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Zhang D, Wang H, Chen Y, Cai Z, Yu B, Liu J, Feng X, Wang C, Gu Y, Zhang J. MicroRNA-2285f regulates milk fat metabolism by targeting MAP2K2 in bovine mammary epithelial cells. Reprod Domest Anim 2024; 59:e14567. [PMID: 38798178 DOI: 10.1111/rda.14567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/01/2024] [Accepted: 03/22/2024] [Indexed: 05/29/2024]
Abstract
In this study, Holstein dairy cows raised in Ningxia were selected as the research object. Mammary epithelial cells (BMECs) were extracted from the milk of eight Holstein cows with significantly different milk fat expression rates and transcribed for sequencing. Bioinformatics analysis was used to analyse the correlation of fat milk percentage, and the critical miR-2285f regulating milk fat was screened out. The target gene binding sites were predicted, and 293T cells and mammary epithelial cells were used as miRNA and target gene models for functional verification in vitro. The tissue difference of miR-2285f Holstein cows was quantitatively analysed by transfecting miR-2285f mimic and inhibitor. Assay (dual luciferase reporter gene assay) and quantitative real-time PCR (quantitative real-time PCR, qRT-PCR), triglyceride (TAG) detection, oil red O detection of lipid droplets, Western Blot assay, Edu and Flow cytometry, The molecular regulatory effects of miR-2285f and target gene MAP2K2 on milk fat metabolism of Holstein dairy cows were studied. The wild-type vector and mutant vector of map2k2-3'utr were constructed, and double luciferase reporting experiments were conducted to verify that MAP2K2 was one of the target genes of miR-2285f. According to qRT-PCR and Western Blot analysis, miR-2285f mainly regulates the expression of MAP2K2 protein in BMECs at the translation level. Bta-miR-2285f can promote cell proliferation and slow cell apoptosis by regulating MAP2K2. Bta-miR-2285f can promote triglyceride (TAG) and lipid droplet accumulation in mammary epithelial cells by targeting MAP2K2. Bta-miR-2285f can regulate protein levels of fat milk marker gene PPARG by targeting MAP2K2. In conclusion, miR-2285f can target the expression of the MAP2K2 gene, promote the proliferation of dairy mammary epithelial cells, inhibit cell apoptosis and regulate the milk fat metabolism in dairy mammary epithelial cells. The results of this study revealed the function of miR-2285f in regulating the differential expression of fat milk in Holstein dairy cows at the cellular level. They provided a theoretical and experimental basis for analysing the regulation network of milk fat synthesis of Holstein dairy cows and the molecular breeding of dairy cows.
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Affiliation(s)
- Di Zhang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - HuiJun Wang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - YaFei Chen
- Yinchuan Animal Husbandry Technology Promotion Service Center, Yinchuan, China
| | - ZhengYun Cai
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - BaoJun Yu
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - JiaMin Liu
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - XiaoFang Feng
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - ChuanChuan Wang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - YaLing Gu
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - Juan Zhang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
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Ojo OE, Hajek L, Johanns S, Pacífico C, Sener-Aydemir A, Ricci S, Rivera-Chacon R, Castillo-Lopez E, Reisinger N, Zebeli Q, Kreuzer-Redmer S. Evaluation of circulating microRNA profiles in blood as potential candidate biomarkers in a subacute ruminal acidosis cow model - a pilot study. BMC Genomics 2023; 24:333. [PMID: 37328742 DOI: 10.1186/s12864-023-09433-y] [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: 08/08/2022] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Subacute ruminal acidosis (SARA) is a metabolic disorder often observed in high-yielding dairy cows, that are fed diets high in concentrates. We hypothesized that circulating miRNAs in blood of cows could serve as potential candidate biomarkers to detect animals with metabolic dysbalances such as SARA. MicroRNAs (miRNAs) are a class of small non-coding RNAs, serving as regulators of a plethora of molecular processes. To test our hypothesis, we performed a pilot study with non-lactating Holstein-Friesian cows fed a forage diet (FD; 0% concentrate, n = 4) or a high-grain diet (HG; 65% concentrate, n = 4) to induce SARA. Comprehensive profiling of miRNA expression in plasma and leucocytes were performed by next generation sequencing (NGS). The success of our model to induce SARA was evaluated based on ruminal pH and was evidenced by increased time spent with a pH threshold of 5.8 for an average period of 320 min/d. RESULTS A total of 520 and 730 miRNAs were found in plasma and leucocytes, respectively. From these, 498 miRNAs were shared by both plasma and leucocytes, with 22 miRNAs expressed exclusively in plasma and 232 miRNAs expressed exclusively in leucocytes. Differential expression analysis revealed 10 miRNAs that were up-regulated and 2 that were down-regulated in plasma of cows when fed the HG diet. A total of 63 circulating miRNAs were detected exclusively in the plasma of cows with SARA, indicating that these animals exhibited a higher number and diversity of circulating miRNAs. Considering the total read counts of miRNAs expressed when fed the HG diet, differentially expressed miRNAs ( log2 fold change) and known function, we have identified bta-miR-11982, bta-miR-1388-5p, bta-miR-12034, bta-miR-2285u, and bta-miR-30b-3p as potential candidates for SARA-biomarker in cows by NGS. These were further subjected to validation using small RNA RT-qPCR, confirming the promising role of bta-miR-30b-3p and bta-miR-2285. CONCLUSION Our data demonstrate that dietary change impacts the release and expression of miRNAs in systemic circulation, which may modulate post-transcriptional gene expression in cows undergoing SARA. Particularly, bta-miR-30b-3p and bta-miR-2285 might serve as promising candidate biomarker predictive for SARA and should be further validated in larger cohorts.
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Affiliation(s)
- O E Ojo
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - L Hajek
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - S Johanns
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - C Pacífico
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
- Biome Diagnostics GmbH, Vienna, Austria
| | - A Sener-Aydemir
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - S Ricci
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - R Rivera-Chacon
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - E Castillo-Lopez
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - N Reisinger
- DSM, BIOMIN Research Center, Tulln an Der Donau, Austria
| | - Q Zebeli
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - S Kreuzer-Redmer
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria.
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria.
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Ojo OE, Kreuzer-Redmer S. MicroRNAs in Ruminants and Their Potential Role in Nutrition and Physiology. Vet Sci 2023; 10:vetsci10010057. [PMID: 36669058 PMCID: PMC9867202 DOI: 10.3390/vetsci10010057] [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: 09/21/2022] [Revised: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The knowledge of how diet choices, dietary supplements, and feed intake influence molecular mechanisms in ruminant nutrition and physiology to maintain ruminant health, is essential to attain. In the present review, we focus on the role of microRNAs in ruminant health and disease; additionally, we discuss the potential of circulating microRNAs as biomarkers of disease in ruminants and the state of technology for their detection, also considering the major difficulties in the transition of biomarker development from bench to clinical practice. MicroRNAs are an inexhaustible class of endogenous non-protein coding small RNAs of 18 to 25 nucleotides that target either the 3' untranslated (UTR) or coding region of genes, ensuring a tight post-transcriptionally controlled regulation of gene expression. The development of new "omics" technologies facilitated a fresh perspective on the nutrition-to-gene relationship, incorporating more extensive data from molecular genetics, animal nutrition, and veterinary sciences. MicroRNAs might serve as important regulators of metabolic processes and may present the inter-phase between nutrition and gene regulation, controlled by the diet. The development of biomarkers holds the potential to revolutionize veterinary practice through faster disease detection, more accurate ruminant health monitoring, enhanced welfare, and increased productivity. Finally, we summarize the latest findings on how microRNAs function as biomarkers, how technological paradigms are reshaping this field of research, and how platforms are being used to identify novel biomarkers. Numerous studies have demonstrated a connection between circulating microRNAs and ruminant diseases such as mastitis, tuberculosis, foot-and-mouth disease, fasciolosis, and metabolic disorders. Therefore, the identification and analysis of a small number of microRNAs can provide crucial information about the stage of a disease, etiology, and prognosis.
