Progress 01/01/22 to 12/31/24
Outputs
Target Audience:The target audience of this project will be the scientific community, especially other beef cattle researchers. They can use the knowledge generated by this study to design applied studies, which will then target dissemination to beef producers Changes/Problems:The project director for this effort stepped down and the project has since been transferred to one of the original PIs. As previously noted the F3 generation sample size was smaller than desired (also noted in anticipated pitfalls), but we were able to perform comparative analysis across generations. What opportunities for training and professional development has the project provided?Training for 5 graduate student and 2 technicians in the areas of sample collection and analysis.Training for 5 graduate student and 2 technicians in the areas of sample collection and analysis. How have the results been disseminated to communities of interest?Data published in peer reviewed journal articles and abstracts. In addition, data used as part of invited presentations to the producer and scientific communities. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Moving from the last report to the current report was the addition of F3 sample analysis to the previously reported analysis of the F1 and F2 generations. The fetal liver and muscle samples from F1, F2, and F3 generations were sequenced for both micro-RNAs (miRNA) and methylation patterns (through Reduced representation bisulfite sequencing, RRBS). The data sets were analyzed following miRDeep2 and methylKit pipelines using miRDeep2.0.1.3 (Friedländer et al., 2012) and methylKit v1.12.0 (Akalin et al., 2012) packages respectively. The data were normalized using the grouping effect and differentially expressed microRNAs (DEM) and differentially methylated regions (DMR) were considered significant at FDR < 0.1 for MG vs. LG fetuses. In the F3 generation, we identified four DEMs where bta-miR-146b was found upregulated while bta-miR-331-3p, bta-miR-1260b, and bta-miR-2478 were found downregulated in MG vs. LG. The upregulation of bta-miR-146b is studied to be associated with the enrichment of fatty acid oxidation and the potential regulation of energy and protein metabolism (Oliveira et al., 2018). The bta-miR-331-3p was found to be associated with post-transcriptional regulation (Zhao et al., 2017), while the bta-miR-1260b and bta-miR-2478 were found associated with energy and lipid metabolism (Muroya et al., 2016). We did not find any differentially expression microRNA significant for MG vs. LG comparison in the F3 generation. In RRBS analyses in the F3 generation, we identified 20633 DMRs and 10698 were hyper-methylated while 9935 were hypo methylated. The mapped genes involving hyper-methylated or potentially downregulated genes were involved in energy metabolic pathways i.e., MAPK, PI3K, Rap1, Wnt, cAMP, and mTOR signaling pathways Other pathways like hippo signaling involving organogenesis, insulin, and thyroid hormone signaling pathways along with mineral absorption pathways. Similarly, the pathways enriched for genes mapped to hypo-methylated DMRs were MAPK, Rap1, mTOR, Wnt, Ras, PI3K, and cAMP signaling. The hippo and VEGF signaling involve organogenesis, fatty acid metabolism, and PPAR signaling pathways. Given these results, we can say that in the F1-generation most of the liver and muscular developmental pathways were upregulated along with fatty acid metabolism to compensate for the negative effect of low gain effect but later in the F2-generation, most of the pathways as associated with energy metabolism and signal transduction as we seem to have sufficient fetal reserves later generation and this continues till F3 generation as well. Similar to DMRs identification and mapping to transcription start sites (TSS) in CpG island regions of gene promoters, we also identified muscular tissue DMR-associated genes to find out the functional pathways involved in MG vs. LG fetuses. We identified 21197 DMRs in the muscular tissue of F3 generations, where 8137 were hyper-methylated while 13060 were hypo-methylated. The mapped genes involving hyper-methylated or potentially downregulated genes were involved in key energy metabolic and fetal developmental pathways like MAPK, Wnt, cAMP, PI3K, Ras, mTOR, longevity regulating, AMPK, VEGF, and Hippo signaling pathways. The genes mapped to hypo-methylated DMRs, potentially upregulated genes (Lim et al., 2010), were involved in energy metabolism pathways like MAPK, Rap1, PI3K, cAMP, Ras, Wnt, mTOR, VEGF, AMPK signaling. The pathways related to fatty acid, nucleotide metabolism, Hippo signaling organogenesis, carbon metabolism, amino acid metabolism, and mineral. These results and associated pathways seem consistent with F1 and F2 generations where energy metabolism and fetal developmental pathways were regulated to meet muscular development in MG vs. LG fetuses. This continued until the F3 generation as most pathways were shared. We also identified some of the DMRs and DMGs shared across generations, shown below in the figure.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2025
