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Passols M, Llobet-Cabau F, Sebastià C, Castelló A, Valdés-Hernández J, Criado-Mesas L, Sánchez A, Folch JM. Identification of genomic regions, genetic variants and gene networks regulating candidate genes for lipid metabolism in pig muscle. Animal 2023; 17:101033. [PMID: 38064855 DOI: 10.1016/j.animal.2023.101033] [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: 07/06/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 12/23/2023] Open
Abstract
The intramuscular fat content and fatty acid composition of porcine meat have a significant impact on its quality and nutritional value. This research aimed to investigate the expression of 45 genes involved in lipid metabolism in the longissimus dorsi muscle of three experimental pig backcrosses, with a 25% of Iberian background. To achieve this objective, we conducted an expression Genome-Wide Association Study (eGWAS) using gene expression levels in muscle measured by high-throughput real-time qPCR for 45 target genes and genotypes from the PorcineSNP60 BeadChip or Axiom Porcine Genotyping Array and 65 single nucleotide polymorphisms (SNPs) located in 20 genes genotyped by a custom-designed Taqman OpenArray in a cohort of 354 animals. The eGWAS analysis identified 301 eSNPs associated with 18 candidate genes (ANK2, APOE, ARNT, CIITA, CPT1A, EGF, ELOVL6, ELOVL7, FADS3, FASN, GPAT3, NR1D2, NR1H2, PLIN1, PPAP2A, RORA, RXRA and UCP3). Three cis-eQTL (expression quantitative trait loci) were identified for GPAT3, RXRA, and UCP3 genes, which indicates that a genetic polymorphism proximal to the same gene is affecting its expression. Furthermore, 24 trans-eQTLs were detected, and eight candidate regulatory genes were located in these genomic regions. Additionally, two trans-regulatory hotspots in Sus scrofa chromosomes 13 and 15 were identified. Moreover, a co-expression analysis performed on 89 candidate genes and the fatty acid composition revealed the regulatory role of four genes (FABP5, PPARG, SCD, and SREBF1). These genes modulate the levels of α-linolenic, arachidonic, and oleic acids, as well as regulating the expression of other candidate genes associated with lipid metabolism. The findings of this study offer novel insights into the functional regulatory mechanism of genes involved in lipid metabolism, thereby enhancing our understanding of this complex biological process.
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Affiliation(s)
- M Passols
- Plant and Animal Genomics, Centre for Research in Agrigenomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, España.
| | - F Llobet-Cabau
- Plant and Animal Genomics, Centre for Research in Agrigenomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, España; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - C Sebastià
- Plant and Animal Genomics, Centre for Research in Agrigenomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, España; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - A Castelló
- Plant and Animal Genomics, Centre for Research in Agrigenomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, España; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - J Valdés-Hernández
- Plant and Animal Genomics, Centre for Research in Agrigenomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, España; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - L Criado-Mesas
- Plant and Animal Genomics, Centre for Research in Agrigenomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, España
| | - A Sánchez
- Plant and Animal Genomics, Centre for Research in Agrigenomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, España; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - J M Folch
- Plant and Animal Genomics, Centre for Research in Agrigenomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, España; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, España
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Alvarenga AB, Oliveira HR, Miller SP, Silva FF, Brito LF. Genetic Modeling and Genomic Analyses of Yearling Temperament in American Angus Cattle and Its Relationship With Productive Efficiency and Resilience Traits. Front Genet 2022; 13:794625. [PMID: 35444687 PMCID: PMC9014094 DOI: 10.3389/fgene.2022.794625] [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: 10/13/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Cattle temperament has been considered by farmers as a key breeding goal due to its relevance for cattlemen's safety, animal welfare, resilience, and longevity and its association with many economically important traits (e.g., production and meat quality). The definition of proper statistical models, accurate variance component estimates, and knowledge on the genetic background of the indicator trait evaluated are of great importance for accurately predicting the genetic merit of breeding animals. Therefore, 266,029 American Angus cattle with yearling temperament records (1-6 score) were used to evaluate statistical models and estimate variance components; investigate the association of sex and farm management with temperament; assess the weighted correlation of estimated breeding values for temperament and productive, reproductive efficiency and resilience traits; and perform a weighted single-step genome-wide association analysis using 69,559 animals genotyped