Search Results (2,532)

Fetal loss, the spontaneous termination of pregnancy between day 42 and 260 of gestation, is poorly understood. Impacts of fetal loss include loss of production, increased health risk, and economic loss. The aims of this study were to identify loci associated with fetal loss in Holstein heifers and primiparous cows to facilitate the selection of reproductively efficient cattle and identify the genetic causes of fetal loss. A genome-wide association analysis (GWAA) compared 5714 heifers that calved at term (controls) to 416 heifers that experienced fetal loss (cases), and for primiparous cows, 2519 controls were compared to 273 cases. The efficient mixed-model association eXpedited approach in the SNP and Variation Suite (v 9.1) statistical software was used with additive, dominant, and recessive inheritance models for the GWAA. In heifers, 16 loci were associated (FDR < 0.05) with fetal loss in the recessive model. In primiparous cows, there were 44 loci associated (FDR < 0.05) with fetal loss in the recessive model. No loci associated with fetal loss were shared between cows and heifers or in the additive and dominant models. These results improve the characterization of genetic factors contributing to fetal loss in Holstein heifers and primiparous cows and provide targets for genomic selection. Full article

Since the molecular mechanisms underlying sex determination in Procambarus clarkii are still unclear, it is important to investigate the genetic basis of sex determination in crustaceans. Currently, the molecular mechanisms of sex determination and the gender-specific markers in this species remain poorly understood. In this study, a total of 14,046,984 SNPs and 2,160,652 InDels were identified through genome-wide resequencing of 89 individuals (45 females and 44 males). Further analysis confirmed that the candidate chromosome was Chr38, the sex determination system was identified as XY, and the sex determination region was located at Chr38: 6,000,000–21,100,000 bp. A pair of sex-specific molecular markers has been identified based on a 21 bp female-specific insertion within the candidate sex-determining region. Additionally, SOAT, NPC1, PTGS2, FANCD1, and VAlRS were identified as candidate sex-determining genes through the screening of candidate genes and RT-qPCR validation analysis. These findings provide a robust foundation for investigating sex-determining mechanisms in crustaceans. Through the integration of genome-wide association studies (GWAS), selection signals, and transcriptome analysis, we identified, for the first time, genes associated with sex determination, growth, and immunity. These genes represent promising candidates for further functional studies and genetic improvement in Procambarus clarkii. Full article

The Fantastic Four gene family encodes small, plant-specific regulatory proteins involved in developmental control; however, their roles in wheat remain poorly understood. In this study, we conducted a comprehensive genome-wide analysis of the Fantastic Four gene family in wheat. A total of 42 TaFAF genes were identified and systematically characterized in terms of their chromosomal distribution, phylogenetic relationships, gene structures, conserved motifs, and promoter cis-regulatory elements. Phylogenetic analysis classified TaFAF genes into four distinct clades, which exhibit high structural conservation but show divergent motif compositions. Expression profiling revealed tissue-specific expression patterns and suggested that a subset of TaFAF genes responded transcriptionally to heat stress in a genotype-dependent manner. Subcellular localization assays showed that representative Fantastic Four proteins were localized in the cytoplasm. Protein–protein interaction analyses indicated that TaFAF-1A.1 and TaFAF-5D.5 physically interact with the key flowering regulator TaFT1. Furthermore, haplotype analysis of TaFAF-5D.5 across 145 wheat accessions revealed a significant association with wheat growth habit, with a favorable haplotype preferentially enriched in winter wheat. Together, these results provide insights into the evolutionary diversification and functional relevance of the Fantastic Four genes and identify TaFAF-5D.5 as a candidate gene potentially associated with developmental adaptation and heat stress responses in wheat. Full article

