Association between maternal growth in the pre-conception and early gestational period of nulliparous dairy heifers with anti-Müllerian hormone in their female offspring.

Anti-Müllerian hormone (AMH) is secreted by granulosa cells of healthy, growing follicles and is positively correlated with the ovarian reserve. Maternal and environmental factors, such as nutrition, disease, parity and endocrine disruptors, are thought to have a profound impact on ovarian reserve development during early foetal life. For genetic progress, it can be advantageous to breed dairy replacements from heifers to expedite the generation interval; however, there is some evidence that nulliparous animals produce female offspring with smaller ovarian reserves compared with multiparous animals. The objective of this prospective, observational study was to determine whether maternal growth in the pre-conception and early gestational period of nulliparous dairy heifers is associated with pre-weaning AMH concentrations in their female offspring. Our hypothesis was that excessive growth in this period would negatively impact AMH concentrations. Seasonal, pasture-based dairy heifer calves (n = 156) born from nulliparous dams, from six Irish farms, were blood sampled at an average of 60 days of age in spring 2022 and tested for AMH. Mixed-effects linear regression models were constructed with Box-Cox transformed AMH concentration as the dependent variable. The independent variables tested included maternal average daily gain (ADG) from pre-breeding examination (PBE) to pregnancy diagnosis (PD) between 30 and 60 days in calf (DIC), ADG from PBE to PD over 60 DIC and ADG between the two PDs. Calf breed and age at sampling were forced into the models, and the farm was treated as a random effect in all models. We found that as ADG increased from the pre-breeding period to their first PD visit, the AMH concentration in their offspring reduced. However, ADG explained only a small amount of the variation in AMH concentrations (marginal R2 = 0.041). In conclusion, the results of our study suggest that excessive growth prior to conception and in early gestation of nulliparous heifers could impact the ovarian reserve of their female offspring, and may imply that farmers should avoid excessive growth in the immediate pre-breeding and early gestational periods.

An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants.

We report the generation of an organism-wide catalog of 976,813 cis-acting regulatory elements for the bovine detected by the assay for transposase accessible chromatin using sequencing (ATAC-seq). We regroup these regulatory elements in 16 components by nonnegative matrix factorization. Correlation between the genome-wide density of peaks and transcription start sites, correlation between peak accessibility and expression of neighboring genes, and enrichment in transcription factor binding motifs support their regulatory potential. Using a previously established catalog of 12,736,643 variants, we show that the proportion of single-nucleotide polymorphisms mapping to ATAC-seq peaks is higher than expected and that this is owing to an approximately 1.3-fold higher mutation rate within peaks. Their site frequency spectrum indicates that variants in ATAC-seq peaks are subject to purifying selection. We generate eQTL data sets for liver and blood and show that variants that drive eQTL fall into liver- and blood-specific ATAC-seq peaks more often than expected by chance. We combine ATAC-seq and eQTL data to estimate that the proportion of regulatory variants mapping to ATAC-seq peaks is approximately one in three and that the proportion of variants mapping to ATAC-seq peaks that are regulatory is approximately one in 25. We discuss the implication of these findings on the utility of ATAC-seq information to improve the accuracy of genomic selection.

Hepatic Global Transcriptomic Profiles of Holstein Cows According to Parity Reveal Age-Related Changes in Early Lactation.

Cows can live for over 20 years, but their productive lifespan averages only around 3 years after first calving. Liver dysfunction can reduce lifespan by increasing the risk of metabolic and infectious disease. This study investigated the changes in hepatic global transcriptomic profiles in early lactation Holstein cows in different lactations. Cows from five herds were grouped as primiparous (lactation number 1, PP, 534.7 ± 6.9 kg, n = 41), or multiparous with lactation numbers 2-3 (MP2-3, 634.5 ± 7.5 kg, n = 87) or 4-7 (MP4-7, 686.6 ± 11.4 kg, n = 40). Liver biopsies were collected at around 14 days after calving for RNA sequencing. Blood metabolites and milk yields were measured, and energy balance was calculated. There were extensive differences in hepatic gene expression between MP and PP cows, with 568 differentially expressed genes (DEGs) between MP2-3 and PP cows, and 719 DEGs between MP4-7 and PP cows, with downregulated DEGs predominating in MP cows. The differences between the two age groups of MP cows were moderate (82 DEGs). The gene expression differences suggested that MP cows had reduced immune functions compared with the PP cows. MP cows had increased gluconeogenesis but also evidence of impaired liver functionality. The MP cows had dysregulated protein synthesis and glycerophospholipid metabolism, and impaired genome and RNA stability and nutrient transport (22 differentially expressed solute carrier transporters). The genes associated with cell cycle arrest, apoptosis, and the production of antimicrobial peptides were upregulated. More surprisingly, evidence of hepatic inflammation leading to fibrosis was present in the primiparous cows as they started their first lactation. This study has therefore shown that the ageing process in the livers of dairy cows is accelerated by successive lactations and increasing milk yields. This was associated with evidence of metabolic and immune disorders together with hepatic dysfunction. These problems are likely to increase involuntary culling, thus reducing the average longevity in dairy herds.