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Alfalfa Xeno-miR168b Target CPT1A to Regulate Milk Fat Synthesis in Bovine Mammary Epithelial Cells. Metabolites 2023; 13:metabo13010076. [PMID: 36677001 PMCID: PMC9866016 DOI: 10.3390/metabo13010076] [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: 12/06/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
It was shown that microRNAs (miRNAs) play an important role in the synthesis of milk fat; thus, this manuscript evaluated whether exogenous miRNA (xeno-miRNAs) from alfalfa could influence the milk fat content in dairy cows. At first, mtr-miR168b was screened from dairy cow milk and blood. Then, EdU staining, flow cytometry, Oil Red O staining, qRT-PCR, and WB were applied to explore the effect of xeno-miR168b on the proliferation, apoptosis, and lipid metabolism of bovine mammary epithelial cells (BMECs). Finally, in order to clarify the pathway that regulated the lipid metabolism of BMECs using xeno-miR168b, a double-luciferase reporter assay was used to verify the target gene related to milk fat. These results showed that overexpression of xeno-miR168b inhibited cell proliferation but promoted apoptosis, which also decreased the expression of several lipid metabolism genes, including PPARγ, SCD1, C/EBPβ, and SREBP1, significantly inhibited lipid droplet formation, and reduced triglyceride content in BMECs. Furthermore, the targeting relationship between CPT1A and xeno-miR168b was determined and it was confirmed that CPT1A silencing reduced the expression of lipid metabolism genes and inhibited fat accumulation in BMECs. These findings identified xeno-miR168b from alfalfa as a cross-kingdom regulatory element that could influence milk fat content in dairy cows by modulating CPT1A expression.
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Variation of miRNA Content in Cow Raw Milk Depending on the Dairy Production System. Int J Mol Sci 2022; 23:ijms231911681. [PMID: 36232984 PMCID: PMC9569736 DOI: 10.3390/ijms231911681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
Pasture-based milk presents several advantages over milk from intensive industrial farming in terms of human health, the environment, animal welfare, and social aspects. This highlights the need for reliable methods to differentiate milk according to its origin on the market. Here, we explored whether miRNA profiles could serve as a marker of milk production systems. We compared levels of previously described miRNAs in milk from four production systems (altogether 112 milk samples): grazing, zero grazing, grass silage or corn silage. Total RNA was extracted from the fat phase, and miRNAs levels were quantified by real-time quantitative PCR. The levels of the miRNAs bta-miR-155 and bta-miR-103 were higher in the grazing system than in corn silage farms. The levels of bta-miR-532, bta-miR-103 and bta-miR-7863 showed differences between different farm managements. The miRNAs bta-miR-155 and bta-miR-103 were predicted to participate in common functions related to fat metabolism and fatty acid elongation. All four differentially expressed miRNAs were predicted to participate in transport, cell differentiation, and metabolism. These results suggest that the dairy production system influences the levels of some miRNAs in milk fat, and that bta-miR-155 and bta-miR-103 may be potential biomarkers to identify milk from pasture-managed systems.
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Winter E, Cisilotto J, Goetten ALF, Veiga Â, Ramos AT, Zimermann FC, Reck C, Creczynski-Pasa TB. MicroRNAs as serum biomarker for Senecio brasiliensis poisoning in cattle. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 94:103906. [PMID: 35697189 DOI: 10.1016/j.etap.2022.103906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/12/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Senecio spp. is one of the most frequent plant-related poisonings in cattle. Its ingestion generates the disease seneciosis, characterized by hepatic damages. Liver biopsies and serum markers dosage are tools used in diagnosis; however, many breeding cattle are undiagnosed. MicroRNAs are non-coding RNA, stable in biological fluids. Their difference in expression levels may indicate the presence of the poisoning. We analyzed the miRNA profiling to identify potential diagnostic biomarkers for Senecio brasiliensis poisoning. The expression of miR-21, miR-885, miR-122, miR-181b, miR-30a, miR-378, and let-7 f were evaluated in the serum of exposed cattle. At least one histological change was found in liver and lower quantity of albumin and high AST and ALP were also detected. MiRNAs miR-30a, miR-378, miR-21, miR-885, and miR-122 presented significantly higher expression in intoxicated animals than in healthy animals. Furthermore, miR-122, miR-885, and, especially, miR-21 signatures demonstrated high sensitivity and specificity, with potential application for detecting poisoning.
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Affiliation(s)
- Evelyn Winter
- Department of Agriculture, Biodiversity and Forest, Postgraduate Program in Conventional and Integrative Veterinary Medicine, Curitibanos, SC 89520-000, Brazil.
