Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition

Maternal prepartum supplementation of protein and energy and body condition score modulated the performance of Bos indicus-influenced cow-calf pairs

Retrospective analyses were performed on a dataset of 1188 fall-calving, Brangus cow-calf pairs. Analyses 1 sorted cows according to their initial body condition score (BCS < 5 vs. ≥ 5) and whether they received (SUP) or not (NOSUP) prepartum supplementation of protein and energy. Analyses 2 sorted cows according to their calving BCS (BCS < 5 or ≥ 5) and BCS change from calving until the start of the breeding season (lost, maintained, or gained). Cows were not estrus synchronized and were assigned to natural breeding for 90 days. Prepartum supplementation increased (P = 0.04) pregnancy percentage in cows with initial BCS < 5 but not (P = 0.20) with initial BCS ≥ 5. Calf weaning weight was greatest (P ≤ 0.04) for calves born from SUP cows with an initial BCS ≥ 5 and did not differ (P ≥ 0.56) among all remaining groups. Among cows with calving BCS < 5, pregnancy percentage were less (P = 0.05) for cows that lost vs. maintained/gained BCS. Postpartum BCS change did not (P ≥ 0.16) impact pregnancy percentage of cows calving at BCS ≥ 5. Calf weaning weight increased (P < 0.01) for cows calving with BCS ≥ 5 vs. < 5 and was not impacted (P = 0.47) by postpartum BCS change. Therefore, precalving supplementation improved reproduction of cows with BCS below optimal and weaning weight of calves born from cows with BCS above optimal, whereas calving BCS was the major factor affecting postpartum BCS change and cow reproductive performance.

Fetal programming effect of rumen-protected methionine on primiparous Angus × Simmental offspring's performance and skeletal muscle gene expression

Primiparous Angus × Simmental dams (n = 22) with an average body weight (BW) of 449 ± 32 kg of BW were divided based on two nutritional treatments: control (CTRL) and rumen-protected methionine (RPM). The control group received bermudagrass hay, corn gluten, and soybean hulls pellets supplementation (base diet); whereas the RPM group received the base diet in addition to 0.07% of DM of RPM at a fixed rate during the last trimester of gestation and the first ~80 d of lactation, in which calves (n = 17) were early weaned. Only male calves were included in this study. After weaning, calves born to RPM dams also received RPM from weaning (day 1) to day 100. Blood sampling and skeletal muscle biopsies for subsequent quantitative polymerase chain reaction (PCR) analysis were conducted on days 1, 25, 50, and 100 on calves. Quantitative PCR data were analyzed using GLIMMIX, and blood metabolites concentrations, BW, and body condition score (BCS) were analyzed using the MIXED procedure of SAS. There was no difference in maternal BW and BCS between treatments. Glucose and blood metabolites that served as biomarkers for liver health (e.g., aspartate transaminase, albumin, alkaline phosphatase, and alanine transaminase) were in the normal levels for all calves (P > 0.40). Calves in the RPM group had a greater expression of adipogenic genes (e.g., PPARG, LPL, and CEBPD) at day 100 compared with CTRL (P < 0.01). In addition, DNA methylation (DNMT1) and oxidative stress-related genes (SOD2 and NOS3) in the RPM group were upregulated at day 100 compared with CTRL (P < 0.01). These results may suggest that calves born to primiparous dams exposed to RPM supplementation are more prone to develop greater adipose tissue than CTRL calves. Furthermore, RPM supplementation may improve methylation processes, as shown by the upregulation of DNMT1. The results shown in our study aim at expanding the knowledge on fetal programming and early-life growth and development of beef cattle under supplementation with RPM.

Rumen-protected methionine modulates body temperature and reduces the incidence of heat stress temperatures during the hottest hours of the day of grazing heat-stressed Bos indicus beef cows

This study evaluated the effects of supplementation of rumen-protected methionine (RPM) on body thermoregulation and conception rate of Nelore cows exposed to high temperature-humidity index (THI). On -31 days before the artificial insemination protocol, 562 lactating, multiparous cows were assigned to receive (MG) or not (CG) RPM supplementation (3 g/cow mixed into 100 g of mineral supplement). Both groups remained in tropical pastures and received supplementation for 77 days. A subset of cows (n = 142) remained with an intravaginal thermometer collecting intravaginal temperature (IT). The respective minimum, average, and maximum environmental THI were 72.8, 78.0, and 83.3. Effects of treatment × hour of the day were detected (P < 0.0001) for IT. From 1330 to 1730 h and 1830 to 1900 h, IT was higher (P < 0.05) for CG versus MG cows when exposed to moderate and high THI. The supplementation with RPM did not affect conception rate (CG = 64.4% vs. MG = 58.2%; P > 0.05). In conclusion, 3 g of RPM supplementation lowered internal body temperature and possibly altered critical THI threshold in Nelore cows with no impact on reproduction.

