Search

Possible phenotypic impairments associated with maternal stress during gestation in beef cattle may be explained by epigenetic effects. This study examined the impact of prenatal transportation stress on DNA methylation of lymphocytes of Brahman cows over the first 5 years of life. Methylation analysis through reduced representation bisulphite sequencing was conducted on DNA from lymphocytes from 28 paired samples from 6 prenatally stressed (PNS) and 8 control (Control) females obtained initially when they were 28 days of age and 5 years of age. There were 14,386 CpG (C = cytosine; p = phosphate; G = guanine) sites differentially methylated (P

Longitudinal studies of gene expression where sampling certain organ systems is precluded may become more feasible if a more accessible, representative biological sample could be identified. The objective of this study was to determine whether peripheral blood leukocytes (PBL) could be an effective surrogate for assessing gene expression differences within neuroendocrine tissues that regulate stress responses. Specifically, leukocyte samples and stress axis tissues, including the paraventricular region of the hypothalamus, anterior pituitary gland, adrenal cortex, and adrenal medulla were isolated from humanely slaughtered 5-yr-old Brahman cows (n = 8). RNA was extracted from each sample and gene expressions were calculated using bioinformatic approaches of RNA-Seq analysis. Differentially expressed genes (DEG) between adrenal axis tissue RNA and PBL RNA were identified using the edgeR Package from Bioconductor, R. More than 3,000 DEGs were identified in each tissue relative to the PBLs. Overall, higher gene expression levels were observed in the hypothalamus vs PBL, while the remaining tissues had reduced expression compared to PBL (Table 1). Pearson correlation values were calculated from the mean normalized gene count in the PBL and tissues for genes (n = 17) important for stress response and metabolism to assess PBL as a possible surrogate for gene expression analyses (Table 2). Only two genes, oxytocin and 11β-hydroxylase, were positively correlated (P < 0.05) between PBL and specific tissue gene expression. As typically observed among different cell types, gene expression differences exist between the PBL and various tissues of the HPA axis. Therefore, it remains to be determined if gene expression in the surrogate PBL will shift in a direction similar to that of specific adrenal axis tissue of mature Brahman cows exposed to stressors during key developmental periods.

The objective of this work was to evaluate efficiency traits of Nellore-Angus crossbred steers (n = 349) on feed. Steers were fed a grain-based diet beginning at approximately 12 months of age for an average of 140 days. Contemporary groups were born in the fall or spring of 2003 through 2007 in full-sibling embryo transfer families or half-sibling families all sired by the same bulls. Individual intake was measured and weights were recorded to permit calculation of average daily gain. Residual feed intake (RFI) was estimated as the residual of models employing regressions on metabolic mid-test weight and ADG. An additional efficiency metric was also constructed and evaluated: model predicted residual consumption (MPRC). Mixed linear models were used to analyze daily dry matter intake, average daily gain (ADG), metabolic mid-test weight, RFI, and MPRC. Large positive associations of DMI with MPRC and RFI were identified along with low positive associations between metabolic mid-weight with ADG and MPRC. Genome wide association analysis revealed 5 regions associated with DMI, but none for the other traits analyzed. Residual feed intake values varied greatly between the contemporary group value and the overall value for the steers, showing the calculation’s dependency on the reference population. However, MPRC as based upon a standardized population, did not fluctuate. More selection phenotypes and strategies are needed for large-scale improvements in global beef cattle production sustainability. The stability of the MPRC metric could be beneficial for future feed efficiency research across multiple and diverse contemporary groups, and diverse production environments.

DNA methylation (DNAm) patterns are tissue specific and aid in tissue specific gene expression changes. The use of DNAm patterns from peripheral blood leukocytes (PBL) as a surrogate for patterns in other tissues is common, especially in longitudinal studies when sampling of tissues is not plausible. Thus, the objective of this study was to investigate the suitability of using DNAm patterns of PBL as a surrogate for the DNAm patterns in neuroendocrine tissues responsible for stress responses and energy metabolism. Samples from the paraventricular region of the hypothalamus, anterior pituitary gland, adrenal cortex, and the adrenal medulla were harvested from 5-yr-old Brahman cows (n = 8) and DNA was extracted from each sample. Methylation was assessed using reduced representation sodium bisulfite sequencing and differentially methylated regions (DMR) between the PBL DNA and tissue DNA were identified using EdgeR from Bioconductor, R. Analysis revealed over 15,000 DMRs located within promoter regions of genes in each tissue, with the majority of the sites having increased methylation in the PBL (Table 1). To further evaluate the use of PBL DNA as a surrogate, Pearson correlation values were calculated for genes (n = 20) pertinent to each respective tissue using the mean methylation of the specific gene in the PBL and in the tissue (Table 2). Three correlations were significant (P ≤ 0.05), two of which were negative. The sizable differences indicate that DNA methylation patterns from PBL do not compare well to patterns from hypothalamic, pituitary, adrenal cortex, and adrenal medulla tissues from 5-yr-old Brahman cows. This is especially the case for the majority of the specific genes examined in this study. Whether DNAm in the surrogate PBL will shift in a direction similar to that of specific tissues of Brahman cows exposed to stressful stimuli during developmental periods remains to be determined.