| | - Julia Cisilotto
- Postgraduate Program in Pharmacy, Federal University of Santa Catarina, Florianópolis, SC 88040-900, Brazil
| | - André L F Goetten
- Department of Agriculture, Biodiversity and Forest, Postgraduate Program in Conventional and Integrative Veterinary Medicine, Curitibanos, SC 89520-000, Brazil
| | - Ângela Veiga
- Department of Agriculture, Biodiversity and Forest, Postgraduate Program in Conventional and Integrative Veterinary Medicine, Curitibanos, SC 89520-000, Brazil
| | - Adriano T Ramos
- Department of Agriculture, Biodiversity and Forest, Postgraduate Program in Conventional and Integrative Veterinary Medicine, Curitibanos, SC 89520-000, Brazil
| | - Francielli C Zimermann
- Department of Agriculture, Biodiversity and Forest, Postgraduate Program in Conventional and Integrative Veterinary Medicine, Curitibanos, SC 89520-000, Brazil
| | - Carolina Reck
- VERTÁ, Laboratory of Veterinary Diagnostic, Institute of Veterinary Research and Diagnostic, Curitibanos, SC 89520-000, Brazil
| | - Tânia B Creczynski-Pasa
- Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, SC 88040-900, Brazil
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Cremonesi P, Capra E, Turri F, Lazzari B, Chessa S, Battelli G, Colombini S, Rapetti L, Castiglioni B. Effect of Diet Enriched With Hemp Seeds on Goat Milk Fatty Acids, Transcriptome, and miRNAs. FRONTIERS IN ANIMAL SCIENCE 2022. [DOI: 10.3389/fanim.2022.909271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In dairy ruminants, a diet supplemented with feed rich in unsaturated fatty acids can be an effective medium to increase the health-promoting properties of milk, although their effect on the pathways/genes involved in these processes has not been properly and completely defined to date. To improve our knowledge of the cell’s activity in specific conditions, next-generation RNA-sequencing technology was used to allow whole transcriptome characterization under given conditions. In addition to this, microRNAs (miRNAs) have recently been known as post-transcriptional regulators in fatty acid and cholesterol metabolism by targeting lipid metabolism genes. In this study, to analyze the transcriptome and miRNAs in goat milk after a supplemental diet enriched with linoleic acid (hemp seeds), next-generation RNA-sequencing was used in order to point out the general biological mechanisms underlying the effects related to milk fat metabolism. Ten pluriparous Alpine goats were fed with the same pretreatment diet for 40 days; then, they were arranged to two dietary treatments consisting of control (C) and hemp seed (H)-supplemented diets. Milk samples were collected at 40 (time point = T0) and 140 days of lactation (time point = T1). Milk fatty acid (FA) profiles revealed a significant effect of hemp seeds that determined a strong increment in the preformed FA, causing a reduction in the concentration of de-novo FA. Monounsaturated and polyunsaturated n−3 FAs were increased by hemp treatment, determining a reduction in the n−6/n−3 ratio. After removing milk fats and proteins, RNA was extracted from the milk cells and transcriptomic analysis was conducted using Illumina RNA-sequencing. A total of 3,835 genes were highly differentially expressed (p-value < 0.05, fold change > 1.5, and FDR < 0.05) in the H group. Functional analyses evidenced changes in metabolism, immune, and inflammatory responses. Furthermore, modifications in feeding strategies affected also key transcription factors regulating the expression of several genes involved in milk fat metabolism, such as peroxisome proliferator-activated receptors (PPARs). Moreover, 38 (15 known and 23 novel) differentially expressed miRNAs were uncovered in the H group and their potential functions were also predicted. This study gives the possibility to improve our knowledge of the molecular changes occurring after a hemp seed supplementation in the goat diet and increase our understanding of the relationship between nutrient variation and phenotypic effects.
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Liu X, Tang Y, Wu J, Liu JX, Sun HZ. Feedomics provides bidirectional omics strategies between genetics and nutrition for improved production in cattle. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 9:314-319. [PMID: 35600547 PMCID: PMC9097626 DOI: 10.1016/j.aninu.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/10/2022] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
Increasing the efficiency and sustainability of cattle production is an effective way to produce valuable animal proteins for a growing human population. Genetics and nutrition are the 2 major research topics in selecting cattle with beneficial phenotypes and developing genetic potentials for improved performance. There is an inextricable link between genetics and nutrition, which urgently requires researchers to uncover the underlying molecular mechanisms to optimize cattle production. Feedomics integrates a range of omic techniques to reveal the mechanisms at different molecular levels related to animal production and health, which can provide novel insights into the relationships of genes and nutrition/nutrients. In this review, we summarized the applications of feedomics techniques to reveal the effect of genetic elements on the response to nutrition and investigate how nutrients affect the functional genome of cattle from the perspective of both nutrigenetics and nutrigenomics. We highlighted the roles of rumen microbiome in the interactions between host genes and nutrition. Herein, we discuss the importance of feedomics in cattle nutrition research, with a view to ensure that cattle exhibit the best production traits for human consumption from both genetic and nutritional aspects.
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Wang B, Sun H, Wang D, Liu H, Liu J. Constraints on the utilization of cereal straw in lactating dairy cows: A review from the perspective of systems biology. ANIMAL NUTRITION 2022; 9:240-248. [PMID: 35600542 PMCID: PMC9097690 DOI: 10.1016/j.aninu.2022.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/17/2021] [Accepted: 01/24/2022] [Indexed: 10/24/2022]
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10
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Zhu Y, Bu D, Ma L. Integration of Multiplied Omics, a Step Forward in Systematic Dairy Research. Metabolites 2022; 12:metabo12030225. [PMID: 35323668 PMCID: PMC8955540 DOI: 10.3390/metabo12030225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/07/2023] Open
Abstract
Due to their unique multi-gastric digestion system highly adapted for rumination, dairy livestock has complicated physiology different from monogastric animals. However, the microbiome-based mechanism of the digestion system is congenial for biology approaches. Different omics and their integration have been widely applied in the dairy sciences since the previous decade for investigating their physiology, pathology, and the development of feed and management protocols. The rumen microbiome can digest dietary components into utilizable sugars, proteins, and volatile fatty acids, contributing to the energy intake and feed efficiency of dairy animals, which has become one target of the basis for omics applications in dairy science. Rumen, liver, and mammary gland are also frequently targeted in omics because of their crucial impact on dairy animals’ energy metabolism, production performance, and health status. The application of omics has made outstanding contributions to a more profound understanding of the physiology, etiology, and optimizing the management strategy of dairy animals, while the multi-omics method could draw information of different levels and organs together, providing an unprecedented broad scope on traits of dairy animals. This article reviewed recent omics and multi-omics researches on physiology, feeding, and pathology on dairy animals and also performed the potential of multi-omics on systematic dairy research.
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Affiliation(s)
- Yingkun Zhu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- School of Agriculture & Food Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Joint Laboratory on Integrated Crop-Tree-Livestock Systems of the Chinese Academy of Agricultural Sciences (CAAS), Ethiopian Institute of Agricultural Research (EIAR), and World Agroforestry Center (ICRAF), Beijing 100193, China
- Correspondence: (D.B.); (L.M.)
| | - Lu Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (D.B.); (L.M.)
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The Role of microRNAs in the Mammary Gland Development, Health, and Function of Cattle, Goats, and Sheep. Noncoding RNA 2021; 7:ncrna7040078. [PMID: 34940759 PMCID: PMC8708473 DOI: 10.3390/ncrna7040078] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023] Open
Abstract
Milk is an integral and therefore complex structural element of mammalian nutrition. Therefore, it is simple to conclude that lactation, the process of producing milk, is as complex as the mammary gland, the organ responsible for this biochemical activity. Nutrition, genetics, epigenetics, disease pathogens, climatic conditions, and other environmental variables all impact breast productivity. In the last decade, the number of studies devoted to epigenetics has increased dramatically. Reports are increasingly describing the direct participation of microRNAs (miRNAs), small noncoding RNAs that regulate gene expression post-transcriptionally, in the regulation of mammary gland development and function. This paper presents a summary of the current state of knowledge about the roles of miRNAs in mammary gland development, health, and functions, particularly during lactation. The significance of miRNAs in signaling pathways, cellular proliferation, and the lipid metabolism in agricultural ruminants, which are crucial in light of their role in the nutrition of humans as consumers of dairy products, is discussed.
