Advancing Dairy and Beef Genetics Through Genomic Technologies.

The US beef and dairy industries have made remarkable advances in sustainability and productivity through technological advancements, including selective breeding. Yet, challenges persist due to the complex nature of quantitative traits. While the beef industry has progressed in adopting genomic technologies, the availability of phenotypic data remains an obstacle. To meet the need for sustainable production systems, novel traits are being targeted for selection. Additionally, emerging approaches such as genome editing and high-throughput phenotyping hold promise for further genetic progress. Future research should address the challenges of translating functional genomic findings into practical applications, while simultaneously harnessing analytical methods.

Effects of rate of body weight gain during the first trimester of gestation on beef heifer and offspring performance, concentrations of hormones and metabolites, and response to vaccination.

Our study objectives were to evaluate the effects of divergent rates of body weight (BW) gain during early gestation in beef heifers on F0 performance, metabolic and endocrine status, colostrum immunoglobulins, and subsequent F1 calf characteristics, growth performance, concentrations of hormones and metabolites, and response to vaccination. Angus-based heifers (n = 100; BW = 369 ±â€…2.5 kg) were adapted to individual feeding for 14 d and bred using artificial insemination with female-sexed semen. Heifers were ranked by BW and assigned to either a basal diet targeting 0.28 kg/d gain (low [LG], n = 50) or the basal diet plus an energy/protein supplement targeting 0.79 kg/d gain (moderate gain [MG], n = 50) until day 84 of gestation. Dam BW and blood samples were collected at 6 time points during gestation; body composition was evaluated on days -10 and 84; and fetal measurements were taken on days 42, 63, and 84. At calving (LG, n = 23; MG, n = 23), dam and calf BW were recorded; and colostrum, calf body measurements, and blood samples were collected. Cow-calf pairs were managed on a common diet from calving to weaning, followed by a common postnatal development period for all F1 female offspring. Growth performance, hormone and metabolite profiles, feeding behavior, and reproductive performance were assessed from birth to prebreeding in F1 heifers. Offspring were vaccinated against respiratory disease and bovine viral diarrhea pathogens on days 62.3 ±â€…4.13 and 220.3 ±â€…4.13 postcalving. By design, MG dams were heavier (P < 0.0001) than LG on day 84, and the BW advantage persisted until subsequent weaning of F1 calves. Concentrations of serum IGF-1 and glucose were increased throughout gestation (P < 0.001) in MG dams, whereas concentrations of NEFA were decreased (P < 0.001) in LG dams. Calves from MG dams were 2.14 kg heavier (P = 0.03) and had larger chest circumference (P = 0.04) at birth compared with LG cohorts. Heifers from MG dams continued to have greater (P ≤ 0.03) BW gain and feed efficiency during the development period, but no differences were observed (P ≥ 0.13) in body composition, concentrations of hormones and metabolites, feeding behavior, puberty attainment, and response to vaccination in F1 offspring. Hence, early gestation rate of gain impacted BW and concentrations of glucose and IGF-1 throughout gestation in the F0 dam, resulting in altered F1 calf BW and measurements at birth and increased gain and efficiency during the development period.

Generally, beef heifers are managed on grazing pastures during early gestation, which are subject to fluctuations in forage quantity and quality. Variations in the nutrients available to the dam can impact the developing offspring during early gestation. Providing energy/protein supplements to grazing cattle is a method to ensure nutrient requirements are being met and to enhance the rate of gain. This study modeled the effects of pasture supplementation in beef heifers during early gestation to determine whether 2 rates of body weight (BW) gain alter maternal body composition and concentrations of hormones and metabolites, as well as changes to postnatal characteristics of the subsequent F1 generation heifer calves. The rate of gain affected the heifer's BW, body composition, and concentrations of key metabolites and hormones, which likely altered the nutritional environment experienced by the fetus. Subsequently, F1 offspring from supplemented dams had greater morphometric characteristics at birth and had greater BW gain, feed efficiency, and eating rate during the postweaning development period. However, body composition, concentrations of hormones and metabolites, other feeding behaviors, puberty attainment, and response to vaccination of offspring were not affected. Further research is warranted to investigate how the early gestational rate of BW gain impacts key metabolic organs and mechanisms involved in transferring programming outcomes to subsequent generations.

lncRNA-gene network analysis reveals the effects of early maternal nutrition on mineral homeostasis and energy metabolism in the fetal liver transcriptome of beef heifers.