This study investigated whether DNA methylation patterns changed over the first five yr of life within prenatally stressed (PNS) heifer calves compared to change within a Control group. Prenatal stress was induced by the transportation of pregnant Brahman cows for 2-hr periods at 60±5, 80± 5, 100±5, 120±5, and140±5d of gestation. White blood cells were sampled from the same 6 PNS heifer calves and 8 Control heifer calves at 28 d and 5 yr of age. The DNA methylation data were generated through Reduced Representation Bisulfite Sequencing. Based on results of mapping and bioinformatics analyses, 73,758 hypermethylated and 73,367 hypomethylated CpG sites, 375 hypermethylated and 377 hypomethylated CHG sites, 735 hypermethylated and 842 hypomethylated CHH (C = cytosine; G = guanine; H = either adenine, thymine, or cytosine) sites were obtained from 28-d-old PNS calves compared to when they had matured into 5-yr-old PNS cows (P ≤ 0.05). The 28-d-old Control heifer calves contained 53,005 hypermethylated and 57,103 hypomethylated CpG sites, 200 hypermethylated and 202 hypomethylated CHG sites, 439 hypermethylated and 535 hypomethylated CHH sites compared to when they matured into 5-yr-old Control cows (P ≤ 0.05). As DNA methylation of gene promoter regions is associated with reduced transcription activity, strongly hypermethylated and hypomethylated CpG sites located in promoter regions underwent Ingenuity Pathway Analysis. The top canonical pathways altered by strongly hypermethylated and hypomethylated CpG sites between 28-d-old and 5-yr-old PNS cows were 4-1BB Signaling in T Lymphocytes (P = 0.00169) and Transcriptional Regulatory Network in Embryonic Stem Cells (P = 0.000744). Mineralocorticoid Biosynthesis (P = 0.00901) and Transcriptional Regulatory Network in Embryonic Stem Cells (P = 0.000804) were the other top canonical pathways altered between 28-d-old and 5-yr-old Control cows. PNS calves appeared to develop an altered epigenome compared to Control group calves during the first five yr from birth.

Prenatal stress in beef cattle has the potential to result in unexpected, long term phenotypic changes to an animal’s performance. One possible explanation for this phenomenon is stress induced epigenetic changes to the genome (e.g., methylation or histone modifications). The objective of this experiment was to identify differential DNA methylation patterns in prenatally stressed (PNS) Brahman females. Multiparous Brahman cows (n = 48) were transported for a 2hr periods on 60 ± 5, 80 ± 5, 100 ± 5, 120 ± 5, and 140 ± 5 d of gestation. A non-transported group (n = 48) was maintained as a control. DNA was extracted from the white blood cells of their 28-d old heifer calves (Control n = 8, PNS n = 6) and methylation was assessed using reduced representation sodium bisulfite sequencing. Mean methylation ratios at locations across the genome in PNS and Control females were compared using a student’s t-test. Analysis revealed 16,377 CpG sites, 311 CHG, and 612 CHH (C= cytosine; G= guanine; H = adenine, cytosine or thymine) sites that were differentially methylated in PNS females compared to the Control females (P ≤ 0.05). The top 2,000 differentially methylated regions (DMRs) were classified by functional location in introns, exons, CpG islands, promoters, and 5’UTR regions. Methylation differences in these regions are known to cause gene expression differences. The identified regions were analyzed using Ingenuity Pathway Analysis (IPA) in order to identify involvement in canonical pathways. Certain regions identified from the hypermethylated DMRs showed the strongest overlap (P = 1.93E-6) with the complex pathway of axonal guidance signaling (important for neural development). These results suggest that prenatal transportation stress does alter the epigenome of Brahman heifers and can influence biological pathways, potentially impacting animal performance.