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Cai W, Li C, Li J, Song J, Zhang S. Integrated Small RNA Sequencing, Transcriptome and GWAS Data Reveal microRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle. Front Genet 2021; 12:726706. [PMID: 34712266 PMCID: PMC8546187 DOI: 10.3389/fgene.2021.726706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/21/2021] [Indexed: 01/04/2023] Open
Abstract
Milk protein is one of the most important economic traits in the dairy industry. Yet, the regulatory network of miRNAs for the synthesis of milk protein in mammary is poorly understood. Samples from 12 Chinese Holstein cows with three high ( ≥ 3.5%) and three low ( ≤ 3.0%) phenotypic values for milk protein percentage in lactation and non-lactation were examined through deep small RNA sequencing. We characterized 388 known and 212 novel miRNAs in the mammary gland. Differentially expressed analysis detected 28 miRNAs in lactation and 52 miRNAs in the non-lactating period with a highly significant correlation with milk protein concentration. Target prediction and correlation analysis identified some key miRNAs and their targets potentially involved in the synthesis of milk protein. We analyzed for enrichments of GWAS signals in miRNAs and their correlated targets. Our results demonstrated that genomic regions harboring DE miRNA genes in lactation were significantly enriched with GWAS signals for milk protein percentage traits and that enrichments within DE miRNA targets were significantly higher than in random gene sets for the majority of milk production traits. This integrated study on the transcriptome and posttranscriptional regulatory profiles between significantly differential phenotypes of milk protein concentration provides new insights into the mechanism of milk protein synthesis, which should reveal the regulatory mechanisms of milk secretion.
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Affiliation(s)
- Wentao Cai
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Department of Animal and Avian Science, University of Maryland, College Park, MD, United States
| | - Cong Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, MD, United States
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Integrative analysis of miRNAs and mRNAs revealed regulation of lipid metabolism in dairy cattle. Funct Integr Genomics 2021; 21:393-404. [PMID: 33963462 DOI: 10.1007/s10142-021-00786-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
Lipid metabolism in bovine mammary epithelial cells has been the primary focus of the research of milk fat percentage of dairy cattle. Functional microRNAs can affect lipid metabolism by regulating the expression of candidate genes. The purpose of the study was to screen and identify differentially expressed miRNAs, candidate genes, and co-regulatory pathways related to the metabolism of milk fat. To achieve this aim, we used miRNA and transcriptome data from the mammary epithelial cells of dairy cattle with high (H, 4.85%) and low milk fat percentages (L, 3.41%) during mid-lactation. One hundred ninety differentially expressed genes and 33 differentially expressed miRNAs were significantly enriched in related regulatory networks, of which 27 candidate genes regulated by 18 differentially expressed miRNAs significantly enriched in pathways related to lipid metabolism (p < 0.05). Target relationships between PDE4D and bta-miR-148a, PEG10 and bta-miR-877, SOD3 and bta-miR-2382-5p, and ADAMTS1 and bta-miR-2425-5p were verified using luciferase reporter assays and quantitative RT-PCR. The detection of triglyceride production in BMECs showed that bta-miR-21-3p and bta-miR-148a promote triglyceride synthesis, whereas bta-miR-124a, bta-miR-877, bta-miR-2382-5p, and bta-miR-2425-5p inhibit triglyceride synthesis. The conjoint analysis could identify functional miRNAs and regulatory candidate genes involved in lipid metabolism within the co-expression networks of the dairy cattle mammary system, which contributes to the understanding of potential regulatory mechanisms of genetic element and gene signaling networks involved in milk fat metabolism.
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14
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Wang D, Cai J, Wang B, Ding S, Guan LL, Liu J. Integrative network analysis revealed molecular mechanisms of urine urea output in lactating dairy cows: Potential solutions to reduce environmental nitrate contamination. Genomics 2021; 113:1522-1533. [PMID: 33774166 DOI: 10.1016/j.ygeno.2021.03.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/08/2021] [Accepted: 03/21/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND The enriched nitrogenous compounds in the dairy farms negatively affect the surrounding soil quality and air condition. The objective of this study is to investigate the transcriptomes of five key tissues involved in nitrogen metabolism and their changes under different diets to elucidate the molecular regulatory mechanisms of urine urea nitrogen (UUN) yield, one of the indicators of nitrogenous compound secretion of dairy cows. RESULTS Cows fed high quality forage-based diet had lower UUN content and UUN yield, compared to those fed low quality forage (crop byproducts) based diets. From the transcriptomes of rumen, duodenum, jejunum, liver and udder, key driver genes and their UUN yield-associated functional gene networks were identified. In addition, the functional networks and expression of key drivers in various tissues (such as S100A8, CA1 and BPIFA2C in the duodenum; A2ML1, HMGCS2 and S100A12 in the jejunum; CYP2B6 and GLYCAM1 in the liver; APOE in the udder) changed in the cows fed crop byproducts based diet, which might be the predominant molecules to drive the increase UUN yield in these cows. CONCLUSION The information suggested that gut, liver and udder play important roles in regulating UUN yield, which could regulate nitrogen excretion waste. These findings provide fundamental information on future nutritional intervention strategies to reduce the UUN yield from dairy cows fed human inedible crop byproducts, which is vital for a sustainable and environmentally friendly dairy industry.
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Affiliation(s)
- Diming Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Jie Cai
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bing Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shengsen Ding
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.
| | - Jianxin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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15
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Wang O, Zhou M, Chen Y, McAllister TA, Plastow G, Stanford K, Selinger B, Guan LL. MicroRNAomes of Cattle Intestinal Tissues Revealed Possible miRNA Regulated Mechanisms Involved in Escherichia coli O157 Fecal Shedding. Front Cell Infect Microbiol 2021; 11:634505. [PMID: 33732664 PMCID: PMC7959717 DOI: 10.3389/fcimb.2021.634505] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/11/2021] [Indexed: 01/02/2023] Open
Abstract
Cattle have been suggested as the primary reservoirs of E. coli O157 mainly as a result of colonization of the recto-anal junction (RAJ) and subsequent shedding into the environment. Although a recent study reported different gene expression at RAJ between super-shedders (SS) and non-shedders (NS), the regulatory mechanisms of altered gene expression is unknown. This study aimed to investigate whether bovine non-coding RNAs play a role in regulating the differentially expressed (DE) genes between SS and NS, thus further influencing E. coli O157 shedding behavior in the animals through studying miRNAomes of the whole gastrointestinal tract including duodenum, proximal jejunum, distal jejunum, cecum, spiral colon, descending colon and rectum. The number of miRNAs detected in each intestinal region ranged from 390 ± 13 (duodenum) to 413 ± 49 (descending colon). Comparison between SS and NS revealed the number of differentially expressed (DE) miRNAs ranged from one (in descending colon) to eight (in distal jejunum), and through the whole gut, seven miRNAs were up-regulated and seven were down-regulated in SS. The distal jejunum and rectum were the regions where the most DE miRNAs were identified (eight and seven, respectively). The miRNAs, bta-miR-378b, bta-miR-2284j, and bta-miR-2284d were down-regulated in both distal jejunum and rectum of SS (log2fold-change: −2.7 to −3.8), bta-miR-2887 was down-regulated in the rectum of SS (log2fold-change: −3.2), and bta-miR-211 and bta-miR-29d-3p were up-regulated in the rectum of SS (log2fold-change: 4.5 and 2.2). Functional analysis of these miRNAs indicated their potential regulatory role in host immune functions, including hematological system development and immune cell trafficking. Our findings suggest that altered expression of miRNA in the gut of SS may lead to differential regulation of immune functions involved in E. coli O157 super-shedding in cattle.
