Search Results (1,275)

The largefin longbarbel catfish (Hemibagrus macropterus), a freshwater species endemic to China with fundamental economic importance, requires investigation into its genetic structure for effective management. In this study, we employed mitochondrial cytochrome b (Cytb) gene sequences and 14 microsatellite loci to elucidate the genetic structure of 195 individuals across eight distinct populations. The Cytb analysis revealed a haplotype number (H) of 31, haplotype diversity (Hd) of 0.853, and nucleotide diversity (π) of 0.0127. Population neutrality tests indicated that Tajima’s D (−0.59467) and Fu and Li’s D* (0.56621) were not statistically significant, and the mismatch distribution exhibited a multimodal pattern. Microsatellite analysis revealed that the mean number of alleles (Na), observed heterozygosity (Ho), and polymorphic information content (PIC) across all loci were 18.500, 0.761, and 0.808, respectively. The UPGMA phylogram constructed based on genetic distance identified two distinct clusters, with paired Fst values ranging from 0.108 to 0.138. These results suggest that the largefin longbarbel catfish is in a state of dynamic equilibrium with high genetic diversity. Furthermore, there was significant genetic differentiation between the YB population and the other seven populations, indicating that the population in the upper reaches of the Yangtze River should be managed as a distinct unit. Full article

Yellow seabream (Acanthopagrus latus), a species of significant economic importance, predominantly inhabits the warm waters of the Indo-Western Pacific. While previous studies have explored the genetic diversity of A. latus using microsatellites and other nuclear markers, a comprehensive understanding of its genetic characteristics and adaptive evolution using whole-genome resequencing (WGR) remains limited. In this study, we collected 60 individuals from six distinct geographic locations and performed WGR, achieving an average sequencing depth of 12.59×, which resulted in the identification of 19,488,059 high-quality single-nucleotide polymorphisms (SNPs). The nucleotide polymorphism (π_θ) across all populations was consistent, ranging from 0.003042 to 0.003155, indicating low genetic differentiation among populations. Comparative analyses revealed that populations other than that in Xiamen (XM) have undergone adaptive evolution, potentially linked to traits such as growth and development, feeding, immunity, and movement. This study explores the population genetics and adaptive evolutionary patterns of Acanthopagrus latus at the genomic level, providing an essential foundation for the conservation and management of this economically important species in the future. Full article

Herbivorous livestock, such as cattle, sheep, goats, horses, and donkeys, play a crucial role in agricultural production and possess remarkable resilience to extreme environmental conditions, driven by complex genetic mechanisms. Recent advancements in high-throughput sequencing, genome assembly, and environmental data integration have enabled a deeper understanding of the genetic basis of their environmental adaptation. This review identifies key genes associated with high-altitude, heat, cold, and drought adaptation, providing insights into the molecular mechanisms underlying these traits. By elucidating these genetic adaptations, our study aims to support conservation efforts, inform selective breeding programs, and enhance agricultural productivity, ultimately contributing to sustainable livestock farming and economic benefits for farmers. Full article

Circular RNA (circRNA) has a significant impact on the maturation of skeletal muscle, although their precise functions within this framework remain largely uncharted. This study presents an investigation of the regulatory effect of circAGGF1 on myogenesis in myoblasts, including the potential molecular mechanisms involved. It is revealed that circAGGF1 facilitates the differentiation of myoblasts into other states while simultaneously enhancing the manifestation of type I muscle fibers. In vivo investigations with mice revealed the promotion of skeletal muscle expansion and maturation by circAGGF1, bolstering its regenerative capacity. Mechanistically, circAGGF1 interacts with miR-199a-3p by acting as a sponge, promoting the subsequent expression of Fgf7. Furthermore, rescue experiments indicated a counteraction of the myogenesis induced by circAGGF1 overexpression by miR-199a-3p. To summarize, this research highlights the role played by circAGGF1 in the development of skeletal muscle, providing a valuable resource for enhancing our understanding of skeletal muscle biology. Full article

