versus pCR. As revealed by PLSR analysis in breast cancer cell lines, out of 105 deregulated genes, 42 were associated with sensitivity to docetaxel, doxorubicin, paclitaxel, and/or cyclophosphamide. We found that 24 out of 42 sensitivity-associated genes displayed intermediate or strong expression in breast malignant cells using single-cell RNAseq re-analysis. Finally, 10 out of 24 genes were significantly associated with overall survival in TNBC TCGA dataset. Our RNA-seq-based findings suggest that there might be transcriptomic signature consisted of 24 genes specifically expressed in tumor malignant cells for predicting neoadjuvant response in FFPE samples from TNBC patients prior to treatment initiation. Additionally, nine out of 24 genes were potential survival predictors in TNBC. This group of 24 genes should be further investigated for its potential to be translated into a predictive test(s).