for 54,609 single-nucleotide polymorphisms. Sex and extrinsic factors were significantly associated with temperament, including conception type, age of dam, birth season, and additional animal-human interactions. Similar results were observed among models including only the direct additive genetic effect and when adding other maternal effects. Estimated heritability of temperament was equal to 0.39 on the liability scale. Favorable genetic correlations were observed between temperament and other relevant traits, including growth, feed efficiency, meat quality, and reproductive traits. The highest approximated genetic correlations were observed between temperament and growth traits (weaning weight, 0.28; yearling weight, 0.28). Altogether, we identified 11 genomic regions, located across nine chromosomes including BTAX, explaining 3.33% of the total additive genetic variance. The candidate genes identified were enriched in pathways related to vision, which could be associated with reception of stimulus and/or cognitive abilities. This study encompasses large and diverse phenotypic, genomic, and pedigree datasets of US Angus cattle. Yearling temperament is a highly heritable and polygenic trait that can be improved through genetic selection. Direct selection for temperament is not expected to result in unfavorable responses on other relevant traits due to the favorable or low genetic correlations observed. In summary, this study contributes to a better understanding of the impact of maternal effects, extrinsic factors, and various genomic regions associated with yearling temperament in North American Angus cattle.
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Affiliation(s)
- Amanda B Alvarenga
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Stephen P Miller
- American Angus Association, Angus Genetics Inc., St Joseph, MO, United States
| | - Fabyano F Silva
- Department of Animal Sciences, Federal University of Vicosa, Viçosa, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Alvarenga AB, Oliveira HR, Chen SY, Miller SP, Marchant-Forde JN, Grigoletto L, Brito LF. A Systematic Review of Genomic Regions and Candidate Genes Underlying Behavioral Traits in Farmed Mammals and Their Link with Human Disorders. Animals (Basel) 2021; 11:ani11030715. [PMID: 33800722 PMCID: PMC7999279 DOI: 10.3390/ani11030715] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/21/2021] [Accepted: 02/27/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary This study is a comprehensive review of genomic regions associated with animal behavior in farmed mammals (beef and dairy cattle, pigs, and sheep) which contributes to a better understanding of the biological mechanisms influencing the target indicator trait and to gene expression studies by suggesting genes likely controlling the trait, and it will be useful in optimizing genomic predictions of breeding values incorporating biological information. Behavioral mechanisms are complex traits, genetically controlled by multiple genes spread across the whole genome. The majority of the genes identified in cattle, pigs, and sheep in association with a plethora of behavioral measurements (e.g., temperament, terrain use, milking speed, tail biting, and sucking reflex) are likely controlling stimuli reception (e.g., olfactory), internal recognition of stimuli (e.g., neuroactive ligand–receptor interaction), and body response to a stimulus (e.g., blood pressure, fatty acidy metabolism, hormone signaling, and inflammatory pathways). Six genes were commonly identified between cattle and pigs. About half of the genes for behavior identified in farmed mammals were also identified in humans for behavioral, mental, and neuronal disorders. Our findings indicate that the majority of the genes identified are likely controlling animal behavioral outcomes because their biological functions as well as potentially differing allele frequencies between two breed groups (subjectively) clustered based on their temperament characteristics. Abstract The main objectives of this study were to perform a systematic review of genomic regions associated with various behavioral traits in the main farmed mammals and identify key candidate genes and potential causal mutations by contrasting the frequency of polymorphisms in cattle breeds with divergent behavioral traits (based on a subjective clustering approach). A total of 687 (cattle), 1391 (pigs), and 148 (sheep) genomic regions associated with 37 (cattle), 55 (pigs), and 22 (sheep) behavioral traits were identified in the literature. In total, 383, 317, and 15 genes overlap with genomic regions identified for cattle, pigs, and sheep, respectively. Six common genes (e.g., NR3C2, PITPNM3, RERG, SPNS3, U6, and ZFAT) were found for cattle and pigs. A combined gene-set of 634 human genes was produced through identified homologous genes. A total of 313 out of 634 genes have previously been associated with behavioral, mental, and neurologic disorders (e.g., anxiety and schizophrenia) in humans. Additionally, a total of 491 candidate genes had at least one statistically significant polymorphism (p-value < 0.05). Out of those, 110 genes were defined as having polymorphic regions differing in greater than 50% of exon regions. Therefore, conserved genomic regions controlling behavior were found across farmed mammal species and humans.
