Journal of Dairy Science

Milk urea concentration (MUC) is an indicator of dietary protein utilization and nitrogen use efficiency in dairy cows. We performed genome-wide association studies (GWAS) on MUC in early, mid, and late lactation in the Holstein (HOL) and Brown Swiss (BSW) dairy cattle breeds using imputed sequence variants. We identified 11 and 17 independent quantitative trait loci (QTL) for MUC across the three lactation stages in BSW and HOL, respectively. While many of these QTL have previously been reported for MUC and other dairy traits, our study provides evidence that some QTL exert lactation-stage specific effects. Our findings suggest that variants at the DGAT1 locus on BTA14 have pleiotropic effects on MUC and other dairy traits. This QTL showed an early lactation-specific association with MUC but impacted milk and fat yield across the entire lactation. We fine-mapped two QTL for MUC in early and mid-lactation in BSW on BTA9 (lead SNP: 9:21392941, Pcorrected = 1.1E-17) and BTA28 (lead SNP: 28:6518357; Pcorrected = 3E-11). We identified lncRNA ENSBTAG00000058688 and IBTK as positional and functional candidate genes for the BTA9 QTL, and KCNK1 as positional and functional candidate gene that harbors a highly significant missense variant for the BTA28 QTL. In conclusion, our results shed light on the genetic architecture of MUC and highlighted QTL harboring potential functional variants underpinning milk urea variation within and across breeds.

Data from 80,713 first-calving cows (1984 to1989) of the Holstein, Mambi, and Siboney breeds, belonging to seven large dairy enterprises in Cuba and progenies of 1,297 sires, were analyzed. For each cow, the average across all lactations for at least 14 years after first calving was defined as individual productivity (PI), and the corresponding lifetime sum as accumulated productivity (PA); both traits were. Two genetic models were fitted: a classical Animal Model (M1) and a Sire maternal grandsire model (Sire MGS; M2), aimed at partitioning additive genetic variance into paternal and maternal-line components. Heritability estimates under model M1 were moderate (h2 {approx} 0.135 to 0.140), whereas M2 yielded higher values (h2 {approx} 0.158 to 0.170), reflecting increased additive variance due to a better connectedness across herds. Using estimated breeding values (EBV) for PI and PA, a global cow merit index (H1) was defined under M1. Under M2, a parental index (IM2) combining four standardized predictors (paternal and maternal-grandsire EBV for PI and PA) was constructed. Multiple regression of H1 on IM2 showed that the paternal and maternal-grandsire paths accounted for 73% and 27% of the variation, respectively, indicating a non-negligible maternal-line contribution. Model M2 provided the best overall fit according to information criteria and cross validation using two independent subsamples and the full population yielded correlations of 0.870 to 0.881, demonstrating strong predictive ability and stability of IM2 rankings. These results support the Sire MGS model as a structural extension of the Animal Model for breeding programs targeting lifetime productivity in tropical dairy cattle.

Introducing cognitive enrichment from an early age has the potential to enhance an animals capacity to learn both simple and complex tasks, promote neural plasticity, and support cognitive development. This is applicable for young cattle who are at a critical stage in their development and could benefit from the influence cognitive enrichment has on their behavioral expression. This study aims to explore the effects cognitive enrichment has on weaned dairy calves through analyzing behavioral measures of voluntary participation and short-term behavioral reactions to enrichment exposure. Our study involved a total of five pairs of weaned calves (n=8 treatment; n=2 control). The treatment groups were presented with three variations of a puzzle box, each equipped with unique challenges that offer different solutions (push, slide, pull). These boxes were provided to the calves twice daily over the span of nine days in an isolated corridor located behind their pen. We hypothesized that motivated calves would consistently engage with cognitive enrichment voluntarily over time and express directed natural behaviors, reflecting sustained participation across repeated trials. Results demonstrated that calves consistently visited the cognitive enrichment area across trials, with an average latency of 75.7 {+/-} 47.0s from the pen to the enrichment. Secondly, the calves spent a significant proportion of trial time within the enrichment area at 65% (870.1 {+/-} 21s). Lastly, all calves expressed a broad range of behaviors in line with their natural exploration within the enrichment area, while the puzzle box treatment groups expressed higher durations of behavioral expressions when compared to the control (F=11.7, p<0.0001). Combined, these results indicate the calves motivations to voluntarily participate in a cognitive challenge. While these are promising findings for cognitive enrichment and its applicability to dairy calves, further work is needed to understand broader parameters. Specifically, how can social dynamics influence enrichment interaction in groups, how can this type of enrichment be implemented on farms, and what are the long-term effects to providing cognitive enrichment in the early stages of development.