Transfer of bovine embryos into a uterus primed with high progesterone concentrations positively impacts fetal development at 42 days of gestation.

Elevated circulating progesterone (P4) concentrations in the first week after conception have been associated with accelerated post-hatching conceptus elongation. However, the consequences, if any, on the development of the fetus are unknown. The objective of this study was to determine the relationship between early circulating P4 and fetal and placental morphometric characteristics at 42 days of gestation. A previously validated model of asynchronous embryo transfer (ET), known to alter uterine exposure to P4, was used in 107 heifers divided in two replicates (replicate 1: n = 51, replicate 2: n = 56). Heifers were randomly assigned to one of the two following groups: those receiving a Day 7 embryo on Day 7 of the cycle (synchronous; ET_D7, n = 49) and those transferred a Day 7 embryo on Day 9 of the cycle (asynchronous; ET_D9, n = 58). The synchronization protocol was started two days earlier for heifers in the ET_D9 group such that ET was done on the same day for both groups. P4 concentrations were determined from Day 3 after estrus to the day of ET. Pregnant heifers were slaughtered at Day 42 of gestation for fetal and placental morphometric measurements. The effects of the group, replicate, fetal sex, and interactions between these variables on fetal and placental characteristics were determined by ANOVA, while Pearson correlation was employed to assess the linear relationship between P4 concentrations two days before and on the day of ET on the fetal parameters. The uteri of heifers in the ET_D9 group were exposed to higher concentrations (P < 0.0001) of P4 from four days before ET, than heifers in the ET_D7 group. Both group and fetal sex variables impacted on fetal crown-rump length (CRL) (group: P < 0.0001, sex: P = 0.001) and fetal weight (group: P = 0.006, sex: P = 0.003). Fetal sex influenced the amniotic sac area (P = 0.003) and amniotic sac weight (P = 0.004); while the group affected the number of cotyledons (P = 0.0009), and the fetal heart weight (P = 0.018). All these parameters were larger in the ET_D9 group compared with ET_D7, and in males compared with females. There was a positive correlation between P4 concentrations two days before ET and fetal weight and CRL, for each sex or considering all fetuses (R2 ∼0.4, p < 0.05). In conclusion, bovine embryos transferred into a uterus primed with higher P4 concentrations underwent enhanced development reflected in higher weight and size at the beginning of the fetal period.

Proportion of Concentrate in the Diet of Early Lactation Dairy Cows Has Contrasting Effects on Circulating Leukocyte Global Transcriptomic Profiles, Health and Fertility According to Parity.

The functionality of circulating leukocytes in dairy cows is suppressed after calving, with negative energy balance as a risk factor. Leukocyte transcriptomic profiles were compared separately in 44 multiparous (MP) and 18 primiparous (PP) Holstein-Friesian cows receiving diets differing in concentrate proportion to test whether immune dysfunction could be mitigated by appropriate nutrition. After calving, cows were offered either (1) low concentrate (LC); (2) medium concentrate (MC) or (3) high concentrate (HC) diets with proportions of concentrate to grass silage of 30%:70%, 50%:50% and 70%:30%, respectively. Cow phenotype data collected included circulating metabolites, milk yield and health and fertility records. RNA sequencing of circulating leukocytes at 14 days in milk was performed. The HC diet improved energy balance in both age groups. There were more differentially expressed genes in PP than MP cows (460 vs. 173, HC vs. LC comparison) with few overlaps. The MP cows on the LC diet showed upregulation of the complement and coagulation cascade and innate immune defence mechanisms against pathogens and had a trend of more cases of mastitis and poorer fertility. In contrast, the PP cows on the HC diet showed greater immune responses based on both gene expression and phenotypic data and longer interval of calving to conception. The leukocytes of MP and PP cows therefore responded differentially to the diets between age, nutrient supply and immunity affecting their health and subsequent fertility.

Multiple Country Approach to Improve the Test-Day Prediction of Dairy Cows' Dry Matter Intake.