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Affiliation(s)
- Ou Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Mi Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Yanhong Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Tim A McAllister
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Kim Stanford
- Research and Innovation Services, University of Lethbridge, Lethbridge, AB, Canada
| | - Brent Selinger
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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16
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The neglected nutrigenomics of milk: What is the role of inter-species transfer of small non-coding RNA? FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2020.100796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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17
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Kosovsky GY, Glazko VI, Glazko GV, Zybaylov BL, Glazko TT. Leukocytosis and Expression of Bovine Leukemia Virus microRNAs in Cattle. Front Vet Sci 2020; 7:272. [PMID: 32582774 PMCID: PMC7296161 DOI: 10.3389/fvets.2020.00272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/23/2020] [Indexed: 11/13/2022] Open
Abstract
Bovine Leukemia Virus (BLV) is an established model for studying retroviral infections, in particular the infection by the human T-cell leukemia type 1 (HTLV-1) virus. Here, we quantified gene expression of several BLV-related genes: effector protein of T and NK-killer cells NK-lysin (Nklys), reverse BLV transcriptase pol, BLV receptor (blvr), and also key enzymes of the microRNA maturation, Dicer (dc1) and Argonaut (ago2). The differences in the expression of the above genes were compared between five groups: (1) BLV infected cows with high and (2) low lymphocyte count, (3) with and (4) without BLV microRNA expressions, and (5) cows without BLV infections (control group). As compared to control, infected cows with high lymphocyte count and BLV microRNA expression had significantly decreased Nklys gene expression and increased dc1 and ago2 gene expressions. Few infected animals without pol gene expression nevertheless transcribed BLV microRNA, while others with pol gene expression didn't transcribe BLV microRNA. Notably, Pol expression significantly (P < 0.05) correlated with dc1 expression. For infected animals, there were no direct correlations between the number of leukocytes and pol, Nklys, and BLV microRNA gene expressions. Blvr gene expression is typical for juvenile lymphocytes and decreases during terminal differentiation. Our data suggest that BLV infects primarily juvenile lymphocytes, which further divide into two groups. One group expresses BLV DNA and another one expressed BLV microRNA that decreases host immune response against cells, expressing BLV proteins. It is suspected that regulatory microRNAs play a significant role in the bovine leukemia infections, yet the precise mechanisms and targets of the microRNAs remain poorly defined. Vaccines that are currently in use have a low response rate. Understanding of microRNA regulatory mechanisms and targets would allow to develop more effective vaccines for retroviral infections.
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Affiliation(s)
- Gleb Yu Kosovsky
- FSBEI HPE Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Valery I Glazko
- FSBEI HPE Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia.,FSBSI V.A. Afanasyev RI for Fur and Rabbit Farming, Moscow, Russia
| | - Galina V Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Boris L Zybaylov
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Tatiana T Glazko
- FSBEI HPE Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia.,FSBSI V.A. Afanasyev RI for Fur and Rabbit Farming, Moscow, Russia
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18
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Lai YC, Lai YT, Rahman MM, Chen HW, Husna AA, Fujikawa T, Ando T, Kitahara G, Koiwa M, Kubota C, Miura N. Bovine milk transcriptome analysis reveals microRNAs and RNU2 involved in mastitis. FEBS J 2019; 287:1899-1918. [PMID: 31663680 DOI: 10.1111/febs.15114] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 07/09/2019] [Accepted: 10/29/2019] [Indexed: 12/22/2022]
Abstract
Mastitis is a common inflammatory infectious disease in dairy cows. To understand the microRNA (miRNA) expression profile changes during bovine mastitis, we undertook a genome-wide miRNA study of normal milk and milk that tested positive on the California mastitis test for bovine mastitis (CMT+). Twenty-five miRNAs were differentially expressed (23 miRNAs upregulated and two downregulated) during bovine mastitis relative to their expression in normal milk. Upregulated mature miR-1246 probably derived from a U2 small nuclear RNA rather than an miR-1246 precursor. The significantly upregulated miRNA precursors and RNU2 were significantly enriched on bovine chromosome 19, which is homologous to human chromosome 17. A gene ontology analysis of the putative mRNA targets of the significantly upregulated miRNAs showed that these miRNAs were involved in binding target mRNA transcripts and regulating target gene expression, and a Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the upregulated miRNAs were predominantly related to cancer and immune system pathways. Three novel miRNAs were associated with bovine mastitis and were relatively highly expressed in milk. We confirmed that one of the novel mastitis-related miRNAs was significantly upregulated using a digital PCR system. The differentially expressed miRNAs were involved in human cancers, infections, and immune-related diseases. The genome-wide analysis of miRNA profiles in this study provides insight into bovine mastitis and inflammatory diseases. DATABASES: The miRNAseq generated for this study can be found in the Sequence Read Archive (SRA) under BioProject Number PRJNA421075 and SRA Study Number SRP126134 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA421075).
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Affiliation(s)
- Yu-Chang Lai
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
| | | | - Md Mahfuzur Rahman
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Japan
| | - Hui-Wen Chen
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan.,Joint Graduate School of Veterinary Medicine, Kagoshima University, Japan
| | - Al Asmaul Husna
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Japan
| | - Takuro Fujikawa
- The United Graduate School of Veterinary Science, Yamaguchi University, Japan.,Laboratory of Veterinary Theriogenology, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
| | - Takaaki Ando
- Laboratory of Veterinary Theriogenology, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
| | - Go Kitahara
- Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Japan
| | - Masateru Koiwa
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Chikara Kubota
- Laboratory of Veterinary Theriogenology, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
| | - Naoki Miura
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
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19
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Sun HZ, Plastow G, Guan LL. Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health. J Dairy Sci 2019; 102:5853-5870. [PMID: 31030919 DOI: 10.3168/jds.2018-16126] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/02/2019] [Indexed: 12/22/2022]
Abstract
Dairy cattle science has evolved greatly over the past century, contributing significantly to the improvement in milk production achieved today. However, a new approach is needed to meet the increasing demand for milk production and address the increased concerns about animal health and welfare. It is now easy to collect and access large and complex data sets consisting of molecular, physiological, and metabolic data as well as animal-level data (such as behavior). This provides new opportunities to better understand the mechanisms regulating cow performance. The recently proposed concept of feedomics could help achieve this goal by increasing our understanding of interactions between the different components or levels and their impact on animal production. Feedomics is an emerging field that integrates a range of omics technologies (e.g., genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, and metatranscriptomics) to provide these insights. In this way, we can identify the best strategies to improve overall animal productivity, product quality, welfare, and health. This approach can help research communities elucidate the complex interactions among nutrition, environment, management, animal genetics, metabolism, physiology, and the symbiotic microbiota. In this review, we summarize the outcomes of the most recent research on omics in dairy cows and highlight how an integrated feedomics approach could be applied in the future to improve dairy cow production and health. Specifically, we focus on 2 topics: (1) improving milk yield and milk quality, and (2) understanding metabolic physiology in transition dairy cows, which are 2 important challenges faced by the dairy industry worldwide.
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Affiliation(s)
- H Z Sun
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5
| | - G Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5
| | - L L Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5.
