Search Results (254)

To clarify the genetic background and biological characteristics of grape germplasm resources and provide theoretical support for germplasm innovation and new-variety breeding, we conducted systematic morphological identification and SSR molecular-marker analysis on 38 core grape germplasms (29 fresh-eating cultivars, 1 local cultivar, and 8 wild germplasms) from the National Southeast Mountainous Crop Germplasm Repository (Jiangxi·Yichun) and other regions. For morphological identification, 14 quantitative traits and 5 descriptive traits of leaves, floral organs and fruits were determined in strict accordance with the NY/T 2932-2016 Descriptors for Grape Germplasm Resources. For SSR molecular-marker analysis, eight pairs of internationally universal core primers were used for PCR amplification and fluorescence detection referring to the NY/T 3640-2020 Identification of Grape Cultivars Using SSR Markers, and genetic diversity analysis was conducted on 11 local and wild grape germplasms. The results revealed abundant phenotypic diversity among the tested germplasms: the functional leaves of cultivars were predominantly pentagonal and cuneate, while those of wild germplasms were mostly reniform and cordate, with 3–5 lobes for most germplasms; all germplasms were hermaphroditic, except for two wild accessions with unisexual flowers. Significant variations were observed in fruit traits, with the coefficient of variation (CV) of cluster weight and berry weight reaching 67.64% and 50.53%, respectively. The genetic plasticity of weight-related traits was much higher than that of shape- and length-related traits, and the average Shannon–Wiener index (H′) of 19 morphological traits was 3.47, indicating a high level of overall phenotypic diversity. SSR analysis showed that the eight primer pairs amplified a total of 42 genotypes (5.25 per primer pair on average). The population had a mean observed number of alleles (Na) of 5.28, a mean effective number of alleles (Ne) of 7.25, and a mean polymorphism information content (PIC) of 0.74, demonstrating rich genetic diversity and high polymorphism of the tested loci. Cluster analysis divided the 11 local germplasms into four groups, which clearly reflected the genetic relationships among them, and genetic admixture was found in some germplasms due to unclear introduction traceability. In this study, fresh-eating grape cultivars suitable for the climatic conditions of Jiangxi Province were screened, the utilization value of local germplasm resources was clarified, and a two-dimensional evaluation system based on phenotypic traits and SSR molecular markers was constructed. The findings provide basic data and a scientific basis for the precise evaluation, elite gene mining, and new-variety breeding of grape germplasm resources in Jiangxi Province. Full article

Background/Objectives: Coronary artery disease (CAD) remains the leading cause of mortality worldwide, with South Asia bearing a disproportionately high and rising burden, particularly at younger ages. The present study aimed to investigate genetic variants associated with premature coronary artery disease (PCAD) using whole-genome sequencing (WGS). Methods: WGS was conducted on 12 people (five PCAD cases, seven matched controls) to assess feasibility and methodology for future large-scale research. High-quality genomic DNA was sequenced at a minimum read depth of 10× with a quality threshold of Q30. Variant calling with stringent quality control identified single-nucleotide polymorphisms (SNPs), followed by annotation against gnomAD for allele frequencies and ClinVar for pathogenicity. Protein-coding variants were filtered, and candidate genes were prioritized for comparative analysis between cases and controls. Results: An average of over 8.8 million SNPs per individual was identified, with comparable overall variant distributions between cases and controls. Initial analyses revealed 120 SNPs exclusively present in PCAD cases. All protein-coding variants were rare (allele frequency < 0.0001), and none were previously classified as pathogenic in ClinVar. After filtration, 87 candidate genes were prioritized. Enriched or unique variants in PCAD cases are mapped to genes involved in lipid metabolism, endothelial dysfunction, inflammatory signaling, immune regulation, thrombosis, vascular remodeling, and metabolic processes. Additional variants were identified in genes related to smooth muscle proliferation, oxidative stress, and other biological pathways. Conclusions: This WGS pilot study provides an initial overview of the genomic landscape of PCAD in a South Asian cohort, highlighting rare variants across multiple biological pathways implicated in atherosclerosis that need validation in a large-scale study. Full article

