Structural variations(SVs≥50 bp)are a critical but underexplored source of genetic diversity in cattle,shaping traits vital for productivity,adaptability,and health.Advances in long-read sequencing,pangenome graph co...Structural variations(SVs≥50 bp)are a critical but underexplored source of genetic diversity in cattle,shaping traits vital for productivity,adaptability,and health.Advances in long-read sequencing,pangenome graph construction,and near-complete genome assemblies now allow accurate SV detection and genotyping.These innovations overcome the limitations of single-reference genomes,enabling the discovery of complex SVs,including nested and overlapping variants,and providing access to previously inaccessible genomic regions such as centromeres and telomeres.This review highlights the current landscape of cattle SV research,with emphasis on integrating longread sequencing and pangenome frameworks to uncover breed-specific and population-level variation.While many SVs are linked to economically important traits such as feed efficiency and disease resistance,their broader regulatory impacts remain an active area of investigation.Emerging functional genomics approaches,including transcriptomics,epigenomics,and genome editing,will clarify how SVs influence gene regulation and phenotype.Looking forward,the integration of SV catalogs with multi-omics data,imputation resources,and artificial intelligence-driven models will be essential for translating discoveries into breeding and conservation applications.Integrating structural variants into breeding pipelines promises to revolutionize livestock genomics,enabling precision selection and sustainable agriculture despite challenges in cost,data sharing,and functional validation.展开更多
Background Excessive abdominal fat in broilers not only reduces feed efficiency and increases processing costs but also raises environmental concerns.This pathological overaccumulation results from complex metabolic d...Background Excessive abdominal fat in broilers not only reduces feed efficiency and increases processing costs but also raises environmental concerns.This pathological overaccumulation results from complex metabolic dysregulation across multiple organs.While current research largely centers on adipogenesis within adipose tissue,a comprehensive understanding of the cross-organ regulatory factors influencing this process remains elusive.Results Here,we employed a high-fat diet(HFD)model and multi-omics approaches to investigate cross-organ regulatory mechanisms underlying abdominal fat deposition in broilers.Our results demonstrated that HFD not only promoted fat accumulation but also altered meat quality traits.Through 16S rRNA amplicon sequencing,we identified significant gut microbiota dysbiosis in HFD-fed chickens,manifested by an increased abundance of Lactobacillus and a decreased abundance of Enterococcus.However,jejunal microbiota transplantation from HFD donors did not induce abdominal fat deposition in recipient chickens.Metabolomic profiling revealed that HFD elevated the level of succinic acid,a metabolite positively correlated with Lactobacillus abundance and potentially generated by Lactobacillus.This increase in succinic acid(SA)further triggered metabolic inflammation response in both jejunal tissue and serum.In vivo validation established succinic acid as a key inflammatory mediator facilitating HFD-induced cross-organ communication between the jejunum and abdominal adipose tissue,enhancing intestinal lipid uptake and subsequent abdominal fat deposition.Bulk and single-nucleus RNA sequencing(snRNA-seq)revealed that HFD induced macrophage population expansion and intensified adipocyte-macrophage crosstalk.Adipocyte-macrophage co-culture systems further elucidated that macrophages are an indispensable factor in succinic acid-induced fat deposition.Conclusion This study delineates a succinic acid-driven"gut-fat axis"governing abdominal fat deposition in broilers,integrating gut microbiota dysbiosis and macrophage-mediated inflammatory adipogenesis.By identifying succinic acid as a cross-organ signaling molecule that enhances lipid absorption and activates macrophage-dependent adipogenesis,we establish systemic metabolic-immune crosstalk as a pivotal regulatory mechanism.These findings redefine fat deposition as a process extending beyond adipose-centric models,advancing multi-omics-guided strategies for sustainable poultry production.展开更多
As a critical global ecosystem,grasslands rely on complex aboveground-belowground interactions that underpin multifunctionality,yet their mechanisms remain poorly understood.Our investigation employed the plateau pika...As a critical global ecosystem,grasslands rely on complex aboveground-belowground interactions that underpin multifunctionality,yet their mechanisms remain poorly understood.Our investigation employed the plateau pika(Ochotona curzoniae),a small herbivore widely distributed throughout the Qinghai-Tibetan Plateau,as a model organism to examine the consequences of disturbance on plant diversity,soil properties,microbial diversity,and multifunctionality of grassland ecosystems.We found that high pika burrow density significantly reduced plant diversity(Shannon-Wiener and Chao1 indices)and aboveground biomass.It also increased soil pH and reduced ammonium nitrogen content.The soil microbial diversity,encompassing both bacteria and fungi,was markedly decreased in areas characterized by a high concentration of burrows.Microbial interaction networks demonstrated greater complexity in areas with high burrow densities,as revealed by the network analysis.Conversely,in regions characterized by low burrow density,a significant negative correlation was observed between the intricacy of soil bacterial networks and the multifunctionality of grassland ecosystems.Structural equation modelling showed that pika disturbance indirectly affected multifunctionality via changes in plant biomass and soil properties-notably,nitrate nitrogen explained 40%of multifunctionality variation under high disturbance.This investigation advances our understanding of complex aboveground-belowground linkages in grassland ecosystems,revealing novel mechanisms through which biodiversity governs ecosystem multifunctionality.Our findings underscore the critical role of small herbivores in shaping grassland ecosystem functions and emphasize the importance of maintaining balanced disturbance regimes to sustain ecosystem multifunctionality.This has immediate implications for global conservation policies on the Qinghai-Tibetan Plateau and analogous ecosystems.展开更多
Sperm is essential for successful artificial insemination in dairy cattle,and its quality can be influenced by both epi-genetic modification and epigenetic inheritance.The bovine germline differentiation is characteri...Sperm is essential for successful artificial insemination in dairy cattle,and its quality can be influenced by both epi-genetic modification and epigenetic inheritance.The bovine germline differentiation is characterized by epigenetic reprogramming,while intergenerational and transgenerational epigenetic inheritance can influence the offspring’s development through the transmission of epigenetic features to the offspring via the germline.Therefore,the selec-tion of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers.We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.展开更多
Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the...Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle.To comprehensively characterize the genomic variation within Bos indicus and,specifically,dairy breeds,we aim to identify non-reference sequences and construct a comprehensive pangenome.Results Five representative genomes of prominent dairy breeds,including Gir,Kankrej,Tharparkar,Sahiwal,and Red Sindhi,were sequenced using 10X Genomics‘linked-read’technology.Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb,comparable to the Bos indicus Brahman reference genome.A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods,revealing 8 Mb and 17.7 Mb of novel sequence respectively.A confident set of 6,844 Non-reference Unique Insertions(NUIs)spanning 7.57 Mb was identified through both methods,representing the pange-nome of Indian Bos indicus breeds.Comparative analysis with previously published pangenomes unveiled 2.8 Mb(37%)commonality with the Chinese indicine pangenome and only 1%commonality with the Bos taurus pange-nome.Among these,2,312 NUIs encompassing~2 Mb,were commonly found in 98 samples of the 5 breeds and des-ignated as Bos indicus Common Insertions(BICIs)in the population.Furthermore,926 BICIs were identified within 682 protein-coding genes,54 long non-coding RNAs(lncRNA),and 18 pseudogenes.These protein-coding genes were enriched for functions such as chemical synaptic transmission,cell junction organization,cell-cell adhesion,and cell morphogenesis.The protein-coding genes were found in various prominent quantitative trait locus(QTL)regions,suggesting potential roles of BICIs in traits related to milk production,reproduction,exterior,health,meat,and carcass.Notably,63.21%of the bases within the BICIs call set contained interspersed repeats,predominantly Long Inter-spersed Nuclear Elements(LINEs).Additionally,70.28%of BICIs are shared with other domesticated and wild species,highlighting their evolutionary significance.Conclusions This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India.The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.展开更多
