Machine-learning methods applied to integrated transcriptomic data from bovine blastocysts and elongating conceptuses to identify genes predictive of embryonic competence.

Early pregnancy loss markedly impacts reproductive efficiency in cattle. The objectives were to model a biologically relevant gene signature predicting embryonic competence for survival after integrating transcriptomic data from blastocysts and elongating conceptuses with different developmental capacities and to validate the potential biomarkers with independent embryonic data sets through the application of machine-learning algorithms. First, two data sets from in vivo-produced blastocysts competent or not to sustain a pregnancy were integrated with a data set from long and short day-15 conceptuses. A statistical contrast determined differentially expressed genes (DEG) increasing in expression from a competent blastocyst to a long conceptus and vice versa; these were enriched for KEGG pathways related to glycolysis/gluconeogenesis and RNA processing, respectively. Next, the most discriminative DEG between blastocysts that resulted or did not in pregnancy were selected by linear discriminant analysis. These eight putative biomarker genes were validated by modeling their expression in competent or noncompetent blastocysts through Bayesian logistic regression or neural networks and predicting embryo developmental fate in four external data sets consisting of in vitro-produced blastocysts (i) competent or not, or (ii) exposed or not to detrimental conditions during culture, and elongated conceptuses (iii) of different length, or (iv) developed in the uteri of high- or subfertile heifers. Predictions for each data set were more than 85% accurate, suggesting that these genes play a key role in embryo development and pregnancy establishment. In conclusion, this study integrated transcriptomic data from seven independent experiments to identify a small set of genes capable of predicting embryonic competence for survival.

Maternal blood transcriptome as a sensor of fetal organ maturation at the end of organogenesis in cattle†.

Harnessing information from the maternal blood to predict fetal growth is attractive yet scarcely explored in livestock. The objectives were to determine the transcriptomic modifications in maternal blood and fetal liver, gonads, and heart according to fetal weight and to model a molecular signature based on the fetal organs allowing the prediction of fetal weight from the maternal blood transcriptome in cattle. In addition to a contemporaneous maternal blood sample, organ samples were collected from 10 male fetuses at 42 days of gestation for RNA-sequencing. Fetal weight ranged from 1.25 to 1.69 g (mean = 1.44 ± 0.15 g). Clustering data analysis revealed clusters of co-expressed genes positively correlated with fetal weight and enriching ontological terms biologically relevant for the organ. For the heart, the 1346 co-expressed genes were involved in energy generation and protein synthesis. For the gonads, the 1042 co-expressed genes enriched seminiferous tubule development. The 459 co-expressed genes identified in the liver were associated with lipid synthesis and metabolism. Finally, the cluster of 571 co-expressed genes determined in maternal blood enriched oxidative phosphorylation and thermogenesis. Next, data from the fetal organs were used to train a regression model of fetal weight, which was predicted with the maternal blood data. The best prediction was achieved when the model was trained with 35 co-expressed genes overlapping between heart and maternal blood (root-mean-square error = 0.04, R2 = 0.93). In conclusion, linking transcriptomic information from maternal blood with that from the fetal heart unveiled maternal blood as a predictor of fetal development.

The oocyte: the key player in the success of assisted reproduction technologies.

The ovulation of a mature oocyte at metaphase II of meiosis, with optimal potential to undergo fertilisation by a sperm cell, complete meiosis and sustain the switch to mitotic division, and support early embryo development, involves a protracted and disrupted/delayed series of processes. Many of these are targeted for exploitation in vivo , or recapitulation in vitro , by the livestock industry. Reproductive technologies, including AI, multiple ovulation embryo transfer, ovum pick-up, in vitro embryo production, and oestrus and ovulation synchronisation, offer practitioners and producers the opportunity to produce offspring from genetically valuable dams in much greater numbers than they would normally have in their lifetime, while in vitro oocyte and follicle culture are important platforms for researchers to interrogate the physiological mechanisms driving fertility. The majority of these technologies target the ovarian follicle and the oocyte within; thus, the quality and capability of the recovered oocyte determine the success of the reproductive intervention. Molecular and microscopical technologies have grown exponentially, providing powerful platforms to interrogate the molecular mechanisms which are integral to or affected by ART. The development of the bovine oocyte from its differentiation in the ovary to ovulation is described in the light of its relevance to key aspects of individual interventions, while highlighting the historical timeline.

