Search Results (117)

Seed oil represents a key trait in soybeans, which holds substantial economic significance, contributing to roughly 60% of global oilseed production. This research employed genome-wide association mapping to identify genetic loci associated with oil content in soybean seeds. A panel comprising 341 soybean accessions, primarily sourced from Northeast China, was assessed for seed oil content at Heilongjiang Province in three replications over two growing seasons (2021 and 2023) and underwent genotyping via whole-genome resequencing, resulting in 1,048,576 high-quality SNP markers. Phenotypic analysis indicated notable variation in oil content, ranging from 11.00% to 21.77%, with an average increase of 1.73% to 2.28% across all growing regions between 2021 and 2023. A genome-wide association study (GWAS) analysis revealed 119 significant single-nucleotide polymorphism (SNP) loci associated with oil content, with a prominent cluster of 77 SNPs located on chromosome 8. Candidate gene analysis identified four key genes potentially implicated in oil content regulation, selected based on proximity to significant SNPs (≤10 kb) and functional annotation related to lipid metabolism and signal transduction. Notably, Glyma.08G123500, encoding a receptor-like kinase involved in signal transduction, contained multiple significant SNPs with PROVEAN scores ranging from deleterious (−1.633) to neutral (0.933), indicating complex functional impacts on protein function. Additional candidate genes include Glyma.08G110000 (hydroxycinnamoyl-CoA transferase), Glyma.08G117400 (PPR repeat protein), and Glyma.08G117600 (WD40 repeat protein), each showing distinct expression patterns and functional roles. Some SNP clusters were associated with increased oil content, while others correlated with decreased oil content, indicating complex genetic regulation of this trait. The findings provide molecular markers with potential for marker-assisted selection (MAS) in breeding programs aimed at increasing soybean oil content and enhancing our understanding of the genetic architecture governing this critical agricultural trait. Full article

The tufted deer (Elaphodus cephalophus), a Near-Threatened (NT) species endemic to China and Myanmar, requires robust genetic data for effective conservation. However, the genetic landscape of key populations, such as those in Chongqing, remains poorly understood. This study aimed to comprehensively evaluate the genetic diversity, population structure, gene flow, and demographic history of tufted deer across this critical region. We analyzed mitochondrial DNA (mtDNA) from 46 non-invasively collected fecal samples from three distinct populations: Jinfo Mountain (JF, n = 13), Simian Mountain (SM, n = 21), and the Northeastern Mountainous region (NEM, n = 12). Genetic variation was assessed using the cytochrome b (Cyt b) and D-loop regions, with analyses including F_st, gene flow (N_m), neutrality tests, and Bayesian Skyline Plots (BSP). Our results revealed the highest genetic diversity in the SM population, establishing it as a genetic hub. In contrast, the JF population exhibited the lowest diversity and significant genetic differentiation (>0.23) from the SM and NEM populations, indicating profound isolation. Gene flow was substantial between SM and NEM but severely restricted for the JF population. Demographic analyses, including BSP, indicated a long history of demographic stability followed by a significant expansion beginning in the Middle to Late Pleistocene. We conclude that the SM/NEM metapopulation serves as the genetic core for the species in this region, while the highly isolated JF population constitutes a distinct and vulnerable Management Unit (MU). This historical demographic expansion is likely linked to climatic and environmental changes during the Pleistocene, rather than recent anthropogenic factors. These findings underscore the urgent need for a dual conservation strategy: targeted management for the isolated JF population and the establishment of ecological corridors to connect the Jinfo Mountain and Simian Mountain populations, ensuring the long-term persistence of this unique species. Full article

Background/Objectives: Chemically or genetically detoxified pertussis toxin (PTx) is a crucial antigen component of the acellular pertussis vaccine. Chemical detoxification using glutaraldehyde generally causes significant structural changes to the toxin. However, how these structural changes in PTx affect its antigenic properties remains unclear. Additionally, there is limited knowledge regarding how many alterations in antigenic properties impact immunogenicity. Methods: To investigate the impact of structural changes on antigenic properties, we developed a sandwich ELISA to quantify the neutralizing epitopes on PTx. Subsequently, we analyzed different PTx toxoid (PTd) preparations with the assay. Additionally, we assessed the immunogenicity of various acellular pertussis vaccine candidates containing these PTd preparations. Finally, the assay was applied to evaluate the consistency of commercial batches of PTx and PTd intermediates. Results: The assay demonstrated reasonable specificity, accuracy, and precision, and it was sensitive enough to quantify variations in neutralizing epitopes among different PTd samples that shared the same protein concentration. Importantly, we found a positive correlation between the number of neutralizing epitopes in detoxified PTx and its immunogenicity, indicating that the amount of neutralizing epitopes present determines the immunogenicity of glutaraldehyde-inactivated PTx. Moreover, commercial batches of PTx and PTd intermediates exhibited minor variations in neutralizing epitopes. Conclusions: These findings have significant implications for developing acellular pertussis vaccines as they highlight the importance of preserving the neutralizing epitopes of PTx during detoxification to ensure the vaccine’s effectiveness. This assay is also valuable for the quality control of PTd as it more accurately represents the actual antigenic changes of PTx. Full article