We predicted dry matter intake of dairy cows using parity, week of lactation, milk yield, milk mid-infrared (MIR) spectrum, and MIR-based predictions of bodyweight, fat, protein, lactose, and fatty acids content in milk. The dataset comprised 10,711 samples of 534 dairy cows with a geographical diversity (Australia, Canada, Denmark, and Ireland). We set up partial least square (PLS) regressions with different constructs and a one-hidden-layer artificial neural network (ANN) using the highest contribution variables. In the ANN, we replaced the spectra with their projections to the 25 first PLS factors explaining 99% of the spectral variability to reduce the model complexity. Cow-independent 10 × 10-fold cross-validation (CV) achieved the best performance with root mean square errors (RMSECV) of 3.27 ± 0.08 kg for the PLS regression and 3.25 ± 0.13 kg for ANN. Although the available data were significantly different, we also performed a country-independent validation (CIV) to measure the models' performance fairly. We found RMSECIV varying from 3.73 to 6.03 kg for PLS and 3.69 to 5.08 kg for ANN. Ultimately, based on the country-independent validation, we discussed the developed models' performance with those achieved by the National Research Council's equation.

Effect of plane of nutrition during the first 12 weeks of life on growth, metabolic and reproductive hormone concentrations, and testicular relative mRNA abundance in preweaned Holstein Friesian bull calves.

The objective of this study was to examine the effect of nutrition during the first 12 wk of life on aspects of the physiological and transcriptional regulation of testicular and overall sexual development in the bull calf. Holstein Friesian bull calves with a mean (SD) age and bodyweight of 17.5 (2.85) d and 48.8 (5.30) kg, respectively, were assigned to either a high (HI; n = 15) or moderate (MOD; n = 15) plane of nutrition and were individually fed milk replacer and concentrate to achieve overall target growth rates of at least 1.0 and 0.5 kg/d, respectively. Throughout the trial, animal growth performance, feed intake, and systemic concentrations of metabolites, metabolic hormones, and reproductive hormones were assessed. Additionally, pulsatility of reproductive hormones (luteinizing hormone, follicle-stimulating hormone, and testosterone) was recorded at 15-min intervals during a 10-h period at 10 wk of age. At 87 ± 2.14 d of age, all calves were euthanized, testes were weighed, and testicular tissue was harvested. Differential expression of messenger ribonucleic acid (mRNA) candidate genes involved in testicular development was examined using quantitative polymerase chain reaction assays. All data were analyzed using the MIXED procedure in Statistical Analysis Software using terms for treatment as well as time for repeated measures. Blood metabolites and metabolic hormones generally reflected the improved metabolic status of the calves on the HI plane of nutrition though the concentrations of reproductive hormones were not affected by diet. Calves on the HI diet had greater mean (SED) slaughter weight (112.4 vs. 87.70 [2.98] kg; P < 0.0001) and testicular tissue weight (29.2 vs. 20.1 [2.21] g; P = 0.0003) than those on the MOD diet. Relative mRNA abundance data indicated advanced testicular development through upregulation of genes involved in cellular metabolism (SIRT1; P = 0.0282), cholesterol biosynthesis (EBP; P = 0.007), testicular function (INSL3; P = 0.0077), and Sertoli cell development (CLDN11; P = 0.0054) in HI compared with MOD calves. In conclusion, results demonstrate that offering dairy-bred male calves a high plane of nutrition during the first 3 mo of life not only improves growth performance and metabolic status but also advances testicular development consistent with more precocious sexual maturation.

Global transcriptomic profiles of circulating leucocytes in early lactation cows with clinical or subclinical mastitis.

Bovine mastitis, an inflammatory disease of the mammary gland, is classified as subclinical or clinical. Circulating neutrophils are recruited to the udder to combat infection. We compared the transcriptomic profiles in circulating leukocytes between healthy cows and those with naturally occurring subclinical or clinical mastitis. Holstein Friesian dairy cows from six farms in EU countries were recruited. Based on milk somatic cell count and clinical records, cows were classified as healthy (n = 147), subclinically (n = 45) or clinically mastitic (n = 22). Circulating leukocyte RNA was sequenced with Illumina NextSeq single end reads (30 M). Differentially expressed genes (DEGs) between the groups were identified using CLC Genomics Workbench V21, followed by GO enrichment analysis. Both subclinical and clinical mastitis caused significant changes in the leukocyte transcriptome, with more intensive changes attributed to clinical mastitis. We detected 769 DEGs between clinical and healthy groups, 258 DEGs between subclinical and healthy groups and 193 DEGs between clinical and subclinical groups. Most DEGs were associated with cell killing and immune processes. Many upregulated DEGs in clinical mastitis encoded antimicrobial peptides (AZU1, BCL3, CAMP, CATHL1, CATHL2, CATHL4,CATHL5, CATHL6, CCL1, CXCL2, CXCL13, DEFB1, DEFB10, DEFB4A, DEFB7, LCN2, PGLYRP1, PRTN3, PTX3, S100A8, S100A9, S100A12, SLC11A1, TF and LTF) which were not upregulated in subclinical mastitis. The use of transcriptomic profiles has identified a much greater up-regulation of genes encoding antimicrobial peptides in circulating leukocytes of cows with naturally occurring clinical compared with subclinical mastitis. These could play a key role in combatting disease organisms.

