A review of the pangenome:how it affects our understanding of genomic variation,selection and breeding in domestic animals?

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.

Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement

Background Genomic selection involves choosing as parents those elite individuals with the higher genomic estimated breeding values(GEBV)to accelerate the speed of genetic improvement in domestic animals.But after multi-generation selection,the rate of inbreeding and the occurrence of homozygous harmful alleles might increase,which would reduce performance and genetic diversity.To mitigate the above problems,we can utilize genomic mating(GM)based upon optimal mate allocation to construct the best genotypic combinations in the next generation.In this study,we used stochastic simulation to investigate the impact of various factors on the efficiencies of GM to optimize pairing combinations after genomic selection of candidates in a pig population.These factors included:the algorithm used to derive inbreeding coefficients;the trait heritability(0.1,0.3 or 0.5);the kind of GM scheme(focused average GEBV or inbreeding);the approach for computing the genomic relationship matrix(by SNP or runs of homozygosity(ROH)).The outcomes were compared to three traditional mating schemes(random,positive assortative or negative assortative matings).In addition,the performance of the GM approach was tested on real datasets obtained from a Large White pig breeding population.Results Genomic mating outperforms other approaches in limiting the inbreeding accumulation for the same expected genetic gain.The use of ROH-based genealogical relatedness in GM achieved faster genetic gains than using relatedness based on individual SNPs.The GROH-based GM schemes with the maximum genetic gain resulted in 0.9%-2.6%higher rates of genetic gainΔG,and 13%-83.3%lowerΔF than positive assortative mating regardless of heritability.The rates of inbreeding were always the fastest with positive assortative mating.Results from a purebred Large White pig population,confirmed that GM with ROH-based GRM was more efficient than traditional mating schemes.Conclusion Compared with traditional mating schemes,genomic mating can not only achieve sustainable genetic progress but also effectively control the rates of inbreeding accumulation in the population.Our findings demonstrated that breeders should consider using genomic mating for genetic improvement of pigs.

miR-24-3p promotes proliferation and inhibits apoptosis of porcine granulosa cells by targeting P27

Ovarian follicle development is associated with the physiological functions of granulosa cells(GCs),including proliferation and apoptosis.The level of miR-24-3p in ovarian tissue of high-yielding Yorkshire×Landrace sows was significantly higher than that of low-yielding sows.However,the functions of miR-24-3p on GCs are unclear.In this study,using flow cytometry,5-ethynyl-2′-de-oxyuridine(EdU)staining,and cell count,we showed that miR-24-3p promoted the proliferation of GCs increasing the proportion of cells in the S phase and upregulating the expression of cell cycle genes,moreover,miR-24-3p inhibited GC apoptosis.Mechanistically,on-line prediction,bioinformatics analysis,a luciferase reporter assay,RT-qPCR,and Western blot results showed that the target gene of miR-24-3p in proliferation and apoptosis is cyclin-dependent kinase inhibitor 1B(P27/CDKN1B).Furthermore,the effect of miR-24-3p on GC proliferation and apoptosis was attenuated by P27 overexpression.These findings suggest that miR-24-3p regulates the physiological functions of GCs.

Dynamic transcriptome profiles and novel markers in bovine spermatogenesis revealed by single-cell sequencing

Testicular development is an important biological process in male and requires interaction between the male germ cells and somatic cells.However,the mechanisms of testicular development in livestock,particularly in cattle,are poorly understood.Furthermore,cellular heterogeneity hinders the profiling of different cell types at different developmental stages.In this study,we first performed a single-cell transcriptomic study of the bovine testis development during puberty by using 10×genomics single-cell RNA sequencing(scRNA-seq).By collecting the scRNA-seq data from 11,083 cells from prepubertal and pubertal bovine testes,a high-resolution scRNA-seq atlas was described,identifying 9 somatic and 13 spermatogenic clusters.We also distinguished several stage-specific marker genes for bovine germ cells and somatic cells,such as GRAF2 and MORC1 for SSC(spermatogonial stem cells),HJURP and TCF19 for differentiating spermatogonia,ARSE for immature Sertoli,CLEC12B for mature Sertoli,LOC112441470 for Leydig.In conclusion,we have examined the transcription levels and constructed the single-cell developmental maps of germ cells and somatic cells during testicular development in Angus cattle.The datasets provided new insights into spermatogenesis and testicular somatic cell development in cattle.