RNA-sequencing reveals genes linked with oocyte developmental potential in bovine cumulus cells.

Cumulus cells provide an interesting biological material to perform analyses to understand the molecular clues determining oocyte competence. The objective of this study was to analyze the transcriptional differences between cumulus cells from oocytes exhibiting different developmental potentials following individual in vitro embryo production by RNA-seq. Cumulus cells were allocated into three groups according to the developmental potential of the oocyte following fertilization: (1) oocytes developing to blastocysts (Bl+), (2) oocytes cleaving but arresting development before the blastocyst stage (Bl-), and (3) oocytes not cleaving (Cl-). RNAseq was performed on 4 (Cl-) or 5 samples (Bl+ and Bl-) of cumulus cells pooled from 10 cumulus-oocyte complexes per group. A total of 49, 50, and 18 differentially expressed genes (DEGs) were detected in the comparisons Bl+ versus Bl-, Bl+ versus Cl- and Bl- versus Cl-, respectively, showing a fold change greater than 1.5 at an adjusted p value <0.05. Focussing on DEGs in cumulus cells from Bl+ group, 10 DEGs were common to both comparisons (10/49 from Bl+ vs. Bl-, 10/50 from Bl+ vs. Cl-). These DEGs correspond to 6 upregulated genes (HBE1, ITGA1, PAPPA, AKAP12, ITGA5, and SLC1A4), and 4 downregulated genes (GSTA1, PSMB8, FMOD, and SFRP4) in Bl+ compared to the other groups, from which 7 were validated by quantitative PCR (HBE1, ITGA1, PAPPA, AKAP12, ITGA5, PSMB8 and SFRP4). These genes are involved in critical biological functions such as integrin-mediated cell adhesion, oxygen availability, IGF and Wnt signaling or PKA pathway, highlighting specific biological processes altered in incompetent in vitro maturation oocytes.

MicroRNAs in amniotic fluid and maternal blood plasma associated with sex determination and early gonad differentiation in cattle†.

We hypothesized that sexually dimorphic differences exist in the expression of miRNAs in amniotic fluid (AF) and maternal blood plasma (MP) in association with the process of sex determination and gonad differentiation in cattle. Amniotic fluid and MP were collected from six pregnant heifers (three carrying a single male and three a single female embryo) following slaughter on Day 39 postinsemination, coinciding with the peak of SRY expression. Samples (six AF and six MP) were profiled using an miRNA Serum/Plasma Focus PCR Panel. Differentially expressed (DE) miRNAs were identified in AF (n = 5) and associated MP (n = 56) of male vs. female embryos (P < 0.05). Functional analysis showed that inflammatory and immune response were among the 13 biological processes enriched by miRNAs DE in MP in the male group (FDR < 0.05), suggesting that these sex-dependent DE miRNAs may be implicated in modulating the receptivity of the dam to a male embryo. Further, we compared the downstream targets of the sex-dependent DE miRNAs detected in MP with genes previously identified as DE in male vs. female genital ridges. The analyses revealed potential targets that might be important during this developmental stage such as SHROOM2, DDX3Y, SOX9, SRY, PPP1CB, JARID2, USP9X, KDM6A, and EIF2S3. Results from this study highlight novel aspects of sex determination and embryo-maternal communication in cattle such as the potential role of miRNAs in gonad development as well as in the modulation of the receptivity of the dam to a male embryo.

Invited review: Use of assisted reproduction techniques to accelerate genetic gain and increase value of beef production in dairy herds.