Maternal nutrition during pregnancy influences fetal development; however, the regulatory markers of fetal programming across different gestational phases remain underexplored in livestock models. Herein, we investigated the regulatory role of long non-coding RNAs (lncRNAs) on fetal liver gene expression, the impacts of maternal vitamin and mineral supplementation, and the rate of maternal body weight gain during the periconceptual period. To this end, crossbred Angus heifers (n=31) were randomly assigned to a 2×2 factorial design to evaluate the main effects of the rate of weight gain (low gain [LG, avg. daily gain of 0.28 kg/day] vs. moderate gain [MG, avg. daily gain of 0.79 kg/day]) and vitamins and minerals supplementation (VTM vs. NoVTM). On day 83±0.27 of gestation, fetuses were collected for morphometric measurements, and fetal liver was collected for transcriptomic and mineral analyses. The maternal diet significantly affected fetal liver development and mineral reserves. Using an RNA-Seq approach, we identified 320 unique differentially expressed genes (DEGs) across all six comparisons (FDR <0.05). Furthermore, lncRNAs were predicted through the FEELnc pipeline, revealing 99 unique differentially expressed lncRNAs (DELs). The over-represented pathways and biological processes (BPs) were associated with energy metabolism, Wnt signaling, CoA carboxylase activity, and fatty acid metabolism. The DEL-regulated BPs were associated with metal ion transport, pyrimidine metabolism, and classical energy metabolism-related glycolytic, gluconeogenic, and TCA cycle pathways. Our findings suggest that lncRNAs regulate mineral homeostasis- and energy metabolism-related gene networks in the fetal liver in response to early maternal nutrition.

Influence of Maternal Supplementation with Vitamins, Minerals, and (or) Protein/Energy on Placental Development and Angiogenic Factors in Beef Heifers during Pregnancy.

The effect of vitamins and minerals supplementation (VTM) and/or two rates of body weight gain (GAIN) on bovine placental vascular development and angiogenic factors gene expression were evaluated in two experiments: In Exp. 1, crossbred Angus heifers (n = 34) were assigned to VTM/NoVTM treatments at least 71 days before breeding to allow changes in the mineral status. At breeding, through artificial insemination (AI), heifers were assigned to low-gain (LG) 0.28 kg/d or moderate-gain (MG) 0.79 kg/d treatments, resulting in NoVTM-LG (Control; n = 8), NoVTM-MG (n = 8), VTM-LG (n = 9), and VTM-MG (n = 9) until day 83 of gestation; In Exp. 2, crossbred angus heifers (n = 28), were assigned to control (CON; n = 12), receiving a basal total mixed ration (TMR) or TMR + VTM (VTM; n = 16) from breeding until parturition. Placentomes from Exp. 1 and cotyledons (COT) from Exp. 2 were evaluated by immunohistochemistry for COT vascular density area. COTs from Exp. 1 were evaluated for angiogenic factor (ANGPT-1, ANGPT-2, eNOS2, eNOS3, FLT1, KDR, TEK, VEGFA) gene expression. In Exp. 1, COT vascularity was not affected by the interaction of VTM and GAIN (p = 0.67) or the main effects of VTM (p = 0.50) and GAIN (p = 0.55). Likewise, angiogenic factors were not differentially expressed between treatments (p < 0.05). In Exp. 2, COT vascularity was greater in VTM vs. CON (p = 0.07). In conclusion, there is a suggested later-stage influence of vitamin and mineral supplementation on placental vascularity, emphasizing the importance of supplementation beyond early pregnancy.

Mapping Expression Quantitative Trait Loci Targeting Candidate Genes for Pregnancy in Beef Cows.