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20
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MicroRNA expression profiles across blood and different tissues in cattle. Sci Data 2019; 6:190013. [PMID: 30747916 PMCID: PMC6371894 DOI: 10.1038/sdata.2019.13] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) play essential roles in regulating gene expression involved in various biological functions. The knowledge of miRNA expression profiles across different tissues in cattle is still limited. Using the miRNAs data generated from 158 samples in three studies, we characterized the miRNA expression profiles of bovine sera, exosomes and 11 different tissues. Totally 639 miRNAs were identified and 159 miRNAs were expressed in all samples. After relative log expression normalization, four miRNA expression clusters were generated: 1) sera and exosomes; 2) liver; 3) mammary gland; 4) rumen and gut tissues. The top 10 most abundant miRNAs accounted for >55% of total miRNA expression in each tissue. In addition, this study described a detailed pipeline for identification of both tissue and circulating miRNAs, and the shareable datasets can be re-used by researchers to investigate miRNA-related biological questions in cattle. In addition, a web-based repository was developed, which enables researchers to access the distribution range and raw counts number of the miRNA expression data (https://www.cattleomics.com/micrornaome).
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21
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Salama AAK, Duque M, Wang L, Shahzad K, Olivera M, Loor JJ. Enhanced supply of methionine or arginine alters mechanistic target of rapamycin signaling proteins, messenger RNA, and microRNA abundance in heat-stressed bovine mammary epithelial cells in vitro. J Dairy Sci 2019; 102:2469-2480. [PMID: 30639019 DOI: 10.3168/jds.2018-15219] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022]
Abstract
Heat stress (HS) causes reductions in milk production, but it is unclear whether this effect is due to reduced number or functional capacity (or both) of mammary cells. Methionine supplementation improves milk protein, whereas Arg is taken up in excess by mammary cells to produce energy and nonessential AA that can be incorporated into milk protein. To evaluate molecular mechanisms by which mammary functional capacity is affected by HS and Met or Arg, mammary alveolar (MAC-T) cells were incubated at thermal-neutral (37°C) or HS (42°C) temperatures. Treatments were optimal AA profiles (control; Lys:Met = 2.9:1.0; Lys:Arg = 2.1:1.0), control plus Met (Lys:Met = 2.5:1.0), or control plus Arg (Lys:Arg = 1.0:1.0). After incubation for 6 h, cells were harvested and RNA and protein were extracted for quantitative real-time PCR and Western blotting. Protein abundance of mechanistic target of rapamycin (MTOR), eukaryotic initiation factor 2a, serine-threonine protein kinase (AKT), 4E binding protein 1 (EIF4EBP1), and phosphorylated EIF4EBP1 was lower during HS. The lower phosphorylated EIF4EBP1 with HS would diminish translation initiation and reduce protein synthesis. Both Met and Arg had no effect on MTOR proteins, but the phosphorylated EIF4EBP1 decreased by AA, especially Arg. Additionally, Met but not Arg decreased the abundance of phosphorylated eukaryotic elongation factor 2, which could be positive for protein synthesis. Although HS upregulated the heat shock protein HSPA1A, the apoptotic gene BAX, and the translation inhibitor EIF4EBP1, the mRNA abundance of PPARG, FASN, ACACA (lipogenesis), and BCL2L1 (antiapoptotic) decreased. Greater supply of Met or Arg reversed most of the effects of HS occurring at the mRNA level and upregulated the abundance of HSPA1A. In addition, compared with the control, supply of Met or Arg upregulated genes related to transcription and translation (MAPK1, MTOR, SREBF1, RPS6KB1, JAK2), insulin signaling (AKT2, IRS1), AA transport (SLC1A5, SLC7A1), and cell proliferation (MKI67). Upregulation of microRNA related to cell growth arrest and apoptosis (miR-34a, miR-92a, miR-99, and miR-184) and oxidative stress (miR-141 and miR-200a) coupled with downregulation of fat synthesis-related microRNA (miR-27ab and miR-221) were detected with HS. Results suggest that HS has a direct negative effect on synthesis of protein and fat, mediated in part by coordinated changes in mRNA, microRNA, and protein abundance of key networks. The positive responses with Met and Arg raise the possibility that supplementation with these AA during HS might have a positive effect on mammary metabolism.
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Affiliation(s)
- A A K Salama
- Group of Research in Ruminants (G2R), Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - M Duque
- Grupo de Investigación Biogénesis, Facultad de Ciencias Agrarias, Universidad de Antioquia, Carrera 75 # 65-87, Medellín, Colombia
| | - L Wang
- Department of Animal Science, Southwest University, Rongchang, Chongqing 402460, China
| | - K Shahzad
- Mammalian NutriPhysioGenomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana 61801
| | - M Olivera
- Grupo de Investigación Biogénesis, Facultad de Ciencias Agrarias, Universidad de Antioquia, Carrera 75 # 65-87, Medellín, Colombia
| | - J J Loor
- Mammalian NutriPhysioGenomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana 61801.
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22
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Liu J, Ning C, Li B, Li R, Wu W, Liu H. Hepatic microRNAome reveals potential microRNA-mRNA pairs association with lipid metabolism in pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 32:1458-1468. [PMID: 30208692 PMCID: PMC6722318 DOI: 10.5713/ajas.18.0438] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 09/03/2018] [Indexed: 02/08/2023]
Abstract
Objective As one of the most important metabolic organs, the liver plays vital roles in modulating the lipid metabolism. This study was to compare miRNA expression profiles of the Large White liver between two different developmental periods and to identify candidate miRNAs for lipid metabolism. Methods Eight liver samples were collected from White Large of 70-day fetus (P70) and of 70-day piglets (D70) (with 4 biological repeats at each development period) to construct sRNA libraries. Then the eight prepared sRNA libraries were sequenced using Illumina next-generation sequencing technology on HiSeq 2500 platform. Results As a result, we obtained 346 known and 187 novel miRNAs. Compared with the D70, 55 down- and 61 up-regulated miRNAs were shown to be significantly differentially expressed (DE). Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis indicated that these DE miRNAs were mainly involved in growth, development and diverse metabolic processes. They were predicted to regulate lipid metabolism through adipocytokine signaling pathway, mitogen-activated protein kinase, AMP-activated protein kinase, cyclic adenosine monophosphate, phosphatidylinositol 3 kinase/protein kinase B, and Notch signaling pathway. The four most abundantly expressed miRNAs were miR-122, miR-26a and miR-30a-5p (miR-122 only in P70), which play important roles in lipid metabolism. Integration analysis (details of mRNAs sequencing data were shown in another unpublished paper) revealed that many target genes of the DE miRNAs (miR-181b, miR-145-5p, miR-199a-5p, and miR-98) might be critical regulators in lipid metabolic process, including acyl-CoA synthetase long chain family member 4, ATP-binding casette A4, and stearyl-CoA desaturase. Thus, these miRNAs were the promising candidates for lipid metabolism. Conclusion Our study provides the main differences in the Large White at miRNA level between two different developmental stages. It supplies a valuable database for the further function and mechanism elucidation of miRNAs in porcine liver development and lipid metabolism.