Maternal diet induces persistent DNA methylation changes in the muscle of beef calves

Maternal nutrition during pregnancy can induce epigenetic alterations in the fetal genome, such as changes in DNA methylation. It remains unclear whether these epigenetic alterations due to changes in maternal nutrition are transitory or persist over time. Here, we hypothesized that maternal methionine supplementation during preconception and early pregnancy could alter the fetal epigenome, and some of these alterations could persist throughout different developmental stages of the offspring. Beef cows were randomly assigned to either a control or a methionine-rich diet from - 30 to + 90 d, relative to the beginning of the breeding season. The methylome of loin muscle from the same bull calves (n = 10 per maternal diet) at 30 and 200 days of age were evaluated using whole-genome bisulfite sequencing. Notably, a total of 28,310 cytosines showed persistent methylation differences over time between maternal diets (q-value < 0.10, methylation change > 20%). These differentially methylated cytosines were in the transcription start sites, exons, or splice sites of 341 annotated genes. Over-representation analysis revealed that these differentially methylated genes are involved in muscle contraction, DNA and histone methylation, mitochondrial function, reactive oxygen species homeostasis, autophagy, and PI3K signaling pathway, among other functions. In addition, some of the persistently, differentially methylated cytosines were found in CpG islands upstream of genes implicated in mitochondrial activities and immune response. Overall, our study provides evidence that a maternal methionine-rich diet altered fetal epigenome, and some of these epigenetic changes persisted over time.

One-carbon metabolite supplementation to heifers for the first 14 d of the estrous cycle alters the plasma and hepatic one-carbon metabolite pool and methionine-folate cycle enzyme transcript abundance in a dose-dependent manner

The objective of this study was to determine the dose of folate and vitamin B12 in beef heifers fed rumen protected methionine and choline required to maintain increased B12 levels and intermediates of the methionine-folate cycle in circulation. Angus heifers (n = 30; BW = 392.6 ± 12.6 kg) were individually fed and assigned to one of five treatments: 0XNEG: Total mixed ration (TMR) and saline injections at day 0 and 7 of the estrous cycle, 0XPOS: TMR, rumen protected methionine (MET) fed at 0.08% of the diet DM, rumen protected choline (CHOL) fed at 60 g/d, and saline injections at day 0 and 7, 0.5X: TMR, MET, CHOL, 5 mg B12, and 80 mg folate at day 0 and 7, 1X: TMR, MET CHOL, 10 mg vitamin B12, and 160 mg folate at day 0 and 7, and 2X: TMR, MET, CHOL, 20 mg B12, and 320 mg folate at day 0 and 7. All heifers were estrus synchronized but not bred, and blood was collected on day 0, 2, 5, 7, 9, 12, and 14 of a synchronized estrous cycle. Heifers were slaughtered on day 14 of the estrous cycle for liver collection. Serum B12 concentrations were greater in the 0.5X, 1X, and 2X, compared with 0XNEG and 0XPOS on all days after treatment initiation (P < 0.0001). Serum folate concentrations were greater for the 2X treatment at day 5, 7, and 9 of the cycle compared with all other treatments (P ≤ 0.05). There were no differences (P ≥ 0.19) in hepatic methionine-cycle or choline analyte concentrations by treatment. Concentrations of hepatic folate cycle intermediates were always greater (P ≤ 0.04) in the 2X treatment compared with the 0XNEG and 0XPOS heifers. Serum methionine was greater (P = 0.04) in the 0.5X and 2X heifers compared with 0XNEG, and S-adenosylhomocysteine (SAH) tended (P = 0.06) to be greater in the 0.5X heifers and the S-adenosylmethionine (SAM):SAH ratio was decreased (P = 0.05) in the 0.5X treatment compared with the 0XNEG, 0XPOS, and 2X heifers. The hepatic transcript abundance of MAT2A and MAT2B were decreased (P ≤ 0.02) in the 0.5X heifers compared with the 0XNEG, 0XPOS, and 2X heifers. These data support that beef heifers fed rumen protected methionine and choline require 20 mg B12 and 320 mg folate once weekly to maintain increased concentrations of B12 and folate in serum. Furthermore, these data demonstrate that not all supplementation levels are equal in providing positive responses, and that some levels, such as the 0.5X, may result in a stoichiometric imbalance in the one-carbon metabolism pathway that results in a decreased SAM:SAH ratio.