Despite collective efforts to understand the complex regulation of reproductive traits, no causative genes and/or mutations have been reported yet. By integrating genomics and transcriptomics data, potential regulatory mechanisms may be unveiled, providing opportunities to dissect the genetic factors governing fertility. Herein, we identified regulatory variants from RNA-Seq data associated with gene expression regulation in the uterine luminal epithelial cells of beef cows. We identified 4676 cis and 7682 trans eQTLs (expression quantitative trait loci) affecting the expression of 1120 and 2503 genes, respectively (FDR < 0.05). These variants affected the expression of transcription factor coding genes (71 cis and 193 trans eQTLs) and genes previously reported as differentially expressed between pregnant and nonpregnant cows. Functional over-representation analysis highlighted pathways related to metabolism, immune response, and hormone signaling (estrogen and GnRH) affected by eQTL-regulated genes (p-value ≤ 0.01). Furthermore, eQTLs were enriched in QTL regions for 13 reproduction-related traits from the CattleQTLdb (FDR ≤ 0.05). Our study provides novel insights into the genetic basis of reproductive processes in cattle. The underlying causal mechanisms modulating the expression of uterine genes warrant further investigation.

Supplementing vitamins and minerals to beef heifers during gestation: impacts on mineral status in the dam and offspring, and growth and physiological responses of female offspring from birth to puberty.

We evaluated the effects of feeding a vitamin and mineral supplement to nulliparous beef heifers throughout gestation on the mineral status of the dam, calf, placenta, and colostrum; offspring growth performance; and physiological responses of offspring raised as replacement heifers. Angus-based heifers (n = 31, initial body weight [BW] = 412.5 ±â€…53.68 kg) were adapted to an individual feeding system for 14 d, estrus synchronized and bred with female-sexed semen. Heifers were ranked by BW and randomly assigned to receive either a basal diet (CON; n = 14) or the basal diet plus 113 g heifer-1 d-1 of the vitamin and mineral supplement (VTM; n = 17). Targeted BW gains for both treatments was 0.45 kg heifer-1 d-1. Liver biopsies were obtained from dams at breeding, days 84 and 180 of gestation. At calving, liver biopsies were taken from dams and calves; colostrum, placenta, and blood samples were collected; and calf body measurements were recorded. After calving, all cow-calf pairs received a common diet through weaning, and F1 heifer calves were managed similarly after weaning. Offspring growth performance, feeding behavior, blood metabolites, and hormones were evaluated from birth through 15 mo of age. Data were analyzed using the MIXED procedure in SAS with repeated measures where appropriate. Hepatic concentrations of Se decreased in VTM dams (P ≤ 0.05) from day 84 to calving, while concentrations of Cu decreased in VTM and CON (P ≤ 0.05) from day 84 to calving. Calf liver concentrations of Se, Cu, Zn, and Co at birth were greater for VTM than CON (P ≤ 0.05), but calf birth BW and body measurements were not different (P = 0.45). Placental Se, colostrum quantity, total Se, Cu, Zn, and Mn in colostrum were greater (P ≤ 0.04) in VTM dams than CON. Finally, offspring from VTM dams were heavier than CON (P < 0.0001) from weaning through 15 mo of age. These results were coupled with greater (P ≤ 0.04) blood glucose at birth, decreased (P ≤ 0.05) blood urea nitrogen at pasture turn out and weaning, and altered feeding behaviors in VTM offspring compared with CON. Maternal gestational vitamin and mineral supplementation enhanced mineral status in dams and F1 progeny, augmented postnatal offspring growth and blood metabolites. Consequently, in utero vitamin and mineral supplementation may exert programming outcomes on the performance and productivity of females raised as herd replacements and should be considered when developing diets for gestating cows and heifers.

Great variation exists in management decisions to offer a vitamin and mineral supplement to cow­calf herds in the Northern Great Plains. Decisions to supplement (or not) vitamins/minerals during critical periods of fetal development may have lasting postnatal impacts on the offspring; however, there is a lack of reports focusing on the long-term offspring outcomes. Our objectives were to determine the impacts of supplementing vitamins/minerals during gestation in beef heifers on mineral status in the dam, calf, placenta, and colostrum; offspring postnatal performance and feeding behavior; blood metabolite and endocrine profiles; and puberty attainment in heifer calves. We observed enhanced hepatic mineral status in heifers receiving supplemental vitamins/minerals during pregnancy, at calving, and in their neonatal calves compared with non-supplemented cohorts. Calves born to supplemented dams had improved measures of growth during postnatal development, increased concentrations of key blood metabolites, and differences in body measurements and carcass ultrasound traits at post-weaning evaluation. These results suggest that fetal nutritional environment is pivotal for the long-term growth and success of the offspring. We hypothesize that fetal programming outcomes on the offspring in this experiment may have the potential to affect the subsequent generation of beef calves.

