Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Ruminant”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed2025

Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.

BACKGROUND: Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial inflammation is lacking. Hence, we performed rumen metagenomic, metagenome-assembled genome and metabolomic analyses, with transcriptome and single-nucleus RNA sequence analyses, to explore the microbial mechanism of SARA occurrence and different degrees of inflammation. RESULTS: A total of 36 goats fed two diets with gradually increasing levels of rumen-degradable starch (RDS) were included in this study, and SARA goats fed 70% concentrate diets supplemented with whole corn (HGW-SARA) and SARA goats fed 70% concentrate diets supplemented with crushed corn (HGC-SARA) were identified. Moreover, 11 goats fed a control basal diet, named LGW-CON, were also included. Compared with those in the LGW-CON group, the rumen fermentation capacity was enhanced, accompanied by ruminal epithelial and systemic inflammation, in goats from HGW-SARA and HGC-SARA. Between them, HGC-SARA goats presented less inflammation. Notably, the ruminal inflammation-related pathways were increased only in the HGW-SARA group but not in the HGC-SARA group. Metagenomic analysis revealed that the β diversity of SARA goats was significantly different from that of LGW-CON goats. Ruminococcus significantly increased in both SARA groups, whereas Prevotella and Bacteroidales significantly decreased, which was accompanied by a decrease in cellulose and hemicellulose enzymes and an increase in lysozymes and lipopolysaccharide synthesis enzymes. Multi-omics analysis of the ruminal contents and tissues suggested that epithelial inflammation was caused by disturbed ruminal microbiome-induced Th17 cell differentiation and IL-17 signalling pathway activation. Comparative analyses between the HGW-SARA and HGC-SARA groups highlighted the importance of Selenomonas and Bifidobacterium, as well as bacterial tryptophan metabolism, in the production of 3-indoleacetic acid, which mitigated ruminal epithelial inflammation by modulating Th17 cells and inhibiting IL-17 signalling. Ruminal microbiota transplantation from HGW-SARA goats to healthy dairy goats and mice revealed the role of microbes in epithelial inflammation. Additionally, 3-indoleacetic acid supplementation reduced rumen inflammation and the IL-17 concentration in the serum, improved VFAs absorption, and enhanced milk production. CONCLUSIONS: This study unveiled that after SARA was induced by high-concentrate feeding, the rumen homeostasis was disrupted, and rumen fiber degradation capacity of dairy goats decreased, but the LPS synthesis capacity increased, and inflammation of the rumen epithelium was observed. However, the ruminal microbial species from the Bifidobacterium and Selenomonas genera and bacterial 3-indole acetic acid are pivotal in mitigating ruminal epithelial inflammation during SARA in dairy goats. This could potentially be attributed to the modulation of ruminal Th17 cell proportions and the inhibition of IL-17 signalling pathways. Video Abstract.

Rumen↗
PubMed2026

Genomic characterization and pathogenicity of ruminant Listeria monocytogenes isolates in a murine oral infection model.

Listeria monocytogenes is a major foodborne pathogen; its ruminant isolates display zoonotic characteristics, causing similar clinical signs in humans, including abortion and encephalitis. However, data on whole genome sequencing and pathogenicity of ruminant L. monocytogenes isolates remain sparse. This study aimed to analyze the genotypic characteristics of L. monocytogenes isolates from ruminants with listeriosis. Furthermore, we assessed the in vivo pathogenicity of four ruminant L. monocytogenes isolates, characterized via whole-genome sequencing-based genetic clustering, in orogastrically inoculated mice. The isolate LM18 (serotype 1/2b, ST224, SL6178) had the lowest lethal dose compared to the other three isolates including previous hypervirulence type (serotype 4b, ST1, SL1) and caused secondary bacteremia in lungs, with sustained bacterial loads in the spleen and liver. Genomic (listeria pathogenicity island -1 and -3) and virulence gene (actA and llsX) mutation analyses associated with virulence suggested from well-recognized studies could not elucidate the virulence of the isolates. SSI-1, which only exists in the isolate LM18 (serotype 1/2b, ST224, SL6178), may help L. monocytogenes survive in the gastrointestinal environment, thereby affecting its virulence. Further research should investigate the role of SSI-1 in the pathogenicity of L. monocytogenes. Moreover, additional studies utilizing larger datasets of ruminant isolates are required to validate our genotypic characterization and to obtain a comprehensive picture of further genotypic differences crucial for L. monocytogenes pathogenicity.