Benchmarking DNA Methylation Analysis of 14 Alignment Algorithms for Whole Genome Bisulfite Sequencing in Mammals

Whole genome bisulfite sequencing (WGBS) is an essential technique for methylome studies. Although a series of tools have been developed to overcome the mapping challenges caused by bisulfite treatment, the latest available tools have not been evaluated on the performance of reads mapping as well as on biological insights in multiple mammals. Herein, based on the real and simulated WGBS data of 14.77 billion reads, we undertook 936 mappings to benchmark and evaluate 14 wildly utilized alignment algorithms from reads mapping to biological interpretation in humans, cattle and pigs: Bwa-meth, BSBolt, BSMAP, Walt, Abismal, Batmeth2, Hisat_3n, Hisat_3n_repeat, Bismark-bwt2-e2e, Bismark-his2, BSSeeker2-bwt, BSSeeker2-soap2, BSSeeker2-bwt2-e2e and BSSeeker2-bwt2-local. Specifically, Bwa-meth, BSBolt, BSMAP, Bismark-bwt2-e2e and Walt exhibited higher uniquely mapped reads, mapped precision, recall and F1 score than other nine alignment algorithms, and the influences of distinct alignment algorithms on the methylomes varied considerably at the numbers and methylation levels of CpG sites, the calling of differentially methylated CpGs (DMCs) and regions (DMRs). Moreover, we reported that BSMAP showed the highest accuracy at the detection of CpG coordinates and methylation levels, the calling of DMCs, DMRs, DMR-related genes and signaling pathways. These results suggested that careful selection of algorithms to profile the genome-wide DNA methylation is required, and our works provided investigators with useful information on the choice of alignment algorithms to effectively improve the DNA methylation detection accuracy in mammals.

Identification of eQTLs and differential gene expression associated with fetal programming in beef cattle

This study assessed differential gene expression and identified expression quantitative trait loci (eQTLs) from samples of Longissimus lumborum muscle from bulls at 15 months of age submitted to different prenatal nutrition. Upon confirmation of pregnancy, 126 dams were separated into three diet treatments varying the period of inclusion of energy protein supplementation (NP, PP, and FP). At calving, 63 males were genotyped with GGP LD BeadChip. The skeletal muscle of 15 bulls was sequenced (RNA-seq) at 15 months of age. The EdgeR package was used for differential gene expression and principal component analysis (PCA), and the Matrix eQTL package was used for the eQTLs analysis (R statistical). The functional enrichment analysis was performed using the MetaCore® software. No genes differentially expressed were found between treatments (FDR > 0.05); nevertheless, we found 179 cis-tag-eQTLs and 20,762 trans-tag-eQTLs (FDR < 0.05) after linkage disequilibrium analysis. The functional enrichment analysis identified terms from gene ontology related to genes associated to trans-eQTLs (FDR < 0.05) as well as metabolic pathways (> gScore). Most biological pathways and genes found had been previously associated to fetal programming. The different prenatal supplementation strategies did not impact on muscle transcriptome of bulls. Additionally, there is a link between genotype and gene expression levels related to developmental traits in Nellore cattle.

Timing of maternal supplementation of dried distillers grains during late gestation influences postnatal growth, immunocompetence, and carcass characteristics of Bos indicus-influenced beef calves