The non-random usage of synonymous codons encoding the same amino acid—referred to as codon usage bias (CUB)—varies substantially across genomes and significantly affects translational efficiency by modulating transcriptional and post-transcriptional processes. In chloroplast genomes, the optimization of CUB is critical for improving the efficacy of genetic engineering approaches. However, comprehensive analyses of CUB in Fagopyrum chloroplast genomes remain scarce. In this study, we performed an in-depth comparative analysis of codon usage patterns in the chloroplast genomes of nine Fagopyrum species. Our results revealed a marked AT-rich nucleotide composition, with base content in the order T > A > C > G. We identified 23 optimal codons and 29 high-frequency codons, most of which ended with A or U. Correlation analyses demonstrated that codon usage is strongly influenced by nucleotide skewness (GC and AT skews), protein properties (such as amino acid composition and the number of synonymous codons), and gene expression levels. Neutrality plot analysis (PR2 bias) and evaluations based on the effective number of codons (ENc) indicated that both mutational pressure and natural selection contribute to shaping CUB, with natural selection identified as the predominant evolutionary force. Comparative analyses with four model organisms indicated that Arabidopsis thaliana shares the highest codon usage compatibility with Fagopyrum chloroplast genomes, highlighting its suitability as a potential heterologous expression system. Phylogenetic reconstruction based on codon usage profiles yielded a fully resolved topology with 100% bootstrap support at all nodes, reinforcing the utility of codon usage data in evolutionary inference. This study elucidates the evolutionary determinants of codon usage variation in Fagopyrum plastomes and provides a robust methodological foundation for codon optimization in chloroplast-based synthetic biology. The validated codon adaptation metrics offer promising tools for improving heterologous protein expression and guiding transgene design in advanced breeding strategies. Full article

Tomato leaf curl Palampur virus (ToLCPalV) is an economically important bipartite begomovirus in the agro-ecological regions in south and western Asia. This study was designed to investigate the sequence variation dynamics, regional delineation, genetic diversity, population structure, and cross-border dispersal patterns of ToLCPalV. The research revealed clear geographical structuring, with distinct Indo–Pak subcontinent and Middle Eastern clades, but no host-specific differentiation. Genetic diversity analysis indicated higher diversity in the Indo–Pak subcontinent, particularly in the DNA-B component, suggesting an older, more diverse population of ToLCPalV prevailing in this region. Neutrality tests and selection pressure analyses revealed predominantly purifying selection, with limited positive selection observed in BV1 of DNA-B. The primary source of dispersal of ToLCPalV progenitor was estimated in Varnasi, India in 1955, from where the virus was spread. No recombination events were detected, suggesting that mutation and selection are the primary drivers of ToLCPalV evolution. Furthermore, a detailed SDT-based nucleotide sequence comparison analysis also identified two potential strains of ToLCPalV. This study elucidates the spatiotemporal dynamics and evolutionary history of ToLCPalV, revealing its cross-border spread and adaptive evolution. These findings contribute to a more comprehensive understanding of begomovirus epidemiology and provide valuable insights into ToLCPalV’s phylogeography and evolutionary dynamics. Full article

