Locus Analysis Research Articles

Virulence factor discovery identifies associations between the Fic gene family and Fap2+ fusobacteria in colorectal cancer microbiomes.

Fusobacterium is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. Here, we analyze genomes of Fusobacterium colon tumor isolates and find that a family of post-translational modification enzymes containing Fic domains is associated with Fap2 positivity in these strains. We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2+ Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. Using a global data set of CRC shotgun metagenomes, we show that fusobacterial Fic and Fap2 genes frequently co-occur in the fecal microbiomes of individuals with late-stage CRC. We further characterize specific Fic gene families harbored by Fap2+ Fusobacterium animalis genomes and detect recombination events and elements of horizontal gene transfer via synteny analysis of Fic gene loci. Exposure of a F. animalis strain to a colon adenocarcinoma cell line increases gene expression of fusobacterial Fic and virulence-associated adhesins. Finally, we demonstrate that Fic proteins are synthesized by F. animalis as Fic peptides are detectable in F. animalis monoculture supernatants. Taken together, our study uncovers Fic genes as potential virulence factors in Fap2+ fusobacterial genomes.IMPORTANCEAccumulating data support that bacterial members of the intra-tumoral microbiota critically influence colorectal cancer progression. Yet, relatively little is known about non-adhesin fusobacterial virulence factors that may influence carcinogenesis. Our genomic analysis and expression assays in fusobacteria identify Fic domain-containing genes, well-studied virulence factors in pathogenic bacteria, as potential fusobacterial virulence features. The Fic family proteins that we find are encoded by fusobacteria and expressed by Fusobacterium animalis merit future investigation to assess their roles in colorectal cancer development and progression.

A novel susceptibility locus to Erysiphe necator (SEN2) identified by genetic mapping of automated microscopy computer vision data in grapevines.

Powdery mildew, caused by the fungus Erysiphe necator, is one of the primary causes of grape yield loss across the globe. While numerous resistance loci have been identified in various grapevine species, the genetic determinants of susceptibility to E. necator remain largely unexplored. Understanding the genetics of susceptibility for pathogenesis is equally important for developing durable resistance grapevines against this pathogen. To identify these factors in Vitis interspecific hybrid 'Chambourcin', a controlled leaf disc assay was conducted for two years using an automated microscopy phenotyping system with 273 F1 genotypes from a cross of 'Chambourcin' and V. vinifera 'Cabernet Sauvignon'. Additionally, a high-resolution linkage map using the same number of 'Chambourcin'-derived hybrids was constructed with 355 simple sequence repeats (SSR) and 1,394 RNaseH2-dependent amplicon sequencing (rhAmpSeq)-derived haplotype markers that clustered into 19 linkage groups. A quantitative trait locus (QTL) analysis identified a susceptibility locus (here named Sen2) on linkage group (LG) 7 explaining 8.90 % - 12.57 % of the total phenotypic variance. The markers associated with this susceptibility locus were used to identify 78 accessions in the USDA-ARS cold hardy Vitis collection at Geneva, NY that carry Sen2 and can be used to selectively exclude susceptible progenies. Additionally, 6 accessions carry the alternative haplotype encoding recessive resistance and can be used for resistance breeding. The identification of powdery mildew susceptibility loci is crucial for identifying genes that could be targeted for gene knock-out, gene editing, RNA interference (RNAi), or selection among breeding genotypes to enhance sustainable protection against pathogens.

Genetic diversity and intercontinental dispersal of temperate and subarctic populations of Dibothriocephalus dendriticus (Cestoda; Diphyllobothriidea), a causative agent of dibothriocephalosis.

