Association Analysis Research Articles

Enzymatic loosening mechanism of endosperm weakening plays a key role in promoting carrot (Daucus carota L.) seed germination by hydro-electro hybrid priming

As an innovative physical priming technique, hydro-electro hybrid priming (HEHP) tends to significantly promote the seed germination of carrot. Endosperm weakening at micropylar endosperm is a critical regulatory mechanism for seed germination, but it is unclear whether it plays a role in promoting seed germination through HEHP treatment. In the present work, we conducted association analysis between transcriptome and proteome data of the previous studies and found that HEHP promoted the mannose metabolism in carrot seeds, with key enzymes involved in mannan degradation called β-mannanase (MAN) and the coding genes were both significantly upregulated in HEHP treatment. Based on this, the subcellular structure of micropylar endosperm, the activity of key enzymes in mannan degradation and the expression pattern of MAN coding genes during the germination process were further studied. The results showed that carrot seeds subjected to the priming treatments exhibited more significant endosperm weakening during germination, with significant degradation of the cell wall of micropylar endosperm, and among the three key enzymes involved in mannan degradation, only MAN activity showed significant differences at micropylar endosperm and non-micropylar endosperm. In addition, the priming treatments, especially the HEHP treatment, significantly upregulated the expression of MANs before sowing, and the expression levels of MANs at micropylar endosperm were significantly higher than those at non-micropylar endosperm. Ultimately, it is confirmed that the rapid germination of carrot seeds is closely related to the enzymatic loosening mechanism of endosperm weakening, and that MAN plays a key role in this process. The results ulteriorly deepen the understanding of the rapid germination mechanism of carrot seeds treated with HEHP.

Genome-wide identification and analyses of ZmAPY genes reveal their roles involved in maize development and abiotic stress responses

Apyrase is a class of enzyme that catalyzes the hydrolysis of nucleoside triphosphates/diphosphates (NTP/NDP), which widely involved in regulation of plant growth and stress responses. However, apyrase family genes in maize have not been identified, and their characteristics and functions are largely unknown. In this study, we identified 16 apyrases (named as ZmAPY1-ZmAPY16) in maize genome, and analyzed their phylogenetic relationships, gene structures, chromosomal distribution, upstream regulatory transcription factors and expression patterns. Analysis of the transcriptome database unveiled tissue-specific and abiotic stress-responsive expression of ZmAPY genes in maize. qPCR analysis further confirmed their responsiveness to drought, heat, and cold stresses. Association analyses indicated that variations of ZmAPY5 and ZmAPY16 may regulate maize agronomic traits and drought responses. Our findings shed light on the molecular characteristics and evolutionary history of maize apyrase genes, highlighting their roles in various biological processes and stress responses. This study forms a basis for further exploration of apyrase functions in maize.

Integrative multi-omics analyses to identify the genetic and functional mechanisms underlying ovarian cancer risk regions

To identify credible causal risk variants (CCVs) associated with different histotypes of epithelial ovarian cancer (EOC), we performed genome-wide association analysis for 470,825 genotyped and 10,163,797 imputed SNPs in 25,981 EOC cases and 105,724 controls of European origin. We identified five histotype-specific EOC risk regions (p value <5×10-8) and confirmed previously reported associations for 27 risk regions. Conditional analyses identified an additional 11 signals independent of the primary signal at six risk regions (pvalue <10-5). Fine mapping identified 4,008 CCVs in these regions, of which 1,452 CCVs were located in ovarian cancer-related chromatin marks with significant enrichment in active enhancers, active promoters, and active regions for CCVs from each EOC histotype. Transcriptome-wide association and colocalization analyses across histotypes using tissue-specific and cross-tissue datasets identified 86 candidate susceptibility genes in known EOC risk regions and 32 genes in 23 additional genomic regions that may represent novel EOC risk loci (false discovery rate <0.05). Finally, by integrating genome-wide HiChIP interactome analysis with transcriptome-wide association study (TWAS), variant effect predictor, transcription factor ChIP-seq, and motifbreakR data, we identified candidate gene-CCV interactions at each locus. This included risk loci where TWAS identified one or more candidate susceptibility genes (e.g., HOXD-AS2, HOXD8, and HOXD3 at 2q31) and other loci where no candidate gene was identified (e.g., MYC and PVT1 at 8q24) by TWAS. In summary, this study describes a functional framework and provides a greater understanding of the biological significance of risk alleles and candidate gene targets at EOC susceptibility loci identified by a genome-wide association study.