Animals↗
PubMed2025

Unveiling novel antimicrobial peptides from the ruminant gastrointestinal microbiomes: A deep learning-driven approach yields an anti-MRSA candidate.

INTRODUCTION: Antimicrobial peptides (AMPs) present a promising avenue to combat the growing threat of antibiotic resistance. The ruminant gastrointestinal microbiome serves as a unique ecosystem that offers untapped potential for AMP discovery. OBJECTIVES: The aims of this study are to develop an effective methodology for the identification of novel AMPs from ruminant gastrointestinal microbiomes, followed by evaluating their antimicrobial efficacy and elucidating the mechanisms underlying their activity. METHODS: We developed a deep learning-based model to identify AMP candidates from a dataset comprising 120 metagenomes and 10,373 metagenome-assembled genomes derived from the ruminant gastrointestinal tract. Both in vivo and in vitro experiments were performed to examine and validate the antimicrobial activities of the AMP candidates that were selected through bioinformatic analysis and subsequently synthesized chemically. Additionally, molecular dynamics simulations were conducted to explore the action mechanism of the most potent AMP candidate. RESULTS: The deep learning model identified 27,192 potential secretory AMP candidates. Following bioinformatic analysis, 39 candidates were synthesized and tested. Remarkably, all synthesized peptides demonstrated antimicrobial activity against Staphylococcus aureus, with 79.5% showing effectiveness against multiple pathogens. Notably, Peptide 4, which exhibited the highest antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), confirmed this effect in a mouse model with wound infection, exhibiting a low propensity for resistance development and minimal cytotoxicity and hemolysis towards mammalian cells. Molecular dynamics simulations provided insights into the mechanism of Peptide 4, primarily its ability to disrupt bacterial cell membranes, leading to cell death. CONCLUSION: This study highlights the power of combining deep learning with microbiome research to uncover novel therapeutic candidates, paving the way for the development of next-generation antimicrobials like Peptide 4 to combat the growing threat of MRSA would infections. It also underscores the value of utilizing ruminant microbial resources.

Animals↗
PubMed2025

Genomic insights into Shigella species isolated from small ruminants and manure in the North West Province, South Africa.

This study investigated Shigella species' antibiotic resistance patterns and genomic characteristics from small ruminants and manure collected in Potchefstroom, North West, South Africa. Whole genome sequencing was used to determine resistome profiles of Shigella flexneri isolates from small ruminants' manure and Shigella boydii from sheep faeces. Comparative genomics was employed on the South African 261 S. flexneri strains available from GenBank, including the sequenced strains in this study, by investigating the serovars, antibiotic resistance genes (ARGs), and plasmid replicon types. The S. flexneri strains could not be assigned to known sequence types, suggesting novel or uncharacterized lineages. S. boydii R7-1A was assigned to sequence type 202 (ST202). Serovar 2A was the most common among South African S. flexneri strains, found in 96% of the 250 compared human-derived isolates. The shared mdf(A) was the most prevalent gene, identified in 99% of 261 S. flexneri genomes, including plasmid replicon types ColRNAI_1 (99%) and IncFII_1 (98%). Both species share a core set of resistance determinants mainly involving β-lactams (ampC1, ampC, ampH), macrolides (mphB), polymyxins (eptA, pmrF), multidrug efflux pumps (AcrAB-TolC, Mdt, Emr, Kpn families), and regulatory systems (marA, hns, crp, baeRS, evgAS, cpxA, gadX). However, S. boydii possesses additional resistance genes conferring resistance to tetracyclines (tet(A)), phenicols (floR), sulphonamides (sul2), and aminoglycosides (APH(3'')-Ib, APH(6)-Id), along with the acrEF efflux pump components (acrE, acrF). In contrast, S. flexneri harboured unique genes linked to polymyxin resistance (ugd) and regulatory functions (sdiA, gadW) that were absent in S. boydii. These findings highlight Shigella strains' genomic diversity and antimicrobial resistance potential in livestock-associated environments. Moreover, S. boydii highlights the potential risk of multidrug-resistant bacteria in farming and environmental routes. KEY POINTS: • First whole genome study of Shigella from manure and small ruminants in South Africa. • Shigella boydii strain carried multiple resistance genes to β-lactams and tetracycline. • Multidrug efflux pump gene mdf(A) was detected in 99% of South African Shigella flexneri strains.