The diphyllobothriid tapeworm Dibothriocephalus dendriticus, one of the causative agents of the fish-borne zoonosis dibothriocephalosis, is mainly distributed in the Arctic/subarctic and temperate zones of the Northern Hemisphere (Europe, North America, and Asia), but also in the southern cone region of South America (Patagonia). The genetic structure and gene flow among 589 individuals of D. dendriticus, representing 20 populations, were studied using the mitochondrial cox1 gene as the first choice marker and 10 polymorphic nuclear microsatellite loci as a dominant molecular tool. The haplotype network of 30 cox1 haplotypes and Principal Coordinate Analysis/Structure analysis based on microsatellite data revealed close genetic relationships among populations within continents, namely northern and northwestern Europe (Norway, Finland, and UK/Scotland), North America (USA/Alaska, USA/Oregon, and Greenland), and South America (Argentina and Chile). The population from Iceland, located on the Mid-Atlantic Ridge between North America and Europe, was related to both Europe and North America. The mixed Nearctic and Palaearctic origin of D. dendriticus in Iceland was confirmed by a coalescent-based analysis of the microsatellite loci (in Migrate software). The most likely scenarios suggested that the Icelandic population is a genetic admixture of tapeworms from northwestern Europe and USA/Alaska. These findings corresponded with the distribution and migratory routes of piscivorous birds of the family Laridae, the main definitive hosts of D. dendriticus. The origin of an apparently non-native population of D. dendriticus in Patagonia was investigated in detail. The two most plausible hypotheses based on Migrate analysis represented different scenarios. One of them points to a European origin of the Patagonian population, the other to a North American origin. Future research with more extensive and a geographically broader sampling set is recommended to trace dispersal routes of D. dendriticus in Patagonia.

Association of antihypertensive drug target genes with alzheimer’s disease: a mendelian randomization study

BackgroundEpidemiological and genetic studies have elucidated associations between antihypertensive medication and Alzheimer’s disease (AD), with the directionality of these associations varying upon the specific class of antihypertensive agents.MethodsGenetic instruments for the expression of antihypertensive drug target genes were identified using expression quantitative trait loci (eQTL) in blood, which are associated with systolic blood pressure (SBP). Exposure was derived from existing eQTL data in blood from the eQTLGen consortium and in the brain from the PsychENCODE and subsequently replicated in GTEx V8 and BrainMeta V2. We performed two-sample Mendelian randomization (MR) to estimate the potential effect of different antihypertensive drug classes on AD using summary statistics from a meta-analysis (111,326 cases and 677,663 controls) and further replicated in FinnGen cohorts (9301 cases and 367,976 controls). The reverse causality detection, assessing horizontal pleiotropy, Bayesian co-localization, phenotype scanning, and protein quantitative trait loci (pQTL) analysis were implemented to consolidate the MR findings further.ResultsA 1-standard deviation (SD) lower expression of the angiotensin-converting enzyme (ACE) gene in blood was associated with a lower SBP of 3.92 (95% confidence interval (CI), 2.69–5.15) mmHg but an increased risk of AD (odds ratio (OR), 2.46; 95% CI, 1.82–3.33). A similar direction of association was also observed between ACE expression in prefrontal cortex (OR, 1.19; 95% CI, 1.10–1.28), frontal cortex (OR, 1.19; 95% CI, 1.11–1.27), cerebellum (OR, 1.13; 95% CI, 1.09–1.17), cortex (OR, 1.59; 95% CI, 1.33–1.28) and ACE protein levels in plasma (OR, 1.13; 95% CI, 1.09–1.17) and AD risk. Colocalization supports these results. Similar results were found in external validation. We found no evidence for an association between genetically estimated blood pressure (BP) and AD risk.ConclusionsThere findings suggest an adverse association of lower ACE messenger RNA and protein levels with an elevated risk of AD, irrespective of its BP-lowering effects. These findings warrant greater pharmacovigilance and further investigation into the effect of ACE inhibitors, particularly those that are centrally acting, on neurodegenerative symptoms in patients with AD.

Genetic variants in PD-1 and its ligands, gene-gene and gene-environment interactions in allergic rhinitis.

The etiology of allergic rhinitis (AR), in which genetic and environmental factors are closely intertwined, has not yet been completely clarified. Programmed cell death 1 (PD-1) and its ligands (PD-L1 and PD-L2) regulate the immune and inflammatory responses during the development of immune-related and atopic diseases. To clarify the associations of genetic variants in PD-1, PD-L1 and PD-L2 with susceptibility to AR, gene-gene and gene-environment interactions were investigated. A total of 452 AR patients and 495 controls were enrolled in this hospital-based case-control study. Eight single nucleotide polymorphisms (SNPs) in the PDCD1, PDCD1LG1 and PDCD1LG2 genes were genotyped. The correlations between SNPs and AR incidence, as well as gene-gene and gene-environment interactions were explored. Differentially expressed genes were screened by the Limma package in two Gene Expression Omnibus (GEO) datasets of AR patients. Expression qualitative trait locus (eQTL) analysis was performed via the Genotype-Tissue Expression (GTEx) database. The rs2297136 (A/G) in PDCD1LG1 was associated with a significantly increased risk of AR, whereas the PDCD1LG2 rs16923189 G allele was associated with a reduced risk of AR. In the subgroups according to AR-related phenotypes, the rs2297136 G allele increased, while the rs16923189 G allele reduced AR risk. Gene-gene interactions and gene-environment interactions (e.g., PDCD1LG1 polymorphisms with factors such as smoke, main road and cooking fumes) were verified in AR patients, but they were not significant after Bonferroni correction. PDCD1LG1 rs2297136 and PDCD1LG2 rs16923189 are associated with susceptibility to AR in this Chinese population. The PD-1/PD-L1 and PD-1/PD-L2 signaling pathways may regulate gene-gene and gene-environment interactions in the pathogenesis of AR.