Epigenetics may play a crucial role in livestock adaptation to environmental challenges like heat stress. In recent years, a growing number of studies have investigated the epigenetic mechanisms underlying dairy cow adaptation to heat stress. However, there is still limited knowledge about the effects of heat stress on immune cells and immune-related phenotypes. Herein we aim to identify heat-stress induced DNA methylation variations on blood methylome potentially affecting regulatory regions and associated phenotypes. Blood samples were collected and peripheral blood mononuclear cell (PBMC) isolated from four cows before (D0) and after (D14) a 14-d heat stress challenge (cyclical THI 72-82) and, from four cows kept in thermoneutral conditions (THI 61-64). Heat-stressed cows had ad libitum access to diets supplemented with adequate levels of vitamin D and Ca (12,000 IU/kg of vitamin D and 0.73% Ca, respectively). To eliminate confounding effects due to differences in nutrient intake, cows maintained under thermoneutral conditions were pair-fed (PF) to their heat-stressed counterparts and received adequate concentrations of vitamin D and Ca as well. Reduced representation bisulphite sequencing (RRBS) was used to profile PBMCs methylome. Differential methylation analysis was performed using methylKit and DSS softwares ({Delta}meth [&ge;] 25%, adjusted p-value < 0.01), retaining only commonly detected differentially methylated cytosines (DMCs). A total of 2,908 DMCs were identified when comparing pre- and post-heat stress samples. After excluding 649 DMCs that were also detected under thermoneutral conditions, as these changes were likely associated with feed restriction inherent to the pair-feeding design rather than with heat stress per se, 2,259 heat stress-specific DMCs remained, predominantly hypomethylated. About half of the DMCs are annotated in intronic and intergenic regions; known to harbor regulatory elements. By intersecting the DMRs with publicly available functional annotation data, we observed hypomethylation on regulatory regions putatively affecting cows immune system. As an example, we identified a loss of methylation within an enhancer region of the MSN gene, which is involved in lymphocyte homeostasis, and a loss of methylation in the promoter region of MECP2, a well-established epigenetic regulator with a central role in chromatin organization and gene expression. These findings highlight the impact of heat stress on dairy cow immunity and provide new insights into its epigenetic regulation under environmental stress. Interpretative summaryThis study examined DNA methylation changes induced by heat stress in dairy cows to elucidate epigenetic mechanisms of thermal adaptation. Using RRBS on PBMCs, 2,259 heat stress-specific differentially methylated cytosines were identified, predominantly hypomethylated and enriched in regulatory regions. Functional annotation highlighted immune-related pathways, including hypomethylated regulatory regions near genes (e.g., MSN, ZBTB33, SLC25A5, GNAS, FAM3A, and MECP2) associated with immune function. These findings indicate that heat stress induces targeted epigenetic modifications potentially affecting immune regulation in dairy cows.

BackgroundThis study investigated rumen microbiome reconstitution and methane (CH4) emissions following a complete exchange of rumen contents between low- and high-CH4-yielding Norwegian Red dairy cows. Twenty cows were screened for CH4 yield, and two low and two high emitters were selected for rumen cannulation and content swap. Total rumen contents were swapped after complete evacuation and washing of both the rumen and omasum. Rumen samples were collected twice in weeks -1, 1, 3, and 7 for fermentation analysis, metagenomics, and metaproteomics, and at week 8 CH4 production was measured. ResultsPrior to the swap, low and high emitters produced 21.2 {+/-} 0.7 and 26.3 {+/-} 1.4 g CH4/kg dry-matter intake (DMI), respectively. Eight weeks after swap, CH4 yields were 12.7 {+/-} 0.3 and 28.9 {+/-} 0.3 g CH4/kg DMI, respectively, showing that the CH4 phenotype of each cow was maintained. Analysis of metagenome-derived 16S rRNA gene sequences showed that low emitters gradually re-established their original microbial community, whereas high emitters retained donor-like microbiota. Metaproteomic mapping suggested higher expression of Prevotella-associated succinate-propionate pathway enzymes in low emitters at week 7, though these differences were modest. ConclusionThese findings suggest that host factors influence CH4 output and microbial reconstitution, with low emitters restoring their native microbiome while high emitters retained a donor-associated community yet continued to emit high CH4. Results should be interpreted with caution given the small sample size (n = 2 per phenotype) and require confirmation in larger studies. ImportanceReducing enteric methane from cattle requires understanding whether the rumen microbiome or the host animal is the primary driver of methane output. We exchanged the entire rumen contents between low- and high-methane-yielding dairy cows and measured methane production alongside metagenomic and metaproteomic profiling over two months. Despite receiving each others microbiomes, each cows methane phenotype persisted--low emitters stayed low and high emitters stayed high. Microbiome reconstitution was asymmetric: low emitters restored their original microbial community, while high emitters retained the donor microbiota. Methanogen communities did not differ between phenotypes, pointing to host-level rather than microbial-level control of methane yield. These pilot findings suggest that breeding for favorable host traits may be essential for lasting methane reduction, and that microbiome transfer alone is unlikely to shift an animals methane phenotype. Larger studies are needed to confirm these observations.

