Search Results (2,275)

Porcine reproductive and respiratory syndrome (PRRS) has been prevalent in Germany for over 30 years, posing a significant threat to the local swine industry. There are limited analyses to offer German PRRSV ORF5 genetic and evolutionary characteristics and GP5 structural and functional features. In this study, a total of 518 sequences of the PRRSV GP5 gene were obtained from the GenBank database, encompassing 102 sequences from Germany to investigate the genetic relationships and GP5 structural and functional features. Similarly, phylogenetic and recombination analyses were used to identify genetic relationships. Two German PRRSV-1 lineage 1 strains exhibited more than 98.0% nucleotide similarity with vaccine strains. Eighteen German PRRSV-2 lineage 5 strains exhibited more than 98.0% nucleotide similarity with a prototype vaccine strain. German PRRSV-1 lineage 1 was predominant. GP5 structural and functional features were determined by N-glycosylation sites, B-cell epitopes, and transmembrane domain predictions. The main N-glycosylation patterns and transmembrane domains of German PRRSV-1 lineage 1 were time-dependent. Mutations of German PRRSV-1 lineage 3 in the primary neutralizing epitope were detected. In conclusion, these findings reveal lineage-specific molecular variation and improve the understanding of the molecular evolution of German PRRSV. Full article

Background/Objectives: Hybrid sterility arises when two fully fertile populations produce sterile offspring, representing a key postzygotic barrier to gene flow between emerging species. In the sterile hybrid males of Mus musculus domesticus (M. m. domesticus, represented by the C57BL/6J strain, hereafter B6) and Mus musculus musculus (M. m. musculus, represented by the wild-derived PWD/Ph strain), meiotic prophase I exhibits extensive autosomal asynapsis, pachytene arrest, and an absence of mature spermatozoa. This sterility results from Prdm9 allelic incompatibility, which is modulated by the X-linked Hstx2 locus, recently identified as the Mir465 microRNA. While this two-locus incompatibility is the major cause of sterility, additional modifiers may further contribute to the phenotype. In particular, the DNA mismatch repair protein MSH2 recognizes DNA sequence heterology and enforces anti-recombination in yeast. This raises the possibility that Msh2 could amplify the effects of subspecific sequence divergence in mouse hybrids. Methods: To test this hypothesis, we generated an Msh2 knockout on a B6 genetic background and assessed its effect on the hybrid sterility phenotype in F1 hybrid and backcross males. Results: Loss of MSH2 did not restore fertility in F1 hybrids. Testes weight remained low, and no mature spermatozoa were detected. In contrast, a modest partial rescue was observed in backcross males carrying the critical Prdm9/Mir465 genotype, with improvements in testes weight and sperm count. Conclusions: We examined the role of the Msh2 gene in arresting spermatogenesis in intersubspecific mouse hybrids. The results show that sterility is predominantly governed by the Prdm9-Mir465 incompatibility, and that DNA mismatch repair has a minor, genetic background-dependent effect. Full article

Background/Objectives: Plant architecture and kernel-related traits are important determinants of yield potential and breeding value in peanut (Arachis hypogaea L.). This study aimed to construct a high-density genetic linkage map, identify quantitative trait loci (QTL) associated with these traits, and prioritize candidate genes underlying key genomic regions in cultivated peanut. Methods: A recombinant inbred line population derived from Luojiangjiwo, a sprawling large-pod line, and Fuhuasheng, an erect small-pod line, was used to construct a high-density genetic linkage map and identify QTL associated with plant architecture and kernel traits. Results: Specific-locus amplified fragment sequencing generated 1,295,490,603 clean reads, with an average Q30 of 93.67%. After SNP discovery, filtering, and linkage analysis, 2646 SNP markers were mapped to 20 linkage groups, spanning 1338.86 cM with an average marker interval of 0.51 cM. Phenotypic evaluation of 16 traits revealed broad variation among 200 recombinant inbred lines, with strong positive correlations among pod-size traits and among kernel-size traits. Composite interval mapping detected eight QTL distributed on chr04, chr05, chr13, and chr15, including five QTL for plant architecture traits and three QTL for kernel-related traits. qLBL13 for lateral branch length explained the highest phenotypic variation, whereas qMKL05 for mean kernel length was delimited to a 0.151 Mb interval containing only nine genes. Candidate-gene analysis prioritized AH05G29360, encoding a knotted-1-like homeobox protein; AH05G29380, encoding mitogen-activated protein kinase kinase 9; AH05G29350, encoding COP1-interacting protein 7; and AH05G29410, encoding a pentatricopeptide repeat-containing protein. Additional candidates included AH15G16520, AH15G16460, AH15G16630, and AH15G16770 in the shared qHKW15/qMKW15 interval. Conclusions: This study identified genomic regions and biologically relevant candidate genes associated with plant architecture and kernel-related traits in peanut. These findings provide valuable genomic resources for future functional validation and facilitate marker-assisted breeding for improved plant architecture and kernel characteristics. Full article

