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Artegoitia VM, Newman JW, Foote AP, Shackelford SD, King DA, Wheeler TL, Lewis RM, Freetly HC. Non-invasive metabolomics biomarkers of production efficiency and beef carcass quality traits. Sci Rep 2022; 12:231. [PMID: 34997076 PMCID: PMC8742028 DOI: 10.1038/s41598-021-04049-2] [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: 03/31/2021] [Accepted: 12/14/2021] [Indexed: 11/25/2022] Open
Abstract
The inter-cattle growth variations stem from the interaction of many metabolic processes making animal selection difficult. We hypothesized that growth could be predicted using metabolomics. Urinary biomarkers of cattle feed efficiency were explored using mass spectrometry-based untargeted and targeted metabolomics. Feed intake and weight-gain was measured in steers (n = 75) on forage-based growing rations (stage-1, 84 days) followed by high-concentrate finishing rations (stage-2, 84 days). Urine from days 0, 21, 42, 63, and 83 in each stage were analyzed from steers with the greater (n = 14) and least (n = 14) average-daily-gain (ADG) and comparable dry-matter-intake (DMI; within 0.32 SD of the mean). Steers were slaughtered after stage-2. Adjusted fat-thickness and carcass-yield-grade increased in greater-ADG-cattle selected in stage-1, but carcass traits did not differ between ADG-selected in stage-2. Overall 85 untargeted metabolites segregated greater- and least-ADG animals, with overlap across diets (both stages) and breed type, despite sampling time effects. Total 18-bile acids (BAs) and 5-steroids were quantified and associated with performance and carcass quality across ADG-classification depending on the stage. Stepwise logistic regression of urinary BA and steroids had > 90% accuracy identifying efficient-ADG-steers. Urine metabolomics provides new insight into the physiological mechanisms and potential biomarkers for feed efficiency.
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Affiliation(s)
- Virginia M Artegoitia
- USDA, ARS, Western Human Nutrition Research Center, 430 West Health Sciences Drive, Davis, CA, 95616, USA. .,USDA, ARS, Meat Animal Research Center, Clay Center, NE, 68933, USA. .,Animal Science, University Nebraska, Lincoln, NE, 68583, USA.
| | - J W Newman
- USDA, ARS, Western Human Nutrition Research Center, 430 West Health Sciences Drive, Davis, CA, 95616, USA
| | - A P Foote
- USDA, ARS, Meat Animal Research Center, Clay Center, NE, 68933, USA.,Animal Science, Oklahoma State University, Stillwater, OK, 74078, USA
| | - S D Shackelford
- USDA, ARS, Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - D A King
- USDA, ARS, Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - T L Wheeler
- USDA, ARS, Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - R M Lewis
- Animal Science, University Nebraska, Lincoln, NE, 68583, USA
| | - H C Freetly
- USDA, ARS, Meat Animal Research Center, Clay Center, NE, 68933, USA
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Jia C, Bai Y, Liu J, Cai W, Liu L, He Y, Song J. Metabolic Regulations by lncRNA, miRNA, and ceRNA Under Grass-Fed and Grain-Fed Regimens in Angus Beef Cattle. Front Genet 2021; 12:579393. [PMID: 33747033 PMCID: PMC7969984 DOI: 10.3389/fgene.2021.579393] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
Beef cattle raised under grass-fed and grain-fed have many differences, including metabolic efficiency and meat quality. To investigate these two regimens' intrinsic influence on beef cattle, we used high-throughput sequencing and metabolomics analyses to explore differentially expressed genes (DEGs) and metabolimic networks in the liver. A total of 200 DEGs, 76 differentially expressed miRNAs (DEmiRNAs), and two differentially expressed lncRNAs (DElncRNAs) were detected between regimen groups. Metabolic processes and pathways enriched functional genes including target genes of miRNAs and lncRNAs. We found that many genes were involved in energy, retinol and cholesterol metabolism, and bile acid synthesis. Combined with metabolites such as low glucose concentration, high cholesterol concentration, and increased primary bile acid concentration, these genes were mainly responsible for lowering intramuscular fat, low cholesterol, and yellow meat in grass-fed cattle. Additionally, we identified two lncRNAs and eight DEGs as potential competing endogenous RNAs (ceRNAs) to bind miRNAs by the interaction network analysis. These results revealed that the effects of two feeding regimens on beef cattle were mainly induced by gene expression changes in metabolic pathways mediated via lncRNAs, miRNAs, and ceRNAs, and contents of metabolites in the liver. It may provide a clue on feeding regimens inducing the metabolic regulations.
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Affiliation(s)
- Cunling Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Department of Animal & Avian Science, University of Maryland, College Park, MD, United States
| | - Ying Bai
- Department of Animal & Avian Science, University of Maryland, College Park, MD, United States
| | - Jianan Liu
- Department of Animal & Avian Science, University of Maryland, College Park, MD, United States
| | - Wentao Cai
- Department of Animal & Avian Science, University of Maryland, College Park, MD, United States
| | - Lei Liu
- Department of Animal & Avian Science, University of Maryland, College Park, MD, United States.,Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Science, Shenzhen, China
| | - Yanghua He
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Manoa, HI, United States
| | - Jiuzhou Song
- Department of Animal & Avian Science, University of Maryland, College Park, MD, United States
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Artegoitia VM, Foote AP, Lewis RM, Freetly HC. Metabolomics Profile and Targeted Lipidomics in Multiple Tissues Associated with Feed Efficiency in Beef Steers. ACS OMEGA 2019; 4:3973-3982. [PMID: 31459606 PMCID: PMC6648084 DOI: 10.1021/acsomega.8b02494] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/14/2018] [Indexed: 05/13/2023]
Abstract
A study of multiple tissues was conducted to identify potential metabolic differences in cattle differing in feed efficiency. Individual feed intake and body weight was measured on 144 steers during 105 days on a high-concentrate ration. Steers were selected according to differences in average daily gain (ADG) with those with the greatest ADG (n = 8; 1.96 ± 0.02 kg/day) and least ADG (n = 8; 1.57 ± 0.02 kg/day), whose dry matter intake was within 0.32 SD of the mean intake (10.10 ± 0.05 kg/day). Duodenum, liver, adipose, and longissimus-dorsi were collected at slaughter, and metabolomics profiles were performed by ultra performance liquid chromatography quadrupole-time of-flight mass spectrometry. Principal components analyses, t-tests, and fold changes in tissues profile were used to identify differential metabolites between ADG groups. These were primarily involved in α-linolenic metabolism, which was downregulated in the greatest ADG as compared to least-ADG group in duodenum, adipose, and longissimus-dorsi. However, taurine and glycerophospholipids metabolisms were both upregulated in the greatest ADG compared with least-ADG group in the liver. The phospholipids and cholesterol were quantified in the tissues. Lipid transport and oxidation were the main common metabolic mechanisms associated with cattle feed efficiency. Combining analyses of multiple tissues may offer a powerful approach for defining the molecular basis of differences in performance among cattle for key production attributes.
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Affiliation(s)
- Virginia M. Artegoitia
- Department
of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska 68583, United States
- E-mail:
| | - Andrew P. Foote
- ARS,
U.S. Meat Animal Research Center, USDA, Clay Center, Nebraska 68933, United States
| | - Ronald M. Lewis
- Department
of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska 68583, United States
| | - Harvey C. Freetly
- ARS,
U.S. Meat Animal Research Center, USDA, Clay Center, Nebraska 68933, United States
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