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Sajjanar B, Aalam MT, Khan O, Dhara SK, Ghosh J, Gandham RK, Gupta PK, Chaudhuri P, Dutt T, Singh G, Mishra BP. Genome-wide DNA methylation profiles regulate distinct heat stress response in zebu (Bos indicus) and crossbred (Bos indicus × Bos taurus) cattle. Cell Stress Chaperones 2024; 29:603-614. [PMID: 38936463 PMCID: PMC11264184 DOI: 10.1016/j.cstres.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 05/22/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024] Open
Abstract
Epigenetic variations result from long-term adaptation to environmental factors. The Bos indicus (zebu) adapted to tropical conditions, whereas Bos taurus adapted to temperate conditions; hence native zebu cattle and its crossbred (B indicus × B taurus) show differences in responses to heat stress. The present study evaluated genome-wide DNA methylation profiles of these two breeds of cattle that may explain distinct heat stress responses. Physiological responses to heat stress and estimated values of Iberia heat tolerance coefficient and Benezra's coefficient of adaptability revealed better relative thermotolerance of Hariana compared to the Vrindavani cattle. Genome-wide DNA methylation patterns were different for Hariana and Vrindavani cattle. The comparison between breeds indicated the presence of 4599 significant differentially methylated CpGs with 756 hypermethylated and 3845 hypomethylated in Hariana compared to the Vrindavani cattle. Further, we found 79 genes that showed both differential methylation and differential expression that are involved in cellular stress response functions. Differential methylations in the microRNA coding sequences also revealed their functions in heat stress responses. Taken together, epigenetic differences represent the potential regulation of long-term adaptation of Hariana (B indicus) cattle to the tropical environment and relative thermotolerance.
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Affiliation(s)
- Basavaraj Sajjanar
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India; ICAR-Indian Veterinary Research Institute, Bengaluru Campus, Bengaluru, Karnataka, India.
| | - Mohd Tanzeel Aalam
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Owais Khan
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sujoy K Dhara
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Jyotirmoy Ghosh
- ICAR-National Institute of Animal Nutrition and Physiology, Bengaluru, Karnataka, India
| | - Ravi Kumar Gandham
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Praveen K Gupta
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Pallab Chaudhuri
- ICAR-Indian Veterinary Research Institute, Bengaluru Campus, Bengaluru, Karnataka, India
| | - Triveni Dutt
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Gyanendra Singh
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India.
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Mendoza-Martínez GD, Orzuna-Orzuna JF, Roque-Jiménez JA, Gloria-Trujillo A, Martínez-García JA, Sánchez-López N, Hernández-García PA, Lee-Rangel HA. A Polyherbal Mixture with Nutraceutical Properties for Ruminants: A Meta-Analysis and Review of BioCholine Powder. Animals (Basel) 2024; 14:667. [PMID: 38473052 PMCID: PMC11154432 DOI: 10.3390/ani14050667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
BioCholine Powder is a polyherbal feed additive composed of Achyrantes aspera, Trachyspermum ammi, Azadirachta indica, and Citrullus colocynthis. The objective of this study was to analyze published results that support the hypothesis that the polyherbal product BioCholine Powder has rumen bypass choline metabolites through a meta-analysis and effect size analysis (ES). Using Scopus, Web of Science, ScienceDirect, PubMed, and university dissertation databases, a systematic search was conducted for experiments published in scientific documents that evaluated the effects of BioCholine supplementation on the variables of interest. The analyzed data were extracted from twenty-one publications (fifteen scientific articles, three abstracts, and three graduate dissertations available in institutional libraries). The studies included lamb growing-finishing, lactating ewes and goats, calves, and dairy cows. The effects of BioCholine were analyzed using random effects statistical models to compare the weighted mean difference (WMD) between BioCholine-supplemented ruminants and controls (no BioCholine). Heterogeneity was explored, and three subgroup analyses were performed for doses [(4 (or 5 g/d), 8 (10 g/d)], supplementation in gestating and lactating ewes (pre- and postpartum supplementation), and blood metabolites by species and physiological state (lactating goats, calves, lambs, ewes). Supplementation with BioCholine in sheep increased the average daily lamb gain (p < 0.05), final body weight (p < 0.01), and daily milk yield (p < 0.05) without effects on intake or feed conversion. Milk yield was improved in small ruminants with BioCholine prepartum supplementation (p < 0.10). BioCholine supplementation decreased blood urea (p < 0.01) and increased levels of the liver enzymes alanine transaminase (ALT; p < 0.10) and albumin (p < 0.001). BioCholine doses over 8 g/d increased blood glucose, albumin (p < 0.10), cholesterol, total protein, and globulin (p < 0.05). The ES values of BioCholine in retained energy over the control in growing lambs were +7.15% NEm (p < 0.10) and +9.25% NEg (p < 0.10). In conclusion, adding BioCholine Powder to domestic ruminants' diets improves productive performance, blood metabolite indicators of protein metabolism, and liver health, showing its nutraceutical properties where phosphatidylcholine prevails as an alternative that can meet the choline requirements in ruminants.