Validation of Dairy Cow Bodyweight Prediction Using Traits Easily Recorded by Dairy Herd Improvement Organizations and Its Potential Improvement Using Feature Selection Algorithms.

Knowing the body weight (BW) of a cow at a specific moment or measuring its changes through time is of interest for management purposes. The current work aimed to validate the feasibility of predicting BW using the day in milk, parity, milk yield, and milk mid-infrared (MIR) spectrum from a multiple-country dataset and reduce the number of predictors to limit the risk of over-fitting and potentially improve its accuracy. The BW modeling procedure involved feature selections and herd-independent validation in identifying the most interesting subsets of predictors and then external validation of the models. From 1849 records collected in 9 herds from 360 Holstein cows, the best performing models achieved a root mean square error (RMSE) for the herd-independent validation between 52 ± 2.34 kg to 56 ± 3.16 kg, including from 5 to 62 predictors. Among these models, three performed remarkably well in external validation using an independent dataset (N = 4067), resulting in RMSE ranging from 52 to 56 kg. The results suggest that multiple optimal BW predictive models coexist due to the high correlations between adjacent spectral points.

Cow-level prevalence and risk factors for estrus detection inaccuracy in seasonal calving pasture-based dairy cows.

High submission rates and pregnancies per AI are essential to ensure compact calving is achieved in seasonal calving pasture-based systems. Estrus detection inaccuracy (EDI) is one area that negatively impacts pregnancies per AI as it increases the inseminations per pregnancy with little probability of conception, while also having the potential to disrupt established pregnancies. The aims of this cross-sectional study were to provide cow-level estimates of EDI prevalence and determine cow-level risk factors for EDI in seasonal calving pasture-based systems. A total of 1071 milk samples were obtained from 984 cows on 19 farms in spring 2018 and analyzed by radioimmunoassay to determine the progesterone concentration at the time of artificial insemination. Based on a validation study on a subset of cows, an inaccurate estrus detection was described as a concentration of progesterone in foremilk of ≥3 ng/ml which corresponded to a composite milk progesterone value of 5 ng/ml. To investigate selected risk factors for EDI, we conducted statistical analyses using two multivariate logistic regression models, stratifying by insemination number (first versus repeat). The overall prevalence of EDI was 4.7% with a prevalence of 3.3% of EDI at first insemination and 14.1% at repeat insemination. Absence of a mounting abrasion (Adjusted odds ratio (AOR) = 3.0) was a significant risk factor for EDI on first insemination while abnormal preceding repeat interval (AOR = 9.5), the absence of an observed standing estrus (AOR = 12.5) and the absence of a mounting abrasion (AOR = 4.1) were significant risk factors for EDI on repeat insemination. The results indicate that cow-level estimated prevalence of EDI in a selection of pasture-based herds was low at first insemination but higher for repeat insemination. It confirms that certain cow-level risk factors existed for EDI, thus providing preliminary evidence for potential future investigation into the targeted use of on-farm progesterone assays in pasture-based herds.

Effect of calfhood nutrition on metabolic hormones, gonadotropins, and estradiol concentrations and on reproductive organ development in beef heifer calves.