3D genome organization and its study in livestock breeding

Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associating domains(TADs),and DNA loops.The identification of these hierarchical structures has benefited from the development of experimental approaches,such as 3C-based methods(Hi-C,ChIA-PET,etc.),imaging tools(2D-FISH,3D-FISH,Cryo-FISH,etc.)and ligation-free methods(GAM,SPRITE,etc.).In recent two decades,numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms,such as regulating enhancer activity and promoter-enhancer interactions.However,there are relatively few studies about the 3D genome in livestock species.Therefore,studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.In this review,we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies,drawing inspiration to explore the 3D genomics of livestock species.We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.

Effect of simulated gastrointestinal digestion on antioxidant,and anti-inflammatory activities of bioactive peptides generated in sausages fermented with Staphylococcus simulans QB7

Dry-fermented sausages are a good source of bioactive peptides,whose stability against gastrointestinal(GI)digestion determines their bioaccessibility.This study focused on evaluating the effect of peptide extracts from sausages fermented with Staphylococcus simulans QB7 during in vitro simulated GI digestion,including peptide profiles and antioxidant and anti-inflammatory activities.Peptides present in sausages were degraded during digestion,with molecular weight reduced from>12 kDa to<1.5 kDa.Besides,the content of amino acids increased from 381.15 to 527.07 mg/g,especially tyrosine being found only after GI digestion.The anti-inflammatory activities were increased after GI digestion,however,the changes in antioxidant activities were the opposite.A total number of 255,252 and 386 peptide sequences were identified in undigested,peptic-digested and GI-digested samples,respectively.PeptideRanker,BIOPEP-UWM and admetSAR were used to further predict the functional properties and intestinal absorption of the identified peptide sequences from GI digestion.Finally,18 peptides were discovered to possess either antioxidant or anti-inflammatory capacities.

Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population

Background: Runs of homozygosity(ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms(SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here,we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs(FROH), homozygosity(FHOM), genomic relationship matrix(FGRM)and pedigree(FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes.Results: In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes(SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_totaland FHOM, while the lowest was-0.083 between FGRMand FPED. The correlations between FPEDand FROHusing four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes(SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4.Conclusion: FROHcan be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROHcan provide an alternative to inbreeding estimates.Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.

The phylogenetic status of typical Chinese native pigs: analyzed by Asian and European pig mitochondrial genome sequences

China is one of the most diverse countries, which have developed 88 indigenous pig breeds. Several studies showed that pigs were independently domesticated in multiple regions of the world. The purpose of this study was to investigate the origin and evolution of Chinese pigs using complete mitochondrial genomic sequences （mtDNA） from Asian and European domestic pigs and wild boars. Thirty primer pairs were designed to determine the mtDNA sequences of Xiang pig, Large White, Lantang, Jinhua and Pietrain. The phylogenetic status of Chinese native pigs was investigated by comparing the mtDNA sequences of complete coding regions and D-loop regions respectively amongst Asian breeds, European breeds and wild boars. The analyzed results by two cluster methods contributed to the same conclusion that all pigs were classified into two major groups, European dade and Asian clade. It revealed that Chinese pigs were only recently diverged from each other and distinctly different from European pigs. Berkshire was clustered with Asian pigs and Chinese pigs were involved in the development of Berkshire breeding. The Malaysian wild boar had distant genetic relationship with European and Asian pigs. Jinhua and Lanyu pigs had more nucleotide diversity with Chinese pigs although they all belonged to the Asian major clade. Chinese domestic pigs were clustered with wild boars in Yangtze River region and South China.

Predicting nitrogen use efficiency,nitrogen loss and dry matter intake of individual dairy cows in late lactation by including mid‑infrared spectra of milk samples