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Affiliation(s)
- Jingge Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Caibo Ning
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bojiang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongyang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Honglin Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
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23
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Sun HZ, Wang DM, Liu HY, Liu JX. Metabolomics Integrated with Transcriptomics Reveals a Subtle Liver Metabolic Risk in Dairy Cows Fed Different Crop By-products. Proteomics 2018; 18:e1800122. [DOI: 10.1002/pmic.201800122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/11/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Hui-Zeng Sun
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition; College of Animal Sciences; Zhejiang University; Hangzhou 310058 P. R. China
| | - Di-Ming Wang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition; College of Animal Sciences; Zhejiang University; Hangzhou 310058 P. R. China
| | - Hong-Yun Liu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition; College of Animal Sciences; Zhejiang University; Hangzhou 310058 P. R. China
| | - Jian-Xin Liu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition; College of Animal Sciences; Zhejiang University; Hangzhou 310058 P. R. China
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24
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Cai W, Li C, Liu S, Zhou C, Yin H, Song J, Zhang Q, Zhang S. Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein Cows. Front Genet 2018; 9:281. [PMID: 30105049 PMCID: PMC6077245 DOI: 10.3389/fgene.2018.00281] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/09/2018] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as a novel class of regulatory molecules involved in various biological processes. However, their role in milk performance is unknown. Here, whole transcriptome RNA sequencing was used to generate the lncRNA transcriptome profiles in mammary tissue samples from 6 Chinese Holstein cows with 3 extremely high and 3 low milk protein percentage phenotypes. In this study, 6,450 lncRNA transcripts were identified through 5 stringent steps and filtration by coding potential. In total, 31 lncRNAs and 18 novel genes were identified to be differentially expressed in high milk protein samples (HP) relative to low milk protein samples (LP), respectively. Differentially expressed lncRNAs were selected to predict target genes through bioinformatics analysis, followed by the integration of differentially expressed mRNA data, gene function, gene ontology (GO) and pathway, genome wide association study (GWAS) and quantitative trait locus (QTL) information, as well as network analysis to further characterize potential interactions. Several lncRNAs were found (such as XLOC_059976) that could be used as candidate markers for milk protein content prediction. This is the first study to perform global expression profiling of lncRNAs and mRNAs related to milk protein traits in dairy cows. These results provide important information and insights into the synthesis of milk proteins, and potential targets for the future improvement of milk quality.
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Affiliation(s)
- Wentao Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Cong Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shuli Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chenghao Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hongwei Yin
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, MD, United States
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Dai W, Wang Q, Zhao F, Liu J, Liu H. Understanding the regulatory mechanisms of milk production using integrative transcriptomic and proteomic analyses: improving inefficient utilization of crop by-products as forage in dairy industry. BMC Genomics 2018; 19:403. [PMID: 29843597 PMCID: PMC5975684 DOI: 10.1186/s12864-018-4808-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 05/21/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Bovine milk is an important nutrient source for humans. Forage plays a vital role in dairy husbandry via affecting milk quality and quantity. However, the differences in mammary metabolism of dairy cows fed different forages remain elucidated. In this study, we utilized transcriptomic RNA-seq and iTRAQ proteomic techniques to investigate and integrate the differences of molecular pathways and biological processes in the mammary tissues collected from 12 lactating cows fed corn stover (CS, low-quality, n = 6) and alfalfa hay (AH, high-quality, n = 6). RESULTS A total of 1631 differentially expressed genes (DEGs; 1046 up-regulated and 585 down-regulated) and 346 differentially expressed proteins (DEPs; 138 increased and 208 decreased) were detected in the mammary glands between the CS- and AH-fed animals. Expression patterns of 33 DEPs (18 increased and 15 decreased) were consistent with the expression of their mRNAs. Compared with the mammary gland of AH-fed cows, the marked expression changes found in the mammary gland of CS group were for genes involved in reduced mammary growth/development (COL4A2, MAPK3, IKBKB, LGALS3), less oxidative phosphorylation (ATPsynGL, ATP6VOA1, ATP5H, ATP6VOD1, NDUFC1), enhanced lipid uptake/metabolism (SLC27A6, FABP4, SOD2, ACADM, ACAT1, IDH1, SCP2, ECHDC1), more active fatty acid beta-oxidation (HMGCS1), less amino acid/protein transport (SLC38A2, SLC7A8, RAB5a, VPS18), reduced protein translation (RPS6, RPS12, RPS16, RPS19, RPS20, RPS27), more proteasome- (PSMC2, PSMC6, PSMD14, PSMA2, PSMA3) and ubiquitin-mediated protein degradation (UBE2B, UBE2H, KLHL9, HSPH1, DNAJA1 and CACYBP), and more protein disassembly-related enzymes (SEC63, DNAJC3, DNAJB1, DNAJB11 and DNAJC12). CONCLUSION Our results indicate that the lower milk production in the CS-fed dairy cows compared with the AH-fed cows was associated with a network of mammary gene expression changes, importantly, the prime factors include decreased energy metabolism, attenuated protein synthesis, enhanced protein degradation, and the lower mammary cell growth. The present study provides insights into the effects of the varying quality of forages on mammary metabolisms, which can help the improvement of strategies in feeding dairy cows with CS-based diet.
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Affiliation(s)
- Wenting Dai
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hang Zhou, 310058 People’s Republic of China
| | - Quanjuan Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hang Zhou, 310058 People’s Republic of China
| | - Fengqi Zhao
- Laboratory of Lactation and Metabolic Physiology, Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT 05405 USA
| | - Jianxin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hang Zhou, 310058 People’s Republic of China
| | - Hongyun Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hang Zhou, 310058 People’s Republic of China
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Comparative transcriptome analysis to investigate the potential role of miRNAs in milk protein/fat quality. Sci Rep 2018; 8:6250. [PMID: 29674689 PMCID: PMC5908868 DOI: 10.1038/s41598-018-24727-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/14/2018] [Indexed: 01/06/2023] Open
Abstract
miRNAs play an important role in the processes of cell differentiation, biological development, and physiology. Here we investigated the molecular mechanisms regulating milk secretion and quality in dairy cows via transcriptome analyses of mammary gland tissues from dairy cows during the high-protein/high-fat, low-protein/low-fat or dry periods. To characterize the important roles of miRNAs and mRNAs in milk quality and to elucidate their regulatory networks in relation to milk secretion and quality, an integrated analysis was performed. A total of 25 core miRNAs were found to be differentially expressed (DE) during lactation compared to non-lactation, and these miRNAs were involved in epithelial cell terminal differentiation and mammary gland development. In addition, comprehensive analysis of mRNA and miRNA expression between high-protein/high-fat group and low-protein/low-fat groups indicated that, 38 miRNAs and 944 mRNAs were differentially expressed between them. Furthermore, 38 DE miRNAs putatively negatively regulated 253 DE mRNAs. The putative genes (253 DE mRNAs) were enriched in lipid biosynthetic process and amino acid transmembrane transporter activity. Moreover, putative DE genes were significantly enriched in fatty acid (FA) metabolism, biosynthesis of amino acids, synthesis and degradation of ketone bodies and biosynthesis of unsaturated FAs. Our results suggest that DE miRNAs might play roles as regulators of milk quality and milk secretion during mammary gland differentiation.