This study examined the effect of plane of nutrition on the endocrinological regulation of the hypothalamic-pituitary-ovarian (HPO) axis in beef heifer calves during a critical sexual developmental window early in calf hood. Forty Holstein-Friesian × Angus heifers (mean age 19 d, SEM = 0.63) were assigned to a high (HI; ADG 1.2 kg) or moderate (MOD; ADG 0.50 kg) nutritional level from 3 to 21 wk of life. Intake was recorded using an electronic calf feeding system, BW was recorded weekly, and blood samples were collected on the week of age 5, 10, 15, and 20 for metabolite, reproductive, and metabolic hormone determination. At 19 wk of age, on sequential days, an 8-h window bleed was carried out for luteinizing hormone (LH), follicle-stimulating hormone (FSH), and estradiol analysis. To characterize anterior pituitary gland function, an intravenous GnRH challenge was conducted (19 wk of age). Blood was collected via a jugular catheter every 15 min for 135 min for the analysis of LH, FSH, and estradiol. Calves were subsequently euthanized at 21 wk of age; the anterior pituitary, metabolic organs, and reproductive tract were weighed, and ovarian surface follicular numbers and oocytes recovered were recorded. Mean ADG was 1.18 and 0.50 kg for HI and MOD, respectively, resulting in a 76.6-kg difference in BW (P < 0.001). Blood insulin, glucose, and IGF-1 concentrations were greater (P < 0.001) for HI compared with MOD. There was a diet × time interaction for leptin (P < 0.01); concentrations were greater in HI compared with MOD at 20 wk of age with no difference between treatments before this. Dietary treatment did not alter the concentrations of adiponectin or anti-mullerian hormone. There was a diet × time interaction for FSH, whereby MOD had greater concentrations than HI at 10, 15, and 20, but not at 5 wk of age. Over the duration of an 8-h window bleed (19 wk of age), serum concentrations of LH, LH pulse frequency, and LH pulse amplitude were unaffected by treatment, whereas FSH (0.23 vs. 0.43 ng/mL) and estradiol (0.53 vs. 0.38 ng/mL) concentrations were less than and greater, respectively, for HI than MOD (P < 0.05). Likewise, following a GnRH challenge, the area under the curve analysis revealed greater (P < 0.01) estradiol and lesser (P < 0.01) FSH concentrations in calves on the HI relative to MOD diet, whereas concentrations of LH were unaffected (P = 0.26) between treatments. Ovarian surface follicle numbers were greater (P < 0.05) in HI compared with MOD. Total reproductive tract, uterus, and ovarian tissue expressed relative to BW were greater (P < 0.05) for HI compared with MOD. In conclusion, enhanced nutrition in early calfhood advances the ontogeny development of the HPO axis.

Relationship between plasma concentrations of IGF-I and clinical endometritis, and response to progesterone synchrony in dairy cows during early lactation.

The first aim of this study was to evaluate the relationship between the concentrations of plasma insulin-like growth factor-I (IGF-I) in the transition period and the incidence of clinical endometritis postpartum. The second aim was to evaluate the relationship between the concentration of plasma IGF-I in the transition period and the estrous synchrony response and pregnancy rate to a controlled internal drug release (CIDR) protocol. A total of 402 dairy cows, 250 multiparous and 152 primiparous, were enrolled. A blood sample was taken from all cows 2 and 1 wk precalving and wk 1, 3, 4, and 5 postcalving for subsequent analysis of IGF-I. Vaginal discharge score as a measurement of uterine health was recorded in wk 3, 4, and 5 postcalving. Estrous cycles of all cows were synchronized on ≥37 d in milk (mean = 59; range 37-93) using an 8-d CIDR protocol. All cows were scanned at 32 to 35 d after insemination to confirm pregnancy. Data were analyzed using Proc Mixed and Proc Logistic models in SAS (version 9.3; SAS Institute Inc., Cary, NC). Plasma IGF-I concentrations were significantly greater in the primiparous cows than in the multiparous cows, both before and after calving, and were therefore analyzed separately. In multiparous cows plasma IGF-I concentrations postcalving were significantly lower among cows with uterine infection than in those without infection, and multiparous cows with a plasma IGF-I concentration less than 40 ng/mL 1 wk after calving were 3 times more likely to suffer from a uterine infection 4 to 5 weeks postcalving (odds ratio 2.8; 95% confidence interval 1.0-7.6). Plasma IGF-I concentrations were significantly greater after calving in the 121 primiparous cows that exhibited estrus post-CIDR protocol (mean 125 ng/mL) than in the 25 primiparous cows that did not respond (mean 95 ng/mL). Multiparous cows with greater plasma IGF-I concentrations postcalving had a significantly greater chance of conceiving (mean plasma IGF-I concentration of conceiving cows = 86 ng/mL; nonconceiving = 70 ng/mL). These results show an association between greater concentrations of plasma IGF-I postcalving and response to CIDR protocol in primiparous animals (mean plasma IGF-I concentration of responders = 116 ng/mL; nonresponders = 95 ng/mL). In contrast no association was detected between concentrations of plasma IGF-I in relation to the response to the CIDR protocol in multiparous cows. In conclusion, changes in circulating concentrations of plasma IGF-I early postpartum may help predict reproductive status of dairy cows.

Predicting physiological imbalance in Holstein dairy cows by three different sets of milk biomarkers.