Lactarius hatsudake is an ecologically and economically significant wild edible mushroom in southern China. To elucidate its population genetic diversity, differentiation, and evolutionary history, we analyzed 172 fruiting bodies from eight geographic populations (AQ, BS, DZ, JS, NC, PT, SG, YX) across seven provinces in the western and eastern regions of southern China using five highly polymorphic simple sequence repeat (SSR) markers. Combined with STRUCTURE clustering, discriminant analysis of principal components (DAPC), unweighted pair group method with arithmetic mean (UPGMA), and analysis of molecular variance (AMOVA), the results revealed high polymorphism across the studied loci (mean PIC = 0.842). A total of 75 alleles were identified, averaging 15 alleles per locus. At the population level, the mean effective number of alleles (Ne) was 4.023, and the mean unbiased gene diversity (uH) was 0.768. The NC population exhibited the highest genetic diversity (uH = 0.796), whereas the BS population showed relatively lower diversity (uH = 0.647). Clustering analyses (STRUCTURE, DAPC, and UPGMA) consistently identified two distinct genetic clusters (K = 2). Cluster I consisted of populations AQ, PT, BS, and SG, while Cluster II was composed of the remaining four populations. Notably, individuals from AQ and NC displayed significant genetic admixture, suggesting a transitional zone. AMOVA revealed that the majority of genetic variation (83%) resided within populations and 17% among populations. Moderate population differentiation (ENA-corrected global Fst = 0.102) and admixture signals suggest non-negligible connectivity among populations. Full article

Grain number per spike (GNS) is a key component of wheat yield, yet its genetic architecture remains incompletely understood. This study phenotyped 610 wheat accessions for GNS in four environments and genotyped them using 429,721 single nucleotide polymorphisms (SNPs). The phenotypes were associated with the SNPs using a three-variance multi-locus random-SNP-effect mixed linear model (3VmrMLM) to identify quantitative trait nucleotides (QTNs), as well as QTN-by-environment (QEI) and QTN-by-QTN (QQI) interactions. These genetic components and residual error explained approximately 18%, 31%, 28%, and 23% of the phenotypic variance, respectively. Two and one previously reported genes were found around QTNs and QEIs, respectively. Bioinformatics and haplotype analyses subsequently yielded 25 candidate genes, 22 gene-by-environment interactions (GEIs), and 24 gene-by-gene interactions (GGIs) around the QTNs, QEIs, and QQIs, respectively. Notably, TraesCS1D01G280000, the wheat homolog of OsRopGEF10, was located near a major QTN explaining over 10% of the total phenotypic variation. A gene interaction network constructed from all identified genes highlighted the central role of GGIs in GNS regulation. Environmental variation may reshape the regulatory network through GEIs. Furthermore, superior haplotypes of 12 candidate genes were identified, providing valuable targets for improving wheat yield. Overall, this study dissects the genetic architecture of GNS and offers practical resources for wheat molecular breeding. Full article

Background/Objectives: To establish a foundation for conserving and utilizing local frog germplasm resources in Zhejiang Province, for Quasipaa spinose, which has high commercial and nutritional value, a pan-genome analysis was performed. Methods: Herein, we characterized 405,263 SNPs for the giant spiny frog, Q. spinose, using the Illumina NovaSeq platform. Results: These loci were highly polymorphic in 59 individuals sampled from three different subpopulations, with 0.05 to 0.30 minor alleles per locus. The observed and expected heterozygosities were 0.2379 and 0.2683 (IBD), respectively. These polymorphic loci would be useful for assessing genetic diversity, population structure, gene flow, population assignment, and paternity in giant spiny frogs. Conclusions: Our investigation demonstrated that there are distinct genetic and evolutionary histories between Zhejiang and Jiangxi frogs. Phylogenetic inference effectively differentiated these three subpopulations based on their geographical origins, and the phylogenetic inference level of domesticated Zhejiang frogs was comparatively higher than that of the Jiangxi-derived population. Furthermore, by utilizing three selective signature methods, namely, Obs/Exp het, nucleotide diversity (Pi), and identical by state (IBS), across subpopulations, we concluded that these three breeds were from an identical population, and no genetic bottleneck occurred among these three lineages, in accordance with LD decay analysis. Finally, 2700 potential candidate genes were identified, including MAPK, calcium signaling pathway, Ras signaling pathway and regulation of actin cytoskeleton; we noted that the key genes associated with dilated cardiomyopathy or arrhythmogenic right ventricular cardiomyopathy in humans beings and GnRH signaling pathway-related genes (i.e., CD80, IFNA, and KCNK1) were highly enriched, which could impact cardiac function through immune-associated genes. Full article