Resilience traits in pig populations allow animals to deal better with infectious disease and suboptimal production environments.The data on daily weight,feed intake and feed behaviors in pigs are collected in test pe...Resilience traits in pig populations allow animals to deal better with infectious disease and suboptimal production environments.The data on daily weight,feed intake and feed behaviors in pigs are collected in test period by automated feeding stations,which facilitate to evaluate the resilience traits.In this study,we adopted the root mean square error(RMSE)of ordinary least squares(OLS)and the negative residuals of quantile regression(QR)to generate four different novel resilience traits using daily records of feed intake and feed duration between 90 and 180 days of age in a population of commercial Duroc pigs.The genome-wide association studies(GWAS)based on single-and two-trait mixed models were carried out on 550 pigs using 48,603 single nucleotide polymorphisms(SNPs)to identify genomic regions associated with resilience traits in growing pigs.We further focused on the GWAS signals to conduct gene annotation,colocalization with multi-tissue eQTL summary statistics of PigGTEx project and identification of enhancers and promoters using the publicly available data.The genomic heritabilities of four novel resilience traits ranged from 0.09 to 0.41.The pairwise genetic and phenotypic correlations ranged from 0.16 to 0.95 and from 0.05 to 0.36,respectively.Twenty-seven SNPs were identified to be significantly associated with these resilience traits.They were distributed on nine chromosomes(SSC1,SSC2,SSC6,SSC7,SSC8,SSC12,SSC14,SSC16 and SSC17).After annotation,39 QTLs and 49 candidate genes were identified.Several of these are functionally relevant candidate genes including OTUD4,TIFA and CARD14,which are involved in the host immune response,disease susceptibility and signal transduction.Eight unique SNPs were found to be causal in both GWAS and eQTL analyses across 15 tissues.Notably,one SNP(rs80794541)was associated with eQTLs identified concurrently across seven tissues/cell types,including the macrophage cell type.Furthermore,four significant SNPs(rs81467127,rs81356029,rs80794541 and rs81305085)were linked to the function of the primed enhancer,active element,and poised promoter in five pig tissues.Using the porcine fibroblast HiC dataset,SNP(rs81356029)on SSC2 regulates the CARNS1 and SSH3,while SNP(rs80794541)on SSC7 regulates the H2AC6.In this study,we generated four novel resilience traits and identified SNPs significantly associated with these resilience traits in a Duroc pig population.GWAS signals were associated with candidate genes involving in the immune traits,and were linked to the crucial regulatory elements as well.Our findings will contribute to elucidating the genetic mechanism that can enhance genome-enabled breeding and inform further research on resilience in domestic pigs.展开更多
Following the publication of Liu et al.(2024),an error was identified in Figure 4B,in which the image representing the lung from the E529G group was inadvertently duplicated with the image of the lung from the WT grou...Following the publication of Liu et al.(2024),an error was identified in Figure 4B,in which the image representing the lung from the E529G group was inadvertently duplicated with the image of the lung from the WT group during figure preparation.展开更多
Backgroud Before fertilization,spermatozoa undergo a crucial maturation step called capacitation,which is a unique event regulates the sperm’s ability for successful fertilization.The capacitation process takes place...Backgroud Before fertilization,spermatozoa undergo a crucial maturation step called capacitation,which is a unique event regulates the sperm’s ability for successful fertilization.The capacitation process takes place as the spermatozoa pass through the female reproductive tract(FRT).Dihydrolipoamide dehydrogenase(DLD)protein is a post-pyruvate metabolic enzyme,exhibiting reactive oxygen species(ROS)production which causes capacitation.Additionally,other vital functions of DLD in buffalo spermatozoa are hyperactivation and acrosome reaction.DLD produces the optimum amount of ROS required to induce capacitation process in FRT.Depending on physiological or patho-physiological conditions,DLD can either enhance or attenuate the production of reactive oxygen species(ROS).Aim of this study was to investigate whether changes in the production of ROS in sperm cells can impact their ability to fertilize by triggering the capacitation and acrosome reaction.Results In this study,abundance of DLD protein was quantified between high(n=5)and low fertile bull(n=5)sper-matozoa.It was found that compared to high-fertile(HF)bulls,low-fertile(LF)bulls exhibited significantly(P<0.05)higher DLD abundances.Herein,we optimised the MICA concentration to inhibit DLD function,spermatozoa were treated with MICA in time(0,1,2,3,4,and 5 h)and concentrations(1,2.5,5,and 10 mmol/L)dependent manner.Maximum DLD inhibition was found to be at 4 h in 10 mmol/L MICA concentration,which was used for further exper-imentation in HF and LF.Based on DLD inhibition it was seen that LF bull spermatozoa exhibited significantly(P<0.05)higher ROS production and acrosome reaction in comparison to the HF bull spermatozoa.The kinematic parameters of the spermatozoa such as percent total motility,velocity parameters(VCL,VSL,and VAP)and other parameters(BCF,STR,and LIN)were also decreased in MICA treated spermatozoa in comparison to the control(capacitated)spermatozoa.Conclusions The present study provides an initial evidence explaining the buffalo bull spermatozoa with higher DLD abundance undergo early capacitation,which subsequently reduces their capacity to fertilize.展开更多
Background Semen quality is one of the most important indicators of boar reproductive performance.In the past,boar breeding has mostly emphasized characteristics such as lean meat percentage,feed conversion efficiency...Background Semen quality is one of the most important indicators of boar reproductive performance.In the past,boar breeding has mostly emphasized characteristics such as lean meat percentage,feed conversion efficiency,and growth rate,while overlooking the genetic improvement of reproductive traits.This study employs advanced multi-omics approaches,such as transcriptome-wide association studies(TWAS)and colocalization between genome-wide association studies(GWAS)and expression quantitative trait loci(eQTLs),to provide a comprehensive understanding of the genetic mechanisms governing semen quality traits in boars.Results Here,we collected 190,000 ejaculate records across 11 semen quality traits from 3,604 Duroc boars.The heritability of semen quality traits ranged from 0.095 to 0.343.Genetic correlations between semen quality traits varied from−0.802 to 0.661,and phenotypic correlations ranged from−0.833 to 0.776.Single-trait GWAS identified 19 independent variants,corresponding to 13 quantitative trait loci(QTLs).By integrating PigGTEx and FAANG resources,we combined TWAS and colocalization analyses to reveal genetic regulation of semen quality traits.Notably,both GWAS and colocalization analyses pinpointed the DCAF12 as a crucial gene associated with multiple semen quality traits.Additionally,the ZSCAN9 gene and the variant rs322211455 were found to significantly affect sperm motility(SPMOT),possibly through hypothalamic-pituitary-gonadal axis.PheWAS further highlighted an association between rs322211455 and sperm abnormality rate,demonstrating the crucial role of ZSCAN9 in male fertility.Conclusion This study reveals the genetic basis and regulatory mechanisms underlying semen quality traits in Duroc boars,identifying key candidate genes such as DCAF12 and ZSCAN9.These findings provide important insight into the genetic regulation of semen quality in boars.展开更多
Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreati...Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreatic genes and blood physiology parameters after administering one maximum residue limit of herbicide glyphosate(GLY),two ANTs,and one anticoccidial drug(AD).A total of 260 Ross 308 broilers aged 1-40 d were divided into the following four groups of 65 birds each:control group,which was fed the main diet(MD),and three experimental groups,which were fed MD supplemented with GLY,GLY+ANTs(enrofloxacin and colistin methanesulfonate),and GLY+AD(ammonium maduramicin),respectively.The results showed that the addition of GLY,GLY+ANTs,and GLY+AD caused significant changes in the expression of several genes of physiological and economic importance.In particular,genes related to inflammation and apoptosis(interleukin 6(IL6),prostaglandin-endoperoxide synthase 2(PTGS2),and caspase 6(CASP6))were downregulated by up to 99.1%,and those related to antioxidant protection(catalase(CAT),superoxide dismutase 1(SOD1)and peroxiredoxin 6(PRDX6))by up to 98.6%,compared to controls.There was also a significant decline in the values of immunological characteristics in the blood serum observed in the experimental groups,and certain changes in gene expression were concordant with changes in the functioning of the pancreas and blood.The changes revealed in gene expression and blood indices in response to GLY,ANTs,and AD provide insights into the possible mechanisms of action of these agents at the molecular level.Specifically,these changes may be indicative of physiological mechanisms to overcome the negative effects of GLY,GLY+ANTs,and GLY+AD in broilers.展开更多