QTL-Based Evidence of Population Genetic Divergence in Male Territorial Aggressiveness of the Japanese Freshwater Threespine Stickleback.

Territorial aggression is widespread across the animal kingdom and is expressed in diverse ecological and social contexts. In addition, there are marked variations in the degree of male reproductive territoriality within and between species. These differences are often attributed to genetic components. However, the evolutionary genetic mechanisms in wild animals are poorly understood. This study explored the genetic basis of divergent male territorial aggressiveness between two Japanese freshwater populations, Gifu (GF) and Tomakomai (TM), in the threespine stickleback, which is a well-known model system for both behavioral ecology and evolutionary genetics. First, our field survey indicated that the distribution of reproductive territories differed greatly across breeding habitats between the focal populations, and the density of reproductive territories was much greater in the GF population. Second, a one-on-one arena aquarium experiment on male-male combat using wild-caught and common-garden-reared males revealed that GF males were genetically more aggressive than TM males. Finally, we performed quantitative trait loci (QTL) analysis using an F2 hybrid cross between the two populations to identify the causal genomic regions contributing to the divergence in male territorial aggressiveness. Our QTL analysis identified a single significant locus in an aggression-related behavioral component, that is, the number of bites of focal F2 males toward a GF stimulus intruder. Two notable behavior-related genes, HTR2A and MAO-A, are found near this locus. These genes have often been suggested to influence of aggressive behavior in animals; therefore, they are regarded as important candidate genes for further functional analyses. Thus, we are the first to provide a QTL-based genetic basis for population divergence in male territorial aggressiveness in the threespine stickleback.

Integrated analyses of Mendelian randomization, eQTL, and single-cell transcriptome identify CCN3 as a potential biomarker in aortic dissection

Plasma secretory proteins are associated with various diseases, including aortic dissection (AD). However, current research on the correlation between AD and plasma protein levels is scarce or lacks specificity. This study aimed to explore plasma secretory proteins as potential biomarkers for AD. Through genome-wide association studies, expression quantitative trait locus (eQTL) analysis, and human plasma protein profiling, we identified DBNL, NPC2, SUMF2, and TFPI as high-risk genes and CCN3, PRKCSH, TEX264, and TGFBR3 as low-risk genes for AD. Further cell localization and differential expression analysis of these eight genes were conducted using single-cell data. We also examined their expression in three Gene Expression Omnibus datasets, measured their mRNA levels in AD versus normal tissues using qPCR, and assessed their protein levels in patients’ blood versus healthy individuals using enzyme-linked immunosorbent assay. Our findings suggest that CCN3, consistently downregulated in both mRNA and plasma levels during AD, may have a protective role. Initial enrichment analyses of differentially expressed CCN3 cells suggested their involvement in focal adhesion, actin cytoskeleton regulation, and the PI3K-Akt signaling pathway.

Genome Sequencing Providing Molecular Evidence of Tetrapolar Mating System and Heterothallic Life Cycle for Edible and Medicinal Mushroom Polyporus umbellatus Fr.

