Journal of Applied Genetics最新文献

Mechanical wounding triggers rapid transcriptional and hormonal reprogramming in plants, primarily driven by jasmonate (JA) signalling. While the role of JA, ethylene, and salicylic acid in wound responses is well characterised, the contribution of strigolactones (SLs) remains largely unexplored. Here, for the first time, it was shown that SLs modulate wound-induced transcriptional dynamics in Arabidopsis thaliana. Using transcriptome profiling of wild-type (Columbia-0) and the SL biosynthesis mutant more axillary growth3 (max3), a discrete cohort of genes whose wound induction is SL-dependent was identified. These genes include core JA biosynthetic genes and several JA-responsive transcriptional repressors, indicating that SLs potentiate early JA signalling. Promoter motif and protein-protein interaction analyses revealed that SLs regulate a transcriptional module composed of AP2/ERF, WRKY, and C2H2 zinc-finger factors, which integrate JA signalling, ROS homeostasis, and tissue regeneration. Notably, many of these factors are misregulated in max3 even prior to wounding, suggesting a primed but hypo-responsive state. Presented findings suggest a model in which SLs act upstream of the JA burst, coordinating transcriptional readiness and post-injury activation. This expands the functional scope of SLs in stress response and positions them as potential modulators of hormone crosstalk during wound responses.

Breast cancer (BC) is characterized by the increase of malignant cells in the breast. The malignant cells begin in the lining of the breast milk glands or ducts (ductal epithelium). BC is the most frequent cancer in women, but it may also occur in males. Long non-coding RNAs (lncRNA) have been demonstrated to control the development and incidence of cancer. However, some lncRNAs experience potential changes in BC, but their role has not been well studied. LINC01279 is known as a valuable biomarker in gastric cancer but has not yet been studied in BC. Changes in LINC01279 expression levels in BC samples were investigated by microarray. Q-PCR was also used to evaluate the expression of LINC01279 in the tumor and normal adjacent samples of 30 BC patients. The LINC01279 co-expressed gene module was discovered using weighted gene correlation network analysis (WGCNA) on the relevant dataset. The top ten hub genes were determined using gene ontology (GO) functional enrichments on the co-expressed gene module. The results of the bioinformatics study showed an increase in LINC01279 expression levels (log2FC = 3.228749561, adj.P.Val = 1.69E - 12) in tumor samples compared to normal marginal tissue. Q-PCR results also showed a significant increase in LINC01279 expression (P-value = 0.0005) in tumor samples. WGCNA analysis identified that the black module is the LINC01279 co-expressed module, and functional annotation analysis of black module genes enriched in significant cancer-related pathways and processes, including cell growth and/or maintenance, regulation of immune response, regulation of cell proliferation, and epithelial-to-mesenchymal transition (EMT). Regarding the real-time PCR results, the analysis of expression patterns has illuminated a distinct association between the heightened expression levels of LINC01279, and the stages of cancer progression as well as the metastatic potential of tumors. However, intriguingly, our observations have failed to reveal any statistically significant correlations between the relative expression of LINC01279 and tumor grade classification, or the presence of ER, PR, and HER2 biomarkers. The present study could provide a new perspective on the molecular regulatory. Processes associated with BC pathogenic mechanisms are linked to the LINC01279, although further research is needed on the possible role of this lncRNA in BC.