This study aimed to elucidate the genetic basis of lipid composition in the breast muscles of poultry, including AA broilers, dwarf guinea fowl, quails, and pigeons, and the impact of artificial selection on lipid traits. By employing lipidomics and transcriptomic sequencing, the research analyzed the chest muscle tissues of these four poultry. A total of 1542 lipid molecules were identified, with 711 showing significant differences among species. These lipids primarily belonged to subclasses such as TG, PC, Phosphatidylethanolamine (PE), Ceramides (Cer), and Diglyceride (DG), with each species demonstrating distinct profiles in these subclasses. Additionally, 5790 orthologous genes were identified, with 763, 767, 24, and 8 genes in AA broilers, dwarf guinea fowl, quails, and pigeons, respectively, exhibiting positive selection (Ka/Ks > 1). Notably, 114 genes related to lipid metabolism displayed significant differential expression, particularly between AA broilers and dwarf guinea fowl. The findings revealed that the metabolic pathways of PC and LPC lipid molecules in the glycerophospholipid pathway, as well as TG lipid molecules in the glycerolipid pathway, exhibited marked interspecies differences, potentially contributing to variations in breast muscle lipid composition. These results provide a solid foundation for understanding the lipid composition and molecular regulatory mechanisms in diverse poultry, offering valuable insights for further research in poultry lipid metabolism and artificial breeding programs. Full article

We report the first high-quality genome-wide assembly for Arctica islandica, the longest-lived non-colonial species, with a reported maximum life span of 507 years. The genome was assembled using short- and long-read DNA sequencing and RNA sequencing of four tissues. All assessment approaches indicated that the assembled genome is complete, contiguous, and accurate. The genome size is estimated at 1781.15 million base pairs (Mbps) with a coverage of 247.8×. The heterozygous rate was 1.15% and the repeat content 67.66%. Genome completeness evaluated by complete BUSCOs was 92.7%. The non-redundant gene set consisted of 39,509 genes with an average transcript length of 15,429 bp. More than 98% of the genes could be annotated across databases. Predicted non-coding RNAs included 801 miRNAs, 11,114 tRNAs, 909 rRNAs, and 349 snRNAs. The Arctica islandica genome, along with the assembly of genomes from other clam species, sets the stage for elucidating the molecular basis for the convergence of extreme longevity across these bivalve species. Full article

Brachyura is among the most diverse groups of crustaceans, with over 7000 described species. Crab mitogenomes are important for understanding molecular evolution and phylogenetic relationships. Grapsus albolineatus exhibits specific rearrangements compared with the Pancrustacean ground pattern and other Brachyura species. The gene arrangement of G. albolineatus is similar to that of ancestral crustaceans, barring that of the translocated trnH gene. In phylogenetic analyses, the Bayesian inference estimation was observed to be superior to the maximum likelihood estimation when the nodal support values were compared. Considering the results of the gene rearrangement pattern and phylogenetic analysis, we speculate that G. albolineatus belongs to Grapsidae. Our comparative study indicated that mitogenomes are a useful phylogenetic tool at the subfamily level within Brachyura. The findings indicate that mitogenomes could be a useful tool for systematics in other Brachyuran species. Full article

The analysis of resilience indicators was based on daily milk yields recorded from 3347 lactations of 3080 Holstein cows located on 10 farms between 2022 and 2024. Six farms used an automatic milking system. A random regression function with a fourth-degree Legendre polynomial was used to predict the lactation curve. The indicators were the natural log-transformed variance (LnVar), lag-1 autocorrelation (r-auto), and skewness (skew) of daily milk yield (DMY) deviations from the predicted lactation curve, as well as the log-transformed variance of DMY (Var). The single-step genomic prediction method (ssGBLUP) was used for genomic evaluation. A total of 9845 genotyped animals and 36,839 SNPs were included. Heritability estimates were low (0.02–0.13). The strongest genetic correlation (0.87) was found between LnVar and Var. The genetic correlation between r-auto and skew was also strong but negative (−0.73). Resilience indicators showed a negative correlation with milk yield per lactation and a positive correlation with fat and protein contents. The negative correlation between fertility and two resilience indicators may be due to the evaluation period (50th–150th day of lactation) being when cows are most often bred after calving, and a decrease in production may accompany a significant oestrus. The associations between resilience indicators and health traits (clinical mastitis, claw health) were weak but mostly favourable. Full article

