The livestock sector is a vital component of India's agricultural economy,providing essential support to rural communities and ensuring food security.Efficient reproductive performance is critical to sustaining li...The livestock sector is a vital component of India's agricultural economy,providing essential support to rural communities and ensuring food security.Efficient reproductive performance is critical to sustaining livestock productivity,yet age-related declines in both male and female fertility pose significant challenges.The current review highlights that male reproductive efficiency is closely tied to semen quality,which deteriorates with age due to oxidative stress,leading to reduced fertilizing capacity and embryonic developmental potential.Similarly,female reproductive longevity is predominantly influenced by ovarian health,which declines with age due to diminished oocyte quality and quantity.This decline is exacerbated by oxidative stress and mitochondrial dysfunction,leading to reproductive senescence and reduced offspring viability.Understanding the mechanisms of reproductive aging and developing strategies to mitigate its effects are crucial for enhancing livestock productivity and sustaining the agrarian economy.展开更多
The gut microbiota has emerged as a pivotal regulator of host lipid metabolism and energy homeostasis.A growing body of evidence reveals that variations in the composition and metabolic activity of intestinal microbes...The gut microbiota has emerged as a pivotal regulator of host lipid metabolism and energy homeostasis.A growing body of evidence reveals that variations in the composition and metabolic activity of intestinal microbes are closely associated with differences in adipose tissue deposition across species.Notably,increased abundance of Firmicutes and a reduced proportion of Bacteroidetes and butyrate-producing bacteria have been linked to enhanced fat accumulation.Key microbial metabolites such as short-chain fatty acids(SCFAs)influence lipid metabolism through multiple pathways,including the activation of GPR41/43 receptors,modulation of the bile acid–FXR/TGR5 axis,and regulation of hepatic lipogenesis.Additionally,the gut–brain axis plays a critical role in controlling feeding behavior via neuroendocrine signaling.This review summarizes current advances in understanding the roles of dominant bacterial phyla and beneficial genera—including Clostridium butyricum and Faecalibacterium prausnitzii—in fat metabolism.We further explore the mechanisms by which gut microbiota modulate lipid synthesis and catabolism through SCFA production,bile acid signaling,and AMPK/PPAR-related pathways.These insights highlight the potential of microbiota-targeted strategies to restore lipid metabolic balance,offering novel opportunities for applications in health management,nutritional interventions,and microbial therapeutics.展开更多
Background Follicular atresia,a complex degenerative process regulated by multiple molecular mechanisms,significantly affects female reproductive performance in animals.While granulosa cell(GC)apoptosis has been well ...Background Follicular atresia,a complex degenerative process regulated by multiple molecular mechanisms,significantly affects female reproductive performance in animals.While granulosa cell(GC)apoptosis has been well established as a primary mechanism underlying follicular atresia,the potential involvement of ferroptosis,which is an irondependent form of regulated cell death,remains largely unexplored in chickens.Results Using a tamoxifen(TMX)-induced avian model of follicular atresia,we demonstrated that ferroptosis plays a critical role in follicular degeneration.Inhibition of ferroptosis through pharmacological agents significantly restored follicular function,underscoring its potential as a therapeutic target.Notably,we observed a significant upregulation of ubiquitin-specific peptidase 9,X-linked(USP9X)in GCs during atresia.Through comprehensive in vitro and in vivo investigations,we confirmed that USP9X facilitates follicular atresia by promoting ferroptosis in GCs.Mechanistically,USP9X induces ferroptosis by stabilizing Beclin1 through deubiquitination,thereby activating autophagy-dependent ferroptosis.This pathway was effectively suppressed by autophagy inhibitors,emphasizing the essential role of autophagy in USP9X-mediated ferroptosis.Conclusions Our findings provide the evidence that the USP9X-Beclin1 axis regulates autophagy-dependent ferroptosis during avian follicular atresia.These insights reveal novel molecular targets and potential genetic markers for improving reproductive efficiency in chicken breeding programs.展开更多
The advantages of genome selection(GS) in animal and plant breeding are self-evident.Traditional parametric models have disadvantage in better fit the increasingly large sequencing data and capture complex effects acc...The advantages of genome selection(GS) in animal and plant breeding are self-evident.Traditional parametric models have disadvantage in better fit the increasingly large sequencing data and capture complex effects accurately.Machine learning models have demonstrated remarkable potential in addressing these challenges.In this study,we introduced the concept of mixed kernel functions to explore the performance of support vector machine regression(SVR) in GS.Six single kernel functions(SVR_L,SVR_C,SVR_G,SVR_P,SVR_S,SVR_L) and four mixed kernel functions(SVR_GS,SVR_GP,SVR_LS,SVR_LP) were used to predict genome breeding values.The prediction accuracy,mean squared error(MSE) and mean absolute error(MAE) were used as evaluation indicators to compare with two traditional parametric models(GBLUP,BayesB) and two popular machine learning models(RF,KcRR).The results indicate that in most cases,the performance of the mixed kernel function model significantly outperforms that of GBLUP,BayesB and single kernel function.For instance,for T1 in the pig dataset,the predictive accuracy of SVR_GS is improved by 10% compared to GBLUP,and by approximately 4.4 and 18.6% compared to SVR_G and SVR_S respectively.For E1 in the wheat dataset,SVR_GS achieves 13.3% higher prediction accuracy than GBLUP.Among single kernel functions,the Laplacian and Gaussian kernel functions yield similar results,with the Gaussian kernel function performing better.The mixed kernel function notably reduces the MSE and MAE when compared to all single kernel functions.Furthermore,regarding runtime,SVR_GS and SVR_GP mixed kernel functions run approximately three times faster than GBLUP in the pig dataset,with only a slight increase in runtime compared to the single kernel function model.In summary,the mixed kernel function model of SVR demonstrates speed and accuracy competitiveness,and the model such as SVR_GS has important application potential for GS.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
The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology,contractility,cell proliferation,differentiation,interactions,migration,and death.The three-dimensi...The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology,contractility,cell proliferation,differentiation,interactions,migration,and death.The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes.The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages.Hi-C was used to build chromatin architectures during four representative stages.Ch IP-seq was conducted to identify enhancers and promoters in these four stages,which are occupied by histone H3K27ac and H3K4me3 peaks.Results show that large-scale genome architecture changes are mostly unidirectional,and coupled by complex on/off dynamic patterns of gene expression.Specifically,we observed 258.30 Mb of the genome undergoing A/B compartment switching.Notable alterations(316.57 Mb)of interaction frequencies within TADs were observed.Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development.Some muscle-related gene promoters that interacted with active enhancers during development,and some myopathy/aging-associated genes that were activated in aging muscle were founded.These results provide key insights into skeletal muscle development in vivo,and offer a valuable resource that allows in-depth functional characterization of candidate genes.展开更多