The contribution of the calf enterprise to the profit of the dairy farm is generally considered small, with beef bull selection on dairy farms often not considered a high priority. However, this is likely to change in the future as the rapid rate of expansion of the dairy herd in some countries is set to plateau and improvements in dairy herd fertility combine to reduce the proportion of dairy breed calves required on dairy farms. This presents the opportunity to increase the proportion of beef breed calves born, increasing both the value of calf sales and the marketability of the calves. Beef embryos could become a new breeding tool for dairies as producers need to reassess their breeding policy as a consequence of welfare concerns and poor calf prices. Assisted reproductive technologies can contribute to accelerated genetic gain by allowing an increased number of offspring to be produced from genetically elite dams. There are the following 3 general classes of donor females of interest to an integrated dairy-beef system: (1) elite dairy dams, from which oocytes are recovered from live females using ovum pick-up and fertilized in vitro with semen from elite dairy bulls; (2) elite beef dams, where the oocytes are recovered from live females using ovum pick-up and fertilized with semen from elite beef bulls; and (3) commercial beef dams (≥50% beef genetics), where ovaries are collected from the abattoir postslaughter, and oocytes are fertilized with semen from elite beef bulls that are suitable for use on dairy cows (resulting embryo with ≥75% beef genetics). The expected benefits of these collective developments include accelerated genetic gain for milk and beef production in addition to transformation of the dairy herd calf crop to a combination of good genetic merit dairy female calves and premium-quality beef calves. The aim of this review is to describe how these technologies can be harnessed to intensively select for genetic improvement in both dairy breed and beef breed bulls suitable for use in the dairy herd.

Comprehensive functional analysis reveals that acrosome integrity and viability are key variables distinguishing artificial insemination bulls of varying fertility.

In vitro methods of assessing bull semen quality in artificial insemination (AI) centers are unable to consistently detect individuals of lower fertility, and attempts to reliably predict bull fertility are still ongoing. This highlights the need to identify robust biomarkers that can be readily measured in a practical setting and used to improve current predictions of bull fertility. In this study, we comprehensively analyzed a range of functional, morphological, and intracellular attributes in cryopreserved spermatozoa from a selected cohort of Holstein Friesian AI bulls classified as having either high or low fertility (n = 10 of each fertility phenotype; difference of 11.4% in adjusted pregnancy rate between groups). Here, spermatozoa were assessed for motility and kinematic parameters, morphology, acrosome integrity, plasma membrane lipid packing, viability (or membrane integrity), superoxide production, and DNA integrity. In addition, spermatozoa were used for in vitro fertilization to evaluate their capacity for fertilization and successful embryo development. The information collected from these assessments was then used to phenotypically profile the 2 groups of bulls of divergent fertility status as well as to develop a model to predict bull fertility. According to the results, acrosome integrity and viability were the only sperm attributes that were significantly different between high- and low-fertility bulls. Interestingly, although spermatozoa from low-fertility bulls, on average, had reduced viability and acrosome integrity, this response varied considerably from bull to bull. Principal component analysis revealed a sperm phenotypic profile that represented a high proportion of ejaculates from low-fertility bulls. This was constructed based on the collective influence of several sperm attributes, including the presence of cytoplasmic droplets and superoxide production. Finally, using the combined results as a basis for modeling, we developed a linear model that was able to explain 47% of the variation in bull field fertility in addition to a logistic predictive model that had a 90% chance of distinguishing between fertility groups. Taken together, we conclude that viability and acrosome integrity could serve as fertility biomarkers in the field and, when used alongside other sperm attributes, may be useful in detecting low-fertility bulls. However, the variable nature of low-fertility bulls suggests that additional, in-depth characterization of spermatozoa at a molecular level is required to further understand the etiology of low fertility in dairy bulls.

Location relative to the corpus luteum affects bovine endometrial response to a conceptus.