This 2-yr study investigated the timing of dried distillers grains (DDG) supplementation during the third trimester of gestation of Bos indicus-influenced beef cows and its impact on their offspring performance. On day 0 of each year (84 d before calving), Brangus cows (n = 84/yr; cow age = 8 ± 3 yr) were stratified by initial body weight (BW; 482 ± 75 kg) and body condition score (BCS; 5.3 ± 0.8) and assigned randomly to one of six bahiagrass (Paspalum notatum) pastures (experimental units; 14 cows/pasture). Treatments were assigned randomly to pasture (2 pastures/treatment/yr) and consisted of no prepartum supplementation (CON), 2 kg/d of DDG from day 0 to 42 (LATE42), or 1 kg/d of DDG from day 0 to 84 (LATE84). Following calving (day 84), cow-calf pairs remained in their respective pastures, and cows were offered sugarcane molasses + urea (1.82 kg of dry matter/cow/d) from day 85 until the end of the breeding season (day 224). On day 347, steer calves (n = 38/yr; 11 to 15 steers/treatment/yr) were weaned and transported to the feedlot (1,193 km). Steers were penned according to cow prepartum pasture and managed similarly until the time of harvest. BCS at calving was greater (P < 0.01) for LATE42 and LATE84 vs. CON cows but did not differ (P = 0.16) between LATE42 and LATE84 cows. Calving date, calving percentage, and birth BW of the first offspring did not differ (P ≥ 0.22) among treatments. However, LATE42 cows calved their second offspring 8 d earlier (P = 0.04) compared with CON and LATE84 cows. At weaning (first offspring), LATE84 calves were the heaviest (P ≤ 0.05), CON calves were the lightest, and LATE42 calves had intermediate BW (P ≤ 0.05). Steer plasma concentrations of cortisol and haptoglobin and serum bovine viral diarrhea virus type-1 titers did not differ (P ≥ 0.21) between treatments. Steer serum parainfluenza-3 titers were greater (P = 0.03) for LATE42 vs. CON steers, tended to be greater (P = 0.10) for LATE84 compared with CON steers, and did not differ (P = 0.38) between LATE42 and LATE84 steers. Steer feedlot BW, average daily gain, dry matter intake, and hot carcass weight did not differ (P ≥ 0.36) between treatments. Marbling and the percentage of steers grading choice were greater (P ≤ 0.04) for LATE42 vs. CON steers, whereas LATE84 steers were intermediate. In summary, different timing of DDG supplementation during the third trimester of gestation could be explored to optimize cow BCS and offspring preweaning growth and carcass quality.

Differential Co-Expression Network Analysis Reveals Key Hub-High Traffic Genes as Potential Therapeutic Targets for COVID-19 Pandemic

Background

The recent emergence of COVID-19, rapid worldwide spread, and incomplete knowledge of molecular mechanisms underlying SARS-CoV-2 infection have limited development of therapeutic strategies. Our objective was to systematically investigate molecular regulatory mechanisms of COVID-19, using a combination of high throughput RNA-sequencing-based transcriptomics and systems biology approaches.

Methods

RNA-Seq data from peripheral blood mononuclear cells (PBMCs) of healthy persons, mild and severe 17 COVID-19 patients were analyzed to generate a gene expression matrix. Weighted gene co-expression network analysis (WGCNA) was used to identify co-expression modules in healthy samples as a reference set. For differential co-expression network analysis, module preservation and module-trait relationships approaches were used to identify key modules. Then, protein-protein interaction (PPI) networks, based on co-expressed hub genes, were constructed to identify hub genes/TFs with the highest information transfer (hub-high traffic genes) within candidate modules.

Results

Based on differential co-expression network analysis, connectivity patterns and network density, 72% (15 of 21) of modules identified in healthy samples were altered by SARS-CoV-2 infection. Therefore, SARS-CoV-2 caused systemic perturbations in host biological gene networks. In functional enrichment analysis, among 15 non-preserved modules and two significant highly-correlated modules (identified by MTRs), 9 modules were directly related to the host immune response and COVID-19 immunopathogenesis. Intriguingly, systemic investigation of SARS-CoV-2 infection identified signaling pathways and key genes/proteins associated with COVID-19's main hallmarks, e.g., cytokine storm, respiratory distress syndrome (ARDS), acute lung injury (ALI), lymphopenia, coagulation disorders, thrombosis, and pregnancy complications, as well as comorbidities associated with COVID-19, e.g., asthma, diabetic complications, cardiovascular diseases (CVDs), liver disorders and acute kidney injury (AKI). Topological analysis with betweenness centrality (BC) identified 290 hub-high traffic genes, central in both co-expression and PPI networks. We also identified several transcriptional regulatory factors, including NFKB1, HIF1A, AHR, and TP53, with important immunoregulatory roles in SARS-CoV-2 infection. Moreover, several hub-high traffic genes, including IL6, IL1B, IL10, TNF, SOCS1, SOCS3, ICAM1, PTEN, RHOA, GDI2, SUMO1, CASP1, IRAK3, HSPA5, ADRB2, PRF1, GZMB, OASL, CCL5, HSP90AA1, HSPD1, IFNG, MAPK1, RAB5A, and TNFRSF1A had the highest rates of information transfer in 9 candidate modules and central roles in COVID-19 immunopathogenesis.