Animals↗
PubMed2026

A genetic manipulation tool based on the GP35 recombinase for targeted gene editing in mycoplasmas of ruminants.

Pathogenic ruminant mycoplasmas are major etiological agents in cattle and small ruminants and are responsible for substantial economic losses in the livestock industry. Progress in pathogenesis research and vaccine development has been hampered by a lack of effective genetic tools. The applicability of common genome editing platforms, such as CRISPR, is inherently restricted in these organisms owing to their minimal genomes, the absence of a cell wall, and low homologous recombination efficiency. Although transposon-mediated random mutagenesis and single-base editing are currently used in the editing of bovine mycoplasma, the stochastic nature of transposons, the risk of single-base random deamination, and limitations in editing window selection hinder the genetic manipulation of bovine mycoplasma. Here, we introduce a plasmid-based methodology that employs the GP35 recombinase from bacteriophage SPP1 to mediate long single-stranded DNA (ssDNA) recombineering, thereby enabling precise gene insertions and deletions in Mycoplasma bovis, with a positive-editing rate of 77.78% - 100%. This targeted system eliminates the risk of random deamination. Leveraging this tool, we generated a panel of M. bovis mutants affecting metabolic and virulence genes and obtained key insights into Mb0564, identified as a novel adhesin. The 192 to 287 aa region of GP35 is critical for interaction with SSB. Structural conservation analysis further suggested that this GP35-ssDNA editing system possesses a high potential for translation to other ruminant pathogens. Collectively, our approach expands the existing genetic toolkit for M. bovis, advances synthetic biology and M. bovis pathobiology, facilitates vaccine development, and strengthens the control of high-impact livestock diseases in line with the One Health framework.

Animals↗
PubMed1977

Protected proteins in ruminant nutrition. In vitro evaluation of casein derivatives.

Chemical treatment of proteins in feeds can, by crosslinking protein chains or other chemical effects, decrease their solubility and microbial degradation in the rumen. A need exists to modify proteins systematically under well-defined conditions with inexpensive reagents and to evaluate the treated products nutritionally for possible beneficial effects on wool growth and quality as well as production of meat and milk. As a first step toward this goal we evaluated many derivatives of casein treated at pH 9-10 with various acylating and alkylating agents. Initial tests indicate that all treatments decreased protein digestion by rumen microorganisms. Potentially crosslinking reagents are usually more effective than similar ones that cannot crosslink. A few treatments gave ruminal protection that approached or exceeded that obtained with formaldehyde. This result shows that systematic evaluation of ruminal in vitro digestibility of protein derivatives may disclose new products deserving tests of post-ruminal digestibility and practical nutritive value.

Amino Acids↗
PubMed1976

Effect of oxygen saturation on H+ and Cl- distribution across the red cell membrane in human and ruminant blood.

Alterations of red cell pH (pHc) and distribution ratios of H+ (gammaH+) and Cl (gammaCl-) between plasma and red blood cells with oxygenation of blood were studied in human blood (audult and fetal) and ruminant blood (bovine, goat and sheep). The experiments were carried out at a plasma pH of 7.0 to 7.7 and at 37 degrees C. In human blood pHc of fully oxygenated blood was 0.035 pH lower than that of fully deoxygenated blood in all ranges of plasma pH studied. In ruminant blood, however, the differences in pHc between oxygenated and deoxygenated blood were 0.011 in ox, and 0.003 in goat and sheep, all of them not being significant. The decreases in gammaH+ accompanying oxygenation were in fairly good agreement with those in gammaCl- in human blood and amounted to about 0.05. In ruminant blood, in spite of virtually zero changes in gammaH+ with oxygenation, the decreases in gammaCl- were slightly greater than those in human blood. There might be a species difference in the mechanisms of distribution of Cl- and H+ across the red cell membrane.

Animals↗
PubMed2026

Developmental block in ruminant embryos: Mechanisms, molecular insights and potential interventions.