In cattle, embryo transfer into the uterine horn contralateral to the corpus luteum results in a higher incidence of pregnancy loss compared to transfer into the ipsilateral horn. We have previously reported temporal changes in the endometrial transcriptome during the estrous cycle which differ between uterine horns. The objective of this study was to compare the transcriptomic response of endometrium from the ipsilateral and contralateral horns to an elongating conceptus. Cross-bred beef heifers (n = 16) were synchronized and either used to generate day 14 conceptuses following the transfer of in vitro-produced blastocysts or to obtain day 14 endometrial explants. Conceptuses were recovered on day 14 by post-mortem uterine flushing, placed individually on top of explants collected from the ipsilateral (IPSI-D14) or the contralateral (CONTRA-D14) uterine horn of cyclic heifers, and co-cultured for 6 h. The response to a conceptus was markedly different between uterine horns, with 61 and 239 differentially expressed genes (DEGs; false discovery rate <0.05) in the ipsilateral and contralateral horns, respectively, compared to their controls. Direct comparison between IPSI-D1 and CONTRA-D14 revealed 32 DEGs, including CXCL11, CXCL10, IFIT2, RSAD2 and SAMD9. Gene Ontology analysis of these 32 genes revealed ten enriched biological processes, mainly related to immune response and response to an external stimulus. These data indicate that the endometrial response to the presence of a conceptus varies between uterine horns in the same uterus and may contribute to the higher incidence of pregnancy loss following embryo transfer to the contralateral horn.

High temperature-humidity index compromises sperm quality and fertility of Holstein bulls in temperate climates.

Rising temperatures caused by climate change have adverse effects on cattle physiology, welfare, health, and reproduction. Heat stress in cows affects the oocyte and embryo directly through heat shock on cellular function. Fewer data are available on the effect of high temperatures on male fertility. Temperature-humidity index (THI) is a measure for assessing the risk of heat stress that combines the effects of temperature and humidity. The aim of this study was to determine the relationship between THI and fresh or frozen-thawed sperm quality of Holstein bulls kept in temperate climates. Bull sperm data of 29,170 ejaculates from 933 bulls collected at 3 Dutch artificial insemination centers between 2015 and 2018 were evaluated. The assessed variables included total sperm motility and morphology of fresh semen, and total sperm motility, morphology, and progressive motility of frozen semen 0 and 3 h after thawing. In addition, 56-d nonreturn rates were analyzed. The assessed effects were season and THI on the day of semen collection and during spermatogenesis (30 d before collection), bull, age of bull, year, and location. Bulls were divided into 2 categories according to their age: young (<36 mo) and older (>36 mo). Overall sperm quality of young bulls improved as age increased. No effect of THI on fresh sperm variables was observed in either young or older bulls. However, high THI at spermatogenesis negatively affected the cryotolerance of sperm cells. Sperm cells from young and older bulls showed a pronounced decrease (14-18%) of the assessed variables 3 h after thawing after the increase of THI during spermatogenesis in autumn. Remarkably, older bulls were more sensitive to THI at spermatogenesis compared with semen collection, showing up to a 3.8 times higher negative effect on frozen sperm quality. However, an elevated THI at semen collection produced a tendency toward decreased 56-d nonreturn rates as the age of the bull increased. Although this decrease was up to 4%, rising temperatures may still cause important economic losses in the future. For the first time, the present study confirmed that climate compromises not only sperm quality, but also dairy bull fertility.

Protein Synthesis by Day 16 Bovine Conceptuses during the Time of Maternal Recognition of Pregnancy.

Interferon Tau (IFNT), the conceptus-derived pregnancy recognition signal in cattle, significantly modifies the transcriptome of the endometrium. However, the endometrium also responds to IFNT-independent conceptus-derived products. The aim of this study was to determine what proteins are produced by the bovine conceptus that may facilitate the pregnancy recognition process in cattle. We analysed by mass spectrometry the proteins present in conceptus-conditioned media (CCM) after 6 h culture of Day 16 bovine conceptuses (n = 8) in SILAC media (arginine- and lysine-depleted media supplemented with heavy isotopes) and the protein content of extracellular vesicles (EVs) isolated from uterine luminal fluid (ULF) of Day 16 pregnant (n = 7) and cyclic (n = 6) cross-bred heifers on day 16. In total, 11,122 proteins were identified in the CCM. Of these, 5.95% (662) had peptides with heavy labelled amino acids, i.e., de novo synthesised by the conceptuses. None of these proteins were detected in the EVs isolated from ULF. Pregnancy-associated glycoprotein 11, Trophoblast Kunitz domain protein 1 and DExD-Box Helicase 39A were de novo produced and present in the CCM from all conceptuses and in previously published CCM data following 6 and 24 h. A total of 463 proteins were present in the CCM from all the conceptuses in the present study, and after 6 and 24 h culture in a previous study, while expression of their transcripts was not detected in endometrium indicating that they are likely conceptus-derived. Of the proteins present in the EVs, 67 were uniquely identified in ULF from pregnant heifers; 35 of these had been previously reported in CCM from Day 16 conceptuses. This study has narrowed a set of conceptus-derived proteins that may be involved in EV-mediated IFNT-independent embryo-maternal communication during pregnancy recognition in cattle.