The industrial application of starter cultures requires stable physiological and genetic performance. In this study, Streptococcus salivarius subsp. thermophilus and Lactobacillus delbrueckii subsp. bulgaricus were continuously subcultured. Physiological stability was assessed through colony morphology, fermentation activity, and growth profiling. Genetic stability was evaluated through comparative genomics of carbohydrate metabolism networks and single-nucleotide polymorphism (SNP) analysis. The results showed that after 2000 generations, the cellular morphology of the strains remained intact. Additionally, the strains exhibited enhanced growth performance and fermentation capability. The Gompertz model revealed that adapted S. thermophilus A37 and L. bulgaricus B29 exhibited shortened lag phases, increased maximum specific growth rates, and high stationary-phase cell densities. Phenotypic microarray and comparative genomics revealed that S. thermophilus mainly used mono- and disaccharides, with impaired ribose metabolism due to the absence of the rbsk gene in the pentose phosphate pathway. In contrast, L. bulgaricus metabolized diverse oligosaccharides, sugar alcohols, and plant-derived substrates. Additionally, it effectively catabolized ribose through the phosphoketolase pathway and possessed a trehalose degradation cluster. All strains exhibited genomic stability, with SNPs revealing fewer than 21 variations per isolate. This study provides an important theoretical foundation for evaluating the stability of fermentation starter cultures. Full article

Genome-wide association analysis and transcriptomics were used to investigate salt tolerance traits during germination in 300 Gossypium hirsutum L. germplasm accessions, with the objective of identifying genes and molecular markers associated with salt tolerance. Under 200 mmol L⁻¹ NaCl stress, six traits were evaluated, germination rate, root length, shoot length, root fresh weight, shoot fresh weight, and total fresh weight, as well as their respective salt tolerance indices. A total of 1277 significantly associated single-nucleotide polymorphism (SNP) markers were identified and mapped to 94 quantitative trait loci (QTLs). Of these, 49 QTLs were detected by three or more analytical models, and three QTLs were prioritized for further investigation. Subsequent analysis of these QTLs identified 73 candidate genes potentially involved in cotton salt tolerance. Integration of transcriptomic data revealed that three candidate genes were among the differentially expressed genes (DEGs). Examination of their RNA-seq expression profiles demonstrated significant differences in fragments per kilobase of transcript per million mapped reads (FPKM) values across sampling time points. These three candidate genes are therefore predicted to be associated with salt tolerance during cotton germination. The results provide new insights into the molecular regulatory mechanisms of salt stress tolerance in cotton and offer valuable genetic resources and molecular markers for the genetic improvement of salt tolerance. Full article

As an elite indigenous poultry breed under national protection in China, the Xupu goose is renowned for its large body size, superior fatty liver production, premium meat quality, and high tolerance to roughage. To elucidate its genomic architecture, genetic diversity, and evolutionary selection signatures, we conducted whole-genome resequencing on 15 purposively selected, unrelated male Xupu geese. An average of 6.79 Gb of high-quality sequence data was generated per individual, yielding approximately 4.27 million single-nucleotide polymorphisms (SNPs) with a transition/transversion (Ti/Tv) ratio of 2.49. Population genomic analyses revealed that while the population retains a moderate genetic reservoir (H_E = 0.298), it exhibits a distinct heterozygote deficit (H_O = 0.217) and a moderate genomic inbreeding coefficient F_ROH = 0.204). This structural pattern underscores the genetic impact of historical ex situ closed-flock conservation and the consequent formation of cryptic family lineages. Furthermore, genome-wide integrated haplotype score (iHS) scans detected distinct regions under recent positive selection. Functional annotation of these regions highlighted candidate genes tightly associated with the breed’s hallmark traits, specifically lipid metabolism and hepatic fat deposition (ACSS2, ACSS3, PECR), alongside muscle development (CMYA5, MTPN, LEPR). Conclusively, this study delineates a comprehensive genomic landscape of the Xupu goose, providing a robust foundational resource for future germplasm conservation, molecular marker development, and precision breeding programs. Full article