Polyporus umbellatus is a species whose sclerotia have been extensively employed in traditional Chinese medicine, which has diuretic, antitumor, anticancer, and immune system enhancement properties. However, prolonged asexual reproduction has resulted in significant homogenization and degeneration of seed sclerotia. In contrast, sexual reproduction has emerged as an effective strategy to address these challenges, with a distinct mating system serving as the foundation for the implementation of sexual breeding. This study presents the first sequencing and assembly of the genome of P. umbellatus, thereby providing an opportunity to investigate the mating system at the genomic level. Based on the annotated mating-type loci within the genome, monokaryotic offspring exhibiting different mating-types were identified. Through the integration of traditional mating tests, the tetrapolar mating system of P. umbellatus was distinctly elucidated. The resequencing of monokaryotic strains with four different mating-types, along with comparative analyses of mating-type loci, revealed the HD1 and HD2 (HD, homeodomain) genes determined the mating A types, and the PR4, PR5, and PR6 (PR, pheromone receptor) genes determined the mating B types. Meanwhile, this study offers a successful case study in the molecular investigation of mating systems. Additionally, the number of sterigma and basidiospores on each basidium was examined using scanning electron microscopy, while the nuclei of basidiospores and basidia at various developmental stages were analyzed through DAPI staining. This research clarifies the heterothallic life cycle of P. umbellatus. The findings of this study are expected to facilitate advancements in genetic research, breeding development, strain improvement, and the industry of P. umbellatus.

Identification of inheritance and genetic loci responsible for wrinkled fruit surface phenotype in chili pepper (Capsicum annuum) by quantitative trait locus analysis.

The online version contains supplementary material available at 10.1007/s11032-024-01528-y.

Analysis of Financial Literacy, Financial Attitude, and Locus of Control on Financial Management Behavior

This study was conducted with the aim of determining the effect of Financial Literacy, Financial Attitudes and Locus of Control on Financial Management Behavior. The sampling technique used was purposive sampling, which is a technique for taking data sources by determining samples with certain considerations. The data used is primary data using a questionnaire distributed to 100 respondents, namely the millennial generation in the Jakarta area. The analysis method uses the Statistical Product and Services Solution (SPSS) application. The results of this study are that Financial Literacy has a positive and significant effect on the Financial Management Behavior of the Millennial Generation in the Jakarta area. Financial Attitudes do not affect the Financial Management Behavior of the Millennial Generation in the Jakarta area. Locus of Control has a positive and significant effect on the Financial Management Behavior of the Millennial Generation in the Jakarta area.

Genetic Parameters and Trait Associations in Wheat Under Drought and Low Nitrogen Conditions

Drought and low nitrogen stress are the leading cause of low crop production and productivity worldwide. Developing drought-tolerant wheat germplasm resilient to low nitrogen conditions is essential through genetic enhancement and selection for novel traits. The objective of the research was to investigate genetic diversity, parameters, and trait relationships within a wheat genotype panel to inform drought- and low-N-tolerant variety selection. This study evaluated 50 wheat genotypes under drought-stressed and non-stressed conditions, with varying nitrogen (50 kg ha−1, 100 kg ha−1, and 200 kg ha−1) levels across four testing sites during the 2019/2020 growing season. Statistical analysis (combined ANOVA) revealed substantial genetic variation (p < 0.05) for the majority of tested traits. High heritability and substantial genetic gain for KPS (97.49%, 28.10% GAM) and SE (96.48%, 14.28% GAM) were determined under drought and low nitrogen stress. Under drought-stressed and non-stressed (at 200 kg N ha−1), grain yield expressed high heritability estimates of 80.43% and 75.68% and genetic advance at 21.90% and 21.56%, respectively. Positive and significant correlations (r > 0.5; p < 0.001) were measured between grain yield and yield components, implicating simultaneous direct and indirect selection of desired traits. The positive relationship between grain yield and yield components suggests that further quantitative trait loci analysis and progeny testing are crucial to guide genotype selection and breeding for drought and low-N stress-tolerant wheat genotypes.

Genetic susceptibility of diffuse large B-cell lymphoma: a meta genome-wide association study in Asian population.

Diffuse large B-cell lymphoma (DLBCL) is an aggressive malignancy and the most common form of non-Hodgkin lymphoma (NHL) that occurs worldwide. To discover risk factors and pathogenesis of DLBCL, we performed the largest GWAS of DLBCL to date in samples of East Asian ancestry, consisting of 2,888 patients with DLBCL and 12,458 controls. The meta-analysis identified three novel loci, rs2233434 on 6p21.1 (OR = 1.26, P = 1.17 × 10-8), rs11066015 on 12q24.12 (OR = 1.24, P = 6.57 × 10-9) and rs6032662 on 20q13.12 (OR = 1.24, P = 5.22 × 10-12). Fine mapping analysis revealed that the extensive association within the MHC region was driven by two novel HLA alleles, HLA-A*02 and HLA-DQB1*03. Functional annotation, eQTL and colocalization analyses of the susceptibility loci implicated NFKBIE/TCTE1, ALDH2/BRAP and CD40 as candidate disease genes. The pleiotropic effect analysis of the DLBCL loci revealed shared genetic susceptibility between DLBCL and several autoimmune diseases. Our study also suggested genetic heterogeneity between Asian and European populations by identifying ancestry-specific genetic associations. Overall, this study has implicated novel disease genes and molecular mechanism for DLBCL.