Restlessness is a symptom of chronic boredom in humans and a behavioural phenomenon anecdotally described as a concern in bulls raised for fattening purposes, but it has so far not been addressed in research. The two studies presented in this paper aimed to gain first insights into restlessness in bulls. We operationally defined restlessness by the number of transitions between behaviours in a given time period, and quantified restlessness in bulls of different weight classes (300, 400, 500 kg) on farms keeping bulls on fully-slatted floors (n=8, Study 1) as well as across three different husbandry systems (fully-slatted floor (FS, n=4), straw-based (SB, n=4) and organic pasture (OP, n=3), Study 2). All farms were visited twice, and the behaviour of different individuals was continuously recorded for 15 minutes each between 9 a.m. and 5 p.m. (Study 1) and for 8 minutes each between 6 a.m. and 10 p.m. (Study 2). The effects of weight class and husbandry system were analysed using generalised linear mixed-effects models, and we ran a sequence analysis to cluster observations by the sequence, frequency, and duration of bulls behaviours in Study 1. Bulls kept in fully-slatted floor systems in Study 1 changed their behaviour on average 48.3 times per 10 minutes, with high variability both within and across farms. Weight class did not have a statistically supported effect on the number of transitions, and the sequence analysis revealed four clusters that differed in sequence and in the number of transitions. In Study 2, OP bulls showed fewer transitions than SB and FS bulls (X22 = 23.6, p < 0.001), while SB and FS bulls did not differ. While SB pens were more structured and offered more space per animal, both SB and FS systems can be characterised by monotony, which may explain the similar level of restlessness in both systems. Alternatively, or in addition, the high feeding intensity in SB and FS systems may have caused the higher number of transitions compared to the OP system, potentially elicited by subacute ruminal acidosis and/or laminitis and the resulting pain. However, these explanations are speculative and require systematic disentanglement in future studies. This study provides initial insights into restlessness in bulls and lays the groundwork for future research to identify the causes underlying restlessness and investigate its association with bull welfare.

Accurate real-time monitoring of milk quality during milking is essential for sustainable dairy farming, yet factors such as cow parity may affect the performance of near-infrared (NIR) spectroscopic sensing systems. This study investigated how cow parity (the number of calvings) impacts the reliability and accuracy of NIR spectroscopy in assessing key milk quality indicators: fat content, lactose, and somatic cell count (SCC). Experiments were conducted at Hokkaido University with two cows in their second parity. Milk spectra were recorded across 700-1050 nm using the NIR system, while fat and lactose were measured with a MilkoScan device and SCC with a Fossomatic device. Calibration models were developed using first parity, second parity, and combined datasets through partial least squares regression. Model performance was evaluated via coefficients of determination and standard errors of prediction. Results showed comparable accuracy for milk fat and SCC across parities, whereas lactose measurements were more affected. Cross-validation between first and second parity datasets further confirmed parity-dependent variations, particularly for lactose. These findings suggest that cow parity should be considered when implementing NIR-based milk quality monitoring, supporting more precise, resource-efficient, and sustainable dairy management practices.