WOMBAT is a software package for quantitative genetic analyses of continuous traits, fitting a linear, mixed model; estimates of covariance components and the resulting genetic parameters are obtained by restricted ma...WOMBAT is a software package for quantitative genetic analyses of continuous traits, fitting a linear, mixed model; estimates of covariance components and the resulting genetic parameters are obtained by restricted maximum likelihood. A wide range of models, comprising numerous traits, multiple fixed and random effects, selected genetic covariance structures, random regression models and reduced rank estimation are accommodated. WOMBAT employs up-to-date numerical and computational methods. Together with the use of efficient compilers, this generates fast executable programs, suitable for large scale analyses. Use of WOMBAT is illustrated for a bivariate analysis. The package consists of the executable program, available for LINUX and WINDOWS environments, manual and a set of worked example, and can be downloaded free of charge from http：//agbu. une.edu.au/-kmeyer/wombat.html展开更多
Tree shrew （Tupaia belangeri） is currently placed in Order Scandentia and has a wide distribution in Southeast Asia and Southwest China. Due to its unique characteristics, such as small body size, high brain-to-body...Tree shrew （Tupaia belangeri） is currently placed in Order Scandentia and has a wide distribution in Southeast Asia and Southwest China. Due to its unique characteristics, such as small body size, high brain-to-body mass ratio, short reproductive cycle and life span, and low-cost of maintenance, tree shrew has been proposed to be an alternative experimental animal to primates in biomedical research. However, there are some debates regarding the exact phylogenetic affinity of tree shrew to primates. In this study, we determined the mtDNA entire genomes of three Chinese tree shrews （T. belangeri chinensis） and one Malayan flying lemur （Galeopterus variegatus）. Combined with the published data for species in Euarchonta, we intended to diseen] the phylogenetic relationship among representative species of Dermoptera, Scandentia and Primates. The mtDNA genomes of Chinese tree shrews and Malayan flying lemur shared similar gene organization and structure with those of other mammals. Phylogenetic analysis based on 12 concatenated mitochondrial proteinencoding genes revealed a closer relationship between species of Scandentia and Glires, whereas species of Dermoptera were clustered with Primates. This pattern was consistent with previously reported phylogeny based on mtDNA data, but differed from the one reconstructed on the basis of nuclear genes. Our result suggested that the matrilineal affinity of tree shrew to primates may not be as close as we had thought. The ongoing project for sequencing the entire genome of Chinese tree shrew will provide more information to clarify this important issue.展开更多
Pluripotent stem cells are unspecialized cells withunlimited self-renewal, and they can be triggered to differentiate into desired specialized cell types. These features provide the basis for an unlimited cell source ...Pluripotent stem cells are unspecialized cells withunlimited self-renewal, and they can be triggered to differentiate into desired specialized cell types. These features provide the basis for an unlimited cell source for innovative cell therapies. Pluripotent cells also allow to study developmental pathways, and to employ them or their differentiated cell derivatives in pharmaceutical testing and biotechnological applications. Via blastocyst complementation, pluripotent cells are a favoured tool for the generation of genetically modified mice. The recently established technology to generate an induced pluripotency status by ectopic co-expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc allows to extending these applications to farm animal species, for which the derivation of genuine embryonic stem cells was not successful so far. Most induced pluripotent stem(i PS) cells are generated by retroviral or lentiviral transduction of reprogramming factors. Multiple viral integrations into the genome may cause insertional mutagenesis and may increase the risk of tumour formation. Non-integration methods have been reported to overcome the safety concerns associated with retro and lentiviral-derived i PS cells, such as transient expression of the reprogramming factors using episomal plasmids, and direct delivery of reprogramming m RNAs or proteins. In this review, we focus on the mechanisms of cellular reprogramming and current methods used to induce pluripotency. We also highlight problems associated with the generation of i PS cells. An increased understanding of the fundamental mechanisms underlying pluripotency and refining the methodology of i PS cell generation will have a profound impact on future development and application in regenerative medicine and reproductive biotechnology of farm animals.展开更多
Meat and milk production needs to increase ～ 70–80% relative to its current levels for satisfying the human needs in 2050.However,it is impossible to achieve such genetic gain by conventional animal breeding systems...Meat and milk production needs to increase ～ 70–80% relative to its current levels for satisfying the human needs in 2050.However,it is impossible to achieve such genetic gain by conventional animal breeding systems.Based on recent advances with regard to in vitro induction of germ cell from pluripotent stem cells,herein we propose a novel embryo-stem cell breeding system.Distinct from the conventional breeding system in farm animals that involves selecting and mating individuals,the novel breeding system completes breeding cycles from parental to offspring embryos directly by selecting and mating embryos in a dish.In comparison to the conventional dairy breeding scheme,this system can rapidly achieve 30–40 times more genetic gain by significantly shortening generation interval and enhancing selection intensity.However,several major obstacles must be overcome before we can fully use this system in livestock breeding,which include derivation and mantaince of pluripotent stem cells in domestic animals,as well as in vitro induction of primordial germ cells,and subsequent haploid gametes.Thus,we also discuss the potential efforts needed in solving the obstacles for application this novel system,and elaborate on their groundbreaking potential in livestock breeding.This novel system would provide a revolutionary animal breeding system by offering an unprecedented opportunity for meeting the fast-growing meat and milk demand of humans.展开更多
Advances in molecular biotechnology have introduced new generations of molecular markers for use in the genetic improvement of farm animals. Consequently, more accurate genetic information can be obtained to better un...Advances in molecular biotechnology have introduced new generations of molecular markers for use in the genetic improvement of farm animals. Consequently, more accurate genetic information can be obtained to better understand existing animal genetic resources. This review gives a brief summary on the development of genetic markers including both the classical genetic markers and more advanced DNA-based molecular markers. This review will help us better understand the characteristics of different genetic markers and the genetic diversity of animal genetic resources.展开更多
