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Tian J, Zhu X, Wu H, Wang Y, Hu X. Serum metabolic profile and metabolome genome-wide association study in chicken. J Anim Sci Biotechnol 2023; 14:69. [PMID: 37138301 PMCID: PMC10158329 DOI: 10.1186/s40104-023-00868-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/09/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Chickens provide globally important livestock products. Understanding the genetic and molecular mechanisms underpinning chicken economic traits is crucial for improving their selective breeding. Influenced by a combination of genetic and environmental factors, metabolites are the ultimate expression of physiological processes and can provide key insights into livestock economic traits. However, the serum metabolite profile and genetic architecture of the metabolome in chickens have not been well studied. RESULTS Here, comprehensive metabolome detection was performed using non-targeted LC-MS/MS on serum from a chicken advanced intercross line (AIL). In total, 7,191 metabolites were used to construct a chicken serum metabolomics dataset and to comprehensively characterize the serum metabolism of the chicken AIL population. Regulatory loci affecting metabolites were identified in a metabolome genome-wide association study (mGWAS). There were 10,061 significant SNPs associated with 253 metabolites that were widely distributed across the entire chicken genome. Many functional genes affect metabolite synthesis, metabolism, and regulation. We highlight the key roles of TDH and AASS in amino acids, and ABCB1 and CD36 in lipids. CONCLUSIONS We constructed a chicken serum metabolite dataset containing 7,191 metabolites to provide a reference for future chicken metabolome characterization work. Meanwhile, we used mGWAS to analyze the genetic basis of chicken metabolic traits and metabolites and to improve chicken breeding.
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Affiliation(s)
- Jing Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaoning Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hanyu Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing, 100193, China
| | - Yuzhe Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing, 100193, China.
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing, 100193, China.
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Dervishi E, Bai X, Dyck MK, Harding JCS, Fortin F, Dekkers JCM, Plastow G. GWAS and genetic and phenotypic correlations of plasma metabolites with complete blood count traits in healthy young pigs reveal implications for pig immune response. Front Mol Biosci 2023; 10:1140375. [PMID: 36968283 PMCID: PMC10034349 DOI: 10.3389/fmolb.2023.1140375] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
Introduction: In this study estimated genetic and phenotypic correlations between fifteen complete blood count (CBC) traits and thirty-three heritable plasma metabolites in young healthy nursery pigs. In addition, it provided an opportunity to identify candidate genes associated with variation in metabolite concentration and their potential association with immune response, disease resilience, and production traits.Methods: The blood samples were collected from healthy young pigs and Nuclear Magnetic Resonance (NMR) was used to quantify plasma metabolites. CBC was determined using the ADVIA® 2120i Hematology System. Genetic correlations of metabolite with CBC traits and single step genome-wide association study (ssGWAS) were estimated using the BLUPF90 programs.Results: Results showed low phenotypic correlation estimates between plasma metabolites and CBC traits. The highest phenotypic correlation was observed between lactic acid and plasma basophil concentration (0.36 ± 0.04; p < 0.05). Several significant genetic correlations were found between metabolites and CBC traits. The plasma concentration of proline was genetically positively correlated with hemoglobin concentration (0.94 ± 0.03; p < 0.05) and L-tyrosine was negatively correlated with mean corpuscular hemoglobin (MCH; −0.92 ± 0.74; p < 0.05). The genomic regions identified in this study only explained a small percentage of the genetic variance of metabolites levels that were genetically correlated with CBC, resilience, and production traits.Discussion: The results of this systems approach suggest that several plasma metabolite phenotypes are phenotypically and genetically correlated with CBC traits, suggesting that they may be potential genetic indicators of immune response following disease challenge. Genomic analysis revealed genes and pathways that might interact to modulate CBC, resilience, and production traits.