AO_SCPLOWBSTRACTC_SCPLOWImproving feed efficiency in pigs is essential for reducing production costs and environmental impacts. This study examines the influence of circadian feeding rhythms and genetic polymorphisms on feed efficiency variability using two pig lines divergently selected for Residual Feed Intake (RFI) over ten generations. Feeding behavior was monitored using automatic concentrate dispensers, recording 6,494,097 visits from 3,824 pigs to analyze meal frequency, duration, and diurnal patterns. LRFI pigs ate less frequently, with larger meals and longer durations, they exhibited two distinct feeding peaks: one around 8:00 AM and a higher one at 5:00 PM and they consumed more feed during the diurnal period and less at night. HRFI pigs showed a smoother, less rhythmic feeding behavior with increased nocturnal intake. The differences between the two RFI lines became more pronounced as the number of generations of selection increased, suggesting a genetic basis. Feeding behaviors, including intake during the two main diurnal peaks, were found to be heritable (heritability estimates: 0.30-0.40) and genetic correlations were observed between feed intake and RFI, especially for intake between the two peaks. Then, we investigated the evolution of allele frequencies of single nucleotide polymorphisms (SNPs) in DNA sequences surrounding 10 core clock genes (ARNTL, CLOCK, CRY1, CRY2, NPAS2, NR1D1, PER1, PER2, PER3, RORA) along generations of selection. SNPs with significant frequency changes were mapped to regulatory regions and transposable elements, especially in HRFI line, suggesting potential functional impacts on circadian regulation. These results underscore the role of feeding behavior and genetic variation in feed efficiency, offering insights for breeding programs aimed at improving metabolic efficiency and sustainability in pig production.

BackgroundBlack soldier fly larvae (Hermetia illucens, BSFL) efficiently bio-convert organic waste into high-value protein, which has significant potential in domesticated animal feed formulations. BSFL growth and bioconversion potential can be enhanced through selective breeding, which requires accurate estimates of genetic parameters and knowledge of genotype-by-diet (G x D) interactions. However, comprehensive knowledge of G x D interactions is limited, and reports of genetic parameters are sparse across genetic strains and production environments globally. ResultsThis study estimated heritabilities, dominance effects and genetic correlations for BSFL growth traits and quantified G x D interactions. Phenotypes of 2,097 fifth-instar larvae reared on three diets were recorded, including larval body weight (LBW), length (LL), width (LW), and surface area (LSA). All larvae were genotyped using a custom 6K Allegro SNP panel. Genetic parameters and G x D interactions were estimated by fitting an additive-dominance model in ASReml-R. Heritabilities for growth traits were low across diets (0.05-0.14), with diet-specific estimates ranging from low to moderate (0.06-0.36). Dominance effects were significant across the traits (0.09-0.19), and genetic correlations were high among growth traits (>0.81), except between LW and LL (0.51). G x D interactions were moderate across diets (-0.04-0.49). ConclusionResults suggest that moderate to high genetic gain is achievable over a long-term breeding programme, given the genetic basis of growth traits and BSFs short generation interval (38-45 days). However, G x D interactions must be considered, either through combined or diet-specific selection strategies, and the significant dominance effects suggest heterosis could accelerate improvement.

Stable isotope analysis provides an important tool for reconstructing past livestock management practices and landscape use. However, isotopic data for sheep from Late Iron Age (AD 375/400-1050) Denmark remain limited. Here, we present bulk bone collagen {delta}{superscript 1}3C, {delta}{superscript 1}N, and {delta}3S isotope analyses of 27 sheep (Ovis aries) from six archaeological sites in Denmark, dated to the Germanic Iron Age (AD 375/400-750) and Viking Age (AD 750-1050). The analysed sheep exhibit a consistent pattern of enriched {delta}13C values relative to previously published isotopic datasets for Scandinavian livestock, while {delta}15N values display substantial inter-individual variability. Sulfur isotope values fall within moderate ranges consistent with mixed terrestrial and coastal environmental influences. The decoupling of {delta}13C enrichment from elevated {delta}15N values suggests that the observed carbon isotope signal does not reflect marine protein consumption but rather the incorporation of a 13C-enriched plant resource into sheep diets. We propose that eelgrass (Zostera sp.), either through direct grazing in coastal environments or supplementary foddering with harvested eelgrass, represents a plausible dietary source to explain this isotopic pattern. The results indicate that Late Iron Age sheep management strategies in Denmark incorporated coastal plant resources within flexible pastoral systems, potentially supporting intensified wool production associated with expanding textile economies. HighlightsO_LIStable isotope values of Late Iron Age sheep show some dietary marine input. C_LIO_LIEnriched {delta}13C values suggest eelgrass as supplementary fodder. C_LIO_LI{delta}34S values indicate adaptive grazing across coastal and inland landscapes. C_LI