Introduction Tibetan sheep,economically important animals on the Qinghai–Tibet Plateau,have diversified into numerous local breeds with unique characteristics through prolonged environmental adaptation and selective ...Introduction Tibetan sheep,economically important animals on the Qinghai–Tibet Plateau,have diversified into numerous local breeds with unique characteristics through prolonged environmental adaptation and selective breeding.However,most current research focuses on one or two breeds,and lacks a comprehensive representa-tion of the genetic diversity across multiple Tibetan sheep breeds.This study aims to fill this gap by investigating the genetic structure,diversity and high-altitude adaptation of 6 Tibetan sheep breeds using whole-genome rese-quencing data.Results Six Tibetan sheep breeds were investigated in this study,and whole-genome resequencing data were used to investigate their genetic structure and population diversity.The results showed that the 6 Tibetan sheep breeds exhibited distinct separation in the phylogenetic tree;however,the levels of differentiation among the breeds were minimal,with extensive gene flow observed.Population structure analysis broadly categorized the 6 breeds into 3 distinct ecological types:plateau-type,valley-type and Euler-type.Analysis of unique single-nucleotide polymor-phisms(SNPs)and selective sweeps between Argali and Tibetan sheep revealed that Tibetan sheep domestication was associated primarily with sensory and signal transduction,nutrient absorption and metabolism,and growth and reproductive characteristics.Finally,comprehensive analysis of selective sweep and transcriptome data sug-gested that Tibetan sheep breeds inhabiting different altitudes on the Qinghai–Tibet Plateau adapt by enhancing cardiopulmonary function,regulating body fluid balance through renal reabsorption,and modifying nutrient diges-tion and absorption pathways.Conclusion In this study,we investigated the genetic diversity and population structure of 6 Tibetan sheep breeds in Qinghai Province,China.Additionally,we analyzed the domestication traits and investigated the unique adapta-tion mechanisms residing varying altitudes in the plateau region of Tibetan sheep.This study provides valuable insights into the evolutionary processes of Tibetan sheep in extreme environments.These findings will also contribute to the preservation of genetic diversity and offer a foundation for Tibetan sheep diversity preservation and plateau animal environmental adaptation mechanisms.展开更多
Hypobaric hypoxia encountered at high altitudes impairs reproductive health and fertility across species.Previous findings have demonstrated that maternal hypoxia exposure disrupts granulosa cell(GC)viability and oocy...Hypobaric hypoxia encountered at high altitudes impairs reproductive health and fertility across species.Previous findings have demonstrated that maternal hypoxia exposure disrupts granulosa cell(GC)viability and oocyte maturation in female offspring;however,its transgenerational impact on male reproductive outcomes remains poorly elucidated.In this study,pregnant mice(F0)were subjected to hypoxic conditions,and male progeny across four generations(F1-F4)were evaluated.Results revealed that maternal hypoxia induced mild alterations in sperm DNA methylation in F1 males but caused profound developmental defects in F2 embryos,predominantly affecting males.Following mating of F1males with control females,a substantial proportion of male F2 fetuses were lost at embryonic day(E)13.5,attributed to placental malformations.Integrated RNA sequencing and whole-genome bisulfite sequencing of placentas from male fetuses revealed aberrant expression of imprinted genes,including Gnas,Slc38a4,Jade1,and Kcnq1,which also exhibited differential methylation in F1sperm.These findings demonstrate that maternal hypoxia disrupts epigenetic programming in F1 germ cells,impairing placental development and fetal viability in F2males,thereby leading to an unbalanced sex ratio.Overall,this study elucidates the mechanisms by which environmental hypoxia influences sex ratios and offers critical insights into hypoxia-induced reproductive impairments in mammals.展开更多
A comprehensive taxonomic reassessment of the Hebius optatus species complex,integrating molecular data and morphological data,has led to the recognition and description of a previously overlooked species from norther...A comprehensive taxonomic reassessment of the Hebius optatus species complex,integrating molecular data and morphological data,has led to the recognition and description of a previously overlooked species from northern Vietnam and the Guangxi Zhuang Autonomous Region,China,herein described as Hebius vogeli sp.nov.Phylogenetic analyses reveal that Hebius vogeli sp.nov.is closely related to H.sauteri and H.optatus sensu stricto.Uncorrected p-distances based on cytochrome b sequences indicate a divergence of 10.74%-11.73%between Hebius vogeli sp.nov.and H.optatus.The new species differs from H.optatus by a combination of characters,including a higher number of subcaudal scales,a greater total number of ventral and subcaudal scales,and distinct ventral coloration.Hebius vogeli sp.nov.appears to be geographically restricted to northern Vietnam and the adjacent region of Guangxi Zhuang Autonomous Region,China,making its distribution allopatric from that of H.optatus.The Pearl River is hypothesized to serve as a biogeographic barrier separating the two taxa.Accordingly,we recommend the exclusion of H.optatus from the herpetofauna of Vietnam.Based on IUCN Red List criteria,we propose that Hebius vogeli sp.nov.be assessed as Least Concern(LC).Our results emphasize both the underestimated diversity within Hebius and the need for continued integrative taxonomic efforts,particularly in the Vietnam-China borderlands,where cryptic diversity remains largely unexplored.展开更多
Maternal undernutrition or overnutrition during pregnancy alters organ structure, impairs prenatal and neonatal growth and development, and reduces feed efficiency for lean tissue gains in pigs. These adverse effects ...Maternal undernutrition or overnutrition during pregnancy alters organ structure, impairs prenatal and neonatal growth and development, and reduces feed efficiency for lean tissue gains in pigs. These adverse effects may be carried over to the next generation or beyond. This phenomenon of the transgenerational impacts is known as fetal programming, which is mediated by stable and heritable alterations of gene expression through covalent modifications of DNA and histones without changes in DNA sequences(namely, epigenetics). The mechanisms responsible for the epigenetic regulation of protein expression and functions include chromatin remodeling; DNA methylation(occurring at the 5′-position of cytosine residues within CpG dinucleotides); and histone modifications(acetylation, methylation, phosphorylation, and ubiquitination). Like maternal malnutrition, undernutrition during the neonatal period also reduces growth performance and feed efficiency(weight gain:feed intake; also known as weightgain efficiency) in postweaning pigs by 5–10%, thereby increasing the days necessary to reach the market bodyweight. Supplementing functional amino acids(e.g., arginine and glutamine) and vitamins(e.g., folate) play a key role in activating the mammalian target of rapamycin signaling and regulating the provision of methyl donors for DNA and protein methylation. Therefore, these nutrients are beneficial for the dietary treatment of metabolic disorders in offspring with intrauterine growth restriction or neonatal malnutrition. The mechanism-based strategies hold great promise for the improvement of the efficiency of pork production and the sustainability of the global swine industry.展开更多
Background： The Y chromosome in mammal is paternally inherited and harbors genes related to male fertility and spermatogenesis. The unique intra-chromosomal recombination pattern of Y chromosome and morphological dif...Background： The Y chromosome in mammal is paternally inherited and harbors genes related to male fertility and spermatogenesis. The unique intra-chromosomal recombination pattern of Y chromosome and morphological difference of this chromosome between Bos taurus and Bos indicus make it an ideal model for studying structural variation, especially in crossbred （Bos taurus x Bos indicus） bulls. Copy Number Variation （CNV） is a type of genomic structural variation that gives information complementary to SNP data. The purpose of this study was to find out copy number differences of four Y chromosomal spermatogenesis-related candidate genes in genomic DNA of crossbred and purebred Indicine bulls. Result： Four Y chromosomal candidate genes of spermatogenesis namely, sex determining gene on Ychromosome （SRY）, DEAD box po/ypeptide 3-Y chromosome （DDX3 Y）, Ubiquidn specific peptidase 9, Y-linked （ usPgY）, testis-specific protein on Y chromosome （TSPY） were evaluated. Absolute copy numbers of Y chromosomal genes were determined by standard curve-based quantitative real time PCR. Copy numbers of SRYand TSPYgenes per unit amount of genomic DNA are higher in crossbred than Indicine bulls. However, no difference was observed in DDX3Yand usPgYgene copy numbers between two groups. Conclusion： The present study demonstrates that the structural organization of Y chromosomes differs between crossbred and Indicine bulls which are reproductively healthy as observed from analysis of semen attributes. The absolute copy numbers of SRY and TSPY genes in unit mass of genomic DNA of crossbred bulls are significantly higher than Indicine bulls. No alteration in absolute copies ofDDX3Yand usPgYgene was found between the genome of crossbred and Indicine bulls. This study suggests that the DDX3Yand USPgYare likely to be single copy genes in the genome of crossbred and Indicine bulls and variation in Y chromosome length between crossbred and Indicine bulls may be due to the copy number variation of SRY gene and TSPYarray.展开更多