As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of ...As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of origin and migration,suggesting a possible omission of some population-specific sequences in the current reference genome.Conversely,the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals(core genome)and is also able to display sequence information unique to each individual(variable genome).The progress of pangenome research in humans,plants and domestic animals has proved that the missing genetic components and the identification of large structural variants(SVs)can be explored through pangenomic studies.Many individual specific sequences have been shown to be related to biological adaptability,phenotype and important economic traits.The maturity of technologies and methods such as third-generation sequencing,Tel-omere-to-telomere genomes,graphic genomes,and reference-free assembly will further promote the development of pangenome.In the future,pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals,providing better insights into animal domestication,evolution and breeding.In this review,we mainly discuss how pangenome analysis reveals genetic variations in domestic animals(sheep,cattle,pigs,chickens)and their impacts on phenotypes and how this can contribute to the understanding of species diversity.Additionally,we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.展开更多
Background Sharply increased beef consumption is propelling the genetic improvement projects of beef cattle in China.Three-dimensional genome structure is confirmed to be an important layer of transcription regulation...Background Sharply increased beef consumption is propelling the genetic improvement projects of beef cattle in China.Three-dimensional genome structure is confirmed to be an important layer of transcription regulation.Although genome-wide interaction data of several livestock species have already been produced,the genome structure states and its regulatory rules in cattle muscle are still limited.Results Here we present the first 3D genome data in Longissimus dorsi muscle of fetal and adult cattle(Bos taurus).We showed that compartments,topologically associating domains(TADs),and loop undergo re-organization and the structure dynamics were consistent with transcriptomic divergence during muscle development.Furthermore,we annotated cis-regulatory elements in cattle genome during myogenesis and demonstrated the enrichments of promoter and enhancer in selection sweeps.We further validated the regulatory function of one HMGA2 intronic enhancer near a strong sweep region on primary bovine myoblast proliferation.Conclusions Our data provide key insights of the regulatory function of high order chromatin structure and cattle myogenic biology,which will benefit the progress of genetic improvement of beef cattle.展开更多
This gene pyramiding strategy is based on the idea of efficiently pyramiding genes of interest by crosses and selection to obtain a population with favorable alleles from different breeds or lines, which is called an ...This gene pyramiding strategy is based on the idea of efficiently pyramiding genes of interest by crosses and selection to obtain a population with favorable alleles from different breeds or lines, which is called an ideal population. We investigate impacts of some factors on the pyramiding efficiencies by simulation. These factors include selection strategies （the breeding value selection, the molecular scores selection and the index selection）, proportion selected （2, 10 and 20%）, recombination rates between adjacent target genes （0.1, 0.3 and 0.5） and different mating types （the random mating and the positive assortative mating avoiding sib mating）. The results show that： （1） The more recombination rate and the lower proportion male selected, the better pyramiding efficiency; （2） the ideal population is obtained via various selection strategies, while different selection strategies are suitable for different breeding objectives. From the perspective of pyramiding target genes merely, the molecular scores selection is the best one, for the purpose of pyramiding target genes and recovering genetic background of the target trait, the index selection is the best one, while from the saving cost point of view, the breeding value selection is the best one; （3） the positive assortative mating is more efficient for gene pyramiding compared with the random mating in the terms of the number of generations of intercross for getting the ideal population.展开更多
Castration of male animals is a common practice in the meat industry aimed at reducing aggressive behavior, preventing unpleasant flavor, and controlling undesirable breeding. For many years, mechanical castration and...Castration of male animals is a common practice in the meat industry aimed at reducing aggressive behavior, preventing unpleasant flavor, and controlling undesirable breeding. For many years, mechanical castration and surgical castration have been practiced to sterilize the animals. However, these castration methods are not humane because of the associated risk of death, pain, and stress. Recently, immunocastration targeting the hypothalamic-pituitary-gonadal axis(HPG) axis has been reported as an animal-friendly approach that circumvents many of the concerns with conventional castration, and suggested by researches as an alternative to surgical castration. However, there is no compilation of updated information on the use of immunocastration in sheep and goats. Therefore, this review aims to summarize the developmental process from traditional surgical castration to immunocastration and to screen the process of immune targets. It also compares the respective advantages and disadvantages of traditional castration technologies and immunocastration, in particular including analyses in the characteristics, features application and welfare benefits of immunocastration in sheep and goats were also analyzed.展开更多
Four transplant studies are described that focus on fertilisation and early development or the progression of unfertilised oocytes （eggs） in the oviduct. （1） Pig eggs transplanted from ovulations induced during th...Four transplant studies are described that focus on fertilisation and early development or the progression of unfertilised oocytes （eggs） in the oviduct. （1） Pig eggs transplanted from ovulations induced during the luteal phase of the estrous cycle were fertilised in the oviducts of inseminated recipient animals in estrus. By contrast, pig eggs from donors in estrus became highly polyspermic when transplanted to the oviducts of animals force-mated during the luteal phase. （2） Pig embryos at the stage of hatched blastocysts （ days 7 and 8） could be transplanted successfuUy to synchronous recipients and full embryonic development demonstrated to between days 19 and 23 of pregnancy. Thus, the exposed trophectoderm of developing embryos could withstand the physical ma- nipulation of recovery and transplantation, and the li-fespan of corpora lutea in the unmated recipients could be prolonged by transfer of day 7 and 8 blastocysts. （3） Bovine oocytes aspirated from 2 to 6 mm diameter Graafian follicles and matured in vitro were fertilized normally in the oviducts of inseminated recipient heifers, demonstrating the potential of slaughterhouse ovaries for the generation of embryos. （4） Transplanting equine eggs to a pig oviduct, in which egg descent to the uterus requires only 46 to 48 h, did not reveal a retarded progress of degenerating unferfil- ised horse eggs, suggesting the involvement of nonphysical factors in equine embryo progression to the uterus. Prostaglandins of embryonic origin are now known to be a key. A final section examines the postovulatory role of ovarian follicular cells on the secretory activity of the oviductal epithelium.展开更多