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Affiliation(s)
- E. Dervishi
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - X. Bai
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - M. K. Dyck
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - J. C. S. Harding
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - F. Fortin
- Centre de Developpement du porc du Quebec inc (CDPQ), Quebec City, QC, Canada
| | - J. C. M. Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - G. Plastow
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
- *Correspondence: G. Plastow,
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Dervishi E, Bai X, Cheng J, Fortin F, Dyck MK, Harding JCS, Seddon YM, Dekkers JCM, Canada P, Plastow G. Exploration of plasma metabolite levels in healthy nursery pigs in response to environmental enrichment and disease resilience. J Anim Sci 2023; 101:7008185. [PMID: 36705540 PMCID: PMC9982359 DOI: 10.1093/jas/skad033] [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: 06/02/2022] [Accepted: 01/25/2023] [Indexed: 01/28/2023] Open
Abstract
The purpose of this study was to explore plasma metabolite levels in young healthy pigs and their potential association with disease resilience and estimate genetic and phenotypic correlation with the change in lymphocyte concentration following disease challenge. Plasma samples were collected from 968 healthy nursery pigs over 15 batches at an average of 28 ± 3.23 d of age. Forty-four metabolites were identified and quantified by nuclear magnetic resonance. Pigs were then introduced into a natural disease challenge barn, and were classified into four groups based on the growth rate of each animal in the grow-to-finish phase (GFGR) and treatment rate (TR): resilient (RES), average (MID), susceptible (SUS), and dead (pigs that died before harvest). Blood samples were collected from all pigs before and 2 wk after disease challenge and complete blood count was determined. Environmental enrichment (inedible point source objects) was provided for half of the pigs in seven batches (N = 205) to evaluate its impact on resilience and metabolite concentrations. Concentration of all metabolites was affected by batch, while entry age affected the concentration of 16 metabolites. The concentration of creatinine was significantly lower for pigs classified as "dead" and "susceptible" when compared to "average" (P < 0.05). Pigs that received enrichment had significantly lower concentrations of six metabolites compared with pigs that did not receive enrichment (P ≤ 0.05). Both, group classification and enrichment affected metabolites that are involved in the same pathways of valine, leucine, and isoleucine biosynthesis and degradation. Resilient pigs had higher increase in lymphocyte concentration after disease challenge. The concentration of plasma l-α-aminobutyric acid was significantly negatively genetically correlated with the change in lymphocyte concentration following challenge. In conclusion, creatinine concentration in healthy nursery pigs was lower in pigs classified as susceptible or dead after disease challenge, whilst l-α-aminobutyric may be a genetic biomarker of lymphocyte response after pathogen exposure, and both deserve further investigation. Batch, entry age, and environmental enrichment were important factors affecting the concentration of metabolites and should be taken into consideration in future studies.
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Affiliation(s)
- Elda Dervishi
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Xuechun Bai
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Jian Cheng
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Frederic Fortin
- Centre de developpement du porc du Quebec inc. (CDPQ), Quebec City, QC, Canada
| | - Mike K Dyck
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - John C S Harding
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yolande M Seddon
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - PigGen Canada
- PigGen Canada Research Consortium, Guelph, ON N1H4G8Canada
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Trevisi P, Negrini C, Correa F, Virdis S, Laghi L, Marcello M, Conte G, Mazzoni M, Luise D. Insight into the long-term impact of birth weight on intestinal development, microbial settlement, and the metabolism of weaned piglets. J Anim Sci 2023; 101:skad395. [PMID: 38064718 PMCID: PMC10963063 DOI: 10.1093/jas/skad395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Infant mortality of low birth body weight (LBBW) piglets can reach 10% and is mainly due to gut and immune system immaturity which can lead to a higher risk in the long term. This study aimed to assess the impact of birth body weight (BBW) on piglet metabolism, gut status, and microbial profile from weaning to 21 d postweaning. At birth, 32 piglets were selected for their BBW and inserted into the normal BBW (NBBW:1.38 ± 0.09 g) or the LBBW (0.92 ± 0.07 g) group. The piglets were weighed weekly from weaning (d0) to d21. At d9 and d21, 8 piglets/group were slaughtered to obtain the distal jejunum for morphology, immunohistochemistry, and gene expression analysis, colon content for microbiota and short-chain fatty acid (SCFA) analysis, and intestinal content for pH measurement. Blood was collected for metabolomic, haptoglobin (Hp), and reactive oxygen metabolite (ROM) analysis. The LBBW group had a lower body weight (BW) throughout the study (P < 0.01), a lower average daily gain from d9-d21 (P = 0.002), and lower feed intake (P = 0.02). The LBBW piglets had lower Hp at d9 (P = 0.03), higher ROMs at d21 (P = 0.06), and a net alteration of the amino acid (AA) metabolism at d9 and d21. A higher expression of NFKB2 was observed in the LBBW piglets at d9 (P = 0.003) and d21 (P < 0.001). MYD88 expression was enhanced in NBBW piglets at d9 (P < 0.001). The LBBW piglets had a lower villus height, absorptive mucosal surface (P = 0.01), and villus height:crypt depth ratio (P = 0.02), and a greater number of T-lymphocytes in both the epithelium and the crypts (P < 0.001) at d21. At d21, the LBBW piglets had higher lactic acid, acetate, butyrate, and valerate, and also higher SCFA in the colon (P < 0.05). The LBBW piglets had a higher Shannon index (P = 0.01) at d9 and a higher abundance of SCFA-fermenting bacteria. In conclusion, the present study confirmed that LBBW could impact the gut mucosal structure, immunity, and inflammatory and oxidative status, leading to an altered AA metabolism, and delaying the recovery from weaning.