Road traffic is the main factor causing the decline in amphibian populations worldwide. The proper design of an amphibian tunnel is one of the most efficient measures to mitigate the negative impacts of road traffic o...Road traffic is the main factor causing the decline in amphibian populations worldwide. The proper design of an amphibian tunnel is one of the most efficient measures to mitigate the negative impacts of road traffic on amphibians. However, no study has investigated the effectiveness of amphibian tunnels under semi-controlled conditions in Asian amphibians. Here, we selected two representative amphibian species, the Chinese brown frog, Rana chensinensis, and the Asiatic toad, Bufo gargarizans, which suffer the most severe road mortality along the roads in Northeast China. We placed experimental arrays of culverts of various sizes(diameters of 1.5, 1, and 0.5 m for circular culverts; side lengths of 1.5, 1, and 0.5 m for box culverts), and substrate type(soil, concrete, and metal) to examine the preferences of both species during the migratory season between May and September in 2016 and 2017. The results revealed that the Chinese brown frog preferred mid-and large-sized culverts as well as soil culverts. We concluded that culverts with a side length ≥ 1 m, lined with soil, and accompanied by a ≥ 0.4 m high guide drift fence and ≤ 45° gradient on the roadside ditch wall would best facilitate road crossings for both species and likely for other amphibian species in Northeast China.展开更多
Subgroup J avian leukosis virus(ALV-J) is a highly oncogenic retrovirus that has been devastating the global poultry industry since the late 1990s. The major infection model of ALV-J is vertical transmission, which is...Subgroup J avian leukosis virus(ALV-J) is a highly oncogenic retrovirus that has been devastating the global poultry industry since the late 1990s. The major infection model of ALV-J is vertical transmission, which is responsible for the congenital infection of progeny from generation to generation. Increasing evidence has suggested that extracellular vesicles(EVs) derived from virus-infected cells or biological fluids have been thought to be vehicles of transmission for viruses. However, the role of EVs in infection and transmission of ALV-J remains obscure. In the present study, semen extracellular vesicles(SE) were isolated and purified from ALV-J-infected rooster seminal plasma(SE-ALV-J), which was shown to contain ALV-J genomic RNA and partial viral proteins, as determined by RNA sequencing, reverse transcription-quantitative PCR and Western blotting. Furthermore, SE-ALV-J was proved to be able to transmit ALV-J infection to host cells and establish productive infection.More importantly, artificial insemination experiments showed that SE-ALV-J transmitted ALV-J infection to SPF hens, and subsequently mediated vertical transmission of ALV-J from the SPF hens to the progeny chicks. Taken together, the results of the present study suggested that ALV-J utilized host semen extracellular vesicles as a novel means for vertical transmission, enhancing our understanding on mechanisms underlying ALV-J transmission.展开更多
The ability of human deciduous tooth dental pulp cells（HDDPCs） to differentiate into odontoblasts that generate mineralized tissue holds immense potential for therapeutic use in the field of tooth regenerative medic...The ability of human deciduous tooth dental pulp cells（HDDPCs） to differentiate into odontoblasts that generate mineralized tissue holds immense potential for therapeutic use in the field of tooth regenerative medicine. Realization of this potential depends on efficient and optimized protocols for the genetic manipulation of HDDPCs. In this study, we demonstrate the use of a Piggy Bac（PB）-based gene transfer system as a method for introducing nonviral transposon DNA into HDDPCs and HDDPC-derived inducible pluripotent stem cells. The transfection efficiency of the PB-based system was significantly greater than previously reported for electroporation-based transfection of plasmid DNA. Using the neomycin resistance gene as a selection marker, HDDPCs were stably transfected at a rate nearly 40-fold higher than that achieved using conventional methods. Using this system, it was also possible to introduce two constructs simultaneously into a single cell. The resulting stable transfectants, expressing td Tomato and enhanced green fluorescent protein, exhibited both red and green fluorescence. The established cell line did not lose the acquired phenotype over three months of culture. Based on our results, we concluded that PB is superior to currently available methods for introducing plasmid DNA into HDDPCs. There may be significant challenges in the direct clinical application of this method for human dental tissue engineering due to safety risks and ethical concerns. However, the high level of transfection achieved with PB may have significant advantages in basic scientific research for dental tissue engineering applications, such as functional studies of genes and proteins. Furthermore, it is a useful tool for the isolation of genetically engineered HDDPC-derived stem cells for studies in tooth regenerative medicine.展开更多
Insulin-like growth factor 2 m RNA-binding protein 2(IGF2 BP2,also called IMP2)plays an essential role in the development and maturation of germ cells and embryos and is a candidate gene for goat litter size,based on ...Insulin-like growth factor 2 m RNA-binding protein 2(IGF2 BP2,also called IMP2)plays an essential role in the development and maturation of germ cells and embryos and is a candidate gene for goat litter size,based on a previous genomewide selective sweep analysis.In this study,the m RNA expression level of IGF2 BP2 was found to be significantly higher in a single-lamb group than in a multi-lamb group.Insertions/deletions(indels)within the goat IGF2 BP2 gene,including P4-Ins-13 bp and P5-Del-12 bp,were verified in 918 Shaanbei White Cashmere(SBWC)female goats.The minor allelic frequencies(MAFs)of P4-Ins-13 bp and P5-Del-12 bp loci were 0.349 and 0.295,respectively.Analysis using the Chi-square(χ^(2))test showed that the genotype(χ^(2)=14.479,P=0.006)distribution of P4-Ins-13 bp was significantly different between the single-lamb and multi-lamb groups.Correlation analysis demonstrated that P4-Ins-13 bp was significantly associated with goat litter size(P=0.022),and individual goats with the homozygous deletion/deletion(DD)genotype produced more litters than other goats.Therefore,considered as a potential molecular marker significantly related to lambing traits,the P4-Ins-13 bp mutation of the goat IGF2 BP2 gene can be used in goat breeding with practical molecular marker-assisted selection(MAS)to optimize female reproduction and improve economic efficiency in the goat industry.展开更多
基金supported in part by AFRI grant numbers 2019-7015-29321 and 2021-67015-33409 from the USDA National Institute of Food and Agriculture(NIFA)the SCINet project of the USDA ARS project number 0500-00093-001-00-D。
文摘Structural variations(SVs≥50 bp)are a critical but underexplored source of genetic diversity in cattle,shaping traits vital for productivity,adaptability,and health.Advances in long-read sequencing,pangenome graph construction,and near-complete genome assemblies now allow accurate SV detection and genotyping.These innovations overcome the limitations of single-reference genomes,enabling the discovery of complex SVs,including nested and overlapping variants,and providing access to previously inaccessible genomic regions such as centromeres and telomeres.This review highlights the current landscape of cattle SV research,with emphasis on integrating longread sequencing and pangenome frameworks to uncover breed-specific and population-level variation.While many SVs are linked to economically important traits such as feed efficiency and disease resistance,their broader regulatory impacts remain an active area of investigation.Emerging functional genomics approaches,including transcriptomics,epigenomics,and genome editing,will clarify how SVs influence gene regulation and phenotype.Looking forward,the integration of SV catalogs with multi-omics data,imputation resources,and artificial intelligence-driven models will be essential for translating discoveries into breeding and conservation applications.Integrating structural variants into breeding pipelines promises to revolutionize livestock genomics,enabling precision selection and sustainable agriculture despite challenges in cost,data sharing,and functional validation.