Blood biomarkers may be used to detect physiological imbalance and potential disease. However, blood sampling is difficult and expensive, and not applicable in commercial settings. Instead, individual milk samples are readily available at low cost, can be sampled easily and analysed instantly. The present observational study sampled blood and milk from 234 Holstein dairy cows from experimental herds in six European countries. The objective was to compare the use of three different sets of milk biomarkers for identification of cows in physiological imbalance and thus at risk of developing metabolic or infectious diseases. Random forests was used to predict body energy balance (EBAL), index for physiological imbalance (PI-index) and three clusters differentiating the metabolic status of cows created on basis of concentrations of plasma glucose, ß-hydroxybutyrate (BHB), non-esterified fatty acids (NEFA) and serum IGF-1. These three metabolic clusters were interpreted as cows in balance, physiological imbalance and "intermediate cows" with physiological status in between. The three sets of milk biomarkers used for prediction were: milk Fourier transform mid-IR (FT-MIR) spectra, 19 immunoglobulin G (IgG) N-glycans and 8 milk metabolites and enzymes (MME). Blood biomarkers were sampled twice; around 14 days after calving (days in milk (DIM)) and around 35 DIM. MME and FT-MIR were sampled twice weekly 1-50 DIM whereas IgG N-glycan were measured only four times. Performances of EBAL and PI-index predictions were measured by coefficient of determination (R2cv) and root mean squared error (RMSEcv) from leave-one-cow-out cross-validation (cv). For metabolic clusters, performance was measured by sensitivity, specificity and global accuracy from this cross-validation. Best prediction of PI-index was obtained by MME (R2cv = 0.40 (95 % CI: 0.29-0.50) at 14 DIM and 0.35 (0.23-0.44) at 35 DIM) while FT-MIR showed a better performance than MME for prediction of EBAL (R2cv = 0.28 (0.24-0.33) vs 0.21 (0.18-0.25)). Global accuracies of predicting metabolic clusters from MME and FT-MIR were at the same level ranging from 0.54 (95 % CI: 0.39-0.68) to 0.65 (0.55-0.75) for MME and 0.51 (0.37-0.65) to 0.68 (0.53-0.81) for FT-MIR. R2cv and accuracies were lower for IgG N-glycans. In conclusion, neither EBAL nor PI-index were sufficiently well predicted to be used as a management tool for identification of risk cows. MME and FT-MIR may be used to predict the physiological status of the cows, while the use of IgG N-glycans for prediction still needs development. Nevertheless, accuracies need to be improved and a larger training data set is warranted.

A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach.

The aim of the present study was to identify genomic region(s) associated with the length of the calving interval in primiparous (n = 6866) and multiparous (n = 5071) Holstein cows. The single nucleotide polymorphism (SNP) solutions were estimated using a weighted single-step genomic best linear unbiased prediction (WssGBLUP) approach and imputed high-density panel (777 k) genotypes. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. The results showed that the accuracies of GEBVs with WssGBLUP improved by +5.4 to +5.7, (primiparous cows) and +9.4 to +9.7 (multiparous cows) percent points over accuracies from the pedigree-based BLUP. The most accurate genomic evaluation was provided at the second iteration of WssGBLUP, which was used to identify associated genomic regions using a windows-based GWAS procedure. The proportion of additive genetic variance explained by windows of 50 consecutive SNPs (with an average of 165 Kb) was calculated and the region(s) that accounted for equal to or more than 0.20% of the total additive genetic variance were used to search for candidate genes. Three windows of 50 consecutive SNPs (BTA3, BTA6, and BTA7) were identified to be associated with the length of the calving interval in primi- and multiparous cows, while the window with the highest percentage of explained genetic variance was located on BTA3 position 49.42 to 49.52 Mb. There were five genes including ARHGAP29, SEC24D, METTL14, SLC36A2, and SLC36A3 inside the windows associated with the length of the calving interval. The biological process terms including alanine transport, L-alanine transport, proline transport, and glycine transport were identified as the most important terms enriched by the genes inside the identified windows.

Reproductive management in dairy cows - the future.