Investigation of LTF mRNA expression levels as an anti-T2 asthma biomarker

Lactotransferrin (LTF) has an immunomodulatory function and its expression levels are associated with asthma susceptibility. We sought to investigate LTF mRNA expression levels in human bronchial epithelial cells (BECs) as an anti-type 2 (anti-T2) asthma biomarker. Association analyses between LTF mRNA expression levels in BECs and asthma-related phenotypes were performed in the Severe Asthma Research Program (SARP) cross-sectional (n = 155) and longitudinal (n = 156) cohorts using a generalized linear model. Correlation analyses of mRNA expression levels between LTF and all other genes were performed using Spearman correlation. Low LTF mRNA expression levels were associated with asthma susceptibility and severity (P < 0.025), retrospective and prospective asthma exacerbations, and low lung function (P < 8.3x10-3). Low LTF mRNA expression levels were associated with high airway T2 inflammation biomarkers (sputum eosinophils and fractional exhaled nitric oxide; P < 8.3x10-3) but not associated with blood eosinophils or total serum IgE. LTF mRNA expression levels were negatively correlated with expression levels of Th2 or asthma-associated genes (POSTN, NOS2, and MUC5AC) and eosinophil-related genes (IL1RL1, CCL26, and IKZF2) and positively correlated with expression levels of Th1 and inflammation genes (IL12A, MUC5B, and CC16) and Th17-driven cytokines or chemokines for neutrophils (CXCL1, CXCL6, and CSF3) (P < 3.5x10-6). Low LTF mRNA expression levels in BECs are associated with asthma susceptibility, severity, and exacerbations through upregulation of airway T2 inflammation. LTF is a potential anti-T2 biomarker and its expression levels may help determine the balance of eosinophilic and neutrophilic asthma.

The association analysis between fatigue and body composition loss in patients with nasopharyngeal carcinoma during radiotherapy: An observational longitudinal study

PurposeThis study aimed to reveal the association of fatigue with weekly changes in the body composition in patients with nasopharyngeal carcinoma (NPC) and identified the independent strength. MethodsFour body composition indexes and fatigue were assessed before treatment (T0, baseline) and once a week throughout radiotherapy (T1-T7). Generalized additive mixed models (GAMMs) were used to explore the trajectories and longitudinal relationships of fatigue and weekly changes in body composition. The marginal structural model (MSM) was used to control the effect of depression and anxiety. ResultsThe trajectories of fatigue in 105 participants reached a peak in the fifth week, and changes in body composition started appearing from the second week. Four body composition indexes, weight, body mass index (BMI), body fat rate, and lean body weight loss weekly were positively associated with fatigue. High magnitude of effects was revealed when anxiety and depression were controlled as time-dependent confounders. The positive associations with fatigue were manifested in patients aged >53 years, those with senior high and above education, no drinking, >5000 Y/month of family inflow, ≥ stage III, or those receiving a dose of ≥70 Gy, ≥3 cycles of induced chemotherapy, and ≤1 cycle of concurrent chemotherapy (CCRT). ConclusionsLoss of weight, BMI, body fat rate, and lean body weight could be used to independently evaluate the development of fatigue in patients with NPC during radiotherapy. Positive associations between fatigue and weekly body composition loss were found in patients with certain characteristics.

A multidisciplinary approach to describe population structure of Solea solea in the Mediterranean Sea

Investigating marine species population structure in a multidisciplinary framework can reveal signatures of potential local adaptation and the consequences for management and conservation. In this study we delineate the population structure of common sole (Solea solea) in the Mediterranean Sea using genomic and otolith data, based on single nucleotide polymorphism (SNPs) markers, otolith shape and otolith trace element composition data. We correlated SNPs with environmental and spatial variables to evaluate the impact of the selected features on the actual population structure. Specifically, we used a seascape genetics approach with redundancy (RDA) and genetic-environmental association (GEA) analysis to identify loci potentially involved in local adaptation. Finally, putative functional annotation was investigated to detect genes associated with the detected patterns of neutral and adaptive genetic variation. Results from both genetic and otolith data suggested significant divergence among putative populations of common sole, confirming a clear separation between the Western and Eastern Mediterranean Sea, as well as a distinct genetic cluster corresponding to the Adriatic Sea. Evidence of fine-scale population structure in the Western Mediterranean Sea was observed at outlier loci level and further differentiation in the Adriatic. Longitude and salinity variation accounted for most of the wide and fine spatial structure. The GEA detected significant associated outlier loci potentially involved in local adaptation processes under highly structured differentiation. In the RDA both spatial distribution and environmental features could partially explain the genetic structure. Our study not only indicates that separation among Mediterranean sole population is led primarily by neutral processes because of low connectivity due to spatial segregation and limited dispersal, but it also suggests the presence of local adaptation. These results should be taken into account to support and optimize the assessment of stock units, including a review and possible redefinition of fishery management units.