B-cell lymphoma/leukemia 11B (Bcl11b) plays roles in cell proliferation and apoptosis and holds a pivotal position within the immune system. Our previous studies have demonstrated that Bcl11b can promote cell apoptosis to curb ALV-J infection. To gain insights into the molecular mechanisms underlying Bcl11b expression regulation in chickens, we constructed various truncated dual luciferase reporter vectors and analyzed the promoter region of Bcl11b. We employed promoter-binding TF profiling assay and the dual luciferase assay of site-directed mutagenesis and the expression level of interfering or overexpressing transcription factors were used to study their transcriptional regulation mechanism of chicken Bcl11b and functions in ALV-J infection. Our findings revealed core regulatory regions of the chicken Bcl11b promoter. By examining the −606~−363 bp region, we identified several transcription factors and their binding sites. Mutational and functional analysis further revealed interferon regulatory factor-1 (IRF1) and GATA-binding protein 1 (GATA1) as critical factors for the repression of chicken Bcl11b, thereby affecting cell apoptosis and ALV-J replication. Furthermore, DNA methylation analysis indicated that methylation may also contribute to changes in Bcl11b promoter activity. These findings offer valuable insights into the regulatory mechanisms of chicken Bcl11b and provide promising targets for molecular breeding and genetic improvement of disease resistance in chickens. Full article

Litter size records from two lines of Tunisian Barbarine sheep were analysed across parities using an RRM. A total of 2751 and 2562 litter records from the first to the sixth parity from the prolific and the conventional lines, respectively, were included in the analysis. The total number of animals in the pedigree was 1277 for the prolific line and 1102 for the conventional line. The estimation of genetic parameters was based on Bayesian inference under categorical distribution. Fixed effects included the year and month of lambing and a fixed quadratic regression coefficient for the lambing number with Legendre polynomials. The random additive and permanent environmental effects were modelled by second-order Legendre polynomials. Heritability ranged from 0.04 to 0.18 for the prolific line and from 0.17 to 0.39 for the conventional line. Genetic correlations within trait through parities showed a wide range of values, from 0.25 to 0.96 for the prolific line and from zero to 0.93 for the conventional line. Due to the changes in the variances and the genetic correlations different from unity across parities, the use of an RRM is recommended to analyse litter size in the Barbarine sheep. Full article

Compared to the negative effect of directional selection on genetic diversity, balancing selection acts oppositely and maintains variability across the genome. This study aims to articulate whether balancing selection leads to heterozygosity-rich region islands (HRRIs) forming in the canine genome by investigating 1000 animals belonging to 50 dog breeds via 153,733 autosomal SNPs. A consecutive SNP-based approach was used to identify heterozygosity-rich regions (HRRs). Signals of balancing selection in the genome of studied breeds were then assessed with Tajima’s D statistics. A total of 72,062 HRRs with an average length of 324 kb were detected to be unevenly distributed across the genome. A total of 509 and 450 genomic regions were classified as HRRIs and balancing selection signals, respectively. Although the genome-wide distributions of HRRIs varied across breeds, several HRRIs were found in the same locations across multiple breeds. A total of 109 genomic regions were classified as both HRRIs and signals of balancing selection. Even though the genomic coordinates of HRRIs and balancing selection signals did not fully overlap across all genomic regions, balancing selection may play a significant role in maintaining diversity in regions associated with various cancer diseases, immune response, and bone, skin, and cartilage tissue development. Full article

This study investigates the genetic structure of Belgian Red (BR), Belgian Red and White (BWR), and Qinchuan (QinC) cattle, with a focus on identifying genes associated with reproductive functions, growth, and development. A total of 270 Belgian cattle (91 BR and 179 BWR) and 286 Qinchuan cattle were genotyped using the Illumina Bovine SNP 50K microarray. Data analysis was conducted using PLINK and Beagle 5.1 to estimate linkage disequilibrium (LD) and effective population size (Ne). Candidate SNP loci were identified by selecting the top 5% based on the weighted fixation index (Fst) and nucleotide diversity (θπ ratio), followed by gene annotation. The analysis revealed 160 candidate genes under selection between Qinchuan and Belgian Red cattle, and 98 candidate genes between Qinchuan and Belgian Red and White cattle. Key genes associated with reproductive functions, including NFKBIA, PTHLH, UGT2B10, TRPC4, and ALOX5AP, were identified. Additionally, genes involved in growth and muscle development were highlighted, particularly those influencing protein synthesis, fatty acid metabolism, and collagen synthesis. These findings provide valuable molecular markers for enhancing reproductive efficiency, growth, and meat production through genetic selection and selective breeding strategies. Full article