Biochemical characterization of progesterone-induced alterations in bovine uterine fluid amino acid and carbohydrate composition during the conceptus elongation window†.

Pregnancy establishment in cattle is contingent on conceptus elongation-a fundamental developmental event coinciding with the time during which most pregnancies fail. Elongation in vivo is directly driven by uterine secretions, indirectly influenced by systemic progesterone concentrations, and has yet to be recapitulated in vitro. To better understand the microenvironment evolved to facilitate this phenomenon, the amino acid and carbohydrate composition of uterine fluid was interrogated using high-throughput metabolomics on days 12, 13, and 14 of the estrous cycle from heifers with normal and high circulating progesterone. A total of 99 biochemicals (79 amino acids and 20 carbohydrates) were consistently identified, of which 31 showed a day by progesterone interaction. Fructose and mannitol/sorbitol did not exhibit a day by progesterone interaction, but displayed the greatest individual fluctuations (P ≤ 0.05) with respective fold increases of 18.39 and 28.53 in high vs normal progesterone heifers on day 12, and increases by 10.70-fold and 14.85-fold in the uterine fluid of normal progesterone animals on day 14 vs day 12. Moreover, enrichment analyses revealed that the phenylalanine, glutathione, polyamine, and arginine metabolic pathways were among the most affected by day and progesterone. In conclusion, progesterone had a largely stabilizing effect on amino acid flux, and identified biochemicals of likely importance to conceptus elongation initiation include arginine, fructose, glutamate, and mannitol/sorbitol.

Bovine endometrium responds differentially to age-matched short and long conceptuses†.

This study combined in vitro production of bovine blastocysts, multiple embryo transfer techniques, and a conceptus-endometrial explant co-culture system to test the hypothesis that bovine endometrium exposed to long vs. short day 15 conceptuses would exhibit a different transcriptome profile reflective of potential for successful pregnancy establishment. Bovine endometrial explants collected at the late luteal stage of the estrous cycle were cultured in RPMI medium for 6 h with nothing (control), 100 ng/mL recombinant ovine interferon tau (IFNT), a long day 15 conceptus, or a short day 15 conceptus. Transcriptional profiling of the endometrial explants found that exposure of endometrium to IFNT, long conceptuses, or short conceptuses altered (P < 0.05) expression of 491, 498, and 230 transcripts, respectively, compared to the control. Further analysis revealed three categories of differentially expressed genes (DEG): (i) commonly responsive to exposure to IFNT and conceptuses, irrespective of size (n = 223); (ii) commonly responsive to IFNT and long conceptuses only (n = 168); and genes induced by the presence of a conceptus but independent of IFNT (n = 108). Of those 108 genes, 101 were exclusively induced by long conceptuses and functional analysis revealed that regulation of molecular function, magnesium-ion transmembrane transport, and clathrin coat assembly were the principal gene ontologies associated with these DEG. In conclusion, bovine endometrium responds differently to age-matched conceptuses of varying size in both an IFNT-dependent and -independent manner, which may be reflective of the likelihood of successful pregnancy establishment.

Do differences in the endometrial transcriptome between uterine horns ipsilateral and contralateral to the corpus luteum influence conceptus growth to day 14 in cattle?