Gender-related alterations of serum trace elements and neurometabolism in the anterior cingulate cortex of patients with major depressive disorder

BackgroundIt is widely known that sex differences have a significant impact on patients with major depressive disorder (MDD). This study aims to evaluate the sex-related connection between serum trace elements and changes in neurometabolism in the anterior cingulate cortex (ACC) of MDD patients. Methods109 untreated MDD patients and 59 healthy controls underwent proton magnetic resonance spectroscopy (1H-MRS) under resting conditions. We measured metabolic ratios in the ACC from both sides. Additionally, venous blood samples were taken from all participants to detect calcium (Ca), phosphorus, magnesium (Mg), copper (Cu), ceruloplasmin (CER), zinc (Zn), and iron (Fe) levels. We performed association and interaction analyses to explore the connections between the disease and gender. ResultsIn individuals with MDD, the Cu/Zn ratio increased, while the levels of Mg, CER, Zn and Fe decreased. Male MDD patients had lower Cu levels, while female patients had an increased Cu/Zn ratio. We observed significant gender differences in Cu, CER and the Cu/Zn ratio in MDD. Male patients showed a reduced N-acetyl aspartate (NAA)/phosphocreatine + creatine (PCr + Cr) ratio in the left ACC. The NAA/PCr + Cr ratio decreased in the right ACC in patients with MDD. In the left ACC of male MDD patients, the Cu/Zn ratio was inversely related to the NAA/PCr + Cr ratio, and Fe levels were negatively associated with the GPC + PC/PCr + Cr ratio. ConclusionsOur findings highlight gender-specific changes in Cu homeostasis among male MDD patients. The Cu/Zn ratio and Fe levels in male MDD patients were significantly linked to neurometabolic alterations in the ACC.

Polymorphism rs117585797 of the ANO2 gene as a genetic marker of a high risk of developing combined proliferative diseases of the uterus in women with endometriosis

Introduction. Endometriosis is a common gynecological disease that has important socio-economic significance for both sick women, their families, and society as a whole. It is often combined with other hyperplastic diseases of the uterus.Aim. To analyze the involvement of GWAS-significant polymorphic loci of sex hormone genes in the development of combined proliferative diseases of the uterus in women with endometriosis. Materials and methods. The sample for the study included 395 women, including 103 patients with isolated endometriosis and 292 patients with endometriosis in combination with uterine fibroids and/or endometrial hyperplasia. All women underwent molecular genetic testing of seven GWAS-significant single-nucleotide polymorphic variants of sex hormone genes (rs34670419, rs11031005, rs11031002, rs148982377, rs112295236, rs1641549, rs117585797). The analysis of associations of polymorphic variants with the risk of developing combined proliferative diseases of the uterus in patients with endometriosis was carried out. To assess the functional effects of SNP associated with the formation of combined proliferative diseases of the uterus in women with endometriosis, the online programs HaploReg and Gtex Portal were used.Results and discussion. Genetic variant A rs117585797 of the ANO2 gene is a risk factor for the development of combined proliferative diseases of the uterus in women with endometriosis (p = 0.05, рperm = 0.05, OR = 4.29). According to the data obtained in silico, the rs117585797 locus localized in the intron of the ANO2 gene affects the affinity of the regulatory DNA motif to the transcription factors Crx and Gsc.Conclusions. Polymorphic locus rs117585797 of the ANO2 gene is associated with a high risk of the formation of combined proliferative diseases of the uterus in patients with endometriosis.