N⁶-methyladenosine (m⁶A) is one of the most abundant modifications in eukaryotic RNA molecules and mediates the functional exertion of RNA molecules. We characterized the circPAPPA and validated its potential m⁶A modification sites in secondary hair follicles (SHFs) of cashmere goats. Furthermore, we generated integrated regulatory networks of the circPAPPA along with enrichment analysis of signaling pathways. We also explored the potential relationship of circPAPPA expression with the first intron methylation of the PAPPA gene in SHFs of cashmere goats. Host source analysis revealed that circPAPPA is derived from the complete exon 2 of the PAPPA gene, spliced in reverse orientation, and predominantly localized in the cytoplasm of SHF stem cells in cashmere goats. The circPAPPA was verified to contain at least four m⁶A modification sites in SHFs of cashmere goats, including m⁶A-450/456, m⁶A-852, m⁶A-900, and m⁶A-963. The generated regulatory network indicated complex and diverse regulatory relationships of m⁶A-circPAPPA with its putative regulatory molecules, including miRNAs, mRNAs, and proteins. Enrichment analysis of signaling pathways showed that m⁶A-circPAPPA might play multiple functional roles in the growth and development of SHF in cashmere goats through the putative regulatory network mediated by its target miRNAs and regulatory proteins. The first intron methylation of the PAPPA gene most likely is significantly involved in the dynamic expression of m⁶A-circPAPPA in cashmere goat SHFs. Results from this study provided novel information to elucidate the biological roles and functional regulatory pathways of m⁶A-circPAPPA in SHF development and the growth of cashmere goat fiber. Full article

Non-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they are easy to collect with minimal permission and cause little disturbance to the subject population. However, such studies face limitations due to poor DNA yield, which affects the overall utilization of collected samples and increases data errors. Here, we evaluated the impact of sample age and collection season on the performance of DNA extracted from feces (spraints) of the Eurasian otter (Lutra lutra), a semi-aquatic apex predator in South Korean freshwater ecosystems. We found that PCR amplification success rates decreased more rapidly in summer (79.3–58.2%) compared to winter (99.2–84.8%) with extended environmental exposure. Genotyping error rates were higher in samples collected during summer, with the rate of error increase over time being significantly greater in summer than in winter. The hot and humid South Korean summer fosters microbial growth and fecal degradation, which negatively impacts DNA yield, reducing PCR amplification success and increasing genotyping errors. We recommend collecting otter feces during winter for better DNA quality. If sampling in summer is unavoidable, it is crucial to collect fresh samples, which can be facilitated by conducting frequent surveys of latrine sites. Full article

Goats are widely recognized for their adaptability and resource efficiency, making them an excellent choice for sustainable farming. However, the Hainan Black goat (HNBG), a vital breed in southern China’s tropical regions, faces significant challenges that threaten its productivity and economic viability. Specifically, young HNBGs exhibit stunted growth and poor muscle development, indicating the breed may have more genetic defects that cause the poor phenotypes. The FNDC5 gene, which encodes the protein irisin, plays a key role in promoting mitochondrial biogenesis and oxidative metabolism by activating critical signaling molecules such as PGC-1α, thereby enhancing muscle endurance and metabolic efficiency. This study aimed to investigate the impact of missense mutations in the FNDC5 gene on growth and meat quality traits in HNBGs. We sequenced a population of HNBGs and identified three SNPs that could lead to amino acid substitutions. Notably, SNP1 (p.119A/V) and SNP2 (p.135R/H) showed strong linkage. Predictions on the structural effects of these mutations indicated that SNP1 (p.119A/V) and SNP3 (p.170W/G) could alter the secondary structure of the FNDC5 protein. Association analyses revealed that SNP1 (p.119A/V) and SNP2 (p.135R/H) were significantly associated with morphometric traits and meat quality. The phenotypic values of SNP1 and SNP2 co-mutants were significantly lower than those of other combined genotypes. Furthermore, gene expression levels of FNDC5 varied notably across individuals with different SNP1 genotypes. These findings suggest that FNDC5-SNP1 (p.119A/V) could serve as a promising genetic marker for selecting HNBGs with improved growth and muscle development, offering a potential pathway for enhancing key economic traits in this breed. Full article