基金supported by the National Key Research and Development Program of China(2022YFF1000201)National Scientific Foundation of China(32272861)the China Agriculture Research System of MOF and MARA(CARS-41)。
文摘Background Excessive abdominal fat in broilers not only reduces feed efficiency and increases processing costs but also raises environmental concerns.This pathological overaccumulation results from complex metabolic dysregulation across multiple organs.While current research largely centers on adipogenesis within adipose tissue,a comprehensive understanding of the cross-organ regulatory factors influencing this process remains elusive.Results Here,we employed a high-fat diet(HFD)model and multi-omics approaches to investigate cross-organ regulatory mechanisms underlying abdominal fat deposition in broilers.Our results demonstrated that HFD not only promoted fat accumulation but also altered meat quality traits.Through 16S rRNA amplicon sequencing,we identified significant gut microbiota dysbiosis in HFD-fed chickens,manifested by an increased abundance of Lactobacillus and a decreased abundance of Enterococcus.However,jejunal microbiota transplantation from HFD donors did not induce abdominal fat deposition in recipient chickens.Metabolomic profiling revealed that HFD elevated the level of succinic acid,a metabolite positively correlated with Lactobacillus abundance and potentially generated by Lactobacillus.This increase in succinic acid(SA)further triggered metabolic inflammation response in both jejunal tissue and serum.In vivo validation established succinic acid as a key inflammatory mediator facilitating HFD-induced cross-organ communication between the jejunum and abdominal adipose tissue,enhancing intestinal lipid uptake and subsequent abdominal fat deposition.Bulk and single-nucleus RNA sequencing(snRNA-seq)revealed that HFD induced macrophage population expansion and intensified adipocyte-macrophage crosstalk.Adipocyte-macrophage co-culture systems further elucidated that macrophages are an indispensable factor in succinic acid-induced fat deposition.Conclusion This study delineates a succinic acid-driven"gut-fat axis"governing abdominal fat deposition in broilers,integrating gut microbiota dysbiosis and macrophage-mediated inflammatory adipogenesis.By identifying succinic acid as a cross-organ signaling molecule that enhances lipid absorption and activates macrophage-dependent adipogenesis,we establish systemic metabolic-immune crosstalk as a pivotal regulatory mechanism.These findings redefine fat deposition as a process extending beyond adipose-centric models,advancing multi-omics-guided strategies for sustainable poultry production.
基金supported by the National Natural Science Foundation of China(32471603)Science and Technology Commissioner Special Project of Qinghai Province(2025-NK-P42)+2 种基金Central Financial Funds for Forestry and Grassland Reform and Development in 2024(2024-TG16)Hainan Tibetan Autonomous Prefecture Science and Technology Program Project(2025-KH01-B)the leading Kunlun talents in Qinghai Province.
文摘As a critical global ecosystem,grasslands rely on complex aboveground-belowground interactions that underpin multifunctionality,yet their mechanisms remain poorly understood.Our investigation employed the plateau pika(Ochotona curzoniae),a small herbivore widely distributed throughout the Qinghai-Tibetan Plateau,as a model organism to examine the consequences of disturbance on plant diversity,soil properties,microbial diversity,and multifunctionality of grassland ecosystems.We found that high pika burrow density significantly reduced plant diversity(Shannon-Wiener and Chao1 indices)and aboveground biomass.It also increased soil pH and reduced ammonium nitrogen content.The soil microbial diversity,encompassing both bacteria and fungi,was markedly decreased in areas characterized by a high concentration of burrows.Microbial interaction networks demonstrated greater complexity in areas with high burrow densities,as revealed by the network analysis.Conversely,in regions characterized by low burrow density,a significant negative correlation was observed between the intricacy of soil bacterial networks and the multifunctionality of grassland ecosystems.Structural equation modelling showed that pika disturbance indirectly affected multifunctionality via changes in plant biomass and soil properties-notably,nitrate nitrogen explained 40%of multifunctionality variation under high disturbance.This investigation advances our understanding of complex aboveground-belowground linkages in grassland ecosystems,revealing novel mechanisms through which biodiversity governs ecosystem multifunctionality.Our findings underscore the critical role of small herbivores in shaping grassland ecosystem functions and emphasize the importance of maintaining balanced disturbance regimes to sustain ecosystem multifunctionality.This has immediate implications for global conservation policies on the Qinghai-Tibetan Plateau and analogous ecosystems.
基金funded by the National Key R&D Program of China(2021YFD1200903)Seed Fund(CAU),Shandong Provincial Natural Science Foundation(ZR2021MC070)+3 种基金the National Key R&D Program of China(2021YFF1000701-06)Shandong Provincial Natural Science Foundation(ZR2020MC165)the Earmarked Fund for CARS-36.X.W.is funded by the“Hundred Talents Program”project of Hebei Province(E2020100019)the research project of Zhongnongtongchuang(ZNTC)group(ZNTC2019A10 and ZNTC2021B12)in China.
文摘Sperm is essential for successful artificial insemination in dairy cattle,and its quality can be influenced by both epi-genetic modification and epigenetic inheritance.The bovine germline differentiation is characterized by epigenetic reprogramming,while intergenerational and transgenerational epigenetic inheritance can influence the offspring’s development through the transmission of epigenetic features to the offspring via the germline.Therefore,the selec-tion of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers.We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.
基金the project “Genomics for Conservation of Indigenous Cattle Breeds and for Enhancing Milk Yield, Phase-I” [BT/ PR26466/AAQ/1/704/2017], funded by the Department of Biotechnology (DBT ), Indiathe project “Identification of key molecular factors involved in resistance/susceptibility to paratuberculosis infection in indigenous breeds of cows” [BT/PR32758/AAQ/1/760/2019], which was also funded by Department of Biotechnology (DBT ), India。
文摘Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle.To comprehensively characterize the genomic variation within Bos indicus and,specifically,dairy breeds,we aim to identify non-reference sequences and construct a comprehensive pangenome.Results Five representative genomes of prominent dairy breeds,including Gir,Kankrej,Tharparkar,Sahiwal,and Red Sindhi,were sequenced using 10X Genomics‘linked-read’technology.Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb,comparable to the Bos indicus Brahman reference genome.A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods,revealing 8 Mb and 17.7 Mb of novel sequence respectively.A confident set of 6,844 Non-reference Unique Insertions(NUIs)spanning 7.57 Mb was identified through both methods,representing the pange-nome of Indian Bos indicus breeds.Comparative analysis with previously published pangenomes unveiled 2.8 Mb(37%)commonality with the Chinese indicine pangenome and only 1%commonality with the Bos taurus pange-nome.Among these,2,312 NUIs encompassing~2 Mb,were commonly found in 98 samples of the 5 breeds and des-ignated as Bos indicus Common Insertions(BICIs)in the population.Furthermore,926 BICIs were identified within 682 protein-coding genes,54 long non-coding RNAs(lncRNA),and 18 pseudogenes.These protein-coding genes were enriched for functions such as chemical synaptic transmission,cell junction organization,cell-cell adhesion,and cell morphogenesis.The protein-coding genes were found in various prominent quantitative trait locus(QTL)regions,suggesting potential roles of BICIs in traits related to milk production,reproduction,exterior,health,meat,and carcass.Notably,63.21%of the bases within the BICIs call set contained interspersed repeats,predominantly Long Inter-spersed Nuclear Elements(LINEs).Additionally,70.28%of BICIs are shared with other domesticated and wild species,highlighting their evolutionary significance.Conclusions This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India.The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.