Quantitative analysis of visually normal EEG reveals spectral power abnormalities in temporal lobe epilepsy

ObjectiveTo compare quantitative spectral parameters of visually-normal EEG between Mesial Temporal Lobe Epilepsy (MTLE) patients and healthy controls (HC). MethodWe enrolled 26 MTLE patients and 26 HC. From each recording we calculated total power of all frequency bands and determined alpha-theta (ATR) and alpha-delta (ADR) power ratios in different brain regions. Group-wise differences between spectral parameters were investigated (p < 0.05). To test for associations between spectral-power and cognitive status, we evaluated correlations between neuropsychological tests and quantitative EEG (qEEG) metrics. ResultsIn all comparisons, ATR and ADR were significantly decreased in MTLE patients compared to HC, particularly over the hemisphere ipsilateral to epileptic activity. A positive correlation was seen in MTLE patients between ATR in ipsilateral temporal lobe, and results of neuropsychological tests of auditory verbal learning (RAVLT and RAVLT-D), short term verbal memory (Digit span backwards), and executive function (Weigl's sorting test). ADR values in the contralateral posterior region correlated positively with RAVLT-D and Digit span backwards tests. DiscussionResults confirmed that the power spectrum of qEEG is shifted towards lower frequencies in MTLE patients compared to HC. ConclusionOf note, our results were found in visually-normal recordings, providing further evidence of the value of qEEG for longitudinal monitoring of MTLE patients over time. Exploratory analysis of associations between qEEG and neuropsychological data suggest this could be useful for investigating effects of antiseizure medications on cognitive integrity in patients.

Rare variant association analyses reveal the significant contribution of carbohydrate metabolic disturbance in severe adolescent idiopathic scoliosis

BackgroundAdolescent idiopathic scoliosis (AIS), the predominant genetic-influenced scoliosis, results in spinal deformities without vertebral malformations. However, the molecular aetiology of AIS remains unclear.MethodsUsing genome/exome sequencing, we studied 368 patients with...

Genome sequence analyses identify novel risk loci for multiple system atrophy.

Multiple system atrophy (MSA) is an adult-onset, sporadic synucleinopathy characterized by parkinsonism, cerebellar ataxia, and dysautonomia. The genetic architecture of MSA is poorly understood, and treatments are limited to supportive measures. Here, we performed a comprehensive analysis of whole genome sequence data from 888 European-ancestry MSA cases and 7,128 controls to systematically investigate the genetic underpinnings of this understudied neurodegenerative disease. We identified four significantly associated risk loci using a genome-wide association study approach. Transcriptome-wide association analyses prioritized USP38-DT, KCTD7, and lnc-KCTD7-2 as novel susceptibility genes for MSA within these loci, and single-nucleus RNA sequence analysis found that the associated variants acted as cis-expression quantitative trait loci for multiple genes across neuronal and glial cell types. In conclusion, this study highlights the role of genetic determinants in the pathogenesis of MSA, and the publicly available data from this study represent a valuable resource for investigating synucleinopathies.

Study of the involvement of the LEP gene in the genetics of obesity in the Moroccan population: Genetic association analysis and molecular modelling

Study of the involvement of the LEP gene in the genetics of obesity in the Moroccan population: Genetic association analysis and molecular modelling

Genome-Wide Association Study Identifies IFIH1 and HLA-DQB1*05:02 Loci Associated With Anti-NMDAR Encephalitis.

Anti-N-methyl-d-aspartate receptor (NMDAR) encephalitis is a rare autoimmune neurologic disorder, the genetic etiology of which remains poorly understood. Our study aims to investigate the genetic basis of this disease in the Chinese Han population. We performed a genome-wide association study and fine-mapping study within the major histocompatibility complex (MHC) region of 413 Chinese patients with anti-NMDAR encephalitis recruited from 6 large tertiary hospitals and 7,127 healthy controls. Our genome-wide association analysis identified a strong association at the IFIH1 locus on chromosome 2q24.2 (rs3747517, p = 1.06 × 10-8, OR = 1.55, 95% CI, 1.34-1.80), outside of the human leukocyte antigen (HLA) region. Furthermore, through a fine-mapping study of the MHC region, we discovered associations for 3 specific HLA class I and II alleles. Notably, HLA-DQB1*05:02 (p = 1.43 × 10-12; OR, 2.10; 95% CI 1.70-2.59) demonstrates the strongest association among classical HLA alleles, closely followed by HLA-A*11:01 (p = 4.36 × 10-7; OR, 1.52; 95% CI 1.29-1.79) and HLA-A*02:07 (p = 1.28 × 10-8; OR, 1.87; 95% CI 1.50-2.31). In addition, we uncovered 2 main HLA amino acid variation associated with anti-NMDAR encephalitis including HLA-DQβ1-126H (p = 1.43 × 10-12; OR, 2.10; 95% CI 1.70-2.59), exhibiting a predisposing effect, and HLA-B-97R (p = 3.40 × 10-8; OR, 0.63; 95% CI 0.53-0.74), conferring a protective effect. Computational docking analysis suggested a close relationship between the NR1 subunit of NMDAR and DQB1*05:02. Our findings indicate that genetic variation in IFIH1, involved in the type I interferon signaling pathway and innate immunity, along with variations in the HLA class I and class II genes, has substantial implications for the susceptibility to anti-NMDAR encephalitis in the Chinese Han population.