Analysis of Locus of Control and Self Efficacy on Satisfaction Employee Work and its Impact on Performance Achievement Levels

The Kampar Regency Ministry of Religion Office has the main task of carrying out functions in formulating and establishing vision, mission and technical policies in the field of religious life services and guidance to the community in Kampar Regency as well as providing services, guidance and guidance in the field of Hajj and Umrah. Therefore, employees with optimal performance are very necessary. Many factors influence employee performance, including job satisfaction, locus of control and self-efficacy. This research was conducted at the Ministry of Religion of Kampar Regency which is located on Jalan DI Panjaitan, Bangkinang District. The aim of this research is to find out and analyze the influence of locus of control on employee job satisfaction, the influence of self-efficacy on employee job satisfaction, direct influence of locus of control on employee performance, the direct influence of self-efficacy on employee performance, the influence of job satisfaction on employee performance, the indirect influence of locus of control on employee performance through job satisfaction and , the direct influence of self-efficacy on employee performance through job satisfaction; This research uses primary data and secondary data obtained by distributing questionnaires, observations, interviews and research files. The population in this study were all employees at the Ministry of Religion office in Kampar Regency, totaling 48 people and all of them were used as samples. Data analysis was carried out using the Structural Equation Modeling (SEM) analysis tool and hypothesis testing was carried out at an alpha of 5%. The results of this study concluded that locus of control was proven to have no significant effect on job satisfaction, self-efficacy has been proven to have a significant effect on employee job satisfaction, locus of control has been proven to have a direct and significant effect on employee performance, self-efficacy is proven to have a direct and significant effect on employee performance, job satisfaction has a significant effect on employee performance, locus of control is indirectly proven to have no significant effect on employee performance through job satisfaction and self efficacy is indirectly proven to have a significant effect on employee performance through job satisfaction at the Kampar Regency Ministry of Religion Office.

Genetic variants of FER and SULF1 in the fibroblast-related genes are associated with non-small-cell lung cancer survival.

Fibroblasts are important components in the tumor microenvironment and can affect tumor progression and metastasis. However, the roles of genetic variants of the fibroblast-related genes (FRGs) in the prognosis of non-small-cell lung cancer (NSCLC) patients have not been reported. Therefore, we investigated the associations between 26,544 single nucleotide polymorphisms (SNPs) in 291 FRGs and survival of NSCLC patients from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. In Cox regression multivariable analysis, we found that 661 SNPs were associated with NSCLC overall survival (OS). Then we validated these SNPs in another independent replication dataset of 984 patients from the Harvard Lung Cancer Susceptibility (HLCS) Study. Finally, we identified two independent SNPs (i.e., FER rs7716388 A>G and SULF1 rs11785839 G>C) that remained significantly associated with NSCLC survival with hazards ratios (HRs) of 0.87 (95% confidence interval [CI] = 0.77-0.98, p = 0.018) and 0.88 (95% CI = 0.79-0.99, p = 0.033), respectively. Combined analysis for these two SNPs showed that the number of protective alleles was associated with better OS and disease-specific survival. Expression quantitative trait loci analysis indicated that the FER rs7716388 G allele was associated with the up-regulation of FER mRNA expression levels in lung tissue. Our results indicated that these two functional SNPs in the FRGs may be prognostic biomarkers for the prognosis of NSCLC patients, and the possible mechanism may be through modulating the expression of their corresponding genes.

Genome-Wide In Silico Analysis of Microsatellite Loci in Rabbits.