BACKGROUND: Drivers of change in dairy herd health management include the significant increase in herd/farm size, quota removal (within Europe) and the increase in technologies to aid in dairy cow reproductive management. MAIN BODY: There are a number of key areas for improving fertility management these include: i) handling of substantial volumes of data, ii) genetic selection (including improved phenotypes for use in breeding programmes), iii) nutritional management (including transition cow management), iv) control of infectious disease, v) reproductive management (and automated systems to improve reproductive management), vi) ovulation / oestrous synchronisation, vii) rapid diagnostics of reproductive status, and viii) management of male fertility. This review covers the current status and future outlook of many of these key factors that contribute to dairy cow herd health and reproductive performance. CONCLUSIONS: In addition to improvements in genetic trends for fertility, numerous other future developments are likely in the near future. These include: i) development of new and novel fertility phenotypes that may be measurable in milk; ii) specific fertility genomic markers; iii) earlier and rapid pregnancy detection; iv) increased use of activity monitors; v) improved breeding protocols; vi) automated inline sensors for relevant phenotypes that become more affordable for farmers; and vii) capturing and mining multiple sources of "Big Data" available to dairy farmers. These should facilitate improved performance, health and fertility of dairy cows in the future.

Integrated ovarian mRNA and miRNA transcriptome profiling characterizes the genetic basis of prolificacy traits in sheep (Ovis aries).

BACKGROUND: The highly prolific breeds of domestic sheep (Ovis aries) are globally valuable genetic resources for sheep industry. Genetic, nutritional and other environmental factors affect prolificacy traits in sheep. To improve our knowledge of the sheep prolificacy traits, we conducted mRNA-miRNA integrated profiling of ovarian tissues from two pure breeds with large (Finnsheep) vs. small (Texel) litter sizes and their F1 crosses, half of which were fed a flushing diet. RESULTS: Among the samples, 16,402 genes (60.6% known ovine genes) were expressed, 79 novel miRNAs were found, and a cluster of miRNAs on chromosome 18 was detected. The majority of the differentially expressed genes between breeds were upregulated in the Texel with low prolificacy, owing to the flushing diet effect, whereas a similar pattern was not detected in the Finnsheep. F1 ewes responded similarly to Finnsheep rather than displaying a performance intermediate between the two pure breeds. CONCLUSIONS: The identification and characterization of differentially expressed genes and miRNAs in the ovaries of sheep provided insights into genetic and environmental factors affecting prolificacy traits. The three genes (CST6, MEPE and HBB) that were differentially expressed between the group of Finnsheep and Texel ewes kept in normal diet appeared to be candidate genes of prolificacy traits and will require further validation.

Effects of physiological and/or disease status on the response of postpartum dairy cows to synchronization of estrus using an intravaginal progesterone device.

Progesterone treatments are used to increase submission rates in postpartum dairy cows; however, in many cases the protocol is used as a blanket therapy for all cows without regard for physiological or disease state. The objective of this study was to identify the physiological or disease classes of cows that respond well (or not) to synchronization of estrus via progesterone. Dairy cows (n = 402) were monitored peri and postpartum to establish their physiological or disease status. Animals were classified as having negative energy balance, clinical lameness, uterine infection (UI), anovulatory anestrus, high somatic cell counts, and healthy (H). Blood samples were collected at five different time points and analyzed for metabolites. All animals received an 8-day controlled internal drug release protocol, which included GnRH at insertion and PGF2α the day before removal. Response to the protocol was determined by visual observation of estrus synchronization. Conception rate was determined by ultrasonography between Days 32 and 35 after artificial insemination. Animals without UI were 1.9 times more likely to respond and two times more likely to be confirmed pregnant than those with UI. There was no relationship between negative energy balance and clinical lameness in the visual estrous response, but both conditions were associated with reduced conception rates. Dairy cows in anovulatory anestrus responded successfully to the protocol in both estrous response and conception rates. High glutathione peroxidase concentrations had a positive effect on conception rates, whereas high non-esterified fatty acids and beta-hydroxybutyrate had a negative effect on the estrous response. In conclusion, disease and physiological states of dairy cows determined the response to progesterone-based synchronization. The more disease or physiological problems the cows had, the lower the estrous response and conception rates; cows with these problems were not ideal candidates for synchronization. Both anestrus and healthy dairy cows were good responders to progesterone-based synchronization.

Characterization of follicle and CL development in beef heifers using high resolution three-dimensional ultrasonography.