The elite maize inbred line Zheng58, female parent of the widely cultivated hybrid Zhengdan958, is renowned for conferring short stature and high-density tolerance. Despite its critical role in modern breeding, the genetic basis of its dominant dwarfing effect has remained elusive. In this study, we dissected the genetic architecture of six plant architecture traits in a recombinant inbred line (RIL) population derived from elite inbred lines Zheng58 and PH6WC. Phenotypic evaluations across four environments revealed high heritability with additive effects accounting for 45.5–64.6% of the total genetic variance. A total of 125 QTLs were identified for the traits in single-environment QTL mapping, and multi-environment analysis further detected 77 QTLs for the six traits. Notably, a major dominant-negative pleiotropic QTL was identified on chromosome 2 that consistently explains plant height (PH), plant height above ear (PHAE), and average internode length above ear (AILAE) across multiple environments. The Zheng58 allele at this locus acts dominantly to reduce plant height by approximately 8.7 cm, providing a genetic explanation for Zheng58’s characteristic dwarfing effect. Regional association mapping refined this QTL to a 351.9 kb interval harboring 13 candidate genes. Transcriptome analysis uncovered 205 differentially expressed genes (DEGs) within the QTL region, with only one DEG (Zm00001d005848) located in the pleiotropic hotspot QTL on chromosome 2. This candidate gene encodes a rhomboid protease homolog, and population-wide expression data showed significantly negative correlation with PH. Our study unveils the genetic mystery of Zheng58′s dominant dwarfing phenotype by pinpointing a pleiotropic QTL hotspot, offering a strategic target for molecular breeding of compact, high-density-tolerant hybrids in maize. Full article

Soybean (Glycine max) is a major economic and food crop whose yield is severely affected by frogeye leaf spot (FLS), caused by Cercospora sojina. Current knowledge of resistance genes remains insufficient for effective molecular breeding. In this study, a recombinant inbred line (RIL) population derived from a cross between the resistant parent, Henong 60 (H60), and the susceptible parent, Dongnong L13 (DN L13), was evaluated under field conditions in Acheng (AC) and Xiangyang (XY). Plants were artificially inoculated with physiological race 7 of C. sojina, and disease severity at the R3 growth stage was recorded. Genotyping using the SoySNP660K chip yielded 54,836 high-quality single-nucleotide polymorphism (SNP) markers. A genome-wide association study (GWAS) was performed using the 3VmrMLM model by integrating dual-environment phenotypic data, and four quantitative trait nucleotides (QTNs) significantly associated with resistance to FLS were identified on chromosomes 8 (1), 17 (1), and 20 (2). By the analysis of genomic annotation, functional enrichment, metabolic pathway analyses, haplotype–phenotype association and quantitative real-time PCR (qRT-PCR), Glyma.20G155700 and Glyma.17G070500 are intended to be candidate genes related to soybean resistance to race 7 of FLS. The findings of this study provide insights into the genetic mechanisms underlying resistance to FLS in soybean. The identified molecular markers and candidate genes may provide useful resources for marker-assisted breeding and the development of disease-resistant germplasm. Full article