Managing post-weaning diarrhoea (PWD) in piglets is difficult due to limits on antibiotics and zinc. Chitosan is emerging as a potential feed additive. We analysed a chito-oligosaccharide hydrochloride (COS-HCl), a low molecular weight (LMW) chitosan, and a medium molecular weight (MMW) chitosan, and assessed their effects on growth, faecal consistency, microbiota, and potential interference with enterotoxigenic Escherichia coli (ETEC). The three chitosans were characterised using {superscript 1}H-NMR, SEC-RI-MS, and SEC-RI-MALLS. COS-HCl had an Mw of 0.824 kDa; LMW and MMW showed Mw ranges of 14.4 kDa (0.3-30 kDa) and 116 kDa (15-600 kDa). Degrees of acetylation were 9.5%, 6.5%, and 15%. Two 42-day field studies evaluated average daily gain (ADG), faecal consistency, and microbiota. In the first trial, COS-HCl at 0.025-0.1% did not significantly affect ADG (-33 to - 12 g/d). In the second, LMW and MMW at 0.01% did not significantly change ADG (-7 and +3 g/d). Faecal consistency, ETEC shedding, and microbiota composition were similar to controls. An enzymatic HPLC-MS method enabled quantification of MMW chitosan in premix. Our results highlight the importance of advanced chitosan characterisation for precision nutrition and suggest that a threshold dosemay be needed to benefit growth and gut health in PWD management. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/714014v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@19c9e23org.highwire.dtl.DTLVardef@152461aorg.highwire.dtl.DTLVardef@7886e0org.highwire.dtl.DTLVardef@df0d9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

Enteric methane emissions from ruminant livestock contribute to global warming, creating an urgent need for effective mitigation strategies that do not compromise animal productivity and welfare. Methanogenic archaea within the rumen microbiome drive enteric methane emissions. However, large-scale rumen-fluid sampling in commercial production systems is impractical, due to its invasive nature and the associated logistical challenges. This study hypothesised that rumination enables the capture of rumen microbial signals within the oral cavity and using oral microbiome profiles to provide a practical, non-invasive alternative method for proxy methane phenotyping in commercial production systems. To test the hypothesis, we estimated the oral microbiability, defined as the proportion of phenotypic variance in methane emissions explained by oral microbiome variation. Samples were collected from 209 animals across two trials in Queensland, Australia. Oral microbiome samples were obtained from all animals, with paired rumen samples in one trial, and methane emissions were measured using either the sulphur hexafluoride (SF6) tracer technique or the GreenFeed system. Microbial features were characterised using taxonomic and functional annotations, and microbiability was estimated using mixed linear models incorporating microbiome-based relationship matrices. Although the small sample size limited strong conclusions, the oral microbiability estimates reported in this study were comparable to those derived from rumen samples. Functional microbial profiles generally explained a greater proportion of methane variation than taxonomic profiles, suggesting that microbial function is more closely linked to methane production than community composition alone. However, these differences were not statistically significant due to large standard errors. These findings suggest that oral microbiome sampling potentially provides a practical, minimally invasive, scalable proxy method for methane emissions of individual cattle in grazing systems, where direct methane gas measurements are labour-intensive and difficult to implement. Integrating oral microbiome profiles in the existing breeding model with the host genetics, weight and environmental factors could provide a promising pathway for enabling selection for low emissions and advancing reduced emissions livestock farming under real-world production conditions. Lay summaryCattle produce methane as part of their normal digestion and this contributes to climate change. Reducing methane emission in grazing livestock systems is therefore important. However, measuring methane from individual grazing animals is difficult, costly, and often impractical under commercial conditions. The rumen microbiome has been used as a proxy for estimating methane emissions, but collecting rumen samples is invasive and impractical for large-scale use. Because rumination transfers material from the rumen to the mouth, we investigated whether microbes found in cattle mouths could also be used to estimate how much methane an individual animal produced. We suggest that mouth-swab sampling method can be an alternative to rumen fluid sampling because it was less invasive, relatively quick and practically applicable in commercial conditions. Importantly, the microbiome explained a meaningful proportion of the between-animal variation for methane emission. This suggests that collection of mouth swabs is a potentially scalable alternative proxy method to identify cattle that naturally produce less methane. Overall, our findings support the potential use of oral ruminant microbial information to improve breeding and management strategies aimed at reducing methane emissions while maintaining productive livestock systems. Teaser TextThis study demonstrates that collecting oral swabs from the mouths of grazing beef cattle could provide a scalable method to estimate individual methane emissions in commercial production systems, offering a practical alternative to invasive rumen sampling and complex gas measurement systems. These findings support the development of scalable breeding and management strategies for methane mitigation in large-scale livestock production systems.