基金funded by the National Key Research and Development Program of China(2024YFF1000100 and 2021YFD1301102)the National Natural Science Foundations of China(32172702)the National Agricultural Science and Technology Innovation Program,Chinese Academy of Agricultural Sciences(ASTIP-IAS02).
文摘Resilience traits in pig populations allow animals to deal better with infectious disease and suboptimal production environments.The data on daily weight,feed intake and feed behaviors in pigs are collected in test period by automated feeding stations,which facilitate to evaluate the resilience traits.In this study,we adopted the root mean square error(RMSE)of ordinary least squares(OLS)and the negative residuals of quantile regression(QR)to generate four different novel resilience traits using daily records of feed intake and feed duration between 90 and 180 days of age in a population of commercial Duroc pigs.The genome-wide association studies(GWAS)based on single-and two-trait mixed models were carried out on 550 pigs using 48,603 single nucleotide polymorphisms(SNPs)to identify genomic regions associated with resilience traits in growing pigs.We further focused on the GWAS signals to conduct gene annotation,colocalization with multi-tissue eQTL summary statistics of PigGTEx project and identification of enhancers and promoters using the publicly available data.The genomic heritabilities of four novel resilience traits ranged from 0.09 to 0.41.The pairwise genetic and phenotypic correlations ranged from 0.16 to 0.95 and from 0.05 to 0.36,respectively.Twenty-seven SNPs were identified to be significantly associated with these resilience traits.They were distributed on nine chromosomes(SSC1,SSC2,SSC6,SSC7,SSC8,SSC12,SSC14,SSC16 and SSC17).After annotation,39 QTLs and 49 candidate genes were identified.Several of these are functionally relevant candidate genes including OTUD4,TIFA and CARD14,which are involved in the host immune response,disease susceptibility and signal transduction.Eight unique SNPs were found to be causal in both GWAS and eQTL analyses across 15 tissues.Notably,one SNP(rs80794541)was associated with eQTLs identified concurrently across seven tissues/cell types,including the macrophage cell type.Furthermore,four significant SNPs(rs81467127,rs81356029,rs80794541 and rs81305085)were linked to the function of the primed enhancer,active element,and poised promoter in five pig tissues.Using the porcine fibroblast HiC dataset,SNP(rs81356029)on SSC2 regulates the CARNS1 and SSH3,while SNP(rs80794541)on SSC7 regulates the H2AC6.In this study,we generated four novel resilience traits and identified SNPs significantly associated with these resilience traits in a Duroc pig population.GWAS signals were associated with candidate genes involving in the immune traits,and were linked to the crucial regulatory elements as well.Our findings will contribute to elucidating the genetic mechanism that can enhance genome-enabled breeding and inform further research on resilience in domestic pigs.
文摘Following the publication of Liu et al.(2024),an error was identified in Figure 4B,in which the image representing the lung from the E529G group was inadvertently duplicated with the image of the lung from the WT group during figure preparation.
基金Bill&Melinda Gates Foundation(Grant number OPP1154401).
文摘Backgroud Before fertilization,spermatozoa undergo a crucial maturation step called capacitation,which is a unique event regulates the sperm’s ability for successful fertilization.The capacitation process takes place as the spermatozoa pass through the female reproductive tract(FRT).Dihydrolipoamide dehydrogenase(DLD)protein is a post-pyruvate metabolic enzyme,exhibiting reactive oxygen species(ROS)production which causes capacitation.Additionally,other vital functions of DLD in buffalo spermatozoa are hyperactivation and acrosome reaction.DLD produces the optimum amount of ROS required to induce capacitation process in FRT.Depending on physiological or patho-physiological conditions,DLD can either enhance or attenuate the production of reactive oxygen species(ROS).Aim of this study was to investigate whether changes in the production of ROS in sperm cells can impact their ability to fertilize by triggering the capacitation and acrosome reaction.Results In this study,abundance of DLD protein was quantified between high(n=5)and low fertile bull(n=5)sper-matozoa.It was found that compared to high-fertile(HF)bulls,low-fertile(LF)bulls exhibited significantly(P<0.05)higher DLD abundances.Herein,we optimised the MICA concentration to inhibit DLD function,spermatozoa were treated with MICA in time(0,1,2,3,4,and 5 h)and concentrations(1,2.5,5,and 10 mmol/L)dependent manner.Maximum DLD inhibition was found to be at 4 h in 10 mmol/L MICA concentration,which was used for further exper-imentation in HF and LF.Based on DLD inhibition it was seen that LF bull spermatozoa exhibited significantly(P<0.05)higher ROS production and acrosome reaction in comparison to the HF bull spermatozoa.The kinematic parameters of the spermatozoa such as percent total motility,velocity parameters(VCL,VSL,and VAP)and other parameters(BCF,STR,and LIN)were also decreased in MICA treated spermatozoa in comparison to the control(capacitated)spermatozoa.Conclusions The present study provides an initial evidence explaining the buffalo bull spermatozoa with higher DLD abundance undergo early capacitation,which subsequently reduces their capacity to fertilize.
基金supported by grants from The Sci-Tech Innovation 2030 Agenda(2023ZD04045)Guangxi Key Research and Development Program(AB241484033).
文摘Background Semen quality is one of the most important indicators of boar reproductive performance.In the past,boar breeding has mostly emphasized characteristics such as lean meat percentage,feed conversion efficiency,and growth rate,while overlooking the genetic improvement of reproductive traits.This study employs advanced multi-omics approaches,such as transcriptome-wide association studies(TWAS)and colocalization between genome-wide association studies(GWAS)and expression quantitative trait loci(eQTLs),to provide a comprehensive understanding of the genetic mechanisms governing semen quality traits in boars.Results Here,we collected 190,000 ejaculate records across 11 semen quality traits from 3,604 Duroc boars.The heritability of semen quality traits ranged from 0.095 to 0.343.Genetic correlations between semen quality traits varied from−0.802 to 0.661,and phenotypic correlations ranged from−0.833 to 0.776.Single-trait GWAS identified 19 independent variants,corresponding to 13 quantitative trait loci(QTLs).By integrating PigGTEx and FAANG resources,we combined TWAS and colocalization analyses to reveal genetic regulation of semen quality traits.Notably,both GWAS and colocalization analyses pinpointed the DCAF12 as a crucial gene associated with multiple semen quality traits.Additionally,the ZSCAN9 gene and the variant rs322211455 were found to significantly affect sperm motility(SPMOT),possibly through hypothalamic-pituitary-gonadal axis.PheWAS further highlighted an association between rs322211455 and sperm abnormality rate,demonstrating the crucial role of ZSCAN9 in male fertility.Conclusion This study reveals the genetic basis and regulatory mechanisms underlying semen quality traits in Duroc boars,identifying key candidate genes such as DCAF12 and ZSCAN9.These findings provide important insight into the genetic regulation of semen quality in boars.
基金supported by the Russian Science Foundation(No.22-16-00128),“Investigation of the Toxic Effect of Glyphosates on the Functional State of the Bird Intestinal Microbial Community,Their Growth and Development,and the Development of a Biological Product Based on the Glyphosate Degrading Strain”.
文摘Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreatic genes and blood physiology parameters after administering one maximum residue limit of herbicide glyphosate(GLY),two ANTs,and one anticoccidial drug(AD).A total of 260 Ross 308 broilers aged 1-40 d were divided into the following four groups of 65 birds each:control group,which was fed the main diet(MD),and three experimental groups,which were fed MD supplemented with GLY,GLY+ANTs(enrofloxacin and colistin methanesulfonate),and GLY+AD(ammonium maduramicin),respectively.The results showed that the addition of GLY,GLY+ANTs,and GLY+AD caused significant changes in the expression of several genes of physiological and economic importance.In particular,genes related to inflammation and apoptosis(interleukin 6(IL6),prostaglandin-endoperoxide synthase 2(PTGS2),and caspase 6(CASP6))were downregulated by up to 99.1%,and those related to antioxidant protection(catalase(CAT),superoxide dismutase 1(SOD1)and peroxiredoxin 6(PRDX6))by up to 98.6%,compared to controls.There was also a significant decline in the values of immunological characteristics in the blood serum observed in the experimental groups,and certain changes in gene expression were concordant with changes in the functioning of the pancreas and blood.The changes revealed in gene expression and blood indices in response to GLY,ANTs,and AD provide insights into the possible mechanisms of action of these agents at the molecular level.Specifically,these changes may be indicative of physiological mechanisms to overcome the negative effects of GLY,GLY+ANTs,and GLY+AD in broilers.