Bifidobacterium animalis subsp. lactis is a widely used probiotic, yet its efficacy is highly strain-specific, and growing antibiotic resistance necessitates rigorous safety evaluations. We used whole-genome sequencing and in vitro assays to characterize the safety and probiotic traits of infant feces-sourced strain BD1, which shows preliminary mood-modulating and anti-inflammatory potential. The BD1 genome showed a favorable safety profile. VFDB analysis identified 139 low-similarity homologs, with no major toxins detected. Only four chromosomally encoded antibiotic resistance genes were found; phenotypic testing confirmed resistance solely to tetracycline and mupirocin. Although the tetracycline resistance gene tet(W) was identified in genomic island GI01, the absence of associated mobile genetic elements results in a negligible risk of its mobilization. Functional annotation highlighted a dominant metabolic capacity for carbohydrate and amino acid metabolism. BD1 is rich in CAZymes, enabling superior utilization of diverse substrates (starch, sucrose, galactose). Enrichment in lipid metabolism pathways (glycerolipid, sphingolipid) further suggests potential for enhancing fermented product flavor. In vitro assessment demonstrated moderate gastrointestinal tolerance and strong bile salt tolerance. Surface properties showed pronounced cell surface hydrophobicity and confirmed biofilm-forming potential. In conclusion, BD1 exhibits robust safety, metabolic versatility, and strong probiotic characteristics, supporting its development as a functional probiotic strain. Full article

Fusarium oxysporum f. sp. niveum is an increasingly threatening fungal pathogen that systemically colonizes watermelon plants and severely compromises their productivity by causing destructive vascular wilt disease. While its nonribosomal peptide synthetase NPS6 has been identified as a key virulence factor, the regulatory mechanisms through which it controls downstream gene networks to cause disease remain unclear. To elucidate this regulatory pathway, we constructed a ΔFW-NPS6 knockout mutant and conducted a comparative genome-wide analysis using RNA sequencing, with the wild-type strain as a control. The results revealed 66 NPS6-dependent differentially expressed genes, which were primarily associated with secondary-metabolite biosynthesis (e.g., genes encoding nonribosomal peptide synthetases like NPS2) and pathogen–host interactions (e.g., components of the MAPK signaling pathway), and were enriched in key pathogenic pathways. This finding reveals the virulence regulatory network mediated by NPS6, providing a direct theoretical foundation and crucial molecular targets for developing novel control strategies, such as targeted fungicides or genetic interventions, against Fusarium wilt in watermelon by highlighting NPS6 itself as a potential fungicide target and its downstream pathways (e.g., siderophore biosynthesis) as points for intervention. Full article

The wet gluten content (WGC) of wheat is a key indicator of wheat-processing quality, and its genetic basis is extremely critical in breeding. This study evaluated the WGC of 207 wheat accessions under three growing seasons from a natural population. Nine quantitative trait loci (QTLs) explained 7.61–15.18% of phenotypic variation in a genome-wide association study (GWAS) using a 660K SNP array. Among them, qWGC6B.2 on chromosome 6BL was consistently detected across multiple environments, accounting for 10.08–12.27% of variation. Incorporating grain transcriptome data led to the identification of TaWGC6B.1 (TraesCS6B02G386700), which is highly expressed in developing endosperm and strongly correlated with WGC. A competitive allele specific PCR (KASP) marker development and validation indicated that the Whaas68366_GG allele significantly enhanced gene expression and WGC. This study identified key genes and molecular markers, providing theoretical and technical support for WGC genetic improvement in wheat (Triticum aestivum L.). Full article

Background/Objectives: Metabolism is fundamental to all living organisms. It comprises a highly complex network of fine-tuned chemical reactions that sustain life but also generate by-products that damage cellular biomolecules, including DNA, thereby contributing to aging and disease. As metabolism can be largely modified by dietary alterations, it has the potential to positively or negatively affect health and disease. Interestingly, many aging-associated illnesses known to be influenced by diet also show a causal relation with DNA damage. As DNA keeps all instructions for life, and DNA lesions, if unrepaired, interfere with vital processes such as DNA replication and transcription, DNA damage may be an important mediator of the impact of nutrition on health and aging. Methods: Here, we discuss the genome-protective effects of various oral interventions in mice, aiming to elucidate which nutritional alterations lower DNA damage and promote overall health. Results: Our analysis covers a wide range of interventions with reported positive impacts on genomic stability, including modified diets (e.g., dietary restriction, probiotics, micronutrients, fatty acids, and hormones), NAD+ precursors (e.g., nicotinamide riboside), plant derivatives, and synthetic drugs. Among these, caloric and dietary restriction emerge as the most potent, generic modulators of DNA damage and repair processes, enhancing aspects of repair efficiency through metabolic recalibration and improved cellular resilience. Other interventions, like NAD+ precursors, activate partly similar pathways without necessitating reduced food intake. Conclusions: While many interventions show promise, their effects are often less pronounced or are process-specific compared to caloric or dietary restriction. Additionally, many substances lack comprehensive exploration of their genome-protective effects in mice, with often only a small number of studies examining their impact on genome stability. Moreover, the heterogeneity between studies limits direct comparison. However, the observed overlap in mechanistic effects between treatments lends credibility to their potential efficacy. Ultimately, a deeper understanding of these mechanisms could pave the way for translating these findings into, e.g., combination treatments to promote healthy aging in humans. Full article