The aim was to characterize dominant follicle (DF) and CL development through the estrous cycle of cattle using three-dimensional (3D) ultrasonography while making a comparison with conventional two-dimensional (2D) B-mode ultrasound (US) and to relate the measures taken to systemic concentrations of steroid hormones and gonadotropins. After synchronization of estrus, the ovaries of crossbred beef heifers (N = 5) were assessed using daily US with a GE Voluson i US scanner until the end of the first follicle wave, then every other day until emergence of the final (ovulatory) wave, when daily US resumed until ovulation. Follicle and CL growth were recorded and mapped. Measures of diameter (2D) and volume (3D) of the DF from the first and ovulatory waves of the cycles; and CL development were captured and stored for further analysis. Blood flow to the DF and CL were assessed using 3D power Doppler US measuring vascularization index (VI; %), vascularization flow index (0/100) and flow index (0/100). Jugular blood samples were collected every 24 hours for progesterone from the first estrus until the second ovulation. Concentrations of estradiol (E2) and follicle stimulating hormone (FSH) were measured every 8 hours from estrus to second follicle wave emergence; then, E2 only was measured from final follicle wave emergence until ovulation. Data were analyzed using PROC MIXED and PROC REG in SAS. Dominant follicle blood flow tended to decrease during follicle wave emergence and DF VI increased (P < 0.05) 24 hours before ovulation after peak E2. Measures of the DF and CL volume (3D) were highly predictive of 2D diameter measures throughout the cycle (P < 0.0001). Predictive values (r(2)) for day of wave emergence and day from ovulation were similar for 2D and 3D measures; however, 2D measures had higher repeatability when compared with 3D measures. There was no relationship between CL VI and progesterone early in the cycle (r(2) = 0.12; P = 0.1); however, there was a strong positive relationship approaching ovulation (r(2) = 0.77; P < 0.0001). In conclusion, 3D power Doppler measures of blood flow appears to be representative of vascular changes in the DF and CL throughout the estrous cycle. However, the extra time required to acquire and analyze a 3D image and the relatively little additional information obtained over that achievable with 2D imaging in terms of follicle and CL development might preclude its widespread use other than for detailed research purposes.

Effects of systemic progesterone during the early luteal phase on the availabilities of amino acids and glucose in the bovine uterine lumen.

The uterine histotroph provides essential nutrition to the developing conceptus during the preimplantation period of pregnancy. The objective of the present study was to examine the effects of cycle stage and progesterone (P4) concentrations in the blood on the recoverable quantities of amino acids and glucose in the histotroph during the preimplantaion period of conceptus development. Following oestrus, dairy heifers were assigned to low, control or high P4 groups (n=6 heifers per treatment and time point). The uterine horn ipsilateral to the corpus luteum was flushed on either Day 7 or Day 13. The present study quantified 24 amino acids and glucose in the uterine flushings using HPLC and fluorometry, respectively. Heifers in the low P4 group had lower plasma concentrations of P4 throughout the cycle, whereas heifers in the high group had higher plasma concentrations of P4 between Days 3 and 7 compared with the control group (P<0.05). Total recoverable neutral (Ser, Gln, Gly, Thr, Cit, ß-Ala, Tau, Ala, Tyr, Trp, Met, Val, Phe, Ile, Leu, Pro and Cys), acidic (Glu) and basic (His, Arg, Orn and Lys) amino acids were greater (P<0.05) on Day 13 than on Day 7. There was no significant difference in the amount of Asp or Asn between Day 7 and Day 13. The amount of amino acids recovered on Day 7 was similar across treatment groups. On Day 13, the amount of Asn, His and Thr was lower (P<0.05) in the low P4 heifers compared with the controls and/or high P4 heifers. Quantities of glucose were not altered by cycle stage or P4 treatment. In conclusion, the stage of oestrous cycle and P4 play important roles in modulating amino acids in the histotroph, a potentially critical factor for early embryonic and/or conceptus survival.

The influence of cow and management factors on reproductive performance of Irish seasonal calving dairy cows.

Herd management record analysis facilitates accurate assessment of the current herd reproductive status; a crucial decision making tool to implement effective change. To determine the relative importance of cow and management factors on reproductive indices in moderate-yielding Irish seasonal-calving dairy herds, breeding records of 1173 cows were collected from 10 seasonal calving herds between 2007 and 2009. Backward-stepwise multivariable logistic regression analysis was utilised to determine the effect of cow factors including parity, calving timing, days post partum, heat detection accuracy and herd factors including herd size and heat detection efficiency on key reproductive indices. Mean farm six-week pregnancy and end of season not-in-calf rate were 46% (range 14-72%) and 22% (range 3-40%), respectively. Oestrous detection efficiency (P<0.001), timing of calving (P<0.001) relative to start of breeding, history of abnormal repeat intervals (P<0.001) and length of post partum interval (P<0.001) were each associated with lower six-week pregnancy rates. Timing of calving (P<0.001) and history of abnormal repeat intervals (P<0.001) were associated with higher not-in-calf rates. Herd size and cow parity were not associated (P>0.05) with either outcome when factors including existing calving pattern and heat detection accuracy and efficiency were accounted for. The existing spread in calving pattern, heat detection quality and length of voluntary waiting period were the most influential factors that reduced fertility performance in seasonal-calving herds.