基金supported by the Natural Science Foundation of Qinghai Province(No.2022-ZJ-901)the National Breeding Joint Research Project。
文摘Introduction Tibetan sheep,economically important animals on the Qinghai–Tibet Plateau,have diversified into numerous local breeds with unique characteristics through prolonged environmental adaptation and selective breeding.However,most current research focuses on one or two breeds,and lacks a comprehensive representa-tion of the genetic diversity across multiple Tibetan sheep breeds.This study aims to fill this gap by investigating the genetic structure,diversity and high-altitude adaptation of 6 Tibetan sheep breeds using whole-genome rese-quencing data.Results Six Tibetan sheep breeds were investigated in this study,and whole-genome resequencing data were used to investigate their genetic structure and population diversity.The results showed that the 6 Tibetan sheep breeds exhibited distinct separation in the phylogenetic tree;however,the levels of differentiation among the breeds were minimal,with extensive gene flow observed.Population structure analysis broadly categorized the 6 breeds into 3 distinct ecological types:plateau-type,valley-type and Euler-type.Analysis of unique single-nucleotide polymor-phisms(SNPs)and selective sweeps between Argali and Tibetan sheep revealed that Tibetan sheep domestication was associated primarily with sensory and signal transduction,nutrient absorption and metabolism,and growth and reproductive characteristics.Finally,comprehensive analysis of selective sweep and transcriptome data sug-gested that Tibetan sheep breeds inhabiting different altitudes on the Qinghai–Tibet Plateau adapt by enhancing cardiopulmonary function,regulating body fluid balance through renal reabsorption,and modifying nutrient diges-tion and absorption pathways.Conclusion In this study,we investigated the genetic diversity and population structure of 6 Tibetan sheep breeds in Qinghai Province,China.Additionally,we analyzed the domestication traits and investigated the unique adapta-tion mechanisms residing varying altitudes in the plateau region of Tibetan sheep.This study provides valuable insights into the evolutionary processes of Tibetan sheep in extreme environments.These findings will also contribute to the preservation of genetic diversity and offer a foundation for Tibetan sheep diversity preservation and plateau animal environmental adaptation mechanisms.
基金supported by the National Natural Science Foundation of China(32400711,U22A20447)Natural Science Foundation of Qinghai(2025-ZJ-910Q)“Kunlun Talents”Project from the Qinghai Provincial Government(to Q.E.Y.)。
文摘Hypobaric hypoxia encountered at high altitudes impairs reproductive health and fertility across species.Previous findings have demonstrated that maternal hypoxia exposure disrupts granulosa cell(GC)viability and oocyte maturation in female offspring;however,its transgenerational impact on male reproductive outcomes remains poorly elucidated.In this study,pregnant mice(F0)were subjected to hypoxic conditions,and male progeny across four generations(F1-F4)were evaluated.Results revealed that maternal hypoxia induced mild alterations in sperm DNA methylation in F1 males but caused profound developmental defects in F2 embryos,predominantly affecting males.Following mating of F1males with control females,a substantial proportion of male F2 fetuses were lost at embryonic day(E)13.5,attributed to placental malformations.Integrated RNA sequencing and whole-genome bisulfite sequencing of placentas from male fetuses revealed aberrant expression of imprinted genes,including Gnas,Slc38a4,Jade1,and Kcnq1,which also exhibited differential methylation in F1sperm.These findings demonstrate that maternal hypoxia disrupts epigenetic programming in F1 germ cells,impairing placental development and fetal viability in F2males,thereby leading to an unbalanced sex ratio.Overall,this study elucidates the mechanisms by which environmental hypoxia influences sex ratios and offers critical insights into hypoxia-induced reproductive impairments in mammals.
基金supported by the Rufford Foundation(Grant No.45888-2:data analysis)the Russian Science Foundation(RSF Grant No.22-14-00037-P:data analysis)+3 种基金the National Natural Science Foundation of China(32300370)International Partnership Program of Chinese Academy of Sciences(071GJHZ2023041MI),ChinaPostdoctoral Science Foundation(2023M743416)the 2023 award fund of Qinghai Provincial Key Laboratory of Animal Ecological Genomics.
文摘A comprehensive taxonomic reassessment of the Hebius optatus species complex,integrating molecular data and morphological data,has led to the recognition and description of a previously overlooked species from northern Vietnam and the Guangxi Zhuang Autonomous Region,China,herein described as Hebius vogeli sp.nov.Phylogenetic analyses reveal that Hebius vogeli sp.nov.is closely related to H.sauteri and H.optatus sensu stricto.Uncorrected p-distances based on cytochrome b sequences indicate a divergence of 10.74%-11.73%between Hebius vogeli sp.nov.and H.optatus.The new species differs from H.optatus by a combination of characters,including a higher number of subcaudal scales,a greater total number of ventral and subcaudal scales,and distinct ventral coloration.Hebius vogeli sp.nov.appears to be geographically restricted to northern Vietnam and the adjacent region of Guangxi Zhuang Autonomous Region,China,making its distribution allopatric from that of H.optatus.The Pearl River is hypothesized to serve as a biogeographic barrier separating the two taxa.Accordingly,we recommend the exclusion of H.optatus from the herpetofauna of Vietnam.Based on IUCN Red List criteria,we propose that Hebius vogeli sp.nov.be assessed as Least Concern(LC).Our results emphasize both the underestimated diversity within Hebius and the need for continued integrative taxonomic efforts,particularly in the Vietnam-China borderlands,where cryptic diversity remains largely unexplored.
基金supported by the National Basic Research Program of China(2013CB127302)the National Natural Science Foundation of China(31272450 and 31572412)+2 种基金Competitive Grants from the Animal Reproduction Program(no.2014-67015-21770)Animal Growth & Nutrient Utilization Programs(no.2015-67015-23276)of the USDA National Institute of Food and AgricultureTexas A&M AgriL ife Research(H-8200)
文摘Maternal undernutrition or overnutrition during pregnancy alters organ structure, impairs prenatal and neonatal growth and development, and reduces feed efficiency for lean tissue gains in pigs. These adverse effects may be carried over to the next generation or beyond. This phenomenon of the transgenerational impacts is known as fetal programming, which is mediated by stable and heritable alterations of gene expression through covalent modifications of DNA and histones without changes in DNA sequences(namely, epigenetics). The mechanisms responsible for the epigenetic regulation of protein expression and functions include chromatin remodeling; DNA methylation(occurring at the 5′-position of cytosine residues within CpG dinucleotides); and histone modifications(acetylation, methylation, phosphorylation, and ubiquitination). Like maternal malnutrition, undernutrition during the neonatal period also reduces growth performance and feed efficiency(weight gain:feed intake; also known as weightgain efficiency) in postweaning pigs by 5–10%, thereby increasing the days necessary to reach the market bodyweight. Supplementing functional amino acids(e.g., arginine and glutamine) and vitamins(e.g., folate) play a key role in activating the mammalian target of rapamycin signaling and regulating the provision of methyl donors for DNA and protein methylation. Therefore, these nutrients are beneficial for the dietary treatment of metabolic disorders in offspring with intrauterine growth restriction or neonatal malnutrition. The mechanism-based strategies hold great promise for the improvement of the efficiency of pork production and the sustainability of the global swine industry.