[ Objective] This study analyzed the differences in DDX3 Y gene sequences among male horse, male donkey, male mule, male hinny and male foal to investigate the relationship between DDX3Y gene structure and the mechani...[ Objective] This study analyzed the differences in DDX3 Y gene sequences among male horse, male donkey, male mule, male hinny and male foal to investigate the relationship between DDX3Y gene structure and the mechanism of infertility in male Equus fetus × asirms. [ Method] Partial sequences of DDX3Y gene in male horse, male donkey, male mule, male hinny and male foal were obtained by genome comparison, sequencing and cloning, and compared by bioinformatics methods. [ Result] The CDS regions varied in 5 base pairs and two amino acids. DDX3Y protein was predicted to be an unstable protein. In addition, the results also showed that DDX3 Y gene in male horse displayed a closer phylogenetic relationship to male mule and male foal; DDX3Y gene in male donkey displayed a closer phylogenetic relationship to male hinny. [ Conclusion] This study provided scientific basis for further exploring the function of DDX3 Y gene and the mecha- nism of reproductive regulation in male Equus ferus × asinus.展开更多
The low egg production of goose greatly limits the development of the industry.China possesses the most abundant goose breeds resources.In this study,genome resequencing data of swan goose(Anser cygnoides)and domestic...The low egg production of goose greatly limits the development of the industry.China possesses the most abundant goose breeds resources.In this study,genome resequencing data of swan goose(Anser cygnoides)and domesticated high and low laying goose breeds(Anser cygnoides domestiation)were used to identify key genes related to egg laying ability in geese and verify their functions.Selective sweep analyses revealed 416 genes that were specifically selected during the domestication process from swan geese to high laying geese.Furthermore,SNPs and Indels markers were used in GWAS analyses between high and low laying breed geese.The results showed that RTCB,BPIFC,SYN3,SYNE1,VIP,and ESR1 may be related to the differences in laying ability of geese.Notably,only ESR1 was identified simultaneously by GWAS and selective sweep analysis.The genotype of Indelchr3:54429172,located downstream of ESR1,was confirmed to affect the expression of ESR1 in the ovarian stroma and showed significant correlation with body weight at first egg and laying frequency of geese.CCK-8,EdU,and flow cytometry confirmed that ESR1 can promote the apoptosis of goose pre-hierarchical follicles ganulosa cells(phGCs)and inhibit their proliferation.Combined with transcriptome data,it was found ESR1 involved in the function of goose phGCs may be related to MAPK and TGF-beta signaling pathways.Overall,our study used genomic information from different goose breeds to identify an indel located in the downstream of ESR1 associated with goose laying ability.The main pathways and biological processes of ESR1 involved in the regulation of goose laying ability were identified by cell biology and transcriptomics methods.These results are helpful to further understand the laying ability characteristics of goose and improve the egg production of geese.展开更多
Background N^(6)-methyladenosine(m^(6)A)methylation is a key epigenetic modification that can modulate gene expression and strongly affect mammalian developmental processes.However,the genome-wide methylation of long ...Background N^(6)-methyladenosine(m^(6)A)methylation is a key epigenetic modification that can modulate gene expression and strongly affect mammalian developmental processes.However,the genome-wide methylation of long non-coding RNAs(lncRNAs)and its implications for the development of skeletal muscle remain poorly understood.Bovine skeletal muscle samples from five developmental stages were analyzed in this study to establish lncRNA methylome and transcriptomic maps.Results Globally,59.67%of lncRNAs in skeletal muscle with m^(6)A modifications,and this percentage decreased progressively during development.lncRNA expression levels were positively associated with the number of m^(6)A peaks,with lncRNAs possessing 3 or more peaks showing significantly higher expression levels than those with 1 or 2 peaks.Specific lncRNAs involved in skeletal muscle development were identified through two analytical approaches.The first approach employed weighted gene co-expression network analysis(WGCNA)of transcriptomic data to identify correlations between annotated lncRNAs and growth-related traits,resulting in 21 candidate hub lncRNAs.The intersection of these 21 hub lncRNAs with 151 differentially methylated lncRNAs(DM-lncRNAs)identified 10 shared candidate lncRNAs.The second approach integrated MeRIP-seq and RNA-seq data to identify 36 lncRNAs that were both differentially m^(6)A modified and differentially expressed(dme-lncRNAs).GO and KEGG enrichment analyses of cis-target genes associated with these dme-lncRNAs identified eight candidate lncRNAs.Combining the results from the two approaches identified 16 key m^(6)A-modified lncRNAs likely involved in skeletal muscle development.Conclusions These findings highlight the regulatory and functional significance of dynamic lncRNA methylation in skeletal muscle development.展开更多
Yaks are well-adapted to the harsh environment of the Tibetan Plateau,and they emit less enteric methane(CH_(4))and digest poor-quality forage better than cattle.To examine the potential of yak rumen inoculum to mitig...Yaks are well-adapted to the harsh environment of the Tibetan Plateau,and they emit less enteric methane(CH_(4))and digest poor-quality forage better than cattle.To examine the potential of yak rumen inoculum to mitigate CH_(4)production and improve digestibility in cattle,we incubated substrate with rumen inoculum from yak(YRI)and cattle(CRI)in vitro in five ratios(YRI:CRI):(1)0:100(control),(2)25:75,(3)50:50,(4)75:25 and(5)100:0 for 72 h.The YRI:CRI ratios of 50:50,75:25 and 100:0 produced less total gas and CH_(4)and accumulated less hydrogen(H_(2))than0:100(control)at most time points.From 12 h onwards,there was a linear decrease(P<0.05)in carbon dioxide(CO_(2))production with increasing YRI:CRI ratio.At 72 h,the ratios of 50:50 and 75:25 had higher dry matter(+7.71%and+4.11%,respectively),as well as higher acid detergent fiber digestibility(+15.5%and+7.61%,respectively),when compared to the 0:100 ratio(P<0.05).Increasing the proportion of YRI generally increased total VFA concentrations,and,concomitantly,decreased the proportion of metabolic hydrogen([2H])incorporated into CH_(4),and decreased the recovery of[2H].The lower[2H]recovery indicates unknown[2H]sinks in the culture.Estimated Gibbs free energy changes(ΔG)for reductive acetogenesis were negative,indicating the thermodynamic feasibility of this process.It would be beneficial to identify:1)the alternative[2H]sinks,which could help mitigate CH_(4)emission,and 2)core microbes involved in fiber digestion.This experiment supported lower CH_(4)emission and greater nutrient digestibility of yaks compared to cattle.Multi-omics combined with microbial culture technologies developed in recent years could help to better understand fermentation differences among species.展开更多
文摘The livestock sector is a vital component of India's agricultural economy,providing essential support to rural communities and ensuring food security.Efficient reproductive performance is critical to sustaining livestock productivity,yet age-related declines in both male and female fertility pose significant challenges.The current review highlights that male reproductive efficiency is closely tied to semen quality,which deteriorates with age due to oxidative stress,leading to reduced fertilizing capacity and embryonic developmental potential.Similarly,female reproductive longevity is predominantly influenced by ovarian health,which declines with age due to diminished oocyte quality and quantity.This decline is exacerbated by oxidative stress and mitochondrial dysfunction,leading to reproductive senescence and reduced offspring viability.Understanding the mechanisms of reproductive aging and developing strategies to mitigate its effects are crucial for enhancing livestock productivity and sustaining the agrarian economy.