Transcriptomic analyses are widely used to elucidate the molecular mechanisms driving gametogenesis and reproduction in fish, yet their accuracy depends heavily on appropriate normalization of gene expression data. Conventional approaches that rely on single or multiple reference genes are problematic during teleost oogenesis, as profound structural and physiological remodeling of the ovary challenges the assumption that commonly used reference transcripts remain stable. In this study, we assessed by qPCR the transcriptional variability of four widely used reference genes (actb, ef-1, gapdh, and 18S rRNA) throughout the oogenic cycle of the thicklip grey mullet (Chelon labrosus), using geNorm and NormFinder analyses, and we additionally evaluated total cDNA concentration as an alternative normalization factor. To examine the performance and interpretive consequences of each normalization strategy, we compared expression patterns of key steroidogenic genes (star, cyp19a1a, and cyp11b) normalized by individual reference genes, combinations of reference genes, or total cDNA concentration. All evaluated reference genes displayed notable transcriptional variability across oogenesis, confirming their limited suitability as sole internal controls. In contrast, normalization approaches integrating multiple reference genes and/or total cDNA concentration consistently provided greater stability and more reliable biological interpretation. These results support a refined and more robust normalization framework for transcriptional analyses in fish ovaries, particularly during stages of extensive tissue remodeling. Our findings demonstrate cDNA-based normalization is straightforward, rapid, and easy to implement across laboratories, providing a practical alternative for achieving accurate, reproducible transcript quantification in fish ovary studies.

BackgroundGene expression levels are affected by genetics and environmental effects. However, quantification of the influence of genetics and environmental effects on gene expression remains limited, especially in farm animals. Here, the relative influence of genetic and heat-related environmental variations on gene expression levels was investigated in pigs, using a backcross herd of diverse heat adaptation levels. Backcross animals were raised in either a tropical or temperate environment. Animals raised in temperate environment were subjected to an experimental heat stress at the end of their growth. ResultsWe identified 1,967 differentially expressed genes (DEGs) between pigs raised in the tropical (n = 181) and temperate (n = 180) facilities, and 472 DEGs throughout a 3 weeks experimental heat stress. Transcriptome-wide association (TWAS) study identified 139 associations between gene expression levels and thermoregulation/production traits. We detected 6,014 expression quantitative trait loci (eQTLs) associated with the expression level of 3,297 genes. Genetic variance was estimated to explain 36.3% of gene expression variance on average, and was the main source of variance for 27.7% of transcripts. Most eQTLs found are located in proximal regions (cis-eQTLs) and few within distal regions (trans-eQTLs) to their assigned genes. A trans-eQTL hotspot highlighted a hematopoietic mechanism driven by GPATCH8. An integration of GWAS and TWAS pointed to TMCO1 and ZNF184 as candidate genes for backfat thickness. ConclusionsThis study provides a better understanding of the impact of climate, heat stress and genetic influences on the pig whole blood transcriptome.

Mycoplasma bovis was first detected in cattle in New Zealand in 2017, prompting an eradication programme that incorporated extensive surveillance and a test-and-cull policy. Genome sequence data and phylodynamic models were used to inform decision making throughout the eradication programme. Isolates from 697 cattle on 126 farms were collected and sequenced between July 2017 and December 2023. Phylodynamic models were used to estimate the time of most recent common ancestor, the effective reproduction number (Reff) and effective population size, and long-range and local between-farm transmission dynamics. The analysis revealed the dramatic impact of movement restrictions and culling up to early 2020, with a sharp reduction in the Reff to less than 1 in 2018/9 and the extinction of two of three major lineages in 2020. This was followed by three-years of residual infection in farms in the South Island, associated with persistent infection of a large feedlot farm and nearby farms. The comprehensive dataset of genomic and epidemiological data provided a unique opportunity to study the dynamics of a country-wide outbreak of a single-host pathogen from first detection to potential eradication, underlining the utility of integrated genomic surveillance during an outbreak response. Author summaryThe economically important cattle pathogen, Mycoplasma bovis, was first detected in New Zealand in 2017. This led to a large-scale, successful control programme aimed at eradication of the pathogen. The decision to undertake an eradication programme was informed by initial analyses of whole genome sequences from isolates collected as part of the surveillance programme. The analysis showed that the bacteria had entered New Zealand relatively recently and was unlikely to be widespread. Over the subsequent years, genome sequencing and modelling of transmission dynamics informed important policy decisions made by the New Zealand Government and the cattle industry, and helped to monitor progress of the eradication programme. The impact of the detection, movement control and culling programme was profound, with sharp reductions in transmission between 2018 and 2020. This was followed by a long tail of localised infection in the South Island, involving transmission from a large feedlot farm. Provisional eradication was achieved after depopulation of this feedlot. This analysis highlights the role of genomic surveillance and modelling to inform decision making during an infectious disease outbreak.