Although commercial vaccines against porcine circovirus type 2 (PCV2) have been widely implemented globally, PCV2 remains endemic in swine populations, accompanied by ongoing genotype replacement. Meanwhile, the emergence of novel porcine circoviruses (PCVs), including PCV3 and PCV4, has further complicated the prevention and control of porcine circovirus-associated diseases (PCVAD). This study systematically characterized the epidemiological patterns and genetic diversity of PCVs circulating in Eastern China. A total of 739 clinical samples collected between 2010 and 2016 were screened for PCV2. Additionally, 653 samples obtained during 2023–2024 were analyzed using a triplex real-time quantitative PCR (qPCR) assay for the simultaneous detection of PCV2, PCV3, and PCV4. Full-genome amplification and sequencing were subsequently performed on all PCR-positive samples. Epidemiological analysis revealed an overall PCV2 positivity rate of 37.62% during 2010–2016. In the 2023–2024 cohort, the positivity rates for PCV2 and PCV3 were 35.99% and 16.39%, respectively, with a co-infection rate of 10.26%. Notably, no PCV4-positive samples were detected. Phylogenetic analysis demonstrated that PCV2d is the predominant genotype in Eastern China. Furthermore, PCV2g strains were identified in clinical samples for the first time in mainland China, while PCV3b were determined to be the dominant circulating subtype of PCV3. Multiple critical amino acid substitutions were identified within the neutralizing epitopes of the PCV2 Cap protein, and a recombination event involving a PCV2d vaccine strain and a PCV2c reference strain was detected. In contrast, the PCV3 genome exhibited a high degree of genetic conservation. Collectively, these findings expand the molecular epidemiological landscape of PCVs in Eastern China and elucidate the evolutionary dynamics of circulating PCV strains, providing important insights for the development of next-generation vaccines and region-specific PCVAD control strategies. Full article

Porcine epidemic diarrhea virus (PEDV) continues to undergo genetic evolution and remains a major etiological agent of enteric disease in swine, causing significant economic losses worldwide. This study investigated the molecular epidemiology and genetic characteristics of PEDV circulating in Chongqing, China, between 2022 and 2024. A total of 296 diarrheic piglet samples collected from nine regions were screened using RT-qPCR, of which 48.31% (143/296) tested positive for PEDV. A subset of positive samples was subjected to S gene amplification and sequencing, yielding 15 complete sequences. Phylogenetic analysis revealed that all sequenced strains clustered within the G2c lineage and showed high nucleotide similarity (93.37–94.09%) to the classical CV777 strain. Recombination analysis indicated potential recombination events among field strains involving S-INDEL and G2b-like parental lineages, although these findings are based on a limited number of sequences. Sequence analysis identified multiple amino acid substitutions within the COE antigenic region, while other neutralizing epitopes (SS2, SS6, and 2C10) remained largely conserved. In addition, variation in predicted N-glycosylation sites was observed among some strains. Structural modelling suggested that these changes may influence spike protein conformation and antigenic properties; however, these interpretations are based on in silico analysis and require experimental validation. Overall, the findings indicate ongoing genetic evolution of PEDV in Chongqing and suggest circulation of G2c-associated variants in diarrheic piglets. However, given the limited and non-random nature of sequencing, these results may not fully represent the broader viral population. Continued large-scale molecular surveillance and functional studies are needed to better understand PEDV evolution and to support the development of improved control strategies and vaccines. Full article

Genetic recombination occurs in many organisms, from simple RNA viruses to mammals and plants with DNA genomes. In sexual reproduction, two parental genomes come together and undergo recombination, producing an offspring genome with a combination of information from the two parental genomes. Genome recombination that occurs during sexual reproduction can involve any one of several mechanisms, including copy-choice recombination as well as breakage and exchange. Across widely different organisms, recombination is generally promoted by factors that damage the genetic material. In organisms such as bacteriophage and Paramecium, it was experimentally demonstrated that recombinational repair during sexual reproduction can overcome otherwise deleterious or lethal damage. For many decades, it has been recognized that there are higher biological costs of sexual reproduction than for asexual reproduction. Theories assuming that genetic variation, due to recombination, is the main adaptive benefit of sexual reproduction have been widely accepted. Such a benefit was considered to compensate for the high cost of sexual reproduction. However, it has been difficult to find a strong, consistent benefit of variation. The repair of lethal damage, involving recombinational interactions of two different genomes, now appears to be the major selective factor underlying sexual reproduction in organisms both simple and complex. Full article