基金supported by National Key R&D Program of China(2024YFF1001500)Sichuan Science and Technology Program(2021YFYZ0007,2024NSFSC0298,SCCXTD-2025-8)+1 种基金China Agriculture Research System(CARS-35)National Natural Science Foundation of China(32421005)。
文摘The gut microbiota has emerged as a pivotal regulator of host lipid metabolism and energy homeostasis.A growing body of evidence reveals that variations in the composition and metabolic activity of intestinal microbes are closely associated with differences in adipose tissue deposition across species.Notably,increased abundance of Firmicutes and a reduced proportion of Bacteroidetes and butyrate-producing bacteria have been linked to enhanced fat accumulation.Key microbial metabolites such as short-chain fatty acids(SCFAs)influence lipid metabolism through multiple pathways,including the activation of GPR41/43 receptors,modulation of the bile acid–FXR/TGR5 axis,and regulation of hepatic lipogenesis.Additionally,the gut–brain axis plays a critical role in controlling feeding behavior via neuroendocrine signaling.This review summarizes current advances in understanding the roles of dominant bacterial phyla and beneficial genera—including Clostridium butyricum and Faecalibacterium prausnitzii—in fat metabolism.We further explore the mechanisms by which gut microbiota modulate lipid synthesis and catabolism through SCFA production,bile acid signaling,and AMPK/PPAR-related pathways.These insights highlight the potential of microbiota-targeted strategies to restore lipid metabolic balance,offering novel opportunities for applications in health management,nutritional interventions,and microbial therapeutics.
基金funded by The National Key Research and Development Program of China,grant number 2022YFF1000202Sichuan Science and Technology Program,grant number 2023NSFSC1940,2021YFYZ0007 and 2024YFNH0025+1 种基金National Natural Science Foundation of China Grants,grant number 32402745China Agriculture Research System of MOF and MARA,grant number CARS-40。
文摘Background Follicular atresia,a complex degenerative process regulated by multiple molecular mechanisms,significantly affects female reproductive performance in animals.While granulosa cell(GC)apoptosis has been well established as a primary mechanism underlying follicular atresia,the potential involvement of ferroptosis,which is an irondependent form of regulated cell death,remains largely unexplored in chickens.Results Using a tamoxifen(TMX)-induced avian model of follicular atresia,we demonstrated that ferroptosis plays a critical role in follicular degeneration.Inhibition of ferroptosis through pharmacological agents significantly restored follicular function,underscoring its potential as a therapeutic target.Notably,we observed a significant upregulation of ubiquitin-specific peptidase 9,X-linked(USP9X)in GCs during atresia.Through comprehensive in vitro and in vivo investigations,we confirmed that USP9X facilitates follicular atresia by promoting ferroptosis in GCs.Mechanistically,USP9X induces ferroptosis by stabilizing Beclin1 through deubiquitination,thereby activating autophagy-dependent ferroptosis.This pathway was effectively suppressed by autophagy inhibitors,emphasizing the essential role of autophagy in USP9X-mediated ferroptosis.Conclusions Our findings provide the evidence that the USP9X-Beclin1 axis regulates autophagy-dependent ferroptosis during avian follicular atresia.These insights reveal novel molecular targets and potential genetic markers for improving reproductive efficiency in chicken breeding programs.
基金supported by the China Agriculture Research System of MOF and MARAthe National Natural Science Foundation of China (31872337 and 31501919)the Agricultural Science and Technology Innovation Project,China (ASTIP-IAS02)。
文摘The advantages of genome selection(GS) in animal and plant breeding are self-evident.Traditional parametric models have disadvantage in better fit the increasingly large sequencing data and capture complex effects accurately.Machine learning models have demonstrated remarkable potential in addressing these challenges.In this study,we introduced the concept of mixed kernel functions to explore the performance of support vector machine regression(SVR) in GS.Six single kernel functions(SVR_L,SVR_C,SVR_G,SVR_P,SVR_S,SVR_L) and four mixed kernel functions(SVR_GS,SVR_GP,SVR_LS,SVR_LP) were used to predict genome breeding values.The prediction accuracy,mean squared error(MSE) and mean absolute error(MAE) were used as evaluation indicators to compare with two traditional parametric models(GBLUP,BayesB) and two popular machine learning models(RF,KcRR).The results indicate that in most cases,the performance of the mixed kernel function model significantly outperforms that of GBLUP,BayesB and single kernel function.For instance,for T1 in the pig dataset,the predictive accuracy of SVR_GS is improved by 10% compared to GBLUP,and by approximately 4.4 and 18.6% compared to SVR_G and SVR_S respectively.For E1 in the wheat dataset,SVR_GS achieves 13.3% higher prediction accuracy than GBLUP.Among single kernel functions,the Laplacian and Gaussian kernel functions yield similar results,with the Gaussian kernel function performing better.The mixed kernel function notably reduces the MSE and MAE when compared to all single kernel functions.Furthermore,regarding runtime,SVR_GS and SVR_GP mixed kernel functions run approximately three times faster than GBLUP in the pig dataset,with only a slight increase in runtime compared to the single kernel function model.In summary,the mixed kernel function model of SVR demonstrates speed and accuracy competitiveness,and the model such as SVR_GS has important application potential for GS.
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 Key R&D Program of China(2023YFD1300040 and 2022YFF1000100)the Sichuan Science and Technology Program,China(2022NSFSC0132,2021YFYZ0009 and 2022JDJQ0054)the National Natural Science Foundation of China(32225046)。
文摘The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology,contractility,cell proliferation,differentiation,interactions,migration,and death.The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes.The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages.Hi-C was used to build chromatin architectures during four representative stages.Ch IP-seq was conducted to identify enhancers and promoters in these four stages,which are occupied by histone H3K27ac and H3K4me3 peaks.Results show that large-scale genome architecture changes are mostly unidirectional,and coupled by complex on/off dynamic patterns of gene expression.Specifically,we observed 258.30 Mb of the genome undergoing A/B compartment switching.Notable alterations(316.57 Mb)of interaction frequencies within TADs were observed.Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development.Some muscle-related gene promoters that interacted with active enhancers during development,and some myopathy/aging-associated genes that were activated in aging muscle were founded.These results provide key insights into skeletal muscle development in vivo,and offer a valuable resource that allows in-depth functional characterization of candidate genes.