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Affiliation(s)
- Amanda B. Alvarenga
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 625014, China
| | | | - Jeremy N. Marchant-Forde
- Livestock Behavior Research Unit, United States Department of Agriculture—Agricultural Research Service (USDA–ARS), West Lafayette, IN 47907, USA;
| | - Lais Grigoletto
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 05508, São Paulo, Brazil
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
- Correspondence:
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Shi C, Lu Y, Zhai G, Huang J, Shang G, Lou Q, Li D, Jin X, He J, Du Z, Gui J, Yin Z. Hyperandrogenism in POMCa-deficient zebrafish enhances somatic growth without increasing adiposity. J Mol Cell Biol 2020; 12:291-304. [PMID: 31237951 PMCID: PMC7232124 DOI: 10.1093/jmcb/mjz053] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/17/2019] [Accepted: 05/17/2019] [Indexed: 01/29/2023] Open
Abstract
The endocrine regulatory roles of the hypothalamic-pituitary-adrenocortical axis on anxiety-like behavior and metabolic status have been found throughout animal taxa. However, the precise effects of the balancing adrenal corticosteroid biosynthesis under the influence of adrenocorticotrophic hormone (ACTH), a pro-opiomelanocortin (POMC)-derived peptide, on animal energy expenditure and somatic growth remain unknown. POMC has also been identified as one of the candidate loci for polycystic ovary syndrome, which features hyperandrogenism and some prevalence of obesity in patients. Here we show that zebrafish lacking functional POMCa exhibit similar phenotypes of stress response and body weight gain but not obesity as observed in mammalian models. In contrast with the impaired anorexigenic signaling cascade of melanocyte-stimulating hormones and leptin, which are responsible for their obesity-prone weight gain observed in various pomc mutant mammals, analyses with our pomca mutant series indicate that ACTH is the key regulator for the phenotype with enhanced somatic growth without obesity in pomca-deficient zebrafish. Hypocortisolism associated with hyperandrogenism has been observed in the pomca-deficient zebrafish, with enhanced activation of mammalian target of rapamycin complex 1; reutilization of amino acids and fatty acid β-oxidation are observed in the muscle tissue of the pomca-deficient fish. After reducing hyperandrogenism by crossing our pomca mutant fish with a cyp17a1-deficient background, the phenotype of enhanced somatic growth in pomca-deficient fish was no longer observed. Thus, our work also demonstrated that the role of POMCa in stress response seems to be conserved in vertebrates, whereas its effect on adipostasis is unique to teleosts.