Yield-related traits of rice (Oryza sativa L.) are pivotal to safeguarding global food security. As a powerful and efficient strategy, genome-wide association study (GWAS) has identified numerous genes for yield-related traits in rice over recent decades, providing critical resources for germplasm improvement. Most yield-related traits are complex quantitative traits controlled by multiple genes with diverse effect sizes, and traditional GWAS approaches have limited power to detect small-effect loci. In this study, we employed Fast3VmrMLM, a compressed mixed linear model integrating genome-wide scanning and machine learning, to perform GWAS for 10 key yield-related traits using a panel of 529 rice accessions and 4,945,006 single-nucleotide polymorphisms (SNPs). The traits included heading date, plant height, panicle number, effective panicle number, yield per plant, spikelet length, grain length, grain width, grain weight, and grain thickness. We detected 141 significant quantitative trait nucleotides (QTNs) associated with target traits and identified 92 previously validated genes located near these QTNs. As a key environmental regulator, photoperiod directly controls flowering and indirectly modulates yield-related traits, and we further identified 182 photoperiod-responsive candidate genes via differential expression and Gene Ontology (GO) enrichment analysis. Through tissue-specific expression analysis, homology analysis with Arabidopsis genes, and haplotype-phenotype differential analysis, six pleiotropic candidate genes were confirmed; notably, LOC_Os02g02210 appears to contribute substantially to grain width and yield-related traits. In conclusion, Fast3VmrMLM proved effective for dissecting the genetic basis of yield-related traits, especially in detecting small-effect loci. These results not only establish a potential genetic link between photoperiod regulation and rice yield formation but also provide high-confidence candidate genes and loci that will accelerate functional genomic studies and precision molecular breeding for high-yield rice. Full article

Oat (Avena sativa L.), as an essential dual-purpose grain and forage crop, exhibits lodging resistance as a key factor directly impacting yield and quality. Therefore, breeding new oat varieties with lodging resistance is important to increase crop productivity and economic benefits. Using 130 oat germplasm as materials, 7 lodging resistance-related traits of oat, including plant height (PH), the fresh weight of single stem (FWSS), the length of basal second internode (LBSI), diameter of basal second internode (DBSI), wall thickness of basal second internode (WTBSI), stem breaking strength (SBS), and stalk puncture strength (SPS), were investigated in two experimental sites for one year. The results indicate that the seven lodging resistance-related traits exhibit a continuous distribution overall and generally follow a typical distribution pattern. A total of 36,928,068 high-quality Single-nucleotide polymorphisms (SNPs) generated from whole-genome resequencing were used for genome-wide association study (GWAS). Based on the BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway) model threshold (−log₁₀(P) ≥ 6), 379 quantitative trait nucleotides (QTNs) associated with lodging resistance-related traits were identified. Among them, 38, 34, 78, 66, 55, 18, and 94 QTNs were associated with PH, FWSS, SBS, SPS, LBSI, DBSI, and WTBSI, respectively. Notably, three QTNs associated with FWSS and one QTN associated with SBS were stably detected across both environments, representing valuable markers for molecular breeding. From these loci, 54 candidate genes were annotated. Ranked by the number of candidate genes per trait, LBSI contained the highest number (14), followed by WTBSI (12), SPS (11), SBS (7), PH (5), and FWSS (5). Our findings provide critical support for analyzing the genetic mechanism of oat lodging resistance. Moreover, this study also offers a material and theoretical basis for the subsequent development of molecular markers and the breeding of new lodging-resistant oat varieties. Full article