基金Project (No. BFGEN.100B) supported by the Meat and LivestockLtd., Australia (MLA)
文摘WOMBAT is a software package for quantitative genetic analyses of continuous traits, fitting a linear, mixed model; estimates of covariance components and the resulting genetic parameters are obtained by restricted maximum likelihood. A wide range of models, comprising numerous traits, multiple fixed and random effects, selected genetic covariance structures, random regression models and reduced rank estimation are accommodated. WOMBAT employs up-to-date numerical and computational methods. Together with the use of efficient compilers, this generates fast executable programs, suitable for large scale analyses. Use of WOMBAT is illustrated for a bivariate analysis. The package consists of the executable program, available for LINUX and WINDOWS environments, manual and a set of worked example, and can be downloaded free of charge from http：//agbu. une.edu.au/-kmeyer/wombat.html
基金supported by grants from Chinese Academy of Sciences (Nos.KSCX2-EW-R-11 and KSCX2-EW-J-23)the National 863 Project of China (No.2012AA021801)Yunnan Province (No.2009CI119)
文摘Tree shrew （Tupaia belangeri） is currently placed in Order Scandentia and has a wide distribution in Southeast Asia and Southwest China. Due to its unique characteristics, such as small body size, high brain-to-body mass ratio, short reproductive cycle and life span, and low-cost of maintenance, tree shrew has been proposed to be an alternative experimental animal to primates in biomedical research. However, there are some debates regarding the exact phylogenetic affinity of tree shrew to primates. In this study, we determined the mtDNA entire genomes of three Chinese tree shrews （T. belangeri chinensis） and one Malayan flying lemur （Galeopterus variegatus）. Combined with the published data for species in Euarchonta, we intended to diseen] the phylogenetic relationship among representative species of Dermoptera, Scandentia and Primates. The mtDNA genomes of Chinese tree shrews and Malayan flying lemur shared similar gene organization and structure with those of other mammals. Phylogenetic analysis based on 12 concatenated mitochondrial proteinencoding genes revealed a closer relationship between species of Scandentia and Glires, whereas species of Dermoptera were clustered with Primates. This pattern was consistent with previously reported phylogeny based on mtDNA data, but differed from the one reconstructed on the basis of nuclear genes. Our result suggested that the matrilineal affinity of tree shrew to primates may not be as close as we had thought. The ongoing project for sequencing the entire genome of Chinese tree shrew will provide more information to clarify this important issue.
基金Supported by CREST fellowship from Department of Biotechnology,Ministry of Science and Technology,Government of India(DK)International fellowship for Ph D from ICAR(TRT),Government of IndiaInternational training in generation of i PS cells from NAIP,ICAR,Government of India(TA)
文摘Pluripotent stem cells are unspecialized cells withunlimited self-renewal, and they can be triggered to differentiate into desired specialized cell types. These features provide the basis for an unlimited cell source for innovative cell therapies. Pluripotent cells also allow to study developmental pathways, and to employ them or their differentiated cell derivatives in pharmaceutical testing and biotechnological applications. Via blastocyst complementation, pluripotent cells are a favoured tool for the generation of genetically modified mice. The recently established technology to generate an induced pluripotency status by ectopic co-expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc allows to extending these applications to farm animal species, for which the derivation of genuine embryonic stem cells was not successful so far. Most induced pluripotent stem(i PS) cells are generated by retroviral or lentiviral transduction of reprogramming factors. Multiple viral integrations into the genome may cause insertional mutagenesis and may increase the risk of tumour formation. Non-integration methods have been reported to overcome the safety concerns associated with retro and lentiviral-derived i PS cells, such as transient expression of the reprogramming factors using episomal plasmids, and direct delivery of reprogramming m RNAs or proteins. In this review, we focus on the mechanisms of cellular reprogramming and current methods used to induce pluripotency. We also highlight problems associated with the generation of i PS cells. An increased understanding of the fundamental mechanisms underlying pluripotency and refining the methodology of i PS cell generation will have a profound impact on future development and application in regenerative medicine and reproductive biotechnology of farm animals.
基金supported by Strategy Research on Disruptive Technology in Agriculture(China Academy of Engineering,2017-ZD-10-07)supported by grants from the National Key R&D Program(2017YFD0501901+1 种基金2017YFD0501905)the Earmarked Fund for the Innovative Teams of Beijing Swine Industrialization Research Program.National Waterfowl-industry Technology Research System(CARS-42)
文摘Meat and milk production needs to increase ～ 70–80% relative to its current levels for satisfying the human needs in 2050.However,it is impossible to achieve such genetic gain by conventional animal breeding systems.Based on recent advances with regard to in vitro induction of germ cell from pluripotent stem cells,herein we propose a novel embryo-stem cell breeding system.Distinct from the conventional breeding system in farm animals that involves selecting and mating individuals,the novel breeding system completes breeding cycles from parental to offspring embryos directly by selecting and mating embryos in a dish.In comparison to the conventional dairy breeding scheme,this system can rapidly achieve 30–40 times more genetic gain by significantly shortening generation interval and enhancing selection intensity.However,several major obstacles must be overcome before we can fully use this system in livestock breeding,which include derivation and mantaince of pluripotent stem cells in domestic animals,as well as in vitro induction of primordial germ cells,and subsequent haploid gametes.Thus,we also discuss the potential efforts needed in solving the obstacles for application this novel system,and elaborate on their groundbreaking potential in livestock breeding.This novel system would provide a revolutionary animal breeding system by offering an unprecedented opportunity for meeting the fast-growing meat and milk demand of humans.
基金supported by National High Technology and Science Development Plan of China(No.2011AA100302)Program for New Century Excellent Talents in University(No.NCET-11-0480)Program for Changjiang Scholar and Innovation Research Team in University(IRT1191)and project(CARS-41-K01)
文摘Advances in molecular biotechnology have introduced new generations of molecular markers for use in the genetic improvement of farm animals. Consequently, more accurate genetic information can be obtained to better understand existing animal genetic resources. This review gives a brief summary on the development of genetic markers including both the classical genetic markers and more advanced DNA-based molecular markers. This review will help us better understand the characteristics of different genetic markers and the genetic diversity of animal genetic resources.