Harnessing Genomics and Transcriptomics Approaches to Improve Female Fertility in Beef Cattle-A Review.

Female fertility is the foundation of the cow-calf industry, impacting both efficiency and profitability. Reproductive failure is the primary reason why beef cows are sold in the U.S. and the cause of an estimated annual gross loss of USD 2.8 billion. In this review, we discuss the status of the genomics, transcriptomics, and systems genomics approaches currently applied to female fertility and the tools available to cow-calf producers to maximize genetic progress. We highlight the opportunities and limitations associated with using genomic and transcriptomic approaches to discover genes and regulatory mechanisms related to beef fertility. Considering the complex nature of fertility, significant advances in precision breeding will rely on holistic, multidisciplinary approaches to further advance our ability to understand, predict, and improve reproductive performance. While these technologies have advanced our knowledge, the next step is to translate research findings from bench to on-farm applications.

Ruminal and feces metabolites associated with feed efficiency, water intake and methane emission in Nelore bulls.

The objectives of this study were twofold: (1) to identify potential differences in the ruminal and fecal metabolite profiles of Nelore bulls under different nutritional interventions; and (2) to identify metabolites associated with cattle sustainability related-traits. We used different nutritional interventions in the feedlot: conventional (Conv; n = 26), and by-product (ByPr, n = 26). Thirty-eight ruminal fluid and 27 fecal metabolites were significantly different (P < 0.05) between the ByPr and Conv groups. Individual dry matter intake (DMI), residual feed intake (RFI), observed water intake (OWI), predicted water intake (WI), and residual water intake (RWI) phenotypes were lower (P < 0.05) in the Conv group, while the ByPr group exhibited lower methane emission (ME) (P < 0.05). Ruminal fluid dimethylamine was significantly associated (P < 0.05) with DMI, RFI, FE (feed efficiency), OWI and WI. Aspartate was associated (P < 0.05) with DMI, RFI, FE and WI. Fecal C22:1n9 was significantly associated with OWI and RWI (P < 0.05). Fatty acid C14:0 and hypoxanthine were significantly associated with DMI and RFI (P < 0.05). The results demonstrated that different nutritional interventions alter ruminal and fecal metabolites and provided new insights into the relationship of these metabolites with feed efficiency and water intake traits in Nelore bulls.

Dataset for miRNA expression analysis in the peripheral white blood cells of beef heifers at weaning.

Subfertility in beef heifers leads to a substantial economic loss for producers and beef industry. To overcome this problem, producers require an efficient system to discriminate beef heifers with varying reproductive potential as early as possible. MicroRNAs are short non-coding RNAs that post-transcriptionally regulate gene expression. Herein, we profiled the miRNAs in peripheral white blood cells (PWBC) of beef heifers at weaning to investigate the differences in the beef heifers with varying reproductive outcomes. Blood samples from Angus-Simmental crossbred heifers were collected at weaning. The blood was processed to extract the PWBC pellet and was stored at -80 °C until further processing. After the synchronization of estrus and breeding protocol (artificial insemination (AI) followed by natural bull service) and pregnancy diagnosis, the heifers were categorized as fertile (pregnant to AI) or subfertile (not pregnant to AI or bull exposure). Total RNA was extracted from PWBC collected at the time of weaning from the fertile and subfertile heifers. After quality assessment, the total RNA was used to prepare libraries. The quality-checked libraries (n = 14; 7 samples per fertile and subfertile group) were pooled and sequenced (single-end 50 bp) using a NextSeq 500 platform. The raw sequence reads were analyzed using a bioinformatics workflow utilizing FastQC and MultiQC for quality control, Cutadapt for adapter trimming, miRDeep2 for alignment, and DESeq2 for differential expression analysis. The raw and normalized miRNA counts were deposited and made publicly available on the gene expression omnibus database (GEO; GSE225854). This is the first dataset investigating the miRNA expression level in PWBC at weaning in beef heifers to predict the future reproductive outcome. The results from the data presented here are reported in the research article titled "miRNA expression profiles of peripheral white blood cells from beef heifers with varying reproductive potential" [1].