Background Nitrate leaching to groundwater and surface water and ammonia volatilization from dairy farms have negative impacts on the environment.Meanwhile,the increasing demand for dairy products will result in more pollution if N losses are not controlled.Therefore,a more efficient,and environmentally friendly production system is needed,in which nitrogen use efficiency(NUE)of dairy cows plays a key role.To genetically improve NUE,extensively recorded and cost-effective proxies are essential,which can be obtained by including mid-infrared(MIR)spectra of milk in prediction models for NUE.This study aimed to develop and validate the best prediction model of NUE,nitrogen loss(NL)and dry matter intake(DMI)for individual dairy cows in China.Results A total of 86 lactating Chinese Holstein cows were used in this study.After data editing,704 records were obtained for calibration and validation.Six prediction models with three different machine learning algorithms and three kinds of pre-processed MIR spectra were developed for each trait.Results showed that the coefficient of determination(R2)of the best model in within-herd validation was 0.66 for NUE,0.58 for NL and 0.63 for DMI.For external validation,reasonable prediction results were only observed for NUE,with R2 ranging from 0.58 to 0.63,while the R2 of the other two traits was below 0.50.The infrared waves from 973.54 to 988.46 cm−1 and daily milk yield were the most important variables for prediction.Conclusion The results showed that individual NUE can be predicted with a moderate accuracy in both within-herd and external validations.The model of NUE could be used for the datasets that are similar to the calibration dataset.The prediction models for NL and 3-day moving average of DMI(DMI_a)generated lower accuracies in within-herd validation.Results also indicated that information of MIR spectra variables increased the predictive ability of models.Additionally,pre-processed MIR spectra do not result in higher accuracy than original MIR spectra in the external validation.These models will be applied to large-scale data to further investigate the genetic architecture of N efficiency and further reduce the adverse impacts on the environment after more data is collected.

A post-GWAS confirming the genetic effects and functional polymorphisms of AGPAT3 gene on milk fatty acids in dairy cattle

Background: People are paying more attention to the healthy and balanced diet with the improvement of their living standards. Milk fatty acids(FAs) have been reported that they were related to some atherosclerosis and coronary heart diseases in human. In our previous genome-wide association study(GWAS) on milk FAs in dairy cattle, 83 genomewide significant single nucleotide polymorphisms(SNPs) were detected. Among them, two SNPs, ARS-BFGL-NGS-109493 and BTA-56389-no-rs associated with C18 index(P = 0.0459), were located in the upstream of 1-acylglycerol-3-phosphate O-acyltransferase 3(AGPAT3) gene. AGPAT3 is involved in glycerol-lipid, glycerol-phospholipid metabolism and phospholipase D signaling pathways. Hence, it was inferred as a candidate gene for milk FAs. The aim of this study was to further confirm the genetic effects of the AGPAT3 gene on milk FA traits in dairy cattle.Results: Through re-sequencing the complete coding region, and 3000 bp of 5′ and 3′ regulatory regions of the AGPA T3 gene, a total of 17 SNPs were identified, including four in 5′ regulatory region, one in 5′ untranslated region(UTR),three in introns, one in 3′ UTR, and eight in 3′ regulatory region. By the linkage disequilibrium(LD) analysis with Haploview4.1 software, two haplotype blocks were observed that were formed by four and 12 identified SNPs,respectively. Using SAS9.2, we performed single locus-based and haplotype-based association analysis on 24 milk FAs in 1065 Chinese Holstein cows, and discovered that all the SNPs and the haplotype blocks were significantly associated with C6:0, C8:0 and C10:0(P < 0.0001–0.0384). Further, with Genomatix, we predicted that four SNPs in 5′ regulatory region(g.146702957 G > A, g.146704373 A > G, g.146704618 A > G and g.146704699 G > A) changed the transcription factor binding sites(TFBSs) for transcription factors SMARCA3, REX1, VMYB, BRACH, NKX26, ZBED4, SP1, USF1, ARNT and FOXA1. Out of them, two SNPs were validated to impact transcriptional activity by performing luciferase assay that the alleles A of both SNPs, g.146704373 A > G and g.146704618 A > G, increased the transcriptional activities of AGPAT3 promoter compared with alleles G(P = 0.0004).Conclusions: In conclusion, our findings first demonstrated the significant genetic associations of the AGPAT3 gene with milk FAs in dairy cattle, and two potential causal mutations were detected.