Developmental block remains one of the major hurdles that makes it hard to develop embryos in vitro more efficiently. In ruminants, it is predominantly observed during the 8-16 cell stage, coinciding with the maternal-to-zygotic transition (MZT) and embryonic genome activation (EGA). In addition, reducing maternal transcripts and initiating embryonic transcription correctly is a major reason for developmental arrest. A broad array of molecular mechanisms has been implicated, encompassing incomplete epigenetic regulation, mitochondrial dysfunction, oxidative stress, improper cell cycle progression, and dysregulated apoptosis. During this process, several key genes, including ZAR1, NPM2, DPPA3, DNMTs, Cyclin B1, BCL2, and antioxidant enzymes (SOD1, GPX1, and CAT) have been recognized as essential regulators of the block. External factors, especially poor in vitro culture conditions, high oxygen levels, and the secretion of harmful metabolites, make developmental failure even worse. Recent research has underscored the significance of antioxidant supplementation, epigenetic modulators, and enhanced culture systems in mitigating developmental barriers. Therefore, the current review summarises the contemporary insights into the factors and molecular mechanisms responsible for ruminant embryonic developmental block, focusing on MZT, oxidative stress, and epigenetic regulation. It also addresses potential strategies to enhance the developmental competence of ruminant embryos in vitro.

Embryo↗
PubMed1976

A kinetic concepto of lipid transport in ruminants.

Summarization of the literature shows a strong correlation between dietary fatty acid intake and total lipid concentration in plasma in lactating cows whereas total milk fat secreted is related to neither of these. In the process of plasma triglyceride removal, chylomicra and very low density lipoproteins are converted to low density lipoproteins. Limited kinetic data indicate that the fractional removal rates for chulomicra and very low density lipoproteins are rapid in lactating cows whereas fractional removal of low density lipoproteins is slower, resulting in accumulation of the latter in plasma. Under such conditions, low density lipoprotein concentrations of plasma would not be expected to reflect quantitatively the transfer of plasma triglyceride fatty acids to milk fat. Quantitative analysis or triglyceride fatty acid turnover in density less than 1.006 lipoproteins should delineate the role of plasma lipid transport in milk fat synthesis. High fat diets protected from rumen biohydrogenation have proven to be a useful approach in studying ruminant fat metabolism and may be used more extensively to elucidate the role of cholesterol in plasma lipid transport and the metabolism of essential fatty acids in ruminants.

Acetyl-CoA Carboxylase↗
PubMed1975

Transfer of drugs across the ruminal wall in goats.

The rates at which pentobarbital, salicylate, antipyrine, and quinine were transferred from the rumen of intact, conscious goats were measured. The rates at which the same drugs diffused from the blood plasma (under conditions of constant drug concentration) into the ruminal solution were also evaluated. These compounds were absorbed by simple diffusion, and the rates of transfer were a function of pH of the intraruminal solution. The diffusion of drugs from plasma into the reticulorumen allowed steady-state distributions to be established in some goats. The theoretical and observed steady-state distributions were compared. There were good correlations for pentobarbital and antipyrine, but not for salicylate and quinine. These findings confirm in vivo the general principles of drug transfer across ruminal epithelium that were derived from previous studies conducted in vitro.

Animals↗
PubMed2026

Expression profiles of miRNAs in ruminant intermediate hosts with cystic echinococcosis.

Cystic echinococcosis (CE), caused by the larval stage of Echinococcus granulosus sensu lato (s.l.), is a parasitic zoonotic disease recognized by the World Health Organization as a neglected tropical disease of significant public health concern. Despite ongoing control programs, CE remains endemic, underlining the need for integrated control strategies that involve new diagnostic and therapeutic tools. Recent investigations have spotlighted microRNAs (miRNAs) as key regulators in parasite development, immunomodulation, and as potential diagnostic and therapeutic targets. In the present research, a molecular study was conducted to investigate hydatid cyst samples (protoscoleces and germinal membranes) collected in southern Italy from different ruminant species (sheep, cattle, and water buffaloes), naturally infected with CE, with the ultimate goal of establishing a more comprehensive picture of miRNA expression patterns in these intermediate hosts. The bioinformatic analysis of hydatid cyst samples revealed 168 mature miRNAs. Among these, egr-miR-10-5p, egr-let-7-5p, and egr-miR-71-5p were the most abundant, with egr-miR-10-5p showing particularly high expression levels. No significant differences in miRNA abundance between host species were found. In contrast, when focusing on the comparison between protoscoleces and sterile germinal membranes, 24 miRNAs were found to be differentially expressed. Targeted qPCR of four selected miRNAs (egr-miR-71-5p, egr-let-7-5p, egr-miR-125-5p, and egr-miR-10-5p) showed clear overexpression in protoscoleces and in fertile germinal membranes compared with sterile ones. The differential miRNA expression patterns provide insight into the molecular mechanisms controlling the parasite's lifecycle and may guide the development of novel intervention methods to enhance CE control in endemic areas.