Porcine group A rotavirus (PoRVA) is a significant cause of viral diarrhea in piglets, necessitating urgent global implementation of effective control strategies. This review assesses advancements in PoRVA in vitro cultivation and amplification, crucial for PoRVA vaccine development. Traditional PoRVA cultivation commonly employs primary porcine kidney cells or finite cell lines like MA-104, posing well-documented challenges in scalability, production cost, and their ability to recapitulate the natural intestinal microenvironment. Consequently, research has increasingly focused on adapting PoRVA to alternative systems, particularly immortalized porcine cell lines or physiologically relevant porcine intestinal organoids. This adaptation process, involving serial passaging, can induce genomic alterations and virulence attenuation in piglets, essential for generating live attenuated vaccine (LAV) candidates. Modern biotechnological tools, such as reverse genetics and synthetic genomics, have expedited the creation of recombinant PoRVA strains with defined antigenic profiles and enhanced in vitro growth characteristics. However, a significant concern regarding LAV candidates derived from cell culture adaptation is the risk of virulence reversion upon pig back-passage, necessitating thorough safety and genetic stability evaluations. Nevertheless, utilizing stable cell lines or organoid platforms presents a feasible and cost-effective approach for large-scale PoRVA vaccine production. Future research should focus on identifying vaccine candidates that provide broad protection and exceptional safety, with an emphasis on cross-protection against divergent epidemic genotypes, while ensuring the economic feasibility of innovative manufacturing approaches. Full article

Improving soybean plant architecture is critical for enhancing yield potential. To dissect the genetics of related traits, a recombinant inbred line population of 175 F₉:₁₂ families (derived from Glycine max cultivars Jidou 12 [female] × Ji NF58 [male]) was used for quantitative trait locus (QTL) mapping. Four key traits—plant height, bottom pod height, node number on main stem, and branch number—were analyzed across six environments (two growing seasons × three locations) via two methods: composite interval mapping (CIM, QTL Cartographer v2.5) and mixed-model-based composite interval mapping (MCIM, QTLNetwork 2.0). A total of 22 stable QTLs were detected, with phenotypic variation explained (PVE) of 1.2–52.5%. Co-localized QTLs (due to significant trait correlations) concentrated in three genomic intervals: Satt286-Sat_251 (LG C2/chromosome 06), Satt156-Satt229 (LG L/chromosome 19), and Satt581-Sat_190 (LG O/chromosome 10). A novel QTL (qBPH-O-2) for bottom pod height was identified on LG O. Major QTLs with QTL-by-environment (QE) interactions were found on LG A1 (plant height, node number on main stem) and qBN-C2-1 (branch number, high additive effects + QE interactions). These findings support marker-assisted selection (MAS), targeted plant architecture improvement, and gene pyramiding in soybean breeding. Full article