This study aimed to characterize microsatellites in the rabbit genome using an in silico approach and to develop and validate microsatellite markers. Blood samples were collected from 15 Baladi rabbits and 18 New Zealand White (NZW rabbits). The GMATA software was used to define SSRs in the extracted sequences. Twelve primer pairs were used to validate the loci identified and the primers developed. The total number of the detected microsatellite loci overall chromosomes was 1,136,253. The di-nucleotide microsatellite repeats dominated and exceeded 88% of the detected microsatellites in all chromosomes. There were no microsatellites detected in mitochondrial DNA. The highest relative microsatellite abundance was obtained for chromosome 19, followed by 13 and 6. The highest estimated SSR density was obtained for chromosome 14, and the lowest was for mitochondrial DNA, followed by chromosome 13. The polymorphism was 81.63% and 75.51% for Baladi and NZW rabbits, respectively. The number of detected alleles ranged between two and seven alleles/loci, and polymorphic information content was from 35% to 71%. The AMOVA analysis showed that the total variance of all levels of population structure was 15.734. The results definitely confirmed higher genetic diversity in Baladi compared with NZW rabbits.

Long-Chain Polysaturated Fatty Acid in Atrial Fibrillation-Associated Stroke: Lipidomic-GWAS Study.

Background and Purpose This study aimed to explore the relationship between lipidomic domains, particularly free fatty acids (FFAs), and the presence of AF in patients with acute stroke, and to identify mechanisms of AF-associated stroke through genetic studies. Methods A total of 483 patients of stroke in patients without AF (n = 391) and with AF (n = 92) were selected from a prospectively collected stroke registry. Lipidomic profiling was conducted and the lipid components associated with AF were explored using fold-change analyses and clustering. Genotyping was conducted through trait comparison. Colocalization was also performed. Results Among the lipidomic domains, the free fatty acid (FFA) class was positively associated with AF. Long-chain fatty acids with 14-24 carbons and unsaturated FFAs distinguished AF. Clustering analysis based on FFAs revealed differences in AF proportion across groups. GWAS identified two loci associated with clustered groups of FFA metabolites: near MIR548F3 associated with FFA 20:1, FFA 20:2, FFA 22:5, and FFA 22:6; and near RPL37A associated with FFA 22:5 and FFA 22:6. These loci were associated with increased fibrinogen levels. In the GWAS for the FFA metabolite-quantitative trial locus analysis, loci near rs28456 and rs3770088, and FFA 20:4-QTLs were co-localized with the eQTLs of FADS2, a gene involved in the peroxisome proliferative-activated receptor gamma-related signaling pathway, in the whole blood, left ventricle, and atrial appendage tissue. Conclusion Elevated FFA levels, especially those of long-chain unsaturated FFAs, are strongly associated with AF-associated stroke. This relationship is regulated by the peroxisome proliferator-activated receptor gamma-related signaling pathway.

The analysis of the genetic loci affecting phenotypic plasticity of soybean isoflavone content by dQTG.seq model.

The dQTG.seq model was utilized to investigate the genetic underpinnings of phenotypic plasticity in soybean isoflavone content, leading to the identification of 100 marker sites associated with phenotypic plasticity, including 27 transcription factors. Overexpression of Glyma.18G091600 (GmERF7) hairy roots under low temperature, salt, and drought stress confirmed the regulatory role of GmERF7 in the phenotypic plasticity of soybean isoflavone content. Phenotypic plasticity is characteristic of organisms that undergo phenotypic changes in response to environmental fluctuations. This phenomenon is pivotal in evolutionary processes and the emergence of new traits. Isoflavones, significant secondary metabolites found in soybeans, have garnered considerable attention owing to their beneficial physiological effects on human health. The variation in isoflavone content among different soybean varieties is influenced by diverse environmental factors, thereby influencing the evaluation of high and low isoflavone varieties. In this study, we measured the phenotypic plasticity of isoflavone content in recombinant inbred lines Hefeng 25 and L-28 in three different environments over two years. Utilizing the dQTG.seq model, 100 statistically significant markers were identified, and 101 potential genes, including 27 transcription factors, were screened. Through qRT-PCR analysis, elevated expression levels of Glyma.18G091600, Glyma.09G196200, and Glyma.05G229500 were observed in various parts of soybean plants. Under low temperature, drought or salt stress conditions, the related enzymes involved in the isoflavone synthesis pathway were notably upregulated in Glyma.18G091600 (GmERF7) overexpressed hairy roots compared to wild-type controls, resulting to higher phenotypic plasticity values for DZ, GC, GT, and TI. These results suggest that GmERF7 influences the phenotypic plasticity of soybean isoflavone content, enhancing adaptation to adverse environments, while also promoting the synthesis and accumulation of soybean isoflavones.