Dataset of RNA-Seq transcriptome of the fetal liver at day 83 of gestation associated with periconceptual maternal nutrition in beef heifers.

Herein, we present a dataset based on the RNA-Seq analysis of liver tissue from bovine female fetuses at day 83 of gestation. The findings were reported in the main article, "Periconceptual maternal nutrition affects fetal liver programming of energy- and lipid-related genes" [1]. These data were generated to investigate the effects of periconceptual maternal vitamin and mineral supplementation and rates of body weight gain on the transcript abundance of genes associated with fetal hepatic metabolism and function. To this end, crossbred Angus beef heifers (n = 35) were randomly assigned to 1 of 4 treatments in a 2 × 2 factorial design. The main effects tested were vitamin and mineral supplementation (VTM or NoVTM - at least 71 days pre-breeding to day 83 of gestation) and rate of weight gain (low (LG - 0.28 kg/d) or moderate (MG - 0.79 kg/d) - from breeding to day 83). The fetal liver was collected on day 83 ± 0.27 of gestation. After total RNA isolation and quality control, strand-specific RNA libraries were prepared and sequenced on the Illumina® NovaSeq 6000 platform to generate paired-end 150-bp reads. After read mapping and counting, differential expression analysis was performed with edgeR. We identified 591 unique differentially expressed genes across all six vitamin-gain contrasts (FDR ≤ 0.1). To our knowledge, this is the first dataset investigating the fetal liver transcriptome in response to periconceptual maternal vitamin and mineral supplementation and/or the rate of weight gain. The data described in this article provides genes and molecular pathways differentially programming liver development and function.

Maternal Mineral Nutrition Regulates Fetal Genomic Programming in Cattle: A Review.

Maternal mineral nutrition during the critical phases of fetal development may leave lifetime impacts on the productivity of an individual. Most research within the developmental origins of the health and disease (DOHaD) field is focused on the role of macronutrients in the genome function and programming of the developing fetus. On the other hand, there is a paucity of knowledge about the role of micronutrients and, specifically, minerals in regulating the epigenome of livestock species, especially cattle. Therefore, this review will address the effects of the maternal dietary mineral supply on the fetal developmental programming from the embryonic to the postnatal phases in cattle. To this end, we will draw a parallel between findings from our cattle model research with data from model animals, cell lines, and other livestock species. The coordinated role and function of different mineral elements in feto-maternal genomic regulation underlies the establishment of pregnancy and organogenesis and, ultimately, affects the development and functioning of metabolically important tissues, such as the fetal liver, skeletal muscle, and, importantly, the placenta. Through this review, we will delineate the key regulatory pathways involved in fetal programming based on the dietary maternal mineral supply and its crosstalk with epigenomic regulation in cattle.

miRNA expression profiles of peripheral white blood cells from beef heifers with varying reproductive potential.