Animals↗
PubMed2026

Hemotropic mono- and coinfections in Colombian ruminants: descriptive occurrence and host-related factors associated with coinfection in cattle.

Hemotropic pathogens such as Anaplasma, Babesia, Mycoplasma, and Trypanosoma are endemic to cattle and can cause coinfections, complicating disease dynamics and control. However, the host-related factors influencing these infections under tropical conditions remain poorly understood. This study aimed to investigate the occurrence of hemotropic monoinfections and coinfections in ruminants tested for hemotropic pathogens and to identify host-related factors associated with coinfection in cattle under field conditions in Colombia. A total of 104 animals were included: 91 cattle, 10 buffaloes, and 3 goats. Among the cattle, 34 (37.4%) exhibited monoinfections, 47 (51.6%) had coinfections, and 10 tested negative. In buffaloes, seven (70%) presented monoinfections, and two (20%) presented coinfections; in goats, one had a monoinfection, and one had a coinfection, most frequently involving Mycoplasma spp. The predominant coinfection patterns were Anaplasma&#x2009;+&#x2009;Mycoplasma and Mycoplasma&#x2009;+&#x2009;Trypanosoma, particularly in Bos indicus cattle. Bivariate and multivariable analyses revealed that breed was the strongest predictor of coinfection, with animals of less common breeds showing 93% lower odds (aOR&#x2009;=&#x2009;0.07; 95% CI: 0.02-0.30; p&#x2009;<&#x2009;0.001). Bos taurus individuals also tended toward lower odds of coinfection in the multivariable model, although this trend did not reach statistical significance. Our findings demonstrate a high frequency of hemotropic coinfections in cattle, particularly those involving Mycoplasma spp., and highlight the influence of host-related factors on infection dynamics. These results underscore the importance of integrating demographic and genetic information into surveillance and prevention strategies to improve the management of hemotropic infections in tropical livestock systems.

Animals↗
PubMed1976

Bacterial fermentation of cheese whey for production of a ruminant feed supplement rich in curde protein.

A simple and efficient process for the production of a ruminant feed supplement, rich in crude protein (defined as total N X 6.25), by bacterial fermentation of cheese whey has been developed. The lactose in unpasteurized whey is fermented to lactate acid by Lactobacillus bulgaricus at a temperature of 43 degrees C and pH 5.5. The lactic acid produced is continually neutralized with ammonia to form ammonium lactate. The fermented product is concentrated by evaporation to a solids content of about 70% and adjusted to pH 6.8 with additional ammonia. The concentrated product contains about 55% crude protein. Approximately 6 to 8% of the crude protein is derived from bacterial cells. 17% from whey proteins, and 75 to 77% from ammonium lactate. The efficiency of conversion of lactose to lactic acid usually exceeds 95%. The fermentation time is greatly reduced upon the addition of 0.2% yeast extract or 0.1% corn steep liquor as a source of growth factors. Whey containing lactose at concentrations up to 7% can be fermented efficiently, but at higher concentrations lactose is fermented incompletely. The process has been scaled up to a pilot plant level, and 40 tons of concentrated product were produced fro animal feeding trials, without ever encountering putrefactive spoilage.

Animal Feed↗
PubMed2026

Near-Whole-Genome Sequencing of Peste Des Petits Ruminants Virus Lineage IV From the Savannah District, Northern C&#xf4;te d'Ivoire in 2023.