Association analysis of FXYD5 with prognosis and immunological characteristics across pan-cancer

BackgroundThe FXYD domain-containing ion transport regulator 5 (FXYD5) gene is a cancer promoter. However, evidence for an association between FXYD5 and various types of cancer is still lacking. Using multi-omics bioinformatics, our study aimed to reveal the expression distribution, prognostic value, immune infiltration correlation, and molecular functions of FXYD5. MethodsUsing pan-cancer multi-omics data (including The Cancer Genome Atlas, PrognoScan, Gene Expression Profiling Interactive Analysis, cBioPortal, Gene Expression Omnibus, TIMER and scTIME Portal), we assessed the differences in the expression and prognostic value of FXYD5 in malignant tumors. Furthermore, at the single-cell level, we analyze the expression distribution of FXYD5 across different cell types within the tumor microenvironment, and its relationship with the immune microenvironment. Finally, focusing on ovarian cancer, we conducted preliminary validation of the above findings using cell and molecular biology techniques. ResultsOur results indicated that FXYD5 was up-regulated in various tumor types and was positively associated with tumor progression. We also revealed that FXYD5 was ubiquitously expressed in microenvironmental cells at the single-cell level, and its upregulation was associated with enhanced immune infiltration, cancer-associated fibroblast infiltration, and dysfunction of tumor-infiltrating cytotoxic T lymphocyte. Additionally, its expression was positively correlated with immune checkpoint genes, DNA mismatch repair genes, MSI (microsatellite instability) and TMB (tumor mutational burden) across various cancers. Its higher expression in cytotoxic T lymphocytes attenuated its ability to predict patient survival with PD-L1 (programmed death-ligand 1) blockade therapy, and FXYD5 was found to be a potential regulator of tumor immune escape and resistance to cancer immunotherapies. Based on GSEA (gene set enrichment analysis) and experimental verification, FXYD5 activated TGF‐β/SMAD signaling and drove EMT (epithelial-mesenchymal transition) to promote ovarian cancer progression. ConclusionIn summary, our study revealed that FXYD5-TGFβ axis may coregulate the interaction between tumors, CAFs (carcinoma-associated fibroblasts) and immune cells to reshape the tumor immune microenvironment and promote tumorigenesis and tumor progression. Thus, FXYD5 could be used as an immune-related biomarker for diagnosing and predicting the prognosis of multiple cancer types. Therefore, our findings suggest that targeting FXYD5 in TME (tumor microenvironment) may be a promising therapeutic strategy.

A hierarchical attention network integrating multi-scale relationship for drug response prediction

Anticancer drug response prediction with deep learning technology has become the foundation of precision medicine. It is essential for anticancer drug response prediction to incorporate multi-scale relationships within feature items and biomedical entities. Therefore, we propose MultiDRP that develops the hierarchical attention networks integrating multi-scale relationship for drug response prediction. MultiDRP can fuse both internal correlation of feature items and external relationship of biomedical entities by hierarchically integrating graph attention and self-attention networks to improve the anticancer drug response prediction. A variety of results showed that MultiDRP generated the great representation by integrating multi-scale relationships, and achieved higher performance compared to existing methods on various prediction scenarios. The results of network proximity, gene ontology biological process (GOBP) enrichment, and drug pathway association analysis show that MultiDRP can accurately screen the sensitive and resistant drugs for cancer cell lines. In vitro experiments, eight novel drugs predicted by MultiDRP exhibited high sensitivity to lung cancer cell line NCI-H23, seven of which showed IC50 values of less than 10nM. These results further suggest that MultiDRP can serve as a powerful tool for anticancer drug response prediction. The source data and code are available at https://github.com/pengsl-lab/MultiDRP.git

Oral and non-oral lichen planus show genetic heterogeneity and differential risk for autoimmune disease and oral cancer.