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Affiliation(s)
- Chuang Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Zhai
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jianfei Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guohui Shang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiyong Lou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dongliang Li
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xia Jin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jiangyan He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhenyu Du
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jianfang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhan Yin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100864, China
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Srikanth K, Lee SH, Chung KY, Park JE, Jang GW, Park MR, Kim NY, Kim TH, Chai HH, Park WC, Lim D. A Gene-Set Enrichment and Protein-Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle. Genes (Basel) 2020; 11:E316. [PMID: 32188084 PMCID: PMC7140899 DOI: 10.3390/genes11030316] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in a genome-wide association study (GWAS) to identify loci associated with backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). A total of 15, 176, and 1 SNPs were found to be significantly associated (p < 1.11 × 10-7) with BFT, CWT, and EMA, respectively. The significant loci were BTA4 (CWT), BTA6 (CWT), BTA14 (CWT and EMA), and BTA19 (BFT). BayesR estimated that 1.1%~1.9% of the SNPs contributed to more than 0.01% of the phenotypic variance. So, the GWAS was complemented by a gene-set enrichment (GSEA) and protein-protein interaction network (PPIN) analysis in identifying the pathways affecting carcass traits. At p < 0.005 (~2,261 SNPs), 25 GO and 18 KEGG categories, including calcium signaling, cell proliferation, and folate biosynthesis, were found to be enriched through GSEA. The PPIN analysis showed enrichment for 81 candidate genes involved in various pathways, including the PI3K-AKT, calcium, and FoxO signaling pathways. Our finding provides insight into the effects of regulatory SNPs on carcass traits.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Seung-Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea;
| | - Ki-Yong Chung
- Department of Beef Science, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea;
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Gul-Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Mi-Rim Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Na Yeon Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Tae-Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Won Cheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
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Carmelo VAO, Banerjee P, da Silva Diniz WJ, Kadarmideen HN. Metabolomic networks and pathways associated with feed efficiency and related-traits in Duroc and Landrace pigs. Sci Rep 2020; 10:255. [PMID: 31937890 PMCID: PMC6959238 DOI: 10.1038/s41598-019-57182-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 12/23/2019] [Indexed: 02/06/2023] Open
Abstract
Improving feed efficiency (FE) is a major goal of pig breeding, reducing production costs and providing sustainability to the pig industry. Reliable predictors for FE could assist pig producers. We carried out untargeted blood metabolite profiling in uncastrated males from Danbred Duroc (n = 59) and Danbred Landrace (n = 50) pigs at the beginning and end of a FE testing phase to identify biomarkers and biological processes underlying FE and related traits. By applying linear modeling and clustering analyses coupled with WGCNA framework, we identified 102 and 73 relevant metabolites in Duroc and Landrace based on two sampling time points. Among them, choline and pyridoxamine were hub metabolites in Duroc in early testing phase, while, acetoacetate, cholesterol sulfate, xanthine, and deoxyuridine were identified in the end of testing. In Landrace, cholesterol sulfate, thiamine, L-methionine, chenodeoxycholate were identified at early testing phase, while, D-glutamate, pyridoxamine, deoxycytidine, and L-2-aminoadipate were found at the end of testing. Validation of these results in larger populations could establish FE prediction using metabolomics biomarkers. We conclude that it is possible to identify a link between blood metabolite profiles and FE. These results could lead to improved nutrient utilization, reduced production costs, and increased FE.
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Affiliation(s)
- Victor Adriano Okstoft Carmelo
- Quantitative Genomics, Bioinformatics and Computational Biology, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Priyanka Banerjee
- Quantitative Genomics, Bioinformatics and Computational Biology, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Wellison Jarles da Silva Diniz
- Quantitative Genomics, Bioinformatics and Computational Biology, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.,Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Haja N Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.
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Gao K, Pi Y, Mu C, Farzi A, Liu Z, Zhu W. Increasing carbohydrate availability in the hindgut promotes hypothalamic neurotransmitter synthesis: aromatic amino acids linking the microbiota–brain axis. J Neurochem 2019; 149:641-659. [DOI: 10.1111/jnc.14709] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 03/30/2019] [Accepted: 04/16/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Kan Gao
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health College of Animal Science and Technology Nanjing Agricultural University Nanjing China
- National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Yu Pi
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health College of Animal Science and Technology Nanjing Agricultural University Nanjing China
- National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Chun‐Long Mu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health College of Animal Science and Technology Nanjing Agricultural University Nanjing China
- National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Aitak Farzi
- Research Unit of Translational Neurogastroenterology Otto Loewi Research Center Pharmacology Section Medical University of Graz Graz Austria
| | - Zhuang Liu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health College of Animal Science and Technology Nanjing Agricultural University Nanjing China
- National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Wei‐Yun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health College of Animal Science and Technology Nanjing Agricultural University Nanjing China
- National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
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Abstract
Aggression is a heritable trait and genetically related to neurotransmitter-related genes. Behavioural characteristics of some pig breeds are different. To compare the genetic differences between breeds, backtest and aggressive behaviour assessments, and genotyped using Sequenom iPLEX platform were performed in 50 Chinese indigenous Mi pigs and 100 landrace-large white (LLW) cross pigs with 32 SNPs localized in 11 neurotransmitter-related genes. The genetic polymorphisms of 26 SNPs had notable differences (P < 0.05) between Mi and LLW. The most frequent haplotypes were different in DBH, HTR2A, GAD1, HTR2B,MAOA and MAOB genes between Mi and LLW. The mean of backtest scores was significantly lower (P < 0.001) for Mi than LLW pigs. Skin lesion scores were greater (P < 0.01) in LLW pigs than Mi pigs. In this study, we have confirmed that Chinese Mi pigs are less active and less aggressive than European LLW pigs, and the genetic polymorphisms of neurotransmitter-related genes, which have been proved previously associated with aggressive behaviour, have considerable differences between Mi and LLW pigs.