基金supported by the National Natural Science Foundation of China (grant numbers 31961143021)the earmarked fund for Modern Agro-industry Technology Research System (grant numbers CARS-39-01)+1 种基金the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences (grant numbers ASTIP-IAS01) to YM and LJsupported by the Elite Youth Program in Chinese Academy of Agricultural Sciences
文摘As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of origin and migration,suggesting a possible omission of some population-specific sequences in the current reference genome.Conversely,the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals(core genome)and is also able to display sequence information unique to each individual(variable genome).The progress of pangenome research in humans,plants and domestic animals has proved that the missing genetic components and the identification of large structural variants(SVs)can be explored through pangenomic studies.Many individual specific sequences have been shown to be related to biological adaptability,phenotype and important economic traits.The maturity of technologies and methods such as third-generation sequencing,Tel-omere-to-telomere genomes,graphic genomes,and reference-free assembly will further promote the development of pangenome.In the future,pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals,providing better insights into animal domestication,evolution and breeding.In this review,we mainly discuss how pangenome analysis reveals genetic variations in domestic animals(sheep,cattle,pigs,chickens)and their impacts on phenotypes and how this can contribute to the understanding of species diversity.Additionally,we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.
基金supported by the National Natural Science Foundation of China[Grant No.31972558]the Agricultural Improved Seed Project of Shandong Province[Grant No.2020LZGC014-03]。
文摘Background Sharply increased beef consumption is propelling the genetic improvement projects of beef cattle in China.Three-dimensional genome structure is confirmed to be an important layer of transcription regulation.Although genome-wide interaction data of several livestock species have already been produced,the genome structure states and its regulatory rules in cattle muscle are still limited.Results Here we present the first 3D genome data in Longissimus dorsi muscle of fetal and adult cattle(Bos taurus).We showed that compartments,topologically associating domains(TADs),and loop undergo re-organization and the structure dynamics were consistent with transcriptomic divergence during muscle development.Furthermore,we annotated cis-regulatory elements in cattle genome during myogenesis and demonstrated the enrichments of promoter and enhancer in selection sweeps.We further validated the regulatory function of one HMGA2 intronic enhancer near a strong sweep region on primary bovine myoblast proliferation.Conclusions Our data provide key insights of the regulatory function of high order chromatin structure and cattle myogenic biology,which will benefit the progress of genetic improvement of beef cattle.
基金supported by the National Major Special Project of China on New Varieties Cultivation for Transgenic Organisms (2009ZX08009-146B)by the National Non-profit Institute Research Grant,China (2012cj-2)
文摘This gene pyramiding strategy is based on the idea of efficiently pyramiding genes of interest by crosses and selection to obtain a population with favorable alleles from different breeds or lines, which is called an ideal population. We investigate impacts of some factors on the pyramiding efficiencies by simulation. These factors include selection strategies （the breeding value selection, the molecular scores selection and the index selection）, proportion selected （2, 10 and 20%）, recombination rates between adjacent target genes （0.1, 0.3 and 0.5） and different mating types （the random mating and the positive assortative mating avoiding sib mating）. The results show that： （1） The more recombination rate and the lower proportion male selected, the better pyramiding efficiency; （2） the ideal population is obtained via various selection strategies, while different selection strategies are suitable for different breeding objectives. From the perspective of pyramiding target genes merely, the molecular scores selection is the best one, for the purpose of pyramiding target genes and recovering genetic background of the target trait, the index selection is the best one, while from the saving cost point of view, the breeding value selection is the best one; （3） the positive assortative mating is more efficient for gene pyramiding compared with the random mating in the terms of the number of generations of intercross for getting the ideal population.
基金funded by the National Natural Science Foundation of China(31972997 and 31772598)the China Agriculture Research System of MOF and MARA(CARS-38)。
文摘Castration of male animals is a common practice in the meat industry aimed at reducing aggressive behavior, preventing unpleasant flavor, and controlling undesirable breeding. For many years, mechanical castration and surgical castration have been practiced to sterilize the animals. However, these castration methods are not humane because of the associated risk of death, pain, and stress. Recently, immunocastration targeting the hypothalamic-pituitary-gonadal axis(HPG) axis has been reported as an animal-friendly approach that circumvents many of the concerns with conventional castration, and suggested by researches as an alternative to surgical castration. However, there is no compilation of updated information on the use of immunocastration in sheep and goats. Therefore, this review aims to summarize the developmental process from traditional surgical castration to immunocastration and to screen the process of immune targets. It also compares the respective advantages and disadvantages of traditional castration technologies and immunocastration, in particular including analyses in the characteristics, features application and welfare benefits of immunocastration in sheep and goats were also analyzed.
文摘Four transplant studies are described that focus on fertilisation and early development or the progression of unfertilised oocytes （eggs） in the oviduct. （1） Pig eggs transplanted from ovulations induced during the luteal phase of the estrous cycle were fertilised in the oviducts of inseminated recipient animals in estrus. By contrast, pig eggs from donors in estrus became highly polyspermic when transplanted to the oviducts of animals force-mated during the luteal phase. （2） Pig embryos at the stage of hatched blastocysts （ days 7 and 8） could be transplanted successfuUy to synchronous recipients and full embryonic development demonstrated to between days 19 and 23 of pregnancy. Thus, the exposed trophectoderm of developing embryos could withstand the physical ma- nipulation of recovery and transplantation, and the li-fespan of corpora lutea in the unmated recipients could be prolonged by transfer of day 7 and 8 blastocysts. （3） Bovine oocytes aspirated from 2 to 6 mm diameter Graafian follicles and matured in vitro were fertilized normally in the oviducts of inseminated recipient heifers, demonstrating the potential of slaughterhouse ovaries for the generation of embryos. （4） Transplanting equine eggs to a pig oviduct, in which egg descent to the uterus requires only 46 to 48 h, did not reveal a retarded progress of degenerating unferfil- ised horse eggs, suggesting the involvement of nonphysical factors in equine embryo progression to the uterus. Prostaglandins of embryonic origin are now known to be a key. A final section examines the postovulatory role of ovarian follicular cells on the secretory activity of the oviductal epithelium.
基金Supported by Project of Science and Technology Department of Inner Mongolia Autonomous Region
文摘[ Objective] This study analyzed the differences in DDX3 Y gene sequences among male horse, male donkey, male mule, male hinny and male foal to investigate the relationship between DDX3Y gene structure and the mechanism of infertility in male Equus fetus × asirms. [ Method] Partial sequences of DDX3Y gene in male horse, male donkey, male mule, male hinny and male foal were obtained by genome comparison, sequencing and cloning, and compared by bioinformatics methods. [ Result] The CDS regions varied in 5 base pairs and two amino acids. DDX3Y protein was predicted to be an unstable protein. In addition, the results also showed that DDX3 Y gene in male horse displayed a closer phylogenetic relationship to male mule and male foal; DDX3Y gene in male donkey displayed a closer phylogenetic relationship to male hinny. [ Conclusion] This study provided scientific basis for further exploring the function of DDX3 Y gene and the mecha- nism of reproductive regulation in male Equus ferus × asinus.