To elucidate the crucial function of MICAL2 as a potential immunotherapeutic target and a predictive biomarker in PAAD. The expression of MICAL2 in pan-cancer was investigated using public database, and the expression of MICAL2 in PAAD was validated using tissue samples. The diagnostic and prognostic significance of MICAL2 in PAAD was assessed through the application of ROC curves and Kaplan-Meier curves. The correlation between MICAL2 and infiltrating immune cells and immune checkpoints in PAAD was researched using the TIMER and TCGA databases. In vitro studies involved the evaluation of the biological functions of MICAL2 in human PAAD cells through the knockdown of MICAL2 expression using shRNA. Compared to corresponding normal tissues, the expression of MICAL2 exhibits significant differences in various cancers. Specifically, the level of MICAL2 expression is significantly increased in PAAD. Moreover, MICAL2 demonstrates considerable diagnostic potential in PAAD patients, and its elevated expression is indicative of an unfavorable prognosis. The differential expression of MICAL2 is related to infiltrating immune cells, immune cell markers, and immune checkpoints in PAAD. In ASPC-1 and PANC-1 cells, when MICAL2 was knocked down, there was a notable suppression of proliferation, migration, and invasion. MICAL2 functions as a significant predictor and promising immunotherapeutic target for prognosis assessment in PAAD. It has a pivotal function in fostering the growth and migration of PAAD cells.

The Caracu is a taurine breed adapted to Brazil's climatic conditions and has been selected for 40 + years for Body Weight (BW), maintaining performance records across multiple generations in its database. However, selecting young animals for BW can result in excessive growth, potentially impacting carcass and reproductive traits. This study aimed to estimate genetic correlations and, based on these estimates, evaluate how selection for BW (adjusted to 378 and 550 days of age for males and females, respectively) has influenced carcass traits and reproductive efficiency in this breed. The dataset contained records for BW (kg), Ribeye area (REA, cm²), Height-to-width ratio of the Longissimus dorsi muscle (HWR), Backfat thickness (BFT, mm), Rump fat thickness (RFT, mm), Yearly scrotal circumference (SC, cm), and Days to calving (DC, days) from animals born between 1966 and 2022. (Co)variance components were estimated by Bayesian inference using two-trait animal models. Analyses were conducted to estimate genetic parameters for pairs of traits, including BW with carcass traits (BW × REA, BW × HWR, BW × BFT, and BW × RFT) and BW with reproductive traits (BW × DC and BW × SC). Additionally, analyses were performed for pairwise combinations among carcass traits (REA × HWR, REA × BFT, REA × RFT, HWR × BFT, HWR × RFT, and RFT × BFT) and between reproductive traits (DC × SC). The relationship matrix included 4,783 animals, of which 829 were genotyped with the GGP Bovine 100 K SNP panel. Favorable genetic correlations (r_g) were observed between BW and REA (0.51 ± 0.11), HWR (0.45 ± 0.17), SC (0.24 ± 0.13), and RFT (0.15 ± 0.21), with the latter being favorable but low. On the other hand, unfavorable genetic correlations were observed between BW and BFT (-0.07 ± 0.21), which was unfavorable but close to zero relationship, and between BW and DC (0.48 ± 0.15). The significance of carcass and reproductive traits is underscored by the favorable, r_g between BW and the carcass traits REA (BW × REA) and HWR (BW × HWR), while a high, unfavorable r_g was observed between BW and DC cows. These findings emphasize the importance of carefully balancing genetic selection to optimize growth, carcass quality, and adequate reproduction in Caracu cattle.

Cannabidiol (CBD) is a compound found in Cannabis sativa that is known for its neuroprotective, anti-inflammatory, analgesic, and anxiolytic properties. These properties make it a promising treatment for various neurological conditions. This study aimed to examine the effects of CBD on hypothalamic neurons at the transcriptome level using the adult-derived mHypoA-2/12 mouse cell line. The cells were exposed to four different CBD concentrations (ranging from 0.325 to 3 µM) for 6 and 24 h. Apart from the transcriptome analysis, apoptosis (caspase 3/7 activity) and viability (MTT) assays were performed. The obtained results showed that CBD enhanced cell viability, especially after 24 h of treatment and at lower or intermediate concentrations, and reduced apoptosis, with significant effects at the highest concentration. CBD caused moderate transcriptome profile changes (13 to 69 genes per treatment), with more genes affected at higher concentrations and shorter exposure times, indicating a stronger initial cellular response. Further analysis revealed that CBD affects several biological processes, including: intrinsic apoptosis suppression via p53 modulation, impacting genes like Bbc3, Mdm2, Cdkn1a, and Smad3. Additionally, CBD influenced genes involved in extracellular matrix organization, including metalloproteinases (Mmp-3, Mmp-13) and their inhibitors (Timp1), as well as collagen components (Col11a1) and mitochondrial respiratory chain complexes (mt-Nd5, mt-Nd4). Genes related to serotonin and dopamine biosynthesis, as well as Aldh2, were also impacted, linking CBD's effects in hypothalamic neurons to potential benefits in managing alcohol use disorders. These findings suggest the hypothalamus is a significant target for CBD, warranting further investigation.