Conclusion

This study provides comprehensive information on molecular mechanisms of SARS-CoV-2-host interactions and identifies several hub-high traffic genes as promising therapeutic targets for the COVID-19 pandemic.

Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle

Background

The evaluation of alternative splicing, including differential isoform expression and differential exon usage, can provide some insights on the transcriptional changes that occur in response to environmental perturbations. Maternal nutrition is considered a major intrauterine regulator of fetal developmental programming. The objective of this study was to assess potential changes in splicing events in the longissimus dorsi muscle of beef calves gestated under control or methionine-rich diets. RNA sequencing and whole-genome bisulfite sequencing were used to evaluate muscle transcriptome and methylome, respectively.

Results

Alternative splicing patterns were significantly altered by maternal methionine supplementation. Most of the altered genes were directly implicated in muscle development, muscle physiology, ATP activities, RNA splicing and DNA methylation, among other functions. Interestingly, there was a significant association between DNA methylation and differential exon usage. Indeed, among the set of genes that showed differential exon usage, significant differences in methylation level were detected between significant and non-significant exons, and between contiguous and non-contiguous introns to significant exons.

Conclusions

Overall, our findings provide evidence that a prenatal diet rich in methyl donors can significantly alter the offspring transcriptome, including changes in isoform expression and exon usage, and some of these changes are mediated by changes in DNA methylation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08065-4.

Improving Beef Progeny Performance Through Developmental Programming

Maternal nutritional management during gestation appears to modulate fetal development and imprint offspring postnatal health and performance, via altered organ and tissue development and tissue-specific epigenetics. This review highlighted the studies demonstrating how developmental programming could be explored by beef producers to enhance offspring performance (growth, immune function, and reproduction), including altering cow body condition score (BCS) during pregnancy and maternal supplementation of protein and energy, polyunsaturated fatty acids (PUFA), trace minerals, frequency of supplementation, specific amino acids, and vitamins. However, this review also highlighted that programming effects on offspring performance reported in the literature were highly variable and depended on level, duration, timing, and type of nutrient restriction during gestation. It is suggested that maternal BCS gain during gestation, rather than BCS per se, enhances offspring preweaning growth. Opportunities for boosting offspring productive responses through maternal supplementation of protein and energy were identified more consistently for pre- vs. post-weaning phases. Maternal supplementation of specific nutrients (i.e., PUFA, trace minerals, and methionine) demonstrated potential for improving offspring performance, health and carcass characteristics during immunological challenging scenarios. Despite the growing body of evidence in recent years, the complexity of investigating developmental programming in beef cattle production is also growing and potential reasons for current research challenges are highlighted herein. These challenges include: (1) intrinsic difficulty of accurately measuring cow milk production multiple times in cow-calf systems; (2) larger focus on Bos taurus vs. Bos indicus breeds despite the predominance of Bos indicus-influenced beef breeds in tropical/subtropical environments and their specific, and sometimes opposite, physiological and performance outcomes compared to Bos taurus breeds; (3) limited focus on interaction between prenatal and postnatal management; (4) sex-specific outcomes following similar maternal nutrition during gestation; (5) greater focus on nutrient deficiency vs. excess; (6) limited implementation of immunological challenges; and (7) lack of multigeneration and longer periods of offspring evaluation. This review provides multiple evidence that such obstacles need to be overcome in order to significantly advance the scientific knowledge of developmental programming in beef cattle and promote global beef production.