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Fam BS, Paré P, Felkl AB, Vargas-Pinilla P, Paixão-Côrtes VR, Viscardi LH, Bortolini MC. Oxytocin and arginine vasopressin systems in the domestication process. Genet Mol Biol 2018; 41:235-242. [PMID: 29668014 PMCID: PMC5913714 DOI: 10.1590/1678-4685-gmb-2017-0069] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/01/2017] [Indexed: 11/22/2022] Open
Abstract
Domestication is of unquestionable importance to the technological revolution that has given rise to modern human societies. In this study, we analyzed the DNA and protein sequences of six genes of the oxytocin and arginine vasopressin systems (OXT-OXTR; AVP-AVPR1a, AVPR1b and AVPR2) in 40 placental mammals. These systems play an important role in the control of physiology and behavior. According to our analyses, neutrality does not explain the pattern of molecular evolution found in some of these genes. We observed specific sites under positive selection in AVPR1b (ω = 1.429, p = 0.001) and AVPR2 (ω= 1.49, p = 0.001), suggesting that they could be involved in behavior and physiological changes, including those related to the domestication process. Furthermore, AVPR1a, which plays a role in social behavior, is under relaxed selective constraint in domesticated species. These results provide new insights into the nature of the domestication process and its impact on the OXT-AVP system.
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Affiliation(s)
- Bibiana S.O. Fam
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
| | - Pamela Paré
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
| | - Aline B. Felkl
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
| | - Pedro Vargas-Pinilla
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
| | | | | | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do
Sul, Porto Alegre, RS, Brazil
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10
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Martínez-Montes ÁM, Fernández A, Muñoz M, Noguera JL, Folch JM, Fernández AI. Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed. PLoS One 2018. [PMID: 29522525 PMCID: PMC5844516 DOI: 10.1371/journal.pone.0190184] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic backgrounds, backcrosses based on Iberian pigs, which has a major role in the analysis due to its high productive relevance. The results revealed nine common QTL regions, three segregating in all three backcrosses on SSC1, 0–3 Mb, for body weight, on SSC2, 3–9 Mb, for loin bone-in weight, and on SSC7, 3 Mb, for shoulder weight, and six segregating in two of the three backcrosses, on SSC2, SSC4, SSC6 and SSC10 for backfat thickness, shoulder and ham weights. Besides, 18 QTL regions were specifically identified in one of the three backcrosses, five identified only in BC_LD, seven in BC_DU and six in BC_PI. Beyond identifying and validating QTL, candidate genes and gene variants within the most interesting regions have been explored using functional annotation, gene expression data and SNP identification from RNA-Seq data. The results allowed us to propose a promising list of candidate mutations, those identified in PDE10A, DHCR7, MFN2 and CCNY genes located within the common QTL regions and those identified near ssc-mir-103-1 considered PANK3 regulators to be further analysed.