Long non-coding RNA (lncRNA) participates in various biological processes, however, neither the expression profile nor the biological role of lncRNAs in mammalian ovaries has been fully studied. In this work, the lncRNA transcriptomic analysis of postnatal mice ovaries was performed by using bulk RNA sequencing in C57BL/6 mice. A total of 5302 lncRNAs were found in mouse ovaries, and 1836 lncRNAs were differentially expressed during the development and ageing process, of which targets were enriched in the developmental process, reproduction, etc. Developmental stage specific lncRNAs showed functions in system development, inflammatory response, myeloid leukocyte activation, etc. Moreover, a co-expression network analysis based on reproduction-related genes reveals lncRNAs that may regulate multiple mRNA targets in ovaries, including Neat1, Gm11613 and Gm43915. Two cis-acting lncRNAs, Ptgs2os and Gm14705, showed correlated expression pattern with their potential targets Ptgs2 and Aff2 respectively, and these lncRNA-mRNA pairs were conserved in mice and humans. WGCNA further identified 10 co-expressed modules with distinct expression patterns associated with ovarian development and ageing. Taken together, our results reveal a transcriptomic profile of mouse ovaries over the reproductive lifespan, providing insights into the molecular mechanisms of ovarian development and ageing.

Fusarium stalk rot is the main factor reducing the quality of maize grain and leads to significant yield losses, which that ranges from 20 to 100%, depending on the degree of infection and weather conditions. Understanding its genetic mechanism is key to improving grain quality and ultimate yield. An experiment with 26 doubled haploid (DH) lines of maize was conducted in the northern part of the Lower Silesia Province in Poland over a ten-year period (2013-2022). The study assessed resistance to Fusarium stalk rot. The objectives were to evaluate genotype-year interactions for resistance to Fusarium stalk rot in maize DH lines using the additive main effects and multiplicative interaction (AMMI) model, to select DH lines that are stable across all years of testing and specific to particular environmental conditions, and to estimate additive and epistatic effects. AMMI results demonstrated a significant effect of genotype, year, and their interaction on Fusarium stalk rot resistance. The KN16 line is recommended for inclusion in further research within the breeding program due to its excellent stability and high average resistance to Fusarium stalk rot. Estimates of additive gene action effects were statistically significant in each year of the study. Estimates of epistasis (total additive by additive interaction) effects for Fusarium stalk rot resistance were also statistically significant in all ten years of the study. Only in 2013 was the epistasis effect positive (0.168). These results indicate that achieving biological advances in resistance to Fusarium stalk rot should be an important focus of ongoing maize breeding programs.