Embryo transfer to the uterine horn contralateral to the ovary containing the corpus luteum (CL) negatively impacts pregnancy establishment in cattle. Our aim was to compare the transcriptome and ability of the ipsilateral and contralateral uterine horns to support preimplantation conceptus survival and growth to day 14. In experiment 1, endometrial samples from both horns were collected from synchronized heifers slaughtered on day 5, 7, 13, or 16 post-estrus (n = 5 per time) and subjected to RNA sequencing. In experiment 2, 10 day 7 in vitro produced blastocysts were transferred into the uterine horn ipsilateral (n = 9) or contralateral to the CL (n = 8) or into both horns (i.e., bilateral, n = 9) of synchronized recipient heifers. Reproductive tracts were recovered at slaughter on day 14, and the number and dimensions of recovered conceptuses were recorded for each horn. A total of 217, 54, 14, and 18 differentially expressed genes (>2-fold change, FDR P < 0.05) were detected between ipsilateral and contralateral horns on days 5, 7, 13, and 16, respectively, with signaling pathways regulating pluripotency of stem cells, ErbB signaling pathway, and mTOR signaling pathway amongst the top canonical pathways. Site of embryo transfer did not affect recovery rate (48.0%, 168/350) or length of conceptuses (mean ± SE 2.85 ± 0.27 mm). Although differences in gene expression exist between the endometrium of uterine horns ipsilateral and contralateral to the CL in cattle, they do not impact conceptus survival or length between day 7 and 14.

Progesterone alters the bovine uterine fluid lipidome during the period of elongation.

Successful bovine pregnancy establishment hinges on conceptus elongation, a key reproductive phenomenon coinciding with the period during which most pregnancies fail. Elongation is yet to be recapitulated in vitro, whereas in vivo it is directly driven by uterine secretions and indirectly influenced by prior circulating progesterone levels. To better understand the microenvironment evolved to facilitate this fundamental developmental event, uterine fluid was recovered on Days 12-14 of the oestrous cycle - the window of conceptus elongation initiation - from cycling heifers supplemented, or not, with progesterone. Subsequent lipidomic profiling of uterine luminal fluid by advanced high-throughput metabolomics revealed the consistent presence of 75 metabolites, of which 47% were intricately linked to membrane biogenesis, and with seven displaying a day by progesterone interaction (P ≤ 0.05). Four metabolic pathways were correspondingly enriched according to day and P4 - i.e. comprised metabolites whose concentrations differed between groups (normal vs high P4) at different times (Days 12 vs 13 vs 14). These were inositol, phospholipid, glycerolipid and primary bile acid metabolism. Moreover, P4 elevated total uterine luminal fluid lipid content on Day 14 (P < 0.0001) relative to all other comparisons. The data combined suggest that maternal lipid supply during the elongation-initiation window is primarily geared towards conceptus membrane biogenesis. In summary, progesterone supplementation alters the lipidomic profile of bovine uterine fluid during the period of conceptus elongation initiation.

An approach to study the local embryo effect on gene expression in the bovine oviduct epithelium in vivo.

This study aimed to examine the local embryo effect on the transcriptomic response of the epithelial cells of the oviduct in vivo. Fifteen heifers were synchronized and artificially inseminated to a standing heat. All heifers were slaughtered on Day 2.5 after oestrus. The oviducts from 13 animals were isolated, trimmed free of tissue and divided between ampulla/isthmus. The ipsilateral isthmus was divided into smaller sections (2 cm). Each section was sequentially flushed until the embryo was located (4/13) and then opened and scraped longitudinally to obtain the epithelial cells. Cells were snap-frozen in LN2 for gene expression analysis. All recovered embryos were found at the beginning of the isthmus. The 2 cm sections selected for the transcriptomic analysis were as follows: embryo section (in which the embryo was found); proximal section (through which the embryo had passed); distal section (on the uterine side of the embryo); and contralateral section (section from the contralateral isthmus). The expression pattern of eight genes (STK32A, KERA, QRFPR, MCTP1, PRELP, VAT1L, SOCS3 and CCL20) differentially expressed between the isthmus of pregnant (multiple embryo model) and cyclic heifers were assessed by RT-qPCR. One-way ANOVA and t test was used for statistical analysis. Comparisons between ipsilateral and contralateral oviduct or along the ipsilateral oviduct resulted in no differences for all genes. Despite the failure to detect a site-specific response of a single embryo on the abundance of distinct transcripts in the bovine oviduct in vivo on Day 2.5, the current methodology with proposed modifications would be useful for future studies to examine the local embryo effect.