Lichen planus (LP) is a T-cell-mediated inflammatory disease affecting squamous epithelia in many parts of the body, most often the skin and oral mucosa. Cutaneous LP is usually transient and oral LP (OLP) is most often chronic, so we performed a large-scale genetic and epidemiological study of LP to address whether the oral and non-oral subgroups have shared or distinct underlying pathologies and their overlap with autoimmune disease. Using lifelong records covering diagnoses, procedures, and clinic identity from 473,580 individuals in the FinnGen study, genome-wide association analyses were conducted on carefully constructed subcategories of OLP (n= 3,323) and non-oral LP (n= 4,356) and on the combined group. We identified 15 genome-wide significant associations in FinnGen and an additional 12 when meta-analyzed with UKBB (27 independent associations at 25 distinct genomic locations), most of which are shared between oral and non-oral LP. Many associations coincide with known autoimmune disease loci, consistent with the epidemiologic enrichment of LP with hypothyroidism and other autoimmune diseases. Notably, a third of the FinnGen associations demonstrate significant differences between OLP and non-OLP. We also observed a 13.6-fold risk for tongue cancer and an elevated risk for other oral cancers in OLP, in agreement with earlier reports that connect LP with higher cancer incidence. In addition to a large-scale dissection of LP genetics and comorbidities, our study demonstrates the use of comprehensive, multidimensional health registry data to address outstanding clinical questions and reveal underlying biological mechanisms in common but understudied diseases.

Association analysis of MnSOD-Ala16Val genetic variation and the risk of preeclampsia: A case-control study and in silico analysis

BackgroundPreeclampsia, a main contributor to maternal mortality worldwide, impacts women beyond 20 weeks of gestation, presenting with elevated blood pressure and proteinuria. The role of oxidative stress in the development of preeclampsia is considerable due to the increased oxygen requirement of placenta. The aim of this study is to evaluate the association between MnSOD-Ala16Val genetic variation and the risk of preeclampsia in a group of pregnant women in accompanying a bioinformatics analysis. Materials and methodsIn this case-control study, 136 pregnant women with preeclampsia vs. 173 healthy women without any history of known diseases as control group, were selected from cases who have referred to the Shahid Beheshti hospital of Kashan (Isfahan province, Iran). After sampling and DNA extraction, MnSOD-Ala16Val polymorphism was evaluated using PCR-RFLP for genotype assessment. Eventually, some bioinformatics tools were used for evaluation of the above-mentioned polymorphism on gene function. ResultsOur data illustrate the association between CT heterozygote genotype of MnSOD-Ala16Val polymorphism with enhanced risk of susceptibility to preeclampsia (OR = 1.865, 95%CI = 1.03–3.37, p = 0.039). Indeed, bioinformatics analysis demonstrated the significant impact of the above mentioned polymorphism on the structure of protein (Score: 49, Expected accuracy: 71%) and RNA (Distance: 0.1815, p-value: 0.1676; A p-value <0.2 is significant). ConclusionsAs a preliminary study, our findings suggest a potential association between the MnSOD-Ala16Val polymorphism and the risk of preeclampsia. However, more investigations with a larger sample size and in different ethnicities are essential for achievement of more precise outcomes.

Spatial ecology and microhabitat selection of the nocturnal pitviper Viridovipera stejnegeri (Squamata: Viperidae) in relation to prey.