While striped catfish (Pangasianodon hypophthalmus) is an economically important aquaculture species, its genomic resources remain limited. To date, linkage maps, QTL (quantitative trait loci) analyses, and the identification of candidate genes associated with disease resistance traits are very limited. Therefore, the present study aimed to construct a high-density linkage map and identify candidate genes for this species. Our analysis was conducted on a pedigree population consisting of 560 individuals (490 offspring and 70 parents for 40 families), whose genomes were analyzed using a genotyping-by-sequencing platform. After stringent filtering, 9882 high-quality SNPs were retained for linkage analysis. Linkage analysis placed 8786 markers onto 30 linkage groups (LGs), with an average density of 0.43 SNPs per cM. Recombination rates varied across the 30 linkage groups (LGs), averaging of 3.6 cM/Mb in males, 6.7 cM/Mb in females, and 5.1 cM/Mb when sex-averaged. Using the linkage map, our QTL analysis identified three significant QTLs for disease resistance to Edwardsiella ictaluri, the causative agent of Bacillary Necrosis of Pangasius (BNP). The QTLs were located on LG1, LG9 and LG29, and their peak markers explained 17.03% of the phenotypic variance. An LD-based interval of approximately ±25 kb surrounding the QTL peak was identified as the putative candidate region. However, subsequent genome-wide association analysis did not identify significant SNP effects within these regions, suggesting that the QTLs may represent polygenic or small-effect loci that are detectable only in linkage-based analyses. In summary, this study presents the first high-density SNP-based linkage map for striped catfish and reports significant QTL and associated candidate genes related to disease resistance and growth traits. These findings provide valuable insights into the genetic architecture of economically important traits in P. hypophthalmus. Nevertheless, further validation in independent populations is required before incorporating these markers into selective breeding programs. Full article

Fragaria vesca L., a widely distributed model species, serves as a key resource for studying the evolution and genetics of the Fragaria genus. Research has shown that R2R3-MYB transcription factors are crucial for plant growth and development. However, their specific role in cold resistance in F. vesca is not well understood. In this study, we used the latest genome data for the strawberry (F. vesca v6.0). We performed a genome-wide identification of the R2R3-MYB gene family in F. vesca. We identified a total of 106 R2R3-FvMYBs. Based on their predicted functions in plants, we classified these genes into 25 distinct subfamilies. We then conducted a comprehensive bioinformatics analysis of this family. We performed a detailed examination of the R2R3-FvMYBs structures and physicochemical properties. This analysis provided five key parameters for each protein: molecular weight, the number of amino acids, theoretical isoelectric point, grand average of hydropathicity (GRAVY), and instability index. Gene duplication analysis suggested that segmental duplications were a primary driver of the proliferation of this gene family. Promoter cis-acting element prediction revealed that a large proportion of R2R3-FvMYBs possess elements predominantly associated with phytohormone responsiveness and biotic/abiotic stress responses. Quantitative real-time reverse transcription PCR (qRT-PCR) results confirmed that the expression levels of several R2R3-FvMYBs were upregulated under cold stress. Furthermore, compared to wild-type controls, the overexpression of FvMYB103 in Arabidopsis thaliana enhanced cold tolerance, accompanied by increases in the relevant physiological indices. Collectively, these findings support further investigation into R2R3-MYB gene family to directly assess their contribution to cold resistance. Full article