Fusarium head blight (FHB) is a global detrimental disease affecting wheat production. While Guixie 3 shows strong resistance to FHB, its resistance mechanism is not well understood. Hence, this study aims to elucidate the genetic basis of disease resistance in Guixie 3 and identify new genetic resources for FHB resistance in wheat. The study used an F_2:7 recombinant inbred line population developed by crossing Avocet S with Guixie 3. FHB resistance was phenotypically evaluated across 2 years and two locations (i.e., four environments) after single-floret inoculation, and it was genetically mapped using the wheat 55 K single-nucleotide polymorphism array. A total of 15 quantitative trait loci (QTLs) for FHB resistance were detected on chromosomes 1D (2), 2A (2), 2B (3), 2D.1 (2), 3B (1), 4A (1), 4B (1), 4D (1), 5A (1), and 5B.2 (1). Notably, a QTL on chromosome 2D.1, designated as Qfhb.gaas.2D.1-1, was consistently detected in two environments. This QTL spanned the interval AX-86163393 to AX-110072786, with a genetic interval of 45.12-46.51 cM and a physical interval of 35.68-37.04 Mb (1.36 Mb). It explained 14.07-33.00% of the phenotypic variation. Furthermore, 39 candidate genes were identified in this target region, of which eight were predicted to be associated with FHB resistance. These candidate genes will be further analyzed and validated for FHB resistance in future studies.

Retinopathy of prematurity (ROP) is a major cause of childhood blindness worldwide, linked to gene variants in the renin-angiotensin-aldosterone system, including angiotensin-converting enzyme (ACE) and angiotensin II receptor type 1 (AGTR1). This study aims to evaluate the association between ACE insertion/deletion (I/D) and AGTR1 rs5186A > C variants with the occurrence and progression of ROP in a Polish cohort. A total of 377 premature infants were enrolled in the study. The ACE variant was evaluated using PCR, and AGTR1 was assessed using TaqMan probes. Clinical characteristics, including risk factors and comorbidities, were documented. A meta-analysis of the effects of the studied variants on ROP was also conducted. The AGTR1 rs5186C allele was significantly associated with both the progression of ROP and treatment outcomes. Homozygotes exhibited a 2.47-fold increased risk of developing proliferative ROP and a 4.82-fold increased risk of treatment failure. The impact of this allele increased at low birth weight. A meta-analysis, including 191 cases and 1661 controls, indicated an overall risk of 1.7 (95%CI 1.02-2.84) for the recessive effect of the rs5186C allele. The ACE variant did not show a significant association with ROP in our population; however, a meta-analysis of 996 cases and 2787 controls suggested a recessive effect of the insertion allele (an odds ratio of 1.21 (95%CI 1.00-1.60)). These results indicate that gain-of-function AGTR1 variants may play a crucial role in the development of ROP, potentially by promoting angiogenesis and pro-inflammatory effects. Screening for these variants could facilitate the development of personalized risk assessment and treatment strategies for ROP.

Fusarium ear rot (FER) is a global disease caused by the fungal pathogen Fusarium verticillioides. Maize FER resistance is a quantitative trait controlled by polygenes. In this study, a doubled haploid (DH) population involving 159 lines, developed from the inbred lines B73 (susceptible) and CXS161 (highly resistant), was inoculated with Fusarium verticillioides across 4-year-location environment combinations in China during 2021 and 2022. The lines were genotyped using target sequencing with a 10 K SNP array. The results showed that the estimated broad-sense heritability (H²) in each environment ranged from 0.659 to 0.871, with an overall H² of 0.805. The average genetic length between adjacent markers in the genetic map constructed using multiple single-nucleotide polymorphisms (mSNP) was smaller than that constructed using SNP, whereas the maximal genetic length was almost the same. Using a genetic map constructed with a SNP, two quantitative trait loci (QTL) were identified on chromosomes 2 and 5, which explained 7.65% and 9.58% of the phenotypic variation, respectively. Using the genetic map constructed by mSNP, four QTL were identified, explaining 6.04-12.60% of the phenotypic variation. Moreover, two kompetitive allele-specific PCR (KASP) markers were developed using single-marker analysis methods, with one KASP marker validated across a backcross population that can be effectively used to identify FER resistance. In conclusion, using mSNP for genetic map construction does not confer advantages when the population size is limited and the marker density is high. However, the mSNP-constructed map identified more minor-effect QTL despite possessing a lower likelihood of the odds (LOD) values.