Reproductive performance is the most critical factor affecting production efficiency in the cow-calf industry. Heifers with low reproductive efficiency may fail to become pregnant during the breeding season or maintain a pregnancy. The cause of reproductive failure often remains unknown, and the non-pregnant heifers are not identified until several weeks after the breeding season. Therefore, improving heifer fertility utilizing genomic information has become increasingly important. One approach is using microRNAs (miRNA) in the maternal blood that play an important role in regulating the target genes underlying pregnancy success and thereby in selecting reproductively efficient heifers. Therefore, the current study hypothesized that miRNA expression profiles from peripheral white blood cells (PWBC) at weaning could predict the future reproductive outcome of beef heifers. To this end, we measured the miRNA profiles using small RNA-sequencing in Angus-Simmental crossbred heifers sampled at weaning and retrospectively classified as fertile (FH, n = 7) or subfertile (SFH, n = 7). In addition to differentially expressed miRNAs (DEMIs), their target genes were predicted from TargetScan. The PWBC gene expression from the same heifers were retrieved and co-expression networks were constructed between DEMIs and their target genes. We identified 16 differentially expressed miRNAs between the groups (p-value ≤0.05 and absolute (log2 fold change ≥0.05)). Interestingly, based on a strong negative correlation identified from miRNA-gene network analysis with PCIT (partial correlation and information theory), we identified miRNA-target genes in the SFH group. Additionally, TargetScan predictions and differential expression analysis identified bta-miR-1839 with ESR1 , bta-miR-92b with KLF4 and KAT2B, bta-miR-2419-5p with LILRA4, bta-miR-1260b with UBE2E1, SKAP2 and CLEC4D, and bta-let-7a-5p with GATM, MXD1 as miRNA-gene targets. The miRNA-target gene pairs in the FH group are over-represented for MAPK, ErbB, HIF-1, FoxO, p53, mTOR, T-cell receptor, insulin and GnRH signaling pathways, while those in the SFH group include cell cycle, p53 signaling pathway and apoptosis. Some miRNAs, miRNA-target genes and regulated pathways identified in this study have a potential role in fertility; other targets are identified as novel and need to be validated in a bigger cohort that could help to predict the future reproductive outcomes of beef heifers.

Transcriptomic dataset from peripheral white blood cells of beef heifers at weaning.

Reproductive failure of replacement breeding animals is one of the leading causes of loss to the beef production industry. The losses are further increased due to the inability to diagnose the reproductive potential of the beef heifer prior to the breeding season until the pregnancy outcome. To overcome this problem, a system to discriminate beef heifers with varying reproductive potential as early and accurately as possible is demanded. The omics technologies, such as transcriptomics, could predict the future reproductive potential of beef heifers. Therefore, this manuscript provides the gene expression profile dataset using RNA-Seq identified from peripheral white blood cells (PWBC) of beef heifers at weaning. To accomplish this, the blood samples were collected at the time of weaning, processed to extract the PWBC pellet and stored at - 80 °C until further processing. After the breeding protocol (artificial insemination (AI) followed by natural bull service) and pregnancy diagnosis, the heifers that were pregnant to AI (n = 8) or remained open (n = 7) were utilized for this study. Total RNA was extracted from PWBC collected at the time of weaning from these samples and subjected to sequencing using the Illumina Nova-Seq platform. High-quality sequencing data was analyzed using a bioinformatic workflow based on FastQC and MultiQC for quality control, STAR for read alignment, and DESeq2 for differential expression analysis. Genes were considered significantly differentially expressed after adjustment with Bonferroni correction (padj ≤ 0.05) and absolute (log2 fold change) ≥ 0.5. Raw and processed RNA-Seq data were deposited and made publicly available on the gene expression omnibus database (GEO; GSE221903). To our knowledge, this is the first dataset investigating the change in the gene expression level as early as weaning to predict the future reproductive outcome in beef heifers. Interpretation of the main findings based on this data is reported in a research article titled "mRNA Signatures in Peripheral White Blood Cells Predicts Reproductive Potential in Beef Heifers at Weaning" [1].

Periconceptual Maternal Nutrition Affects Fetal Liver Programming of Energy- and Lipid-Related Genes.

During pregnancy, the fetus relies on the dam for its nutrient supply. Nutritional stimuli during fetal organ development can program hepatic metabolism and function. Herein, we investigated the role of vitamin and mineral supplementation (VTM or NoVTM-at least 71 days pre-breeding to day 83 of gestation) and rate of weight gain (low (LG) or moderate (MG)-from breeding to day 83) on the fetal liver transcriptome and the underlying biological pathways. Crossbred Angus beef heifers (n = 35) were randomly assigned to one of four treatments in a 2 × 2 factorial design (VTM_LG, VTM_MG, NoVTM_LG, and NoVTM_MG). Gene expression was measured with RNA-Seq in fetal livers collected on day 83 ± 0.27 of gestation. Our results show that vitamin and mineral supplementation and rate of weight gain led to the differential expression of hepatic genes in all treatments. We identified 591 unique differentially expressed genes across all six VTM-gain contrasts (FDR ≤ 0.1). Over-represented pathways were related to energy metabolism, including PPAR and PI3K-Akt signaling pathways, as well as lipid metabolism, mineral transport, and amino acid transport. Our findings suggest that periconceptual maternal nutrition affects fetal hepatic function through altered expression of energy- and lipid-related genes.

mRNA Signatures in Peripheral White Blood Cells Predict Reproductive Potential in Beef Heifers at Weaning.