Porcine epidemic diarrhea virus (PEDV) is a major pathogen responsible for viral diarrhea in pigs, causing particularly high mortality in neonatal piglets. In recent years, genetic variations in PEDV have resulted in alterations in both its virulence and antigenicity, leading to a reduced efficacy of existing vaccines. In this study, diarrheal samples were collected from four commercial pig farms in the Hubei, Guangxi, and Jiangxi provinces, China, which experienced vaccine failure. RT-qPCR confirmed PEDV infection, and three PEDV strains, 2021-HBMC, 2024-JXYX, and 2024-JXNC, were successfully isolated. Sequence analysis and phylogenetic tree construction classified these strains into the G2c genotype, the predominant subtype in China. The neutralization assays revealed a significant reduction in the neutralizing titers of these strains against the immune serum compared with the AJ1102 reference strain. Further amino acid sequence analysis of the spike (S) protein identified several mutations in key neutralizing epitopes compared with the AJ1102 strain, including S27L, E57A, N139D, M214T, and P229L in the S-NTD epitope; A520S, F539L, K566N, D569E, G612V, P634S, E636V/K in the COE epitope; and Y1376H in the 2C10 epitope, along with several deletions at N-glycosylation sites (347NSSD and 510NITV). Additionally, whole-genome sequencing and recombination analysis indicated that the 2021-HBMC strain may have resulted from a recombination event. The findings of this study underscore the challenge posed by the continuous genetic evolution of PEDV to vaccine efficacy and provide valuable insights for future vaccine development and control strategies. Full article

Background: Human milk oligosaccharides (HMOs) serve as critical bioactive components supporting infant growth and development. However, the influence of maternal metabolic factors during lactation on HMOs remains to be fully elucidated. This study aimed to investigate the association between maternal metabolic factors and HMOs, as well as the potential mediating effects of these factors. Methods: An observational cross-sectional study was conducted in Central South China, enrolling 196 lactating mothers. HMOs were quantified using liquid chromatography-tandem mass spectrometry. Maternal metabolic factors were assessed through physical examinations. Associations between metabolic factors and HMOs were analyzed using linear regression, and mediation effects were evaluated. Results: HMOs from Central South China were predominantly composed of neutral fucosylated HMOs. Significant differences were observed in the levels of several HMOs across maternal age groups and lactation periods. The concentration of 3′-sialyllactose (3′-SL) exhibited a negative association with the pre-pregnancy body mass index (BMI) (β = −0.16, 95% CI: −0.29, −0.03; p = 0.02), while a positive association was found with maternal heart rate (β = 0.14, 95% CI: 0.01, 0.27; p = 0.04). However, these associations were different between secretor and non-secretor mothers. Associations of 3′-SL with pre-pregnancy BMI and maternal HR were only found in the secretor mothers. Triglycerides and low-density lipoprotein cholesterol mediated the associations between maternal pre-pregnancy BMI and 3′-sialyllactose (3′-SL). Conclusions: The variations of several HMOs among mothers from Central South China were associated with maternal age and lactation period. The concentration of 3′-SL was negatively correlated with maternal pre-pregnancy BMI. The potential mechanism underlying the influence of maternal BMI on 3′-SL levels may involve maternal lipid metabolism and genetic factors. Full article

We performed a comprehensive structural analysis of the conformational space of several spike (S) protein variants using molecular dynamics (MD) simulations. Specifically, we examined four well-known variants (Delta, BA.1, XBB.1.5, and JN.1) alongside the wild-type (WT) form of SARS-CoV-2. The conformational states of each variant were characterized by analyzing their distributions within a selected space of collective variables (CVs), such as inter-domain distances between the receptor-binding domain (RBD) and the N-terminal domain (NTD). Our primary focus was to identify conformational states relevant to potential structural transitions and to determine the set of native contacts (NCs) that stabilize these conformations. The results reveal that genetically more distant variants, such as XBB.1.5, BA.1, and JN.1, tend to adopt more compact conformational states compared to the WT. Additionally, these variants exhibit novel NC profiles, characterized by an increased number of specific contacts distributed among ionic, polar, and nonpolar residues. We further analyzed the impact of specific mutations, including T478K, N500Y, and Y504H. These mutations not only enhance interactions with the human host receptor but also alter inter-chain stability by introducing additional NCs compared to the WT. Consequently, these mutations may influence the accessibility of certain protein regions to neutralizing antibodies. Overall, these findings contribute to a deeper understanding of the structural and functional variations among S protein variants. Full article