Investigating structural impact of a valine to isoleucine substitution on anti-Müllerian hormone in silico and genetic association of the variant and AMH expression with egg production in chickens

Anti-Mullerian hormone(AMH)acts in maintaining orderly cyclic recruitment of early follicles,suggesting that it is a promising can didate for in flue ncing an imal reproductive efficiency.This study aimed to elucidate the effect of a missense mutati on of Val566lle on the structure of AMH protein and the genetic association of Val566lle and AMH expression with egg production in chickens.Structural perturbations of Val566lle were predicted by homology modeling.The association of the variant with the number of eggs was tested using a quantitative trait transmission disequilibrium test model.AMH expression in granulosa cells in Lueyang black-boned chickens was compared with that in Nick chickens.The Vai566 of AMH is a non?conservative amino acid among mammals and birds,but its hydrophobicity is completely conservative.The substitution of Vai566 for lie566 pote ntially disrupted hydroge n bonds and solve nt accessibility of 22 residues and created a short a-helix in the C terminus of AMH.Despite having striking structure-disrupting potential,the variant was not statistically associated with the number of eggs(P>0.05)in the Lueyang black-boned chickens.We did not detect differential expression of AMH betwee n Lueya ng black-b oned chicke ns and Nick chickens(P>0.05).These results con firmed the structural impact of Val566lle,but suggested that Val566lle and AMH expression might not be the major genetic determinants for egg production in Lueyang black-boned chickens.

Identification of single nucleotide polymorphisms of PIK3R1 and DUSP1 genes and their genetic associations with milk production traits in dairy cows

Background:Previously,phosphoinositide-3-kinase regulatory subunit 1(PIK3R1)and dual specificity phosphatase 1(DUSP1)were identified as promising candidate genes for milk production traits due to their being differentially expressed between the dry period and the peak of lactation in livers of dairy cows.Hence,in this study,the single nucleotide polymorphisms(SNPs)of PIK3R1 and DUSP1 genes were identified and their genetic associations with milk yield,fat yield,fat percentage,protein yield,and protein percentage,were investigated using 1067 Chinese Holstein cows from 40 sire families.Results:By re-sequencing the entire coding region and 2000 bp of the 5′and 3′flanking regions of the two genes,one SNP in the 5′untranslated region(UTR),three in the 3′UTR,and two in the 3′flanking region of PIK3R1 were identified,and one in the 5′flanking region,one in the 3′UTR,and two in the 3′flanking region of DUSP1 were found.Subsequent single-locus association analyses showed that five SNPs in PIK3 R1,rs42590258,rs210389799,rs208819656,rs41255622,rs133655926,and rs211408208,and four SNPs in DUSP1,rs207593520,rs208460068,rs209154772,and rs210000760,were significantly associated with milk,fat and protein yields in the first or second lactation(P values≤0.0001 and 0.0461).In addition,by the Haploview 4.2 software,the six and four SNPs in PIK3R1 and DUSP1 respectively formed one haplotype block,and the haplotype-based association analyses showed significant associations between their haplotype combinations and the milk traits in both two lactations(P values≤0.0001 and 0.0364).One SNP,rs207593520(T/G),was predicted to alter the transcription factor binding sites(TFBSs)in the 5′flanking region of DUSP1.Further,the dual-luciferase assay showed that the transcription activity of allele T in rs207593520 was significantly higher than that of allele G,suggesting the activation of transcriptional activity of DUSP1 gene by allele T of rs207593520.Thus,the rs207593520 SNP was highlighted as a potential causal mutation that should be further verified.Conclusions:We demonstrated novel and significant genetic effects of the PIK3R1 and DUSP1 genes on milk production traits in dairy cows,and our findings provide information for use in dairy cattle breeding.

Estimates of genomic inbreeding and identification of candidate regions that differ between Chinese indigenous sheep breeds