Integrated Network Analysis to Identify Key Modules and Potential Hub Genes Involved in Bovine Respiratory Disease: A Systems Biology Approach

Background: Bovine respiratory disease (BRD) is the most common disease in the beef and dairy cattle industry. BRD is a multifactorial disease resulting from the interaction between environmental stressors and infectious agents. However, the molecular mechanisms underlying BRD are not fully understood yet. Therefore, this study aimed to use a systems biology approach to systematically evaluate this disorder to better understand the molecular mechanisms responsible for BRD. Methods: Previously published RNA-seq data from whole blood of 18 healthy and 25 BRD samples were downloaded from the Gene Expression Omnibus (GEO) and then analyzed. Next, two distinct methods of weighted gene coexpression network analysis (WGCNA), i.e., module-trait relationships (MTRs) and module preservation (MP) analysis were used to identify significant highly correlated modules with clinical traits of BRD and non-preserved modules between healthy and BRD samples, respectively. After identifying respective modules by the two mentioned methods of WGCNA, functional enrichment analysis was performed to extract the modules that are biologically related to BRD. Gene coexpression networks based on the hub genes from the candidate modules were then integrated with protein-protein interaction (PPI) networks to identify hub-hub genes and potential transcription factors (TFs). Results: Four significant highly correlated modules with clinical traits of BRD as well as 29 non-preserved modules were identified by MTRs and MP methods, respectively. Among them, two significant highly correlated modules (identified by MTRs) and six nonpreserved modules (identified by MP) were biologically associated with immune response, pulmonary inflammation, and pathogenesis of BRD. After aggregation of gene coexpression networks based on the hub genes with PPI networks, a total of 307 hub-hub genes were identified in the eight candidate modules. Interestingly, most of these hub-hub genes were reported to play an important role in the immune response and BRD pathogenesis. Among the eight candidate modules, the turquoise (identified by MTRs) and purple (identified by MP) modules were highly biologically enriched in BRD. Moreover, STAT1, STAT2, STAT3, IRF7, and IRF9 TFs were suggested to play an important role in the immune system during BRD by regulating the coexpressed genes of these modules. Additionally, a gene set containing several hub-hub genes was identified in the eight candidate modules, such as TLR2, TLR4, IL10, SOCS3, GZMB, ANXA1, ANXA5, PTEN, SGK1, IFI6, ISG15, MX1, MX2, OAS2, IFIH1, DDX58, DHX58, RSAD2, IFI44, IFI44L, EIF2AK2, ISG20, IFIT5, IFITM3, OAS1Y, HERC5, and PRF1, which are potentially critical during infection with agents of bovine respiratory disease complex (BRDC). Conclusion: This study not only helps us to better understand the molecular mechanisms responsible for BRD but also suggested eight candidate modules along with several promising hub-hub genes as diagnosis biomarkers and therapeutic targets for BRD.

Effects of maternal gestational diet, with or without methionine, on muscle transcriptome of Bos indicus-influenced beef calves following a vaccine-induced immunological challenge

Maternal nutrition during gestation can cause epigenetic effects that translate to alterations in gene expression in offspring. This 2-year study employed RNA-sequencing technology to evaluate the pre- and post-vaccination muscle transcriptome of early-weaned Bos indicus-influenced beef calves born from dams offered different supplementation strategies from 57 ± 5 d prepartum until 17 ± 5 d postpartum. Seventy-two Brangus heifers (36 heifers/yr) were stratified by body weight and body condition score and assigned to bahiagrass pastures (3 heifers/pasture/yr). Treatments were randomly assigned to pastures and consisted of (i) no pre- or postpartum supplementation (NOSUP), (ii) pre- and postpartum supplementation of protein and energy using 7.2 kg of dry matter/heifer/wk of molasses + urea (MOL), or (iii) MOL fortified with 105 g/heifer/wk of methionine hydroxy analog (MOLMET). Calves were weaned on d 147 of the study. On d 154, 24 calves/yr (8 calves/treatment) were randomly selected and individually limit-fed a high-concentrate diet until d 201. Calves were vaccinated on d 160. Muscle biopsies were collected from the same calves (4 calves/treatment/day/yr) on d 154 (pre-vaccination) and 201 (post-vaccination) for gene expression analysis using RNA sequencing. Molasses maternal supplementation led to a downregulation of genes associated with muscle cell differentiation and development along with intracellular signaling pathways (e.g., Wnt and TGF-β signaling pathway) compared to no maternal supplementation. Maternal fortification with methionine altered functional gene-sets involved in amino acid transport and metabolism and the one-carbon cycle. In addition, muscle transcriptome was impacted by vaccination with a total of 2,396 differentially expressed genes (FDR ≤ 0.05) on d 201 vs. d 154. Genes involved in cell cycle progression, extracellular matrix, and collagen formation were upregulated after vaccination. This study demonstrated that maternal supplementation of energy and protein, with or without, methionine has long-term implications on the muscle transcriptome of offspring and potentially influence postnatal muscle development.