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Affiliation(s)
- Germán David Mendoza-Martínez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana—Xochimilco, Mexico City 04960, Mexico; (G.D.M.-M.); (J.A.R.-J.); (A.G.-T.); (J.A.M.-G.); (N.S.-L.)
| | | | - José Alejandro Roque-Jiménez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana—Xochimilco, Mexico City 04960, Mexico; (G.D.M.-M.); (J.A.R.-J.); (A.G.-T.); (J.A.M.-G.); (N.S.-L.)
- Instituto de Ciencias Agrícolas, Universidad Autónoma de Baja California, Ejido Nuevo León, Mexicali 21705, Mexico
| | - Adrián Gloria-Trujillo
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana—Xochimilco, Mexico City 04960, Mexico; (G.D.M.-M.); (J.A.R.-J.); (A.G.-T.); (J.A.M.-G.); (N.S.-L.)
| | - José Antonio Martínez-García
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana—Xochimilco, Mexico City 04960, Mexico; (G.D.M.-M.); (J.A.R.-J.); (A.G.-T.); (J.A.M.-G.); (N.S.-L.)
| | - Nallely Sánchez-López
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana—Xochimilco, Mexico City 04960, Mexico; (G.D.M.-M.); (J.A.R.-J.); (A.G.-T.); (J.A.M.-G.); (N.S.-L.)
| | | | - Héctor Aaron Lee-Rangel
- Facultad de Agronomía y Veterinaria, Centro de Biociencias, Instituto de Investigaciones en Zonas Desérticas, Universidad Autónoma de San Luis Potosí, S.L.P., Soledad de Graciano Sánchez 78000, Mexico;
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Ren Y, Chen X, Zheng X, Wang F, Sun R, Wei L, Zhang Y, Liu H, Lin Y, Hong L, Huang X, Chao Z. Diverse WGBS profiles of longissimus dorsi muscle in Hainan black goats and hybrid goats. BMC Genom Data 2023; 24:77. [PMID: 38097986 PMCID: PMC10720224 DOI: 10.1186/s12863-023-01182-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Goat products have played a crucial role in meeting the dietary demands of people since the Neolithic era, giving rise to a multitude of goat breeds globally with varying characteristics and meat qualities. The primary objective of this study is to pinpoint the pivotal genes and their functions responsible for regulating muscle fiber growth in the longissimus dorsi muscle (LDM) through DNA methylation modifications in Hainan black goats and hybrid goats. METHODS Whole-genome bisulfite sequencing (WGBS) was employed to scrutinize the impact of methylation on LDM growth. This was accomplished by comparing methylation differences, gene expression, and their associations with growth-related traits. RESULTS In this study, we identified a total of 3,269 genes from differentially methylated regions (DMR), and detected 189 differentially expressed genes (DEGs) through RNA-seq analysis. Hypo DMR genes were primarily enriched in KEGG terms associated with muscle development, such as MAPK and PI3K-Akt signaling pathways. We selected 11 hub genes from the network that intersected the gene sets within DMR and DEGs, and nine genes exhibited significant correlation with one or more of the three LDM growth traits, namely area, height, and weight of loin eye muscle. Particularly, PRKG1 demonstrated a negative correlation with all three traits. The top five most crucial genes played vital roles in muscle fiber growth: FOXO3 safeguarded the myofiber's immune environment, FOXO6 was involved in myotube development and differentiation, and PRKG1 facilitated vasodilatation to release more glucose. This, in turn, accelerated the transfer of glucose from blood vessels to myofibers, regulated by ADCY5 and AKT2, ultimately ensuring glycogen storage and energy provision in muscle fibers. CONCLUSION This study delved into the diverse methylation modifications affecting critical genes, which collectively contribute to the maintenance of glycogen storage around myofibers, ultimately supporting muscle fiber growth.
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Affiliation(s)
- Yuwei Ren
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Xing Chen
- Institute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, 430000, China
| | - Xinli Zheng
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Feng Wang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Ruiping Sun
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Limin Wei
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Yan Zhang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Hailong Liu
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Yanning Lin
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Lingling Hong
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Xiaoxian Huang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Zhe Chao
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China.