Background:A run of homozygosity(ROH)is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents.Genomic inbreeding can be quantified based on ROH.Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands.We carried out ROH analyses in five Chinese indigenous sheep breeds;Altay sheep(n=50 individuals),Large-tailed Han sheep(n=50),Hulun Buir sheep(n=150),Short-tailed grassland sheep(n=150),and Tibetan sheep(n=50),using genotypes from an Ovine Infinium HD SNP BeadChip.Results:A total of 18,288 ROH were identified.The average number of ROH per individual across the five sheep breeds ranged from 39(Hulun Buir sheep)to 78(Large-tailed Han sheep)and the average length of ROH ranged from 0.929 Mb(Hulun Buir sheep)to 2.544 Mb(Large-tailed Han sheep).The effective population size(Ne)of Altay sheep,Large-tailed Han sheep,Hulun Buir sheep,Short-tailed grassland sheep and Tibetan sheep were estimated to be 81,78,253,238 and 70 five generations ago.The highest ROH-based inbreeding estimate(FROH)was 0.0808 in Large-tailed Han sheep,whereas the lowest F_(ROH)was 0.0148 in Hulun Buir sheep.Furthermore,the highest proportion of long ROH fragments(>5 Mb)was observed in the Large-tailed Han sheep breed which indicated recent inbreeding.In total,49 ROH islands(the top 0.1% of the SNPs most commonly observed in ROH)were identified in the five sheep breeds.Three ROH islands were common to all the five sheep breeds,and were located on OAR2:12.2-12.3 Mb,OAR12:78.4-79.1 Mb and OAR13:53.0-53.6 Mb.Three breed-specific ROH islands were observed in Altay sheep(OAR15:3.4-3.8 Mb),Large-tailed Han sheep(ORA17:53.5-53.8 Mb)and Tibetan sheep(ORA5:19.8-20.2 Mb).Collectively,the ROH islands harbored 78 unique genes,including 19 genes that have been documented as having associations with tail types,adaptation,growth,body size,reproduction or immune response.Conclusion:Different ROH patterns were observed in five Chinese indigenous sheep breeds,which reflected their different population histories.Large-tailed Han sheep had the highest genomic inbreeding coefficients and the highest proportion of long ROH fragments indicating recent inbreeding.Candidate genes in ROH islands could be used to illustrate the genetic characteristics of these five sheep breeds.Our findings contribute to the understanding of genetic diversity and population demography,and help design and implement breeding and conservation strategies for Chinese sheep.

Single‑cell sequencing reveals the reproductive variations between primiparous and multiparous Hu ewes

Background In the modern sheep production systems,the reproductive performance of ewes determines the economic profitability of farming.Revealing the genetic mechanisms underlying differences in the litter size is important for the selection and breeding of highly prolific ewes.Hu sheep,a high-quality Chinese sheep breed,is known for its high fecundity and is often used as a model to study prolificacy traits.In the current study,animals were divided into two groups according to their delivery rates in three consecutive lambing seasons(namely,the high and low reproductive groups with≥3 lambs and one lamb per season,n=3,respectively).The ewes were slaughtered within 12 h of estrus,and unilateral ovarian tissues were collected and analyzed by 10×Genomics single-cell RNA sequencing.Results A total of 5 types of somatic cells were identified and corresponding expression profiles were mapped in the ovaries of each group.Noticeably,the differences in the ovary somatic cell expression profiles between the high and low reproductive groups were mainly clustered in the granulosa cells.Furthermore,four granulosa cell subtypes were identified.GeneSwitches analysis revealed that the abundance of JPH1 expression and the reduction of LOC101112291 expression could lead to different evolutionary directions of the granulosa cells.Additionally,the expression levels of FTH1 and FTL in mural granulosa cells of the highly reproductive group were significantly higher.These genes inhibit necroptosis and ferroptosis of mural granulosa cells,which helps prevent follicular atresia.Conclusions This study provides insights into the molecular mechanisms underlying the high fecundity of Hu sheep.The differences in gene expression profiles,particularly in the granulosa cells,suggest that these cells play a critical role in female prolificacy.The findings also highlight the importance of genes such as JPH1,LOC101112291,FTH1,and FTL in regulating granulosa cell function and follicular development.

Hepatic steatosis is associated with dysregulated cholesterol metabolism and altered protein acetylation dynamics in chickens

Background Hepatic steatosis is a prevalent manifestation of fatty liver, that has detrimental effect on the health and productivity of laying hens, resulting in economic losses to the poultry industry. Here, we aimed to systematically investigate the genetic regulatory mechanisms of hepatic steatosis in laying hens.Methods Ninety individuals with the most prominent characteristics were selected from 686 laying hens according to the accumulation of lipid droplets in the liver, and were graded into three groups, including the control, mild hepatic steatosis and severe hepatic steatosis groups. A combination of transcriptome, proteome, acetylome and lipidome analyses, along with bioinformatics analysis were used to screen the key biological processes, modifications and lipids associated with hepatic steatosis.Results The rationality of the hepatic steatosis grouping was verified through liver biochemical assays and RNA-seq. Hepatic steatosis was characterized by increased lipid deposition and multiple metabolic abnormalities. Integration of proteome and acetylome revealed that differentially expressed proteins(DEPs) interacted with differentially acetylated proteins(DAPs) and were involved in maintaining the metabolic balance in the liver. Acetylation alterations mainly occurred in the progression from mild to severe hepatic steatosis, i.e., the enzymes in the fatty acid oxidation and bile acid synthesis pathways were significantly less acetylated in severe hepatic steatosis group than that in mild group(P < 0.05). Lipidomics detected a variety of sphingolipids(SPs) and glycerophospholipids(GPs) were negatively correlated with hepatic steatosis(r ≤-0.5, P < 0.05). Furthermore, the severity of hepatic steatosis was associated with a decrease in cholesterol and bile acid synthesis and an increase in exogenous cholesterol transport.Conclusions In addition to acquiring a global and thorough picture of hepatic steatosis in laying hens, we were able to reveal the role of acetylation in hepatic steatosis and depict the changes in hepatic cholesterol metabolism. The findings provides a wealth of information to facilitate a deeper understanding of the pathophysiology of fatty liver and contributes to the development of therapeutic strategies.