Enterovirus G (EV-G) is an important enteric pathogen widely circulating in swine populations and is characterized by considerable genetic diversity and recombination potential. In recent years, recombinant EV-G strains carrying exogenous papain-like cysteine protease (PLCP) gene insertions have been increasingly reported; however, their genotype distribution and molecular characteristics in major pig-producing regions remain poorly understood. In this study, 356 clinical samples collected from Guangxi, southern China, between 2020 and 2025 were screened for EV-G, and 13 representative strains were subjected to whole-genome sequencing and sequence analysis. The overall EV-G positivity rate in Guangxi was 20.51% (73/356). Phylogenetic analysis showed that the 13 Guangxi EV-G strains were mainly classified into three genotypes, G1, G2, and G8, with G1 being the predominant genotype. Notably, PLCP gene insertions of 573–642 nt were identified at the 2C/3A junction in seven strains belonging to three distinct genotypes, G1, G2, and G8, demonstrating the cross-genotype distribution of PLCP insertions within a single geographic region. Phylogenetic analysis of the PLCP sequences demonstrated that all Guangxi-derived PLCP sequences clustered within the EV-G-PLCP clade and were clearly separated from the torovirus PLCP clade. Recombination analysis retained three potential recombination events with clearer combined support from RDP4 and SimPlot analyses, involving Guangxi strains GX3008, GX3022, and GX4292. Selection pressure analysis showed that the VP1 gene was overall under negative selection. Collectively, these findings demonstrate the co-circulation of multiple EV-G genotypes, the cross-genotype distribution of PLCP insertions, and the presence of potential recombination events in Guangxi. This study provides new evidence for understanding the genetic diversity, genomic plasticity, and regional molecular characteristics of EV-G, and also provides an important basis for future PLCP-related functional studies and continued EV-G surveillance. Full article

Background/Objectives: Porcine circovirus type 2 (PCV2) remains a major viral agent in pig production worldwide due to its association with economically relevant diseases and productivity losses. Nine genotypes (PCV2a–PCV2i) have been reported, with successive genotype shifts characterized by the historical predominance of PCV2a, the expansion of PCV2b, and the emergence of PCV2d as the predominant genotype in several swine-producing countries. The aim of this study was to characterize the ORF2 gene of PCV2 circulating in Jalisco, Mexico, to provide updated information for regional surveillance and control strategies. Methods: Samples were collected from 80 pig farms located in four regions of Jalisco with different pig density levels and production systems. PCV2-positive samples were subjected to ORF2 amplification and sequencing. Genotype assignment, phylogenetic analysis, and in silico recombination screening using multiple detection methods were performed. All sequences were deposited in GenBank. Results: A total of 70 ORF2-PCV2 sequences were obtained and assigned to two genotypes: PCV2d (51/70, 72.9%) and PCV2a (19/70, 27.1%). The sequences were submitted to GenBank under accession numbers PV235521–PV235590. Recombination analysis identified seven recombinant sequences, and unusual ORF2 extensions were detected in some sequences, evidencing the presence of genetic variants circulating in the region. Conclusions: These findings confirm the predominance of PCV2d in Jalisco while highlighting the continued circulation of PCV2a. The coexistence of both genotypes, together with recombinant sequences and ORF2 extensions, indicates ongoing PCV2 genetic diversification in the region. Continuous molecular surveillance remains essential to monitor viral evolution, support genotype-informed control strategies, and strengthen swine health programs. Full article

Picornaviruses pose a significant threat to both human and animal health, causing many diseases in humans and swine. Porcine sapelovirus (PSV) is a globally reported enteric picornavirus commonly associated with subclinical or mild enteric infections in swine populations. Critically, unlike other neurotropic picornaviruses such as Enterovirus A71, no PSV strain has been reported to breach the blood–brain barrier (BBB). Since 2023, outbreaks of diarrhea with concurrent neurological signs like ataxia and lameness have been observed in weaned piglets across China, in particular, on a farm in Zhejiang province in 2025 with 100% morbidity and 20% mortality among the cases. Routine diagnostics ruled out common swine pathogens, but qPCR was positive for PSV. We successfully isolated three PSV strains (ZJ, FJ, SD) from affected piglets. Genetic analysis revealed that the PSV-ZJ is a novel recombinant between strains YC2011/2012 (China, 2011) and XTND/2019 (Vietnam, 2018). Pathogenicity assessment confirmed that the recombinant PSV-ZJ is highly pathogenic, causing severe diarrhea, growth retardation, and significant viral shedding via the respiratory and digestive tracts. qPCR and histopathology confirmed viral presence in intestinal and brain tissues, indicating that PSV-ZJ can cross the blood–brain barrier. This study presents the first quantitative viral load and histopathological data for a highly pathogenic recombinant PSV strain in China and emphasizes the critical role of recombination in driving viral virulence evolution, necessitating enhanced surveillance and the development of targeted preventive strategies. Full article