Heat shock transcription factors (HSFs) play a central role in mediating plant responses to abiotic stress. Anthocyanins, one of the most important secondary metabolites in plants, contribute to both stress tolerance and the enhancement in crop nutritional quality. However, the possible role of HSFs in regulating anthocyanin biosynthesis in sweet potato (Ipomoea batatas L.) remains unknown. This study conducted a genome-wide analysis of the sweet potato HSF gene family to explore their functions related to anthocyanin metabolism and salinity stress. Multiple stress-inducible promoter elements were identified within IbHSF22, including those induced by drought, salt, heat, ABA, and light. For functional characterization of this gene, a 35S-driven overexpression construct was prepared and then transformed into Nicotiana benthamiana. Overexpression of IbHSF22 led to a nearly two-fold increase in anthocyanin content, concurrently with the elevated expression of key structural genes such as NtCHS, NtF3H, NtDFR, and NtANS. Under salt stress, the transgenic plants also exhibited enhanced tolerance, which was associated with maintained antioxidant enzyme activity and concerted induction of stress-responsive genes, events that collectively resulted in decreased oxidative damage. Therefore, the present work identifies IbHSF22 as an integrator of anthocyanin biosynthesis and salt defense mechanisms. These findings provide a conceptual basis and candidate gene strategy for dual improvement in stress resilience and nutritional quality in sweet potato breeding. Full article

Despite the recognized involvement of TTC39 family genes in metabolism related to pigment deposition, their evolutionary features and potential roles in body coloration in teleost fish remain largely unexplored. We identified three TTC39 genes in Plectropomus leopardus, conserved domains, and evolutionary relationships. The three genes (TTC39A, TTC39B, and TTC39C) were mapped to different chromosomes, yet they shared similar conserved protein domains. Phylogenetic and collinearity analyses indicated that TTC39 genes are evolutionarily conserved among Danio rerio. Gene structure and motif analyses further highlighted the homology and distributional diversity within the TTC39 family. Quantitative expression assays comparing red and black skin revealed significant upregulation of TTC39A and TTC39B in red skin, suggesting that these genes play a role in regulating skin color. These findings provide a foundation for future studies examining how TTC39 genes regulate red skin coloration in P. leopardus. Full article

The characteristic green-note aroma of Chinese plum (Prunus salicina) is largely defined by C6 aldehydes and alcohols synthesized through the fatty acid pathway involving lipoxygenase (LOX), hydroperoxide lyase (HPL), and alcohol dehydrogenase (ADH). However, the LOX/HPL/ADH gene families and their potential contributions to C6 volatile formation remain poorly characterized in Chinese plum. Here, we integrated genome-wide identification with cultivar-level volatile profiling and RT–qPCR expression analyses to link candidate genes with C6 volatile accumulation. We identified 8 PsLOX, 3 PsHPL, and 13 PsADH genes and classified them into 2, 1, and 3 subfamilies, respectively. Conserved motifs/domains were shared within each family, whereas gene-structure variation suggested functional divergence; segmental duplication was the main driver of family expansion. To explore their functional relevance to aroma biosynthesis, five major C6 aldehydes and alcohols were analyzed in ten cultivars using solid-phase microextraction/gas chromatography-mass spectrometry (SPME/GC–MS), revealing substantial diversity in green-note composition. Combined with reverse transcription quantitative polymerase chain reaction (qRT–PCR) expression profiling, low PsADH2.7 expression was associated with high hexanal content, whereas elevated PsLOX5 and PsADH2.2 expression corresponded to increased 1-hexanol accumulation. High 2-ethyl-1-hexanol levels were linked to increased PsLOX4.1 and PsHPL1.3 but decreased PsADH1.2 expression. In addition, (Z)-3-hexen-1-ol abundance showed strong positive correlations with PsLOX3.1, PsHPL1.2, and PsADH2.6 expression. This integrated genomic and expression–metabolite analysis highlights candidate genes potentially involved in C6 aldehyde/alcohol biosynthesis underlying the green-note aroma of Chinese plum and provides genetic targets for aroma-oriented breeding. Full article