Spatially resolved transcriptomic profiling of placental development in dairy cow

The placenta plays a crucial role in successful mammalian reproduction.Ruminant animals possess a semi-invasive placenta characterized by a highly vascularized structure formed by maternal endometrial caruncles and fetal placental cotyledons,essential for full-term fetal development.The cow placenta harbors at least two trophoblast cell populations:uninucleate(UNC)and binucleate(BNC)cells.However,the limited capacity to elucidate the transcriptomic dynamics of the placental natural environment has resulted in a poor understanding of both the molecular and cellular interactions between trophoblast cells and niches,and the molecular mechanisms governing trophoblast differentiation and functionalization.To fill this knowledge gap,we employed Stereo-seq to map spatial gene expression patterns at near single-cell resolution in the cow placenta at 90 and 130 days of gestation,attaining high-resolution,spatially resolved gene expression profiles.Based on clustering and cell marker gene expression analyses,key transcription factors,including YBX1 and NPAS2,were shown to regulate the heterogeneity of trophoblast cell subpopulations.Cell communication and trajectory analysis provided a framework for understanding cell-cell interactions and the differentiation of trophoblasts into BNCs in the placental microenvironment.Differential analysis of cell trajectories identified a set of genes involved in regulation of trophoblast differentiation.Additionally,spatial modules and co-variant genes that help shape specific tissue structures were identified.Together,these findings provide foundational insights into important biological pathways critical to the placental development and function in cows.

Integration of genome-wide association study and selection signatures reveals genetic determinants for skeletal muscle production traits in an F2 chicken population

Improving the production of broiler chicken meat has been a goal of broiler breeding programs worldwide for many years. However, the genetic architectures of skeletal muscle production traits in chickens have not yet been fully elucidated. In the present study, a total of 519 F_(2) birds, derived from a cross of Arbor Acres broiler and Baier layer, were re-sequenced(26 F_(0) individuals were re-sequenced at a 10-fold depth;519 F_(2) individuals were re-sequenced at a 3-fold depth) and the coupling of genome-wide association study(GWAS) and selection signatures(FST(fixation index) and θπ(nucleotide diversity)) was carried out to pinpoint the associated loci and genes that contribute to pectoral muscle weight(PMW) and thigh muscle weight(TMW). A total of 7 890 258 single nucleotide polymorphisms(SNPs) remained to be analyzed after quality control and imputation. The integration of GWAS and selection signature analyses revealed that genetic determinants responsible for skeletal muscle production traits were mainly localized on chromosomes 1(168.95–172.43 Mb) and 4(74.37–75.23 Mb). A total of 17 positional candidate genes(PCGs)(LRCH1, CDADC1, CAB39 L, LOC112531568, LOC112531569, FAM124 A, FOXO1, NBEA, GPALPP1, RUBCNL, ARL11, KPNA3, LHFP, GBA3, LOC112532426, KCNIP4, and SLIT2) were identified in these regions. In particular, KPNA3 and FOXO1 were the most promising candidates for meat production in chickens. These findings will help enhance our understanding of the genetic architecture of chicken muscle production traits, and the significant SNPs identified could be promising candidates for integration into practical breeding programs such as genome-wide selection(GS) to improve the meat yield of chickens.