With global warming, high-temperature stress has become a primary abiotic factor limiting maize yield and quality. Exposure to heat stress induces sunscald on maize leaves, which severely impairs photosynthesis and ultimately leads to yield reduction. In this study, we used the heat-tolerant inbred line Zheng58 and the heat-sensitive inbred line HSBN, both of which are cultivated maize (Zea mays L. subsp. mays) inbred lines, as parents to construct F₂ and F_2:3 populations consisting of 257 lines. Phenotyping for sunscald at the flowering stage was performed across three field environments. The F₂ population was genotyped using the Maize 10K SNP array to construct a genetic map containing 1728 single nucleotide polymorphism (SNP) markers. The map spanned 1406.22 cM, with an average marker density of 0.81 cM per marker. Eight quantitative trait loci (QTLs) associated with heat tolerance were identified in the F₂/F_2:3 populations, distributed on chromosomes 1, 4, 5, and 8, collectively explaining 3.43% to 35.44% of the phenotypic variation. Among them, the stable QTL qHT1-2 on chromosome 1 was consistently detected across all three environments, explaining 11.41% to 35.44% of the phenotypic variation. Additionally, a major QTL, qHT1-3, was identified on the same chromosome, accounting for 33.70% of the phenotypic variation. Transcriptome analysis of flowering-stage leaves from both parents revealed 9262 differentially expressed genes (DEGs). Of these, 21 DEGs were co-localized within the eight QTL intervals. The genes Zm00001eb013260, Zm00001eb012720, Zm00001eb013600, and Zm00001eb013100 exhibited highly significant differential expression between the parental lines, these four genes are identified as candidate genes in response to heat stress in maize, and their specific biological functions require further functional validation. Full article

Thrips are cosmopolitan agricultural pests and important vectors of plant viruses, and the increasing coexistence of multiple morphologically similar species has intensified the demand for species-specific molecular identification. However, traditional morphological identification and PCR assays using universal primers are often inadequate for mixed-species samples and field-adaptable application. In this study, we developed a species-specific molecular identification framework targeting a polymorphism-rich region of the mitochondrial cytochrome c oxidase subunit I (COI) gene, which is more time-efficient than sequencing-based COI DNA barcoding, for four economically important thrips species in southern China, including the globally invasive Frankliniella occidentalis. By aligning COI sequences, polymorphism-rich regions were identified and used to design four species-specific primer pairs, each containing a diagnostic 3′-terminal nucleotide. These primers were combined with a PBS-based DNA extraction workflow optimized for single-insect samples that minimizes dependence on column-based purification. The assay achieved a practical detection limit of 1 ng per reaction, demonstrated species-specific amplification, and maintained reproducible amplification at DNA inputs of ≥1 ng per reaction. Notably, PCR inhibition caused by crude extracts was effectively alleviated by fivefold dilution. Although the chemical identities of the inhibitors remain unknown, interspecific variation in inhibition strength was observed, with T. hawaiiensis exhibiting the strongest suppression, possibly due to differences in lysate composition. This integrated framework balances target specificity, operational simplicity, and dilution-mitigated inhibition, providing a field-adaptable tool for thrips species identification and invasive species monitoring. Moreover, it provides a species-specific molecular foundation for downstream integration with visual nucleic acid detection platforms, such as the CRISPR/Cas12a system, thereby facilitating the future development of portable molecular identification workflows for small agricultural pests. Full article

Aging is accompanied by a chronic, low-grade inflammatory state known as “inflammaging,” largely driven by dysregulated signaling of pro-inflammatory cytokines like IL-1 and TNF-α. The biological impact of these cytokines is modulated by the expression of their cellular receptors, which is influenced by genetic polymorphisms. However, the interplay between age, genetic variation, and cell-type-specific receptor expression remains incompletely characterized. This study aimed to determine the relative and absolute expression levels of IL-1 and TNF receptors on major immunocompetent cell populations in healthy donors of different age groups and to assess the influence of receptor gene polymorphisms on this expression. A cohort of 144 healthy donors was stratified into two age clusters using unsupervised clustering: a “young” group (18–31 years, n = 71) and an “older” group (32–59 years, n = 73). Membrane expression of TNFR1, TNFR2, IL-1R1, and IL-1R2 on T-lymphocytes, B-lymphocytes, and monocytes was analyzed by flow cytometry. The analysis included both the percentage of receptor-positive cells and the number of receptors per cell using absolute quantification with calibration beads. Genotyping for eight SNPs in the TNF1, TNFR2, IL1R1, and IL1R2 genes was performed via PCR-RFLP. The most pronounced age-related differences were observed in monocytes, in which the young cohort exhibited a significantly higher percentage of TNFR1- and TNFR2-positive monocytes, as well as a higher number of IL-1R1 receptors. In contrast, T-lymphocytes from the older cluster showed a higher percentage of TNFR2-positive cells. Genetic polymorphisms significantly modulated receptor expression in an age-dependent manner. For example, in the young cluster, polymorphisms primarily affected receptor levels on B-lymphocytes, whereas in the older cluster, the most significant associations were observed in monocytes. This study reveals significant, cell-specific alterations in the IL-1 and TNF receptor landscapes with age, with monocytes being particularly affected. The observed receptor downregulation in older adults is likely to reflect an active process of ligand-induced desensitization driven by chronic inflammation. Furthermore, genetic polymorphisms exert age-dependent effects on receptor expression, highlighting the dynamic interplay between genetics and immunosenescence. These findings provide a foundation for personalized strategies to mitigate inflammaging. Full article