Background: Coronary heart disease (CHD) remains a leading cause of morbidity and mortality worldwide. Mitochondria-associated endoplasmic reticulum membranes (MAMs) have recently emerged as critical mediators in cardiovascular pathophysiology; however, their specific contributions to CHD pathogenesis remain largely unexplored. Objective: This study aimed to identify and validate MAM-related biomarkers in CHD through integrated analysis of transcriptomic sequencing data and Mendelian randomization, and to elucidate their underlying mechanisms. Methods: We analyzed two gene expression microarray datasets (GSE113079 and GSE42148) and one genome-wide association study (GWAS) dataset (ukb-d-I9_CHD) to identify differentially expressed genes (DEGs) associated with CHD. MAM-related DEGs were filtered using weighted gene co-expression network analysis (WGCNA). Functional enrichment analysis, Mendelian randomization, and machine learning algorithms were employed to identify biomarkers with direct causal relationships to CHD. A diagnostic model was constructed to evaluate the clinical utility of the identified biomarkers. Additionally, we validated the two hub genes in peripheral blood samples from CHD patients and normal controls, as well as in aortic tissue samples from a low-density lipoprotein receptor-deficient (LDLR−/−) atherosclerosis mouse model. Results: We identified 4174 DEGs, from which 3326 MAM-related DEGs (DE-MRGs) were further filtered. Mendelian randomization analysis coupled with machine learning identified two biomarkers, DHX36 and GPR68, demonstrating direct causal relationships with CHD. These biomarkers exhibited excellent diagnostic performance with areas under the receiver operating characteristic (ROC) curve exceeding 0.9. A molecular interaction network was constructed to reveal the biological pathways and molecular mechanisms involving these biomarkers. Furthermore, validation using peripheral blood from CHD patients and aortic tissues from the Ldlr−/− atherosclerosis mouse model corroborated these findings. Conclusions: This study provides evidence supporting a mechanistic link between MAM dysfunction and CHD pathogenesis, identifying candidate biomarkers that have the potential to serve as diagnostic tools and therapeutic targets for CHD. While the validated biomarkers offer valuable insights into the molecular pathways underlying disease development, additional studies are needed to confirm their clinical relevance and therapeutic potential in larger, independent cohorts. Full article

Leaf inclination angle (LIA) and leaf area index (LAI) are important components of crop population canopy structure, which affect population photosynthetic production via altering canopy light interception and transmittance, and gas diffusion. In this study, we used a genetically diverse maize population of 378 inbred lines as materials to detect significantly associated SNPs with LIA and LAI using the mixed linear model (MLM) of genome-wide association study (GWAS). A total of 21 SNPs associated with LIA explain 6.07–10.86% of the phenotypic variation, containing two major-effect SNPs over 10%; 38 SNPs associated with LAI explain 2.91–10.36% of the phenotypic variation, containing one major-effect SNP. One candidate gene, GLCT1, significantly associated with LIA was identified, which might involve cell-wall biosynthesis. In addition, a cascade of SNPs significantly associated with LAI was identified in a single environment, and a candidate gene encoding the bHLH144 transcription factor was found. The results provide a theoretical basis for the selection of maize inbred lines with ideal canopy architecture and further investigation of the genetic mechanism of LIA and LAI. Full article

Understanding the genetic basis of agronomic traits in quinoa adapted to the Qinghai–Tibet Plateau is essential for developing high-yield cultivars, as conventional breeding is constrained by limited molecular tools. In this study, 300 cultivated accessions were evaluated for five quantitative traits, and whole-genome resequencing generated 3.69 million high-quality SNPs. Population structure analysis and genome-wide association study (GWAS) were conducted, with integration of seed developmental transcriptomes to refine trait-associated loci. A highly admixed genetic background (K = 7) was revealed, and 11 significant QTLs across seven chromosomes were identified, involving genes related to metabolism, transport, and cell-wall formation. Among these, CesA4 (CQ042210) showed a strong association with thousand grain weight (TGW) and a distinct expression maximum at the early seed-filling stage. These results provide a genomic framework for understanding trait variation in plateau-adapted quinoa and highlight promising targets for marker-assisted breeding. Full article