Reproductive failure is a major contributor to inefficiency within the cow-calf industry. Particularly problematic is the inability to diagnose heifer reproductive issues prior to pregnancy diagnosis following their first breeding season. Therefore, we hypothesized that gene expression from the peripheral white blood cells at weaning could predict the future reproductive potential of beef heifers. To investigate this, the gene expression was measured using RNA-Seq in Angus-Simmental crossbred heifers sampled at weaning and retrospectively classified as fertile (FH, n = 8) or subfertile (SFH, n = 7) after pregnancy diagnosis. We identified 92 differentially expressed genes between the groups. Network co-expression analysis identified 14 and 52 hub targets. ENSBTAG00000052659, OLR1, TFF2, and NAIP were exclusive hubs to the FH group, while 42 hubs were exclusive to the SFH group. The differential connectivity between the networks of each group revealed a gain in connectivity due to the rewiring of major regulators in the SFH group. The exclusive hub targets from FH were over-represented for the CXCR chemokine receptor pathway and inflammasome complex, while for the SFH, they were over-represented for immune response and cytokine production pathways. These multiple interactions revealed novel targets and pathways predicting reproductive potential at an early stage of heifer development.

Machine Learning-Based Co-Expression Network Analysis Unravels Potential Fertility-Related Genes in Beef Cows.

Reproductive failure is still a challenge for beef producers and a significant cause of economic loss. The increased availability of transcriptomic data has shed light on the mechanisms modulating pregnancy success. Furthermore, new analytical tools, such as machine learning (ML), provide opportunities for data mining and uncovering new biological events that explain or predict reproductive outcomes. Herein, we identified potential biomarkers underlying pregnancy status and fertility-related networks by integrating gene expression profiles through ML and gene network modeling. We used public transcriptomic data from uterine luminal epithelial cells of cows retrospectively classified as pregnant (P, n = 25) and non-pregnant (NP, n = 18). First, we used a feature selection function from BioDiscML and identified SERPINE3, PDCD1, FNDC1, MRTFA, ARHGEF7, MEF2B, NAA16, ENSBTAG00000019474, and ENSBTAG00000054585 as candidate biomarker predictors of pregnancy status. Then, based on co-expression networks, we identified seven genes significantly rewired (gaining or losing connections) between the P and NP networks. These biomarkers were co-expressed with genes critical for uterine receptivity, including endometrial tissue remodeling, focal adhesion, and embryo development. We provided insights into the regulatory networks of fertility-related processes and demonstrated the potential of combining different analytical tools to prioritize candidate genes.

Co-Expression Network and Integrative Analysis of Metabolome and Transcriptome Uncovers Biological Pathways for Fertility in Beef Heifers.

Reproductive failure remains a significant challenge to the beef industry. The omics technologies have provided opportunities to improve reproductive efficiency. We used a multistaged analysis from blood profiles to integrate metabolome (plasma) and transcriptome (peripheral white blood cells) in beef heifers. We used untargeted metabolomics and RNA-Seq paired data from six AI-pregnant (AI-P) and six nonpregnant (NP) Angus-Simmental crossbred heifers at artificial insemination (AI). Based on network co-expression analysis, we identified 17 and 37 hub genes in the AI-P and NP groups, respectively. Further, we identified TGM2, TMEM51, TAC3, NDRG4, and PDGFB as more connected in the NP heifers' network. The NP gene network showed a connectivity gain due to the rewiring of major regulators. The metabolomic analysis identified 18 and 15 hub metabolites in the AI-P and NP networks. Tryptophan and allantoic acid exhibited a connectivity gain in the NP and AI-P networks, respectively. The gene-metabolite integration identified tocopherol-a as positively correlated with ENSBTAG00000009943 in the AI-P group. Conversely, tocopherol-a was negatively correlated in the NP group with EXOSC2, TRNAUIAP, and SNX12. In the NP group, α-ketoglutarate-SMG8 and putrescine-HSD17B13 were positively correlated, whereas a-ketoglutarate-ALAS2 and tryptophan-MTMR1 were negatively correlated. These multiple interactions identified novel targets and pathways underlying fertility in bovines.