BackgroudWuzhishan (WZS) pigs are native to Hainan Province of China, and serve as both important agricultural resources and biomedical models. Although the published WZS pig genome (T2T-pig1.0) even achieving telomere-to telomere (T2T) completeness, substantial genetic diversity still exists within the same pig breed, another WZS pig genome named WZS-T2T was assembled in this study. ResultsMultiple sequencing data were used to assemble genome, and finally yielded a [~]2.68 Gb telomere-to-telomere genome, with N50 length [~]142.87 Mb, and annotated protein coding genes of 23,100. Compared to T2T-pig1.0, QV and BUSCO value was higher, and the Y chromosome (ChrY) length was longer in WZS-T2T than that of T2T-pig1.0. ChrY of two WZS pigs shared 11 genes, including sex differentiation-related genes of SHOX, PRKX, and DDX3X, and SRY; however, energy metabolism gene SLC25A4 and the macrophage-related receptor gene CSF2RA of ChrY were specific to WZS-T2T. An inversion SV on chromosome 10 with length [~]33.86 Mb was identified between two WZS pigs, and three proofs were proposed for proving the accuracy sequence orientation of WZS-T2T.The genetic diversity was consistent with LD decay speed in population different analysis. WZS pigs exhibited higher genetic diversity than other four pig populations (Tunchang pigs, Yuxi black pigs, Large White pig, and Duroc pigs) examined in this study, and presented slower LD decay compared to other four breeds. ConclusionsTherefore, WZS-T2T provided a higher-quality assembly, and potential advantages of both agricultural production and biomedical targets for WZS pigs.

In recent years, genetic studies have made significant progress in identifying single-nucleotide polymorphisms (SNPs) associated with cattle health and production traits. However, it is still challenging to identify and validate more complicated forms of variation, such as copy number variation (CNV) and other types of structural variation (SV). In this study, SV regions were identified using 37 New Zealand dairy cattle with linked-read sequence data. A transmission-based framework was used to validate these variants at the population scale. 62,438 putative autosomal SV regions were identified with the LongRanger pipeline following the 10x Genomics recommendations. Copy number states for these regions were subsequently estimated via a read-depth based genotyping method using CNVpytor in a population-representative cohort of 2306 animals using Illumina short-read sequencing technology. Mendelian inheritance of copy number states was assessed using linear mixed models incorporating pedigree information, and transmission levels were used to quantify the biological validity of each CNV region. Transmission levels ranged widely, with a mean of 0.5162 across all regions, where higher transmission levels were proportionally enriched for larger SVs. A total of 7218 CNV regions exhibited high transmission levels (>0.9), indicating strong evidence of inheritance. Among these, 7136 overlapped CNV regions reported in one or more public datasets, while 82 high-confidence regions represent previously unreported variants. High-transmission CNV regions tended to show clear, discrete inheritance patterns in trio families, providing the biological evidence that these CNVs are inherited within the population. Together, these results demonstrate that integrating linked-read sequencing with population-scale transmission-based validation provides a robust framework for identifying high-confidence CNV regions. This catalogue of validated CNV regions represents an important resource for downstream functional analyses and the incorporation of structural variation into genomic selection and breeding programs.

BackgroundAlthough the biological mechanism for heterosis has been debated for a long time, heterosis is widely utilized to increase the global productivity of crops and livestock. Recently, the mechanism has been well characterized in crops and livestock with a male-heterogametic XY system due to genomic assembly advancements, especially the availability of haploid genomes. However, the biological mechanism for heterosis remains unclear in poultry possessing the female-heterogametic ZW system. ResultsHere, we assembled chromosome-level diploid and haploid genomes of the Muscovy duck. We developed an efficient and cost-effective method to assemble 12 variation graph-haploid Muscovy duck genomes from three full-sibling pairs with high quality using short-read Illumina sequences. We further characterized genetic, expression and regulatory patterns of parental alleles at multiple scales. We found that maternal haploid genomes generally had more open chromatin organization and higher accessibility, and higher levels of gene expression, while showing similar DNA methylation levels when compared to paternal haploid genomes. In contrast, the female paternal Z chromosome showed the most, and the male paternal Z chromosome presented more, relaxed chromatin organization and chromatin accessibility, and gene expression compared to the male maternal Z chromosome. Thus, the ZW system largely relies on compensation and balance to regulate gene expression on the sex Z chromosome. Moreover, we identified non-Mendelian regions covering 0.26% of the genome ([~]3.18 Mb). These regions contained lower gene density, GC content, and repeat sequence frequency, but were enriched for DNA motifs bound by transcription factors, likely leading to a compacted chromatin structure and lower chromatin accessibility. ConclusionsOur work here provides a comprehensive profile of parental alleles genetic, expression and regulatory patterns in the female-heterogametic ZW system, and might be useful for the utilization of heterosis in poultry.