CNV analysis of Meishan pig by nextgeneration sequencing and effects of AHR gene CNV on pig reproductive traits

Background:Reproductive performance of livestock is an economically important aspect of global food production.The Chinese Meishan pig is a prolific breed,with an average of three to five more piglets per litter than European breeds;however,the genetic basis for this difference is not well understood.Results:In this study,we investigated copy number variations(CNVs)of 32 Meishan pigs and 29 Duroc pigs by nextgeneration sequencing.A genome-wide analysis of 61 pigs revealed 12,668 copy number variable regions(CNVRs)that were further divided into three categories based on copy number(CN)of the whole population,i.e.,gain(n=7,638),and loss(n=5,030)CNVRs.We then compared Meishan and Duroc pigs and identified 17.17Mb of 6,387 CNVRs that only existing in Meishan pigs CNVRs that overlapped the reproduction-related gene encoding the aryl hydrocarbon receptor(AHR)gene.We found that normal AHR CN was more frequent than CN loss in four different pig breeds.An association analysis showed that AHR CN had a positive effect on litter size(P<0.05)and that a higher CN was associated with higher total number born(P<0.05),number born alive(P<0.05),number of weaned piglets,and birth weight.Conclusions:The present study provides comprehensive CNVRs for Meishan and Duroc pigs through large-scale population resequencing.Our results provide a supplement for the high-resolution map of copy number variation in the porcine genome and valuable information for the investigation of genomic structural variation underlying traits of interest in pig.In addition,the association results provide evidence for AHR as a candidate gene associated with reproductive traits that can be used as a genetic marker in pig breeding programs.

Variance components and correlations of female fertility traits in Chinese Holstein population

Background: The objective of the present study was to estimate(co)variance components of female fertility traits in Chinese Holsteins, considering fertility traits in different parities as different traits. Data on 88,647 females with 215,632 records(parities) were collected during 2000 to 2014 from 32 herds in the Sanyuan Lvhe Dairy Cattle Center, Beijing, China. The analyzed female fertility traits included interval from calving to first insemination, interval from first to last insemination, days open, conception rate at first insemination, number of inseminations per conception and non-return rates within 56 days after first insemination.Results: The descriptive statistics showed that the average fertility of heifers was superior to that of cows. Moreover,the genetic correlations between the performances of a trait in heifers and in cows were all moderate to high but far from one, which suggested that the performances of a trait in heifers and cows should be considered as different but genetically correlated traits in genetic evaluations. On the other hand, genetic correlations between performances of a trait in different parities of cows were greater than 0.87, with only a few exceptions, but variances were not homogeneous across parities for some traits. The estimated heritabilities of female fertility traits were low; all were below 0.049(except for interval from calving to first insemination). Additionally, the heritabilities of the heifer interval traits were lower than those of the corresponding cow interval traits. Moreover, the heritabilities of the interval traits were higher than those of the threshold traits when measuring similar fertility functions. In general, estimated genetic correlations between traits were highly consistent with the biological categories of the female fertility traits.Conclusions: Interval from calving to first insemination, interval from first to last insemination and non-return rates within 56 days after first insemination are recommended to be included in the selection index of the Chinese Holstein population. The parameters estimated in the present study will facilitate the development of a genetic evaluation system for female fertility traits to improve the reproduction efficiency of Chinese Holsteins.

Effects of Mercury on the Structure and Activity of BLM642-1290 Recombinant Helicase

Objective Bloom’s syndrome is an autosomal recessive disorder characterized by genomic instability and a predisposition to many cancers. Mutations of the BLM gene （encoding a BLM helicase） may form a structure of the etiology of this disease. As a global pollutant, mercury poses a major threat to human health. The current study was conducted to elucidate the effects of Hg^2＋ on the structure and activity of BLM642‐1290 recombinant helicase, and to further explore the molecular mechanisms of mercury toxicity to the DNA helicase. Methods The effects of Hg^2＋ on biological activity and structure of BLM642‐1290 recombinant helicase were determined by fluorescence polarized, ultraviolet spectroscopic, and free‐phosphorus assay technologies, respectively. Results The helicase activity, the DNA‐binding activity, and the ATPase activity of BLM642‐1290 recombinant helicase were inhibited by Hg^2＋ treatment. The LMCT （ligand‐to‐metal charge transition） peaks of the helicase were enhanced with the increase of the Hg^2＋ level. The LMCT peaks of the same concentration of helicase gradually increased over time. Conclusions The biological activity of BLM642‐1290 recombinant helicase is inhibited by Hg^2＋ treatment. The conformation of the helicase is significantly altered by Hg^2＋ . There exist two binding sites between Hg^2＋ and the helicase, which are located in the amino acid residues 1063‐1066 and 940‐944 of the helicase, respectively.