DNA methylation dataset of bovine embryonic fibroblast cells treated with epigenetic modifiers and divergent energy supply.

Fetal programming is established early in life, likely through epigenetic mechanisms that control gene expression. Micronutrients can act as epigenetic modifiers (EM) by modulating the genome through mechanisms that include DNA methylation and post-translational modification of chromatin. Among the EM, methionine, choline, folate, and vitamin B12 have been suggested as key players of DNA methylation. However, the effects of supplementing these four EM, involved in the methionine folate cycle on DNA methylation, are still under investigation. This manuscript provides the genome-wide DNA methylation dataset (GSE180362) of bovine embryonic fibroblast cells exposed to different supplementation levels of glucose and methionine, choline, folate, and vitamin B12 (collectively named as Epigenetic Modifiers - EM). The DNA methylation was measured using MSP-I digestion and Reduced Representation Bisulfite Sequencing. Bioinformatics analyses included data quality control, read mapping, methylation calling, and differential methylation analyses. Supplementary file S1 and data analysis codes are within this article. To our knowledge, this is the first dataset investigating the effects of four EM in bovine embryonic fibroblast DNA methylation profiles. Furthermore, this data and its findings provide information on putative candidate genes responsive to DNA methylation due to EM supplementation.

Epigenetic Modifier Supplementation Improves Mitochondrial Respiration and Growth Rates and Alters DNA Methylation of Bovine Embryonic Fibroblast Cells Cultured in Divergent Energy Supply.

Epigenetic modifiers (EM; methionine, choline, folate, and vitamin B12) are important for early embryonic development due to their roles as methyl donors or cofactors in methylation reactions. Additionally, they are essential for the synthesis of nucleotides, polyamines, redox equivalents, and energy metabolites. Despite their importance, investigation into the supplementation of EM in ruminants has been limited to one or two epigenetic modifiers. Like all biochemical pathways, one-carbon metabolism needs to be stoichiometrically balanced. Thus, we investigated the effects of supplementing four EM encompassing the methionine-folate cycle on bovine embryonic fibroblast growth, mitochondrial function, and DNA methylation. We hypothesized that EM supplemented to embryonic fibroblasts cultured in divergent glucose media would increase mitochondrial respiration and cell growth rate and alter DNA methylation as reflected by changes in the gene expression of enzymes involved in methylation reactions, thereby improving the growth parameters beyond Control treated cells. Bovine embryonic fibroblast cells were cultured in Eagle's minimum essential medium with 1 g/L glucose (Low) or 4.5 g/L glucose (High). The control medium contained no additional OCM, whereas the treated media contained supplemented EM at 2.5, 5, and 10 times (×2.5, ×5, and ×10, respectively) the control media, except for methionine (limited to ×2). Therefore, the experimental design was a 2 (levels of glucose) × 4 (levels of EM) factorial arrangement of treatments. Cells were passaged three times in their respective treatment media before analysis for growth rate, cell proliferation, mitochondrial respiration, transcript abundance of methionine-folate cycle enzymes, and DNA methylation by reduced-representation bisulfite sequencing. Total cell growth was greatest in High ×10 and mitochondrial maximal respiration, and reserve capacity was greatest (p < 0.01) for High ×2.5 and ×10 compared with all other treatments. In Low cells, the total growth rate, mitochondrial maximal respiration, and reserve capacity increased quadratically to 2.5 and ×5 and decreased to control levels at ×10. The biological processes identified due to differential methylation included the positive regulation of GTPase activity, molecular function, protein modification processes, phosphorylation, and metabolic processes. These data are interpreted to imply that EM increased the growth rate and mitochondrial function beyond Control treated cells in both Low and High cells, which may be due to changes in the methylation of genes involved with growth and energy metabolism.