It is generally recognized that clovers represent a major nutrient used in ruminants’ diets due to their composition, which is high in protein content and low in fiber content. Investigating the nutritional quality of red and white clover genotypes, and classifying the genetic materials according to their primary quality attributes were the main goals of the current study. During a two-year experiment, we assessed their performance stability. Twelve red clover (Trifolium pratense L.) and twelve white clover (Trifolium repens L.) genetic materials were cultivated in a randomized complete block experimental design. Crude protein (CP%), acid detergent fiber (ADF%) and neutral detergent fiber (NDF%) concentrations were measured, and the relative feed value (RFV) was calculated using the estimates of digestible dry matter (DDM%) and potential dry matter intake (DMI% of body weight) of the forage. The average CP% content for white clover varied between 17.18% (REP-4) and 20.55% (REP-9) during the two years of testing. Regarding the red clover, the populations PRA-4, PRA-3, PRA-5, and PRA-10 exhibited the highest CP% content (19.98%) and the lowest ADF% (less than 29%). Although the variation was stable across the years, the profile of this variation of CP, ADF, and NDF for each clover species differs. The CP% was related negatively to ADF% and thus positively to DDM in both species but not with the same allocation, forming different clusters. PRA-3 and PRA-4 for the red clover and REP-5 for the white clover genetic materials exhibited characteristics belonging to the other species studied regarding their content in protein and fiber. Because of their relationship, CP and DDM could be improved simultaneously by breeders. This study revealed that ROZETA and PRA-4 were more stable genetic materials in red clover, and GRASSLANDS HUIA, RIVENDEL, and REP-5 in white clover. Full article

Early sowing to avoid stress later in the season is limited by low early spring temperatures and unpredictable cold spells within recommended sowing dates. To achieve successful crop production, it is essential to understand plant stress responses, enabling breeders and producers to better address climate change challenges. Researching genetic variability for cold stress is key to developing cold-tolerant crops. In response, a study investigating the effects of low-temperature treatment and cold priming in the early vegetative development on soybean biomass, chlorophyll a fluorescence (ChlF) and pigment-related spectral reflectance indices (PR_SRIs) was conducted in a controlled environment with 12 soybean genotypes. Priming began 16 days after sowing (DAS), followed by a 48-h recovery and a subsequent 48-h low-temperature treatment. During priming and stress treatments, temperatures and relative air humidity were set to 10/5 °C and 70/90% (day/night), with a light intensity of 300 μmol/m²/s. The results showed that low temperatures negatively impacted biomass and physiological parameters, with priming having neutral or negative effects. The parameters ET₀/TR₀, RE₀/RC, TR₀/DI₀, F_m, F_v, ARI1, and ARI2 were identified as relatively appropriate non-destructive alternatives for biomass analysis, aiding in genotype screening and stress detection. Genotypic variation in response to cold stress suggests potential for selecting cold-tolerant varieties. Full article

To better understand the population genetic structure and molecular biological background of Conger myriaster, an economically important marine fish, a total of 217 complete mitochondrial cytochrome b (Cyt b) gene sequences with a length of 1142 bp were obtained to assess the genetic diversity, population differentiation, and demographic history of seven populations along the coastal waters of China. The analysis of population genetic diversity showed a high level of haplotype diversity and a low level of nucleotide diversity. The analysis of molecular variance (AMOVA) and the genetic differentiation coefficient (F_ST) showed that most of the variation came from within populations, and the geographic distribution of haplotypes revealed non-significant genetic differentiation among populations. Tracing the population dynamic history, the results of the neutrality test and mismatch analysis suggested that the populations of C. myriaster in coastal China seas had experienced demographic expansion, and the expansion time can be traced back to the middle Pleistocene period. These results provide supplemental information for the sustainable utilization of fishery resources of this species. Full article

Understanding genetic diversity is crucial for plant adaptation in a changing world. The neutral genetic variation (NGD) is correlated to adaptation capacity, which is crucial for long-term conservation of threatened species. Brazil, a megadiverse nation with habitats encompassing a great variety of ecosystems, harbors a wealth of plant biodiversity, yet studies on NGD remain scarce. This work analyzed published data on NGD in native Brazilian plant populations, identifying 731 papers through a systematic search on the Scopus database. Results indicated microsatellite markers as the most used for population studies, followed by ISSR. The SNP marker is still underutilized, possibly due to its higher costs and labor-intensiveness. Fabaceae, Bromeliaceae, and Arecaceae were the most studied families. Moreover, the two most studied species were Euterpe edulis and Hancornia speciosa, both economically important species. Notably, trees and herbs dominated the studies with a focus on the Atlantic Forest biome. However, Cerrado and Amazon biomes were also well represented, underscoring the importance of broader investigation across all Brazilian ecosystems. These findings reveal a critical gap in knowledge, where traditional molecular markers are most used and few economically important species are intensively studied. The number of threatened species studied is negligible, and most are not endemic. With looming climate and landscape changes, more comprehensive studies of NGD of threatened flora in Brazil are vital. The lack of genetic diversity information of native species may threaten any conservation efforts in the long term. Full article