Early sex-dependent differences in response to environmental stress.

Developmental plasticity enables the appearance of long-term effects in offspring caused by exposure to environmental stressors during embryonic and foetal life. These long-term effects can be traced to pre- and post-implantation development, and in both cases, the effects are usually sex specific. During preimplantation development, male and female embryos exhibit an extensive transcriptional dimorphism mainly driven by incomplete X chromosome inactivation. These early developmental stages are crucial for the establishment of epigenetic marks that will be conserved throughout development, making it a particularly susceptible period for the appearance of long-term epigenetic-based phenotypes. Later in development, gonadal formation generates hormonal differences between the sexes, and male and female placentae exhibit different responses to environmental stressors. The maternal environment, including hormones and environmental insults during pregnancy, contributes to sex-specific placental development that controls genetic and epigenetic programming during foetal development, regulating sex-specific differences, including sex-specific epigenetic responses to environmental hazards, leading to long-term effects. This review summarizes several human and animal studies examining sex-specific responses to environmental stressors during both the periconception period (caused by differences in sex chromosome dosage) and placental development (caused by both sex chromosomes and hormones). The identification of relevant sex-dependent trajectories caused by sex chromosomes and/or sex hormones is essential to define diagnostic markers and prevention/intervention protocols.

Embryonic maternal interaction in cattle and its relationship with fertility.

Embryo mortality is a major contributor to poor reproductive efficiency and profitability in cattle production systems. While conception is achieved (i.e., the oocyte is fertilized) in the vast majority of cases if insemination is carried out correctly, a significant proportion of the resulting embryos fail to develop to term. Appropriate communication between the developing conceptus and the maternal endometrium is essential for the establishment and maintenance of pregnancy in all mammals. Up to the blastocyst stage, around Days 7-9, contact worth the female reproductive system is not required. However, the process of conceptus elongation after hatching and prior to implantation is entirely maternally driven and is essential to ensure that sufficient quantities of interferon-tau (IFNT) are secreted by the developing conceptus to abrogate the mechanisms that bring about luteolysis. While the importance of conceptus-derived IFNT in maternal recognition of pregnancy and prevention of luteolysis in cattle is unequivocal, many questions, such as the threshold level of IFNT required for pregnancy maintenance, remain unanswered. Furthermore, the precise role of IFNT-independent mechanisms in pregnancy establishment remains to be elucidated. Irrespective of this, failure of the conceptus to elongate undoubtedly results in embryonic loss and is thus believed to contribute greatly to reproductive failure in cattle. This review will address some of these answered questions and try to shed some light on those gaps in knowledge that could potentially contribute to improved embryo survival and reproductive efficiency.

Effect of lactation on conceptus-maternal interactions at the initiation of implantation in cattle: I. Effects on the conceptus transcriptome and amino acid composition of the uterine luminal fluid.