Citation:
1. Anas, M., A.K. Ward, K.L. McCarthy, P.P. Borowicz, L.P. Reynolds, J.S. Caton, C.R Dahlen, and W.J.S Diniz. 2025. Intergenerational effects of maternal rate of body weight gain on the multi-omics hepatic profiles of bovine fetuses. Gene 936, 149082. https://doi.org/10.1016/j.gene.2024.149082
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
15. Anas, M., A.K. Ward, K.L. McCarthy, P.P. Borowicz, L.P. Reynolds, J.S. Caton, C.R. Dahlen, and W.J.S. Diniz. 2024. Multigenerational effects of maternal rate of body weight gain on fetal liver miRNA expression. J. Anim. Sci. 102 (Suppl 3):543-544. https://doi.org/10.1093/jas/skae234.610
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Progress 01/01/23 to 12/31/23
Outputs
Target Audience:The target audience of this project will be the scientific community, especially other beef cattle researchers. They can use the knowledge generated by this study to design applied studies, which will then target dissemination to beef producers Changes/Problems:Death loss of F2 generation calves due to illness reduced the number of available heifers to generate F3 pregnancies but we are maximixing the use of available F2/F3 pairs due to the very novel nature of the datasets being generated. What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?The F2 generations heifers for this effort are under-breeding protocol these days to get our F3 liver and muscle tissue towards end of spring 2024 for subsequent analyses as outlined in the project narrative. The F2-heifers left to get F3 samples at d83 of gestation are low in sample size as anticipated in potential pitfalls of project narrative. So, we are trying to get all animals pregnant to get maximum for better results. Abstracts and manuscripts will be written, submitted, and published. We look forward to the challenges ofmulti-omics data integration, as these data sets are following two different approaches from the publication point of view. The data normalization of both data sets later might alter some of the results for multi-omics integration.
Impacts
What was accomplished under these goals?
The fetal liver and muscle samples from F1 and F2 generations were sequenced for both micro-RNAs (miRNA) and methylation pattern (through Reduced representation bisulfite sequencing, RRBS). The data sets were analyzed following miRDeep2 and methylKit pipelines using miRDeep2.0.1.3 and methylKit v1.12.0 packages, respectively. The differentially expressed microRNAs (DEM) and differentially methylated regions (DMR) were considered significant at FDR < 0.1. The DEMs results for liver samples were found consistent for F1 and F2 generations, as bta-miR-206 was the only DEM identified significantly contributing. The bta-miR-206 was found to be upregulated in fetal hepatic tissue of low gain (LG) animals in F1-generation, indicating fetal reserves were modulated to compensate low gain effect. But its expression was found to be downregulated in fetal hepatic tissues of LG animals in F2 generation, indicating that the low gain effects are being compensated and the developing fetuses are now potentially building mineral reserves as anticipated. The DEMs results for muscle samples were not found significant in F1-generation, indicating that the metabolic processes potentially modulated by liver were sufficient enough to meet the normal muscular development in LG animals compared to moderate gain (MG) animals. But the DEMs found significantly associated with muscular development in F2-generation were bta-miR-100, bta-miR-218, and bta-let-7g. In RRBS analyses, the DMRs were mapped to transcription start sites (TSS) in CpG island regions of gene promoters and based on genes involved their potential regulated functions were explored for LG vs. MG animals. Following this, we identified 429 DMR in the hepatic tissue of F1 generation where 213 regions were hyper-methylated while 216 regions were found hypo-methylated in LG vs. MG animals. In F2 samples we identified 1030 DMRs in hepatic tissue, where 511 were hyper-methylated and 519 DMRs were found hypo-methylated.. We identified muscular tissue DMRs associated genes to find out the functional pathways involved in LG vs. MG animals. We identified 2483 DMR in the muscular tissue of F1 generation where 1322 regions were hyper-methylated while 1161 regions were found hypo-methylated in LG vs. MG animals. In F2 muscle samples we identified 1873 DMRs, where 1032 were hyper-methylated while 841 were found hypo-methylated.
Publications
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