Genetic Characterization of Captive South American Fur Seals in Japan Based on Mitochondrial and Microsatellite DNA Analyses.

Molecular genetic analyses are effective in revealing the origin, kinship, and genetic diversity of zoo animals. In this study, we carried out the genetic characterization of captive founder individuals of the South American fur seal (Arctocephalus australis) in Japanese zoos and aquariums based on analyses of mitochondrial sequences and nuclear microsatellite loci. In mitochondrial DNA analysis, the haplotype diversity and nucleotide diversity of the overall population were 0.8949 and 0.0119, respectively. Microsatellite DNA analysis revealed that the observed heterozygosity within the overall population was 0.722. In addition, we did not detect genetic bottlenecks. The results from two kinds of DNA analyses indicated that the genetic diversity in this captive population was equivalent to that previously reported in wild populations. The detected mitochondrial haplotypes were the same as or phylogenetically close to those previously reported in wild populations in southern Brazil, Uruguay, Argentina, and southern Chile but diverged from those previously reported in a wild population in Peru. Genetic clustering analyses using microsatellite genotypes revealed that no clear genetic structures in this captive population.

LD-informed deep learning for Alzheimer's gene loci detection using WGS data.

The exponential growth of genomic datasets necessitates advanced analytical tools to effectively identify genetic loci from large-scale high throughput sequencing data. This study presents Deep-Block, a multi-stage deep learning framework that incorporates biological knowledge into its AI architecture to identify genetic regions as significantly associated with Alzheimer's disease (AD). The framework employs a three-stage approach: (1) genome segmentation based on linkage disequilibrium (LD) patterns, (2) selection of relevant LD blocks using sparse attention mechanisms, and (3) application of TabNet and Random Forest algorithms to quantify single nucleotide polymorphism (SNP) feature importance, thereby identifying genetic factors contributing to AD risk. The Deep-Block was applied to a large-scale whole genome sequencing (WGS) dataset from the Alzheimer's Disease Sequencing Project (ADSP), comprising 7,416 non-Hispanic white participants (3,150 cognitively normal older adults (CN), 4,266 AD). 30,218 LD blocks were identified and then ranked based on their relevance with Alzheimer's disease. Subsequently, the Deep-Block identified novel SNPs within the top 1,500 LD blocks and confirmed previously known variants, including APOE rs429358 and rs769449. Expression Quantitative Trait Loci (eQTL) analysis across 13 brain regions provided functional evidence for the identified variants. The results were cross-validated against established AD-associated loci from the European Alzheimer's and Dementia Biobank (EADB) and the GWAS catalog. The Deep-Block framework effectively processes large-scale high throughput sequencing data while preserving SNP interactions during dimensionality reduction, minimizing bias and information loss. The framework's findings are supported by tissue-specific eQTL evidence across brain regions, indicating the functional relevance of the identified variants. Additionally, the Deep-Block approach has identified both known and novel genetic variants, enhancing our understanding of the genetic architecture and demonstrating its potential for application in large-scale sequencing studies. Keywords: Alzheimer's disease, Whole-Genome Sequencing, Linkage Disequilibrium, Deep Learning, Genetic Loci, Imputation Methods.

Quantitative Trait Locus Analysis for Panicle and Flag Leaf Traits in Barley (Hordeum vulgare L.) Based on a High-Density Genetic Linkage Map

The yield of barley (Hordeum vulgare L.) is determined by many factors, which have always been research hotspots for agronomists and molecular scientists. In this study, five important agronomic traits related to panicle and flag leaf, including awn length (AL), panicle length (PL), panicle neck length (NL), flag leaf length (LL) and flag leaf width (LW), were investigated and quantitative trait locus (QTL) analyses were carried out. Using a high-density genetic map of 134 recombinant inbred lines based on specific-locus amplified fragment sequencing (SLAF-seq) technology, a total of 32 QTLs were identified, which explained 12.4% to 50% of the phenotypic variation. Among them, qAL5, qNL2, qNL3, qNL6, qPL2, and qLW2 were detected in 3 consecutive years and all of the contribution rates were more than 13.8%, revealing that these QTLs were stable major QTLs and were less affected by environmental factors. Furthermore, LL and LW exhibited significant positive correlations and the localization intervals of qLL2 and qLL3 were highly overlapped with those of qLW2 and qLW3, respectively, indicating that qLL2 and qLW2, qLL3 and qLW3 may be regulated by the same genes.