The Xinjiang Brown cattle (XJBC) is one of China’s five major dual-purpose dairy and beef breeds. Analyzing the genetic diversity of the Xinjiang Brown cattle population lays the theoretical groundwork for identifying and conserving its genetic resources. This study employed the Illumina Bovine SNP 150K chip to analyze genetic diversity, inbreeding coefficient, kinship, and genetic distance in a population of 750 Xinjiang Brown cattle from three breeding farms in Xinjiang. Genetic diversity was assessed by calculating minimum allele frequency (MAF), observed heterozygosity (Ho), expected heterozygosity (He), polymorphic information content (PIC), and linkage disequilibrium (LD). Population structure was analyzed using PCA. ROH was calculated to derive ROH-based inbreeding coefficients, pedigree-based inbreeding coefficients (F_PED) were estimated using CFC software for comparison, and candidate genes within high-frequency ROH regions in Xinjiang Brown cattle were identified. A G matrix was constructed to analyze population kinship. Results revealed 94,173 high-quality SNP loci in Xinjiang Brown cattle, with an average MAF of 0.276, PIC of 0.376, Ho of 0.345, and He of 0.376. Breeding farm 3 exhibited the fastest LD decay, indicating relatively high genetic diversity across Xinjiang Brown cattle populations, with farm 3 demonstrating greater diversity. The IBS genetic distance was 0.313. The G matrix results aligned with the IBS distance matrix, both indicating close kinship among some individuals within the Xinjiang Brown cattle population. The ranges for average F_PED and average F_ROH across farms were 0.0017–0.0189 and 0.0609–0.0878, respectively. Short ROH segments (0.5–2 Mb) constituted the largest proportion (51.31%) of all ROHs. Within high-frequency ROH enrichment regions, 61 genes, including LCORL, FAM110B, NR4A1, and PER2, were identified as potentially associated with economic traits in Xinjiang Brown cattle. These findings provide relevant marker sites for genomic selection in Xinjiang Brown cattle and lay a theoretical foundation for subsequent research. Full article

Background: Monoclonal antibodies targeting the calcitonin gene-related peptide (CGRP) pathway, such as erenumab (ERE), are effective migraine-preventive therapies for many patients. Identifying clinical and genetic factors associated with treatment failure is crucial for optimizing patient management. Methods: This multicenter, prospective observational study included patients with episodic or chronic migraine treated with ERE for 12 months. Demographics, migraine history, comorbidities, treatment outcomes, and genetic variants in CGRP receptor-related genes (CALCRL and RAMP1) were evaluated for associations with non-response to ERE, defined as a <50% reduction in monthly migraine days. Results: Of the 140 patients starting ERE, 11 were lost to follow up, 12 stopped ERE due to side effects; 18 patients were non-responders and were compared to 99 responders. Arterial hypertension [adjusted OR (aOR): 7.77, p = 0.007], smoking (aOR: 4.98, p = 0.014), and insomnia requiring medication (aOR: 4.51, p = 0.027) were associated with non-responder status. Genetic analysis revealed a nominal association between the RAMP1 rs6431564 polymorphism and non-responder status (nominal p = 0.025), which did not survive Bonferroni correction. The G allele was linked to a reduced risk (aOR per G allele: 0.28, p = 0.025) and caused the increased expression of RAMP1 in an allele-dose manner. Conclusions: Hypertension, smoking, insomnia requiring medication, and, nominally, the RAMP1 rs6431564 polymorphism were associated with non-responder status to ERE in migraine patients. Further validation of the present results in larger cohorts is needed. Full article