Determining HIV-1 tropism provides the prognosis of HIV infection and is required before prescribing maraviroc, an entry inhibitor that blocks the interaction between the viral gp120 and the CCR5 coreceptor. However, existing prediction algorithms have been developed primarily for the globally most prevalent subtypes (B, C, and CRF01_AE) and often show reduced performance for other HIV-1 genetic variants. Sub-subtype A6 and circulating recombinant form CRF63_02A6 dominate the HIV-1 epidemic in Russia and other Former Soviet Union (FSU) countries, yet the reliability of tropism prediction for these viruses remains virtually unexplored. We phenotypically determined the tropism of 25 clinical isolates (11 R5, 1 X4, and 7 dual-tropic R5/X4) using U87.CD4.CCR5 and U87.CD4.CXCR4 cell lines and performed a comparative analysis of eight existing genotypic tools (Geno2pheno, WebPSSM, T-CUP 2.0, the Delobel/Garrido rules, and others) or their modifications on a combined dataset that included Los Alamos National Laboratory (LANL) reference sequences (subtypes A, B, C, CRF01_AE, and CRF02_AG) and our laboratory-derived isolates. Most models achieved high accuracy for globally prevalent subtypes (≈95% for B, C, and CRF01_AE) but showed markedly reduced performance for sub-subtype A6 (best accuracy among existing models, 85%) and CRF63_02A6 (best accuracy, 72%), with a poor balance between sensitivity and specificity. To address this problem, we developed HIV-V3Augur, an ensemble stacking model based on the Random Forest and Support Vector Machine (SVM) machine learning algorithms, trained on Pseudo Amino Acid Composition (PseAAC) and Relative Synonymous Codon Usage (RSCU) features with 10-fold stratified cross-validation. HIV-V3Augur achieved an accuracy of 77%, sensitivity of 79%, and specificity of 79% on sub-subtype A6, and on CRF63_02A6 it reached an accuracy of 95%, sensitivity of 87%, and specificity of 100%. Cross-validation demonstrated that HIV-V3Augur represents a balanced genotypic tropism prediction tool for understudied HIV-1 variants circulating in the FSU region. HIV-V3Augur can be used locally through a graphical user interface. Full article

Ring finger protein 126 (RNF126) is a RING-type E3 ubiquitin ligase that has recently emerged as a multifaceted regulator of cellular homeostasis, stress adaptation, and disease progression. Through its structurally distinct zinc-finger and catalytic RING domains, RNF126 orchestrates substrate recognition and ubiquitin transfer, generating diverse ubiquitin linkages with both proteolytic and nonproteolytic functions. Initially characterized as a component of the protein quality control (PQC) machinery, RNF126 cooperates with chaperones such as BAG6 and UBQLN1 to eliminate mislocalized and misfolded proteins, thereby maintaining proteostasis. Beyond PQC, RNF126 plays pivotal roles in DNA damage response pathways by regulating homologous recombination, non-homologous end joining, checkpoint signaling, and genome stability through substrates, including MRE11, Ku80, RNF168, and 14-3-3σ. Genetic studies have further demonstrated its importance in embryogenesis and male fertility, and accumulating evidence has identified RNF126 as a critical driver of malignancy in multiple cancers. RNF126 promotes tumor progression by degrading or modulating key regulators, such as p21, PTEN, p53, PDKs, and LKB1, thereby enhancing proliferation, metabolic reprogramming, anoikis resistance, metastasis, and chemo/radioresistance. Intriguingly, RNF126 exhibits context-dependent functions, acting as an oncogene or tumor suppressor depending on the tissue type and substrate selection. In addition to cancer, RNF126 has been implicated in neurodegeneration, cardiac pathology, antiviral immunity and adaptive immune regulation. This review summarizes the current knowledge of RNF126 structure, ubiquitin signaling mechanisms, physiological functions, and pathological roles, while discussing emerging therapeutic strategies and future challenges for targeting RNF126 in precision medicine. Full article