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Chen X, Duan X, Chong Q, Li C, Xiao H, Chen S. Genome-Wide DNA Methylation Differences between Bos indicus and Bos taurus. Animals (Basel) 2023; 13:ani13020203. [PMID: 36670743 PMCID: PMC9854497 DOI: 10.3390/ani13020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
Disease risk is a persistent problem in domestic cattle farming, while economic traits are the main concern. This study aimed to reveal the epigenetic basis for differences between zebu (Bos indicus) and taurine cattle (Bos taurus) in disease, disease resistance, and economic traits, and provide a theoretical basis for the genetic improvement of domestic cattle. In this study, whole genome bisulfite sequencing (WGBS) was used to analyze the whole-genome methylation of spleen and liver samples from Yunnan zebu and Holstein cattle. In the genome-wide methylation pattern analysis, it was found that the methylation pattern of all samples was dominated by the CG type, which accounted for >94.9%. The DNA methylation levels of different functional regions and transcriptional elements in the CG background varied widely. However, the methylation levels of different samples in the same functional regions or transcriptional elements did not differ significantly. In addition, we identified a large number of differentially methylation region (DMR) in both the spleen and liver groups, of which 4713 and 4663 were annotated to functional elements, and most of them were annotated to the intronic and exonic regions of genes. GO and KEGG functional analysis of the same differentially methylation region (DMG) in the spleen and liver groups revealed that significantly enriched pathways were involved in neurological, disease, and growth functions. As a result of the results of DMR localization, we screened six genes (DNM3, INPP4B, PLD, PCYT1B, KCNN2, and SLIT3) that were tissue-specific candidates for economic traits, disease, and disease resistance in Yunnan zebu. In this study, DNA methylation was used to construct links between genotypes and phenotypes in domestic cattle, providing useful information for further screening of epigenetic molecular markers in zebu and taurine cattle.
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Affiliation(s)
- Xiaona Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Xinyu Duan
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Qingqing Chong
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Chunqing Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Heng Xiao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Shanyuan Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Correspondence: ; Tel.: +86-186-8712-2260
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Masroor S, Aalam MT, Khan O, Tanuj GN, Gandham RK, Dhara SK, Gupta PK, Mishra BP, Dutt T, Singh G, Sajjanar BK. Effect of acute heat shock on stress gene expression and DNA methylation in zebu (Bos indicus) and crossbred (Bos indicus × Bos taurus) dairy cattle. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2022; 66:1797-1809. [PMID: 35796826 DOI: 10.1007/s00484-022-02320-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/15/2022] [Accepted: 06/21/2022] [Indexed: 05/19/2023]
Abstract
Environmental temperature is one of the major factors to affect health and productivity of dairy cattle. Gene expression networks within the cells and tissues coordinate stress response, metabolism, and milk production in dairy cattle. Epigenetic DNA methylations were found to mediate the effect of environment by regulating gene expression patterns. In the present study, we compared three Indian native zebu cattle, Bos indicus (Sahiwal, Tharparkar, and Hariana) and one crossbred Bos indicus × Bos taurus (Vrindavani) for stress gene expression and differences in the DNA methylation patterns. The results indicated acute heat shock to cultured PBMC affected their proliferation, stress gene expression, and DNA methylation. Interestingly, expressions of HSP70, HSP90, and STIP1 were found more pronounced in zebu cattle than the crossbred cattle. However, no significant changes were observed in global DNA methylation due to acute heat shock, even though variations were observed in the expression patterns of DNA methyltransferases (DNMT1, DNMT3a) and demethylases (TET1, TET2, and TET3) genes. The treatment 5-AzaC (5-azacitidine) that inhibit DNA methylation in proliferating PBMC caused significant increase in heat shock-induced HSP70 and STIP1 expression indicating that hypomethylation facilitated stress gene expression. Further targeted analysis DNA methylation in the promoter regions revealed no significant differences for HSP70, HSP90, and STIP1. However, there was a significant hypomethylation for BDNF in both zebu and crossbred cattle. Similarly, NR3C1 promoter region showed hypomethylation alone in crossbred cattle. Overall, the results indicated that tropically adapted zebu cattle had comparatively higher expression of stress genes than the crossbred cattle. Furthermore, DNA methylation may play a role in regulating expression of certain genes involved in stress response pathways.
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Affiliation(s)
- Sana Masroor
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Mohd Tanzeel Aalam
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Owais Khan
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Gunturu Narasimha Tanuj
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Ravi Kumar Gandham
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Sujoy K Dhara
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Praveen K Gupta
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Bishnu Prasad Mishra
- ICAR-National Bureau of Animal Genetic Resources, Haryana, Karnal, 132001, India
| | - Triveni Dutt
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Gynendra Singh
- Physiology and Climatology Division, ICAR-Indian Veterinary Research Institute, Izatnagar Bareilly, 243122, Uttar Pradesh, India
| | - Basavaraj K Sajjanar
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India.
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