Although genome-wide studies have identified a number of candidate regions evolving under selection in domesticated animals and cultivated plants, few attempts have been made, from the point of a definite biological process, to assess sequence variation and characterize the regimes of the selection on miRNA-associated motifs. Here, we performed a genome-wide dissection of nucleotide variation and selection of miRNA targets associated with rice flower development. By sampling and resequencing 26 miRNA targets for globally diverse representative populations of Asian cultivated rice and wild relatives, we found that purifying selection has reduced genetic variation at the conserved miRNA binding sites on the whole, and highly conserved miRNA binding sequences were maintained in the studied rice populations. Conversely, non-neutral evolution of positive and/or artificial selection accelerates the elevated variations at nonconserved binding sites in a population-specific behavior which may have contributed to flower development-related phenotypic variation. Taken together, our results elucidate that miRNA targets involved in flower development are under distinctive selection regimes during rice evolution. Full article

Rice (Oryza) is a genus in the Gramineae family, which has grown widely all over the world and is a staple food source for people’s survival. The genetic information of rice has garnered significant attention in recent years, prompting numerous researchers to conduct extensive investigations in this field. But rice mitochondrial codon usage patterns have received little attention. The present study systematically analyzed the codon usage patterns and sources of variance in the mitochondrial genome sequences of five rice species by the CodonW and R software programs. Our results revealed that the GC content of codons in rice mitochondrial genome genes was determined to be 43.60%. Notably, the individual codon positions exhibited distinct GC contents: 48.00% for position 1, 42.65% for position 2, and 40.16% for position 3. These findings suggest the preference of the rice mitochondrial genome for codons ending in A or U. A weak codon bias was observed, with the effective number of codons (ENC) varying between 40.02 and 61.00, with an average value of 54.34. Subsequently, we identified 25 identical high-frequency codons in five rice mitochondrial genomes, with 11 codons ending in A and 12 codons ending in U. The regression lines in the neutrality plot exhibited slopes of less than 0.5 in five rice species, indicating a predominant role of natural selection, while mutation pressure remained relatively insignificant. In the PR2-plot analysis, most of the genes were located in the right half of the plot, indicating that the third base of the synonymous codon was preferred to end in G than C. Additionally, the ENC plot and ENC ratio analysis unveiled that codon preferences in the rice mitochondrial genome were predominantly influenced by natural selection rather than mutational pressure. The analysis of correspondence revealed distinct variations in the codon usage pattern across five rice mitochondrial genomes. Based on the RSCU values of species, a cluster tree was inconsistent with the mitochondrial genetic data, indicating that RSCU data could not be used as a basis for classification at the species level in the Oryza genus. These results will help decide the specific types of natural selection pressures influencing codon usage and improve the expression of exogenous genes in rice mitochondrial genomes by optimizing their codons. Full article

Clonorchis sinensis is an important zoonotic parasite that is mainly prevalent in China, Korea, Vietnam and the Russian Far East. To explore the genetic variation and population structure of C. sinensis, an in silico analysis was conducted based on mitochondrial cytochrome c oxidase subunit 1 (COX1), ribosomal internal transcribed spacer 1 (ITS1) and ribosomal internal transcribed spacer 2 (ITS2) sequences. The sequences obtained from NCBI were truncated for further analyses, including haplotype network, phylogenetic, gene flow, diversity and neutrality analyses. The results showed that there were 20, 11 and 4 haplotypes for COX1, ITS1 and ITS2, respectively. The results of both the haplotype network and phylogenetic analyses indicated that the haplotypes for each type of sequence from the same country were not all clustered together. Haplotype diversity values were all lower than 0.5. Values of nucleotide diversity were higher than 0.005, except for ITS2. Tajima’s D and Fu’s Fs values were all negative, and p-values showed significant differences, indicating that the population of C. sinensis is growing. Fst values were all lower than 0.05. In conclusion, this study found that there are specific variations of C. sinensis in different countries, and the population of this parasite is growing with less genetic variation. The findings provide a crucial foundation for understanding the molecular epidemiology and population dynamics of C. sinensis. Full article