Approximately 65-75 days postpartum (dpp), the estrous cycles of nonlactating (dried off immediately postpartum: n = 12) and lactating (n = 13) Holstein Friesian cows were synchronized and on day 7 a single blastocyst derived from superovulated nulliparous Holstein Friesian heifers was transferred to each cow. A control group of nulliparous heifers (n = 8) were synchronized, inseminated to a standing heat, and slaughtered on the same day as nonlactating and lactating recipients (day 19; estrus = day 0). The uterine horn ipsilateral to the corpus luteum was flushed with 10 ml phosphate-buffered saline and the conceptus, and uterine luminal fluid (ULF) was snap-frozen in liquid nitrogen. Gene expression analysis of the conceptus was performed by RNA sequencing, while amino acid composition of ULF was determined by high-performance liquid chromatography. No differentially expressed genes (DEGs) were observed between conceptuses recovered from nonlactating and lactating cows. Eight DEGs were identified between conceptuses recovered from nonlactating cows and heifers. A total of 269 DEGs (100 up- and 169 downregulated) were identified between conceptuses recovered from lactating cows compared to heifers. Alanine, glycine, serine, threonine, arginine, leucine, and valine were significantly lower in abundance in ULF recovered from heifers compared to nonlactating or lactating cows. This study demonstrates that the environment in which the embryo develops post the blastocyst stage can have an effect on the conceptus transcriptome and amino acid composition of the ULF but this was mainly observed between the two extreme groups in terms of metabolic status (nulliparous heifers vs postpartum lactating cows).

Effect of metabolic status on conceptus-maternal interactions on day 19 in dairy cattle: II. Effects on the endometrial transcriptome.

The aim of this study was to test the hypothesis that the metabolic stresses associated with lactation alter the ability of the endometrium to respond appropriately to the conceptus by examining endometrial gene expression on day 19 of pregnancy. Immediately after calving, primiparous Holstein cows with similar production and fertility estimated breeding values were randomly divided into two groups and either dried off (i.e. never milked) immediately or milked twice daily. Approximately 65-75 days postpartum, grade 1 blastocysts recovered from superovulated Holstein heifer donors (n = 5) were transferred (1 per recipient) into lactating (n = 11) and nonlactating (n = 11) recipients. Control nulliparous Holstein heifers (n = 6) were artificially inseminated. RNA-sequencing was performed on intercaruncular endometrial samples recovered at slaughter from confirmed pregnant animals on day 19 (n = 5 lactating and nonlactating cows; n = 4 heifers). Differentially expressed genes (DEGs) were identified between both postpartum groups compared to heifers and between lactating and nonlactating cows. Functional annotation of DEGs between cows and heifers revealed over-representation of categories, including endosome, cytoplasmic vesicle, endocytosis, regulation of exocytosis, and cytokine receptor activity. Functional categories including transcription factor binding sites, cell motility, and cell migration were enriched for DEGs between endometria from lactating and nonlactating cows. In conclusion, while the evidence for a major effect of lactation on the endometrial transcriptome is relatively weak, these data suggest that the metabolic status of the animal (heifer vs cow) modulates the response of the endometrium to the developing conceptus.

Differentially Expressed Genes in Endometrium and Corpus Luteum of Holstein Cows Selected for High and Low Fertility Are Enriched for Sequence Variants Associated with Fertility.

Despite the importance of fertility in humans and livestock, there has been little success dissecting the genetic basis of fertility. Our hypothesis was that genes differentially expressed in the endometrium and corpus luteum on Day 13 of the estrous cycle between cows with either good or poor genetic merit for fertility would be enriched for genetic variants associated with fertility. We combined a unique genetic model of fertility (cattle that have been selected for high and low fertility and show substantial difference in fertility) with gene expression data from these cattle and genome-wide association study (GWAS) results in ∼20,000 cattle to identify quantitative trait loci (QTL) regions and sequence variants associated with genetic variation in fertility. Two hundred and forty-five QTL regions and 17 sequence variants associated primarily with prostaglandin F2alpha, steroidogenesis, mRNA processing, energy status, and immune-related processes were identified. Ninety-three of the QTL regions were validated by two independent GWAS, with signals for fertility detected primarily on chromosomes 18, 5, 7, 8, and 29. Plausible causative mutations were identified, including one missense variant significantly associated with fertility and predicted to affect the protein function of EIF4EBP3. The results of this study enhance our understanding of 1) the contribution of the endometrium and corpus luteum transcriptome to phenotypic fertility differences and 2) the genetic architecture of fertility in dairy cattle. Including these variants in predictions of genomic breeding values may improve the rate of genetic gain for this critical trait.