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Affiliation(s)
- Paolo Trevisi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Clara Negrini
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Federico Correa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Sara Virdis
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Luca Laghi
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Mele Marcello
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Giuseppe Conte
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Maurizio Mazzoni
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, Italy
| | - Diana Luise
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
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Bai X, Plastow GS. Breeding for disease resilience: opportunities to manage polymicrobial challenge and improve commercial performance in the pig industry. CABI AGRICULTURE AND BIOSCIENCE 2022; 3:6. [PMID: 35072100 PMCID: PMC8761052 DOI: 10.1186/s43170-022-00073-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/06/2022] [Indexed: 05/31/2023]
Abstract
Disease resilience, defined as an animal's ability to maintain productive performance in the face of infection, provides opportunities to manage the polymicrobial challenge common in pig production. Disease resilience can deliver a number of benefits, including more sustainable production as well as improved animal health and the potential for reduced antimicrobial use. However, little progress has been made to date in the application of disease resilience in breeding programs due to a number of factors, including (1) confusion around definitions of disease resilience and its component traits disease resistance and tolerance, and (2) the difficulty in characterizing such a complex trait consisting of multiple biological functions and dynamic elements of rates of response and recovery from infection. Accordingly, this review refines the definitions of disease resistance, tolerance, and resilience based on previous studies to help improve the understanding and application of these breeding goals and traits under different scenarios. We also describe and summarize results from a "natural disease challenge model" designed to provide inputs for selection of disease resilience. The next steps for managing polymicrobial challenges faced by the pig industry will include the development of large-scale multi-omics data, new phenotyping technologies, and mathematical and statistical methods adapted to these data. Genome editing to produce pigs resistant to major diseases may complement selection for disease resilience along with continued efforts in the more traditional areas of biosecurity, vaccination and treatment. Altogether genomic approaches provide exciting opportunities for the pig industry to overcome the challenges provided by hard-to-manage diseases as well as new environmental challenges associated with climate change.
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Affiliation(s)
- Xuechun Bai
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Graham S. Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
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Dervishi E, Reimert I, van der Zande LE, Mathur P, Knol EF, Plastow GS. Relationship between indirect genetic effects for growth, environmental enrichment, coping style and sex with the serum metabolome profile of pigs. Sci Rep 2021; 11:23377. [PMID: 34862433 PMCID: PMC8642533 DOI: 10.1038/s41598-021-02814-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 11/18/2021] [Indexed: 12/27/2022] Open
Abstract
Including Indirect Genetic Effects (IGE) in breeding programs to reduce aggression in group housed animals has been proposed. However, the effect of selection for IGE for growth on animal metabolism and physiology is unknown. The purpose of this study was twofold: (1) To investigate the effects of this new breeding method along with two housing (barren and straw), coping style (high and low resisters) and sex (female and castrated males) options on the metabolome profile of pigs. (2) To identify and map biological processes associated with a regrouping test at 9 weeks of age. We used Nuclear Magnetic Resonance to quantify 49 serum metabolites at week 8, 9 and 22. Also, we quantified 3 catecholamines (tyramine, epinephrine, phenylethylamine) and serotonin and three water soluble vitamins (B2, B5 and B7). Overall, no significant differences were observed between negative and positive IGE animals. The magnitude of change (delta) of many metabolites as a response to the regrouping test was significantly affected by IGE, especially that of the amino acids (P < 0.05), being greater in positive IGE pigs. The regrouping test was associated with alteration in glycine, serine and threonine metabolism. In conclusion positive and negative IGE animals respond differently to the regrouping test.
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Affiliation(s)
- Elda Dervishi
- Livestock Gentec, University of Alberta, 116 St and 85 Ave, Edmonton, AB, T6G 2R3, Canada.
| | - Inonge Reimert
- Adaptation Physiology Group, Department of Animal Sciences, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Lisette E van der Zande
- Adaptation Physiology Group, Department of Animal Sciences, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
- Topigs Norsvin Research Center B.V, 6640 AA, Beuningen, The Netherlands
| | - Pramod Mathur
- Topigs Norsvin Research Center B.V, 6640 AA, Beuningen, The Netherlands
| | - Egbert F Knol
- Topigs Norsvin Research Center B.V, 6640 AA, Beuningen, The Netherlands
| | - Graham S Plastow
- Livestock Gentec, University of Alberta, 116 St and 85 Ave, Edmonton, AB, T6G 2R3, Canada
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