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27
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Sun HZ, Shi K, Wu XH, Xue MY, Wei ZH, Liu JX, Liu HY. Lactation-related metabolic mechanism investigated based on mammary gland metabolomics and 4 biofluids' metabolomics relationships in dairy cows. BMC Genomics 2017; 18:936. [PMID: 29197344 PMCID: PMC5712200 DOI: 10.1186/s12864-017-4314-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 11/16/2017] [Indexed: 01/12/2023] Open
Abstract
Background Lactation is extremely important for dairy cows; however, the understanding of the underlying metabolic mechanisms is very limited. This study was conducted to investigate the inherent metabolic patterns during lactation using the overall biofluid metabolomics and the metabolic differences from non-lactation periods, as determined using partial tissue-metabolomics. We analyzed the metabolomic profiles of four biofluids (rumen fluid, serum, milk and urine) and their relationships in six mid-lactation Holstein cows and compared their mammary gland (MG) metabolomic profiles with those of six non-lactating cows by using gas chromatography-time of flight/mass spectrometry. Results In total, 33 metabolites were shared among the four biofluids, and 274 metabolites were identified in the MG tissues. The sub-clusters of the hierarchical clustering analysis revealed that the rumen fluid and serum metabolomics profiles were grouped together and highly correlated but were separate from those for milk. Urine had the most different profile compared to the other three biofluids. Creatine was identified as the most different metabolite among the four biofluids (VIP = 1.537). Five metabolic pathways, including gluconeogenesis, pyruvate metabolism, the tricarboxylic acid cycle (TCA cycle), glycerolipid metabolism, and aspartate metabolism, showed the most functional enrichment among the four biofluids (false discovery rate < 0.05, fold enrichment >2). Clear discriminations were observed in the MG metabolomics profiles between the lactating and non-lactating cows, with 54 metabolites having a significantly higher abundance (P < 0.05, VIP > 1) in the lactation group. Lactobionic acid, citric acid, orotic acid and oxamide were extracted by the S-plot as potential biomarkers of the metabolic difference between lactation and non-lactation. The TCA cycle, glyoxylate and dicarboxylate metabolism, glutamate metabolism and glycine metabolism were determined to be pathways that were significantly impacted (P < 0.01, impact value >0.1) in the lactation group. Among them, the TCA cycle was the most up-regulated pathway (P < 0.0001), with 7 of the 10 related metabolites increased in the MG tissues of the lactating cows. Conclusions The overall biofluid and MG tissue metabolic mechanisms in the lactating cows were interpreted in this study. Our findings are the first to provide an integrated insight and a better understanding of the metabolic mechanism of lactation, which is beneficial for developing regulated strategies to improve the metabolic status of lactating dairy cows. Electronic supplementary material The online version of this article (10.1186/s12864-017-4314-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui-Zeng Sun
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Kai Shi
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xue-Hui Wu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Ming-Yuan Xue
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zi-Hai Wei
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Jian-Xin Liu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Hong-Yun Liu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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Dai W, Wang Q, Zou Y, White R, Liu J, Liu H. Short communication: Comparative proteomic analysis of the lactating and nonlactating bovine mammary gland. J Dairy Sci 2017; 100:5928-5935. [DOI: 10.3168/jds.2016-12366] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/06/2017] [Indexed: 01/09/2023]
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Do DN, Li R, Dudemaine PL, Ibeagha-Awemu EM. MicroRNA roles in signalling during lactation: an insight from differential expression, time course and pathway analyses of deep sequence data. Sci Rep 2017; 7:44605. [PMID: 28317898 PMCID: PMC5357959 DOI: 10.1038/srep44605] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/09/2017] [Indexed: 01/30/2023] Open
Abstract
The study examined microRNA (miRNA) expression and regulatory patterns during an entire bovine lactation cycle. Total RNA from milk fat samples collected at the lactogenesis (LAC, day1 [D1] and D7), galactopoiesis (GAL, D30, D70, D130, D170 and D230) and involution (INV, D290 and when milk production dropped to 5 kg/day) stages from 9 cows was used for miRNA sequencing. A total of 475 known and 238 novel miRNAs were identified. Fifteen abundantly expressed miRNAs across lactation stages play regulatory roles in basic metabolic, cellular and immunological functions. About 344, 366 and 209 miRNAs were significantly differentially expressed (DE) between GAL and LAC, INV and GAL, and INV and LAC stages, respectively. MiR-29b/miR-363 and miR-874/miR-6254 are important mediators for transition signals from LAC to GAL and from GAL to INV, respectively. Moreover, 58 miRNAs were dynamically DE in all lactation stages and 19 miRNAs were significantly time-dependently DE throughout lactation. Relevant signalling pathways for transition between lactation stages are involved in apoptosis (PTEN and SAPK/JNK), intracellular signalling (protein kinase A, TGF-β and ERK5), cell cycle regulation (STAT3), cytokines, hormones and growth factors (prolactin, growth hormone and glucocorticoid receptor). Overall, our data suggest diverse, temporal and physiological signal-dependent regulatory and mediator functions for miRNAs during lactation.
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Affiliation(s)
- Duy N Do
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, Quebec, J1M 0C8, Canada.,Department of Animal Science, McGill University, 21111, Lakeshore Road, Ste-Anne-de Bellevue, Quebec, J1M 0C8, Canada
| | - Ran Li
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, Quebec, J1M 0C8, Canada.,College of Animal Science and Technology, Northwest A&F University, Xinong road 22, Shaanxi, 712100, China
| | - Pier-Luc Dudemaine
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, Quebec, J1M 0C8, Canada
| | - Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, Quebec, J1M 0C8, Canada
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Complementary transcriptomic and proteomic analyses reveal regulatory mechanisms of milk protein production in dairy cows consuming different forages. Sci Rep 2017; 7:44234. [PMID: 28290485 PMCID: PMC5349593 DOI: 10.1038/srep44234] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/06/2017] [Indexed: 11/19/2022] Open
Abstract
Forage plays a critical role in the milk production of dairy cows; however, the mechanisms regulating bovine milk synthesis in dairy cows fed high forage rations with different basal forage types are not well-understood. In the study, rice straw (RS, low-quality) and alfalfa hay (AH, high-quality) diets were fed to lactating cows to explore how forage quality affected the molecular mechanisms regulating milk production using RNA-seq transcriptomic method with iTRAQ proteomic technique. A total of 554 transcripts (423 increased and 131 decreased) and 517 proteins (231 up-regulated and 286 down-regulated) were differentially expressed in the mammary glands of the two groups. The correlation analysis demonstrated seven proteins (six up-regulated and one down-regulated) had consistent mRNA expression. Functional analysis of the differentially expressed transcripts/proteins suggested that enhanced capacity for energy and fatty acid metabolism, increased protein degradation, reduced protein synthesis, decreased amino acid metabolism and depressed cell growth were related to RS consumption. The results indicated cows consuming RS diets may have had depressed milk protein synthesis because these animals had decreased capacity for protein synthesis, enhanced proteolysis, inefficient energy generation and reduced cell growth. Additional work evaluating RS- and AH-based rations may help better isolate molecular adaptations to low nutrient availability during lactation.
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