基金supported by the China Agriculture Research System of MOF and MARA(CARS-42-4)School Cooperation Project of Ya’an(21SXHZ0028)the Key Technology Support Program of Sichuan Province,China(2021YFYZ0014),for the financial support。
文摘The low egg production of goose greatly limits the development of the industry.China possesses the most abundant goose breeds resources.In this study,genome resequencing data of swan goose(Anser cygnoides)and domesticated high and low laying goose breeds(Anser cygnoides domestiation)were used to identify key genes related to egg laying ability in geese and verify their functions.Selective sweep analyses revealed 416 genes that were specifically selected during the domestication process from swan geese to high laying geese.Furthermore,SNPs and Indels markers were used in GWAS analyses between high and low laying breed geese.The results showed that RTCB,BPIFC,SYN3,SYNE1,VIP,and ESR1 may be related to the differences in laying ability of geese.Notably,only ESR1 was identified simultaneously by GWAS and selective sweep analysis.The genotype of Indelchr3:54429172,located downstream of ESR1,was confirmed to affect the expression of ESR1 in the ovarian stroma and showed significant correlation with body weight at first egg and laying frequency of geese.CCK-8,EdU,and flow cytometry confirmed that ESR1 can promote the apoptosis of goose pre-hierarchical follicles ganulosa cells(phGCs)and inhibit their proliferation.Combined with transcriptome data,it was found ESR1 involved in the function of goose phGCs may be related to MAPK and TGF-beta signaling pathways.Overall,our study used genomic information from different goose breeds to identify an indel located in the downstream of ESR1 associated with goose laying ability.The main pathways and biological processes of ESR1 involved in the regulation of goose laying ability were identified by cell biology and transcriptomics methods.These results are helpful to further understand the laying ability characteristics of goose and improve the egg production of geese.
基金supported by the National Key R&D Program of China(2023YFD1300103)the Science and Technology Plan Project of Yantai City(2023ZDCX024)+5 种基金the National Natural Science Foundation of China(32372852)the Science Fund for Distinguished Young Scholars of Shaanxi Province(2024JC-JCQN-30)Shaanxi Provincial Innovation Leadership Program in Sciences and Technologies for Young and Middle-aged Scientists(2023SR205)the China Agriculture Research System-beef(CARS-37)the Innovation Team of Cattle Industry in Technological System of Shandong Modern Agriculture Industry(SDAIT-09-03)the Key Research and Development Project in Shandong Province(Competitive Innovation Platform)(2022CXPT010).
文摘Background N^(6)-methyladenosine(m^(6)A)methylation is a key epigenetic modification that can modulate gene expression and strongly affect mammalian developmental processes.However,the genome-wide methylation of long non-coding RNAs(lncRNAs)and its implications for the development of skeletal muscle remain poorly understood.Bovine skeletal muscle samples from five developmental stages were analyzed in this study to establish lncRNA methylome and transcriptomic maps.Results Globally,59.67%of lncRNAs in skeletal muscle with m^(6)A modifications,and this percentage decreased progressively during development.lncRNA expression levels were positively associated with the number of m^(6)A peaks,with lncRNAs possessing 3 or more peaks showing significantly higher expression levels than those with 1 or 2 peaks.Specific lncRNAs involved in skeletal muscle development were identified through two analytical approaches.The first approach employed weighted gene co-expression network analysis(WGCNA)of transcriptomic data to identify correlations between annotated lncRNAs and growth-related traits,resulting in 21 candidate hub lncRNAs.The intersection of these 21 hub lncRNAs with 151 differentially methylated lncRNAs(DM-lncRNAs)identified 10 shared candidate lncRNAs.The second approach integrated MeRIP-seq and RNA-seq data to identify 36 lncRNAs that were both differentially m^(6)A modified and differentially expressed(dme-lncRNAs).GO and KEGG enrichment analyses of cis-target genes associated with these dme-lncRNAs identified eight candidate lncRNAs.Combining the results from the two approaches identified 16 key m^(6)A-modified lncRNAs likely involved in skeletal muscle development.Conclusions These findings highlight the regulatory and functional significance of dynamic lncRNA methylation in skeletal muscle development.
基金supported by the National Natural Science Foundation of China(32072757 and U21A20250)。
文摘Yaks are well-adapted to the harsh environment of the Tibetan Plateau,and they emit less enteric methane(CH_(4))and digest poor-quality forage better than cattle.To examine the potential of yak rumen inoculum to mitigate CH_(4)production and improve digestibility in cattle,we incubated substrate with rumen inoculum from yak(YRI)and cattle(CRI)in vitro in five ratios(YRI:CRI):(1)0:100(control),(2)25:75,(3)50:50,(4)75:25 and(5)100:0 for 72 h.The YRI:CRI ratios of 50:50,75:25 and 100:0 produced less total gas and CH_(4)and accumulated less hydrogen(H_(2))than0:100(control)at most time points.From 12 h onwards,there was a linear decrease(P<0.05)in carbon dioxide(CO_(2))production with increasing YRI:CRI ratio.At 72 h,the ratios of 50:50 and 75:25 had higher dry matter(+7.71%and+4.11%,respectively),as well as higher acid detergent fiber digestibility(+15.5%and+7.61%,respectively),when compared to the 0:100 ratio(P<0.05).Increasing the proportion of YRI generally increased total VFA concentrations,and,concomitantly,decreased the proportion of metabolic hydrogen([2H])incorporated into CH_(4),and decreased the recovery of[2H].The lower[2H]recovery indicates unknown[2H]sinks in the culture.Estimated Gibbs free energy changes(ΔG)for reductive acetogenesis were negative,indicating the thermodynamic feasibility of this process.It would be beneficial to identify:1)the alternative[2H]sinks,which could help mitigate CH_(4)emission,and 2)core microbes involved in fiber digestion.This experiment supported lower CH_(4)emission and greater nutrient digestibility of yaks compared to cattle.Multi-omics combined with microbial culture technologies developed in recent years could help to better understand fermentation differences among species.