基金supported by World Bank funded National Agricultural Innovation Project(C4/C30015)
文摘Background： The Y chromosome in mammal is paternally inherited and harbors genes related to male fertility and spermatogenesis. The unique intra-chromosomal recombination pattern of Y chromosome and morphological difference of this chromosome between Bos taurus and Bos indicus make it an ideal model for studying structural variation, especially in crossbred （Bos taurus x Bos indicus） bulls. Copy Number Variation （CNV） is a type of genomic structural variation that gives information complementary to SNP data. The purpose of this study was to find out copy number differences of four Y chromosomal spermatogenesis-related candidate genes in genomic DNA of crossbred and purebred Indicine bulls. Result： Four Y chromosomal candidate genes of spermatogenesis namely, sex determining gene on Ychromosome （SRY）, DEAD box po/ypeptide 3-Y chromosome （DDX3 Y）, Ubiquidn specific peptidase 9, Y-linked （ usPgY）, testis-specific protein on Y chromosome （TSPY） were evaluated. Absolute copy numbers of Y chromosomal genes were determined by standard curve-based quantitative real time PCR. Copy numbers of SRYand TSPYgenes per unit amount of genomic DNA are higher in crossbred than Indicine bulls. However, no difference was observed in DDX3Yand usPgYgene copy numbers between two groups. Conclusion： The present study demonstrates that the structural organization of Y chromosomes differs between crossbred and Indicine bulls which are reproductively healthy as observed from analysis of semen attributes. The absolute copy numbers of SRY and TSPY genes in unit mass of genomic DNA of crossbred bulls are significantly higher than Indicine bulls. No alteration in absolute copies ofDDX3Yand usPgYgene was found between the genome of crossbred and Indicine bulls. This study suggests that the DDX3Yand USPgYare likely to be single copy genes in the genome of crossbred and Indicine bulls and variation in Y chromosome length between crossbred and Indicine bulls may be due to the copy number variation of SRY gene and TSPYarray.
基金funded by the National Natural Science Foundation of China (Grant No. 51508250)the Science and Technology Project of Department of Transportation of Jilin Province (Grant No. 2018-1-14)+1 种基金the Basic Research Program of the Centric Level, Scientific Research Institutes (Grant No. 20180615)the World Wild Fund for Nature Project (Grant No. P03516)
文摘Road traffic is the main factor causing the decline in amphibian populations worldwide. The proper design of an amphibian tunnel is one of the most efficient measures to mitigate the negative impacts of road traffic on amphibians. However, no study has investigated the effectiveness of amphibian tunnels under semi-controlled conditions in Asian amphibians. Here, we selected two representative amphibian species, the Chinese brown frog, Rana chensinensis, and the Asiatic toad, Bufo gargarizans, which suffer the most severe road mortality along the roads in Northeast China. We placed experimental arrays of culverts of various sizes(diameters of 1.5, 1, and 0.5 m for circular culverts; side lengths of 1.5, 1, and 0.5 m for box culverts), and substrate type(soil, concrete, and metal) to examine the preferences of both species during the migratory season between May and September in 2016 and 2017. The results revealed that the Chinese brown frog preferred mid-and large-sized culverts as well as soil culverts. We concluded that culverts with a side length ≥ 1 m, lined with soil, and accompanied by a ≥ 0.4 m high guide drift fence and ≤ 45° gradient on the roadside ditch wall would best facilitate road crossings for both species and likely for other amphibian species in Northeast China.
基金supported by the Key Research and Development Program of Guangdong Province (2020B020222001)the National Natural Science Foundation of China (Grant Nos. 31972659, 31902252, 31672564, 31602053)+5 种基金Guangdong Basic and Applied Basic Research Foundation (2019A1515012006)Natural Science Foundation of Guangdong Province (2018B030315009)China Postdoctoral Science Foundation (2019M652922)the Special Project of National Modern Agricultural Industrial Technology System (CARS-41)the Chief expert Project of Agricultural Industry Technology system in Guangdong Province (2019KJ128)the support of Instrumental Anlysis&Research Center of South China Agriculture University。
文摘Subgroup J avian leukosis virus(ALV-J) is a highly oncogenic retrovirus that has been devastating the global poultry industry since the late 1990s. The major infection model of ALV-J is vertical transmission, which is responsible for the congenital infection of progeny from generation to generation. Increasing evidence has suggested that extracellular vesicles(EVs) derived from virus-infected cells or biological fluids have been thought to be vehicles of transmission for viruses. However, the role of EVs in infection and transmission of ALV-J remains obscure. In the present study, semen extracellular vesicles(SE) were isolated and purified from ALV-J-infected rooster seminal plasma(SE-ALV-J), which was shown to contain ALV-J genomic RNA and partial viral proteins, as determined by RNA sequencing, reverse transcription-quantitative PCR and Western blotting. Furthermore, SE-ALV-J was proved to be able to transmit ALV-J infection to host cells and establish productive infection.More importantly, artificial insemination experiments showed that SE-ALV-J transmitted ALV-J infection to SPF hens, and subsequently mediated vertical transmission of ALV-J from the SPF hens to the progeny chicks. Taken together, the results of the present study suggested that ALV-J utilized host semen extracellular vesicles as a novel means for vertical transmission, enhancing our understanding on mechanisms underlying ALV-J transmission.
基金supported in part by a Grant-in-Aid for Scientific Research (C) (grant no. 25463192) from the Ministry of Education, Science, Sports, Culture, and Technology of Japan
文摘The ability of human deciduous tooth dental pulp cells（HDDPCs） to differentiate into odontoblasts that generate mineralized tissue holds immense potential for therapeutic use in the field of tooth regenerative medicine. Realization of this potential depends on efficient and optimized protocols for the genetic manipulation of HDDPCs. In this study, we demonstrate the use of a Piggy Bac（PB）-based gene transfer system as a method for introducing nonviral transposon DNA into HDDPCs and HDDPC-derived inducible pluripotent stem cells. The transfection efficiency of the PB-based system was significantly greater than previously reported for electroporation-based transfection of plasmid DNA. Using the neomycin resistance gene as a selection marker, HDDPCs were stably transfected at a rate nearly 40-fold higher than that achieved using conventional methods. Using this system, it was also possible to introduce two constructs simultaneously into a single cell. The resulting stable transfectants, expressing td Tomato and enhanced green fluorescent protein, exhibited both red and green fluorescence. The established cell line did not lose the acquired phenotype over three months of culture. Based on our results, we concluded that PB is superior to currently available methods for introducing plasmid DNA into HDDPCs. There may be significant challenges in the direct clinical application of this method for human dental tissue engineering due to safety risks and ethical concerns. However, the high level of transfection achieved with PB may have significant advantages in basic scientific research for dental tissue engineering applications, such as functional studies of genes and proteins. Furthermore, it is a useful tool for the isolation of genetically engineered HDDPC-derived stem cells for studies in tooth regenerative medicine.
基金the National Natural Science Foundation of China(Nos.32060734 and 31760650)。
文摘Insulin-like growth factor 2 m RNA-binding protein 2(IGF2 BP2,also called IMP2)plays an essential role in the development and maturation of germ cells and embryos and is a candidate gene for goat litter size,based on a previous genomewide selective sweep analysis.In this study,the m RNA expression level of IGF2 BP2 was found to be significantly higher in a single-lamb group than in a multi-lamb group.Insertions/deletions(indels)within the goat IGF2 BP2 gene,including P4-Ins-13 bp and P5-Del-12 bp,were verified in 918 Shaanbei White Cashmere(SBWC)female goats.The minor allelic frequencies(MAFs)of P4-Ins-13 bp and P5-Del-12 bp loci were 0.349 and 0.295,respectively.Analysis using the Chi-square(χ^(2))test showed that the genotype(χ^(2)=14.479,P=0.006)distribution of P4-Ins-13 bp was significantly different between the single-lamb and multi-lamb groups.Correlation analysis demonstrated that P4-Ins-13 bp was significantly associated with goat litter size(P=0.022),and individual goats with the homozygous deletion/deletion(DD)genotype produced more litters than other goats.Therefore,considered as a potential molecular marker significantly related to lambing traits,the P4-Ins-13 bp mutation of the goat IGF2 BP2 gene can be used in goat breeding with practical molecular marker-assisted selection(MAS)to optimize female reproduction and improve economic efficiency in the goat industry.