Habitat is fundamental for facilitating various life activities in animals, for instance, snakes procure essential energy for survival and reproduction by selecting ambush microhabitats. While there has been extensive research on the selection of microhabitat for feeding in terrestrial and aquatic snakes, little is known about arboreal snakes. In the present study, we analyzed the ambush microhabitat preferences of Viridovipera stejnegeri, a widely distributed Asian pitviper in China, conducted association analysis between snake microhabitat and prey microhabitat and abundance to determine the ro5le of microhabitat selection in feeding. Employing random forest analysis and habitat selection functions, we further constructed a predictive framework for assessing the probability of ambush site selection by V. stejnegeri. Our results revealed that V. stejnegeri exhibited a distinct microhabitat preference for ambush prey. Among the 13 environmental factors assessed, V. stejnegeri showed pronounced preferences towards 12 of these factors, including climatic factors, geographical factors, and vegetation factors. Furthermore, although the preferences of V. stejnegeri overlapped substantially with those of its prey across multiple habitat factors, food abundance shows no significant association with various habitat factors of V. stejnegeri, and does not have significant predictive effect on habitat selection of V. stejnegeri. Therefore, we infer that V. stejnegeri does not preferentially select microhabitats with the highest food abundance, which does not support the hypothesis that "snakes select habitats based on the spatial distribution of prey abundance." By analyzing the characteristics of vegetation, geography, and climate, we conclude that V. stejnegeri tends to choose microhabitats with better ambush conditions to increase attack success rate, thereby achieving the optimal feeding success rate at the microhabitat scale, which is in line with the predictions of optimal foraging theory. This study provides new insights into the predation ecology and habitat selection of snakes.

MTP family analysis and association study reveal the role of ZmMTP11 in lead (Pb) accumulation

The metal tolerance protein (MTP) gene family plays an essential role in the transport of heavy metals, however the function of the MTP family in transporting lead (Pb) was still unclear in plants. In this study, we identified and characterized 12 ZmMTPs in the whole genome of maize. These ZmMTP genes were divided into three subfamilies in evolution, namely Zn-CDF, Zn/Fe-CDF, Mn-CDF subfamilies, which showed diverse expression patterns in different tissues of maize. Using gene-based association analyses, we identified a Pb accumulation-related MTP member in maize, ZmMTP11, which was located in plasma membrane and had the potential of transporting Pb ion. Under the Pb treatment, ZmMTP11 showed a generally decreased expression relative to the normal conditions. Heterologous expressions of ZmMTP11 in yeast, Arabidopsis, and rice demonstrated that ZmMTP11 enhanced Pb accumulation in the cells without affecting yeast and plant growth under Pb stress. Remarkably, the increased Pb concentration in the plant roots did not cause changes in Pb content in the shoots. Our study provides new insights into the genetic improvement of heavy metal tolerance in plants and contributes to bioremediation of Pb-contaminant soils.

Aspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters

BackgroundAspergillus flavus is an important agricultural and food safety threat due to its production of carcinogenic aflatoxins. It has high level of genetic diversity that is adapted to various environments. Recently, we reported two reference genomes of A. flavus isolates, AF13 (MAT1-2 and highly aflatoxigenic isolate) and NRRL3357 (MAT1-1 and moderate aflatoxin producer). Where, an insertion of 310 kb in AF13 included an aflatoxin producing gene bZIP transcription factor, named atfC. Observations of significant genomic variants between these isolates of contrasting phenotypes prompted an investigation into variation among other agricultural isolates of A. flavus with the goal of discovering novel genes potentially associated with aflatoxin production regulation. Present study was designed with three main objectives: (1) collection of large number of A. flavus isolates from diverse sources including maize plants and field soils; (2) whole genome sequencing of collected isolates and development of a pangenome; and (3) pangenome-wide association study (Pan-GWAS) to identify novel secondary metabolite cluster genes.ResultsPangenome analysis of 346 A. flavus isolates identified a total of 17,855 unique orthologous gene clusters, with mere 41% (7,315) core genes and 59% (10,540) accessory genes indicating accumulation of high genomic diversity during domestication. 5,994 orthologous gene clusters in accessory genome not annotated in either the A. flavus AF13 or NRRL3357 reference genomes. Pan-genome wide association analysis of the genomic variations identified 391 significant associated pan-genes associated with aflatoxin production. Interestingly, most of the significantly associated pan-genes (94%; 369 associations) belonged to accessory genome indicating that genome expansion has resulted in the incorporation of new genes associated with aflatoxin and other secondary metabolites.ConclusionIn summary, this study provides complete pangenome framework for the species of Aspergillus flavus along with associated genes for pathogen survival and aflatoxin production. The large accessory genome indicated large genome diversity in the species A. flavus, however AflaPan is a closed pangenome represents optimum diversity of species A. flavus. Most importantly, the newly identified aflatoxin producing gene clusters will be a new source for seeking aflatoxin mitigation strategies and needs new attention in research.