Peste des petits ruminants (PPR) is a highly contagious viral disease affecting sheep and goats, causing substantial economic losses in endemic countries. In the Savannah district of C&#xf4;te d'Ivoire, knowledge of the genetic diversity and molecular epidemiology of the PPR virus (PPRV) remains limited. This study investigated the genetic diversity and phylogenetic relationships of PPRV circulating in this region using whole-genome sequencing (WGS). A cross-sectional survey was conducted between September and December 2023. Nasal swabs collected from sheep and goats were screened for PPRV ribonucleic acid (RNA) using real-time reverse transcription polymerase chain reaction (RT-qPCR). Samples with low quantification cycle (Cq) values of less than 35 and successful multiplex PCR amplification profiles were selected for sequencing using the Oxford Nanopore MinION platform. Near-complete consensus genomes were generated through reference-based assembly and analysed alongside representative strains from all recognised PPRV lineages. Of the 355 samples analysed, 25 (7.0%) tested positive for PPRV RNA, with positive detections in all three surveyed regions (Poro, Tchologo and Bagou&#xe9;). The four samples with the lowest Cq values, originating from all three administrative regions, were successfully sequenced, generating genomes that covered 82.0%-86.2% of the reference genome at a depth of &#x2265; 10 &#xd7;. The missing regions were mainly located at the 5' and 3' genomic termini, as well as in limited internal regions associated with amplicon dropout. Phylogenetic analysis revealed that all four sequences belonged to lineage IV and exhibited high nucleotide similarity (98.1%-99.9%). The Ivorian strains clustered with recent lineage IV viruses from West, North and Central Africa, whereas historical Ivorian lineages I and II formed distinct clades. These findings confirm the predominance of lineage IV in northern C&#xf4;te d'Ivoire and provide baseline genomic data to support molecular epidemiological surveillance in the region.

PPRV↗
PubMed1978

[Seroepidemiological investigations in domestic ruminants from Egypt, Somalia and Jordan for the demonstration of complement fixing antibodies against Rickettsia and Chlamydia (author's transl)].

1450 random serum samples of domestic ruminants from Egypt, Somalia and Jordan were investigated for complement fixing antibodies against Rickettsia and Chlamydia. Between 1.5 and 3.4% of the samples from the animals investigated had antibodies against the RMSF-group of Rickettsia, with exception of the sera from Somalian cattle and sheep from Jordan. Antibodies against Rickettsia of the Typhus-group were found in 4 cattle and 1 goat from Jordan and 2 sheep from Egypt; by agglutination test with type-specific antigen they were identified as antibodies against R. typhi. Using 2 different antigens, antibodies against Coxiella burnetii were found in every population tested. The prevalence was 2.0 to 12.2%, with the exception of cattle in Somalia, where only 1 positive serum (0.2%) was found. 27% of the serum samples from Jordan and 22% from Egypt but none of the 802 samples from Somalia had antibodies against Chlamydia. The results are discussed under an epidemiological point of view.

Animals↗
PubMed2026

Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.

Livestock reference genomes have transformed the discovery of variants associated with production, reproduction, health, and environmental adaptation. Nevertheless, a single linear reference represents only one mosaic haplotype and incompletely captures sequence diversity within a species, particularly structural variants, copy-number changes, repeat-rich regions, and breed-specific sequences. Pangenomes address this limitation by integrating multiple high-quality assemblies or population-scale variants into a unified sequence or graph representation. Concurrently, multi-omics approaches connect genomic variation with transcriptomic, epigenomic, manuscriptproteomic, metabolomic, and microbiome responses, thereby improving biological interpretation of genotype-phenotype relationships. This review synthesizes recent progress in livestock pangenomics and multi-omics, with emphasis on cattle, goats, sheep, water buffalo, and chickens. It describes advances in long-read and haplotype-resolved sequencing, graph construction, structural-variant discovery and genotyping, functional annotation, and integrative analysis. Recent pangenome studies have uncovered substantial non-reference sequence, reduced reference bias, identified breed- and population-specific structural variants, and resolved candidate variants underlying pigmentation, body size, tail morphology, cashmere production, altitude adaptation, and other economically relevant traits. However, translation into routine breeding remains constrained by uneven population representation, inconsistent structural-variant definitions, limited functional annotation, computational demands, and insufficient validation across environments. Future progress will depend on diverse near-complete assemblies, graph-aware imputation and genomic prediction, long-read transcriptomics, single-cell and spatial omics, rigorous causal validation, and open, interoperable resources. Together, these developments can support more accurate, resilient, and biologically informed livestock improvement. Importantly, current dairy-cattle evidence indicates that pangenome-derived structural variants can substantially improve variant discovery and functional interpretation while yielding only marginal average gains in routine genomic prediction, favoring targeted augmentation rather than wholesale replacement of established SNP-based evaluations.

Animals↗