Cortisol is a major endogenous glucocorticoid that regulates numerous physiological processes. In plasma, cortisol and its inactive metabolite cortisone bind to corticosteroid-binding globulin (CBG) and albumin, leaving only the unbound fraction available for receptor activation and metabolism. Changes in ligand or protein concentrations alter unbound fractions. Existing binding equations are difficult to extend to multi-ligand, multi-protein systems and do not readily capture competitive endogenous binding interactions. The goal of this study was to develop a plasma protein binding model that quantitatively describes binding species and predicts unbound concentrations across physiological states. Total and unbound cortisol and cortisone, CBG and albumin were measured in plasma from healthy premenopausal women (n=13) at baseline and after 7 days of 30 mg hydrocortisone treatment. Reversible 1:1 binding models were implemented in COPASI and MATLAB/Simulink, and dissociation constants (Kd) were estimated by fitting binding models to observed unbound concentrations. A model describing simultaneous binding of cortisol and cortisone to CBG and albumin yielded in vivo Kd values for cortisol:CBG, cortisone:CBG, cortisol:albumin, and cortisone:albumin of 0.0130 {micro}M, 0.169 {micro}M, 172 {micro}M, and 519 {micro}M, respectively. Model predictions agreed with observed unbound cortisol and cortisone, and bootstrap resampling confirmed stable Kd estimates. This work provides a quantitative framework for predicting unbound cortisol and cortisone across physiological and disease states by accounting for both changes in ligand and protein concentrations. This enables extrapolation without reparameterization and supports exploration of conditions such as pregnancy, adrenal insufficiency, and liver disease, informing interpretation of altered cortisol concentrations in these populations. Significance statementThis work establishes a framework to predict in vivo cortisol and cortisone binding. The developed model was applied to predict unbound cortisol and cortisone concentrations in physiological and pathophysiological states and can be integrated into pharmacokinetic models. Our analysis demonstrates that cortisol and cortisone binding affinities estimated in the native plasma environment differ from those measured using purified proteins. These differences have important implications for predicting and analyzing unbound cortisol concentrations. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/718600v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1d9254corg.highwire.dtl.DTLVardef@11fadd5org.highwire.dtl.DTLVardef@cdbc26org.highwire.dtl.DTLVardef@fba0c0_HPS_FORMAT_FIGEXP M_FIG C_FIG Created in BioRender. Authement, A. (2026) https://BioRender.com/zl1bg0k

The human fallopian tube plays a critical role in reproductive biology, yet the structural organization and immune repertoire of this tissue remain incompletely characterized. Here, we performed an in-depth analysis of human fallopian tube tissue from women of reproductive age across three distinct anatomical regions (isthmus, ampulla, and fimbriae) across the menstrual cycle. Using antibody-based imaging for EPCAM, CD8A, and CD20 together with automated image analysis, the epithelial thickness and spatial distribution of T and B lymphocytes was assessed. No significant differences in epithelial thickness were observed between proliferative and secretory phases within any tubal region. In contrast, significant regional differences were identified, with the epithelium being thickest in the isthmus and thinnest in the ampulla. Both CD8A+ T lymphocytes and CD20+ B lymphocytes were detected throughout the fallopian tube, and a strong correlation between T and B lymphocyte abundance was observed across patients. Spatial analysis further revealed that both lymphocyte populations were preferentially localized within the mucosal compartment adjacent to the lumen. Notably, intraepithelial B lymphocytes were identified throughout the fallopian tube. Together, these findings provide new insight into epithelial organization and immune cell distribution in the human fallopian tube, highlighting the complexity of the tubal immune microenvironment and its potential relevance for reproductive biology.