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Affiliation(s)
- Ángel M. Martínez-Montes
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Almudena Fernández
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - María Muñoz
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
- Centro de I+D en Cerdo Ibérico, Zafra, Badajoz, Spain
| | - Jose Luis Noguera
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Lleida, Spain
| | - Josep M. Folch
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Ana I. Fernández
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
- * E-mail:
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11
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Welzenbach J, Neuhoff C, Heidt H, Cinar MU, Looft C, Schellander K, Tholen E, Große-Brinkhaus C. Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs. Int J Mol Sci 2016; 17:E1426. [PMID: 27589727 PMCID: PMC5037705 DOI: 10.3390/ijms17091426] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/12/2016] [Accepted: 08/22/2016] [Indexed: 01/21/2023] Open
Abstract
The aim of this study was to integrate multi omics data to characterize underlying functional pathways and candidate genes for drip loss in pigs. The consideration of different omics levels allows elucidating the black box of phenotype expression. Metabolite and protein profiling was applied in Musculus longissimus dorsi samples of 97 Duroc × Pietrain pigs. In total, 126 and 35 annotated metabolites and proteins were quantified, respectively. In addition, all animals were genotyped with the porcine 60 k Illumina beadchip. An enrichment analysis resulted in 10 pathways, amongst others, sphingolipid metabolism and glycolysis/gluconeogenesis, with significant influence on drip loss. Drip loss and 22 metabolic components were analyzed as intermediate phenotypes within a genome-wide association study (GWAS). We detected significantly associated genetic markers and candidate genes for drip loss and for most of the metabolic components. On chromosome 18, a region with promising candidate genes was identified based on SNPs associated with drip loss, the protein "phosphoglycerate mutase 2" and the metabolite glycine. We hypothesize that association studies based on intermediate phenotypes are able to provide comprehensive insights in the genetic variation of genes directly involved in the metabolism of performance traits. In this way, the analyses contribute to identify reliable candidate genes.
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Affiliation(s)
- Julia Welzenbach
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
| | - Christiane Neuhoff
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
| | - Hanna Heidt
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
- Institute for Organic Agriculture Luxembourg, Association sans but lucratif (A.S.B.L.), 13 Rue Gabriel Lippmann, L-5365 Munsbach, Luxembourg.
| | - Mehmet Ulas Cinar
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Talas Bulvari No. 99, 38039 Kayseri, Turkey.
| | - Christian Looft
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
| | - Karl Schellander
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
| | - Ernst Tholen
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
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12
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Hewagalamulage SD, Lee TK, Clarke IJ, Henry BA. Stress, cortisol, and obesity: a role for cortisol responsiveness in identifying individuals prone to obesity. Domest Anim Endocrinol 2016; 56 Suppl:S112-20. [PMID: 27345309 DOI: 10.1016/j.domaniend.2016.03.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 03/14/2016] [Accepted: 03/18/2016] [Indexed: 11/22/2022]
Abstract
There is a strong inter-relationship between activation of the hypothalamo-pituitary-adrenal axis and energy homeostasis. Patients with abdominal obesity have elevated cortisol levels. Furthermore, stress and glucocorticoids act to control both food intake and energy expenditure. In particular, glucocorticoids are known to increase the consumption of foods enriched in fat and sugar. It is well-known that, in all species, the cortisol response to stress or adrenocorticotropin is highly variable. It has now emerged that cortisol responsiveness is an important determinant in the metabolic sequelae to stress. Sheep that are characterized as high-cortisol responders (HRs) have greater propensity to weight gain and obesity than low-cortisol responders (LRs). This difference in susceptibility to become obese is associated with a distinct metabolic, neuroendocrine, and behavioral phenotype. In women and ewes, HR individuals eat more in response to stress than LR. Furthermore, HR sheep have impaired melanocortin signaling and reduced skeletal muscle thermogenesis. High-cortisol responder sheep exhibit reactive coping strategies, whereas LRs exhibit proactive coping strategies. This complex set of traits leads to increased food intake and reduced energy expenditure in HR and thus, predisposition to obesity. We predict that cortisol responsiveness may be used as a marker to identify individuals who are at risk of weight gain and subsequent obesity.
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Affiliation(s)
| | - T K Lee
- Department of Physiology, Monash University, VIC 3800, Australia
| | - I J Clarke
- Department of Physiology, Monash University, VIC 3800, Australia
| | - B A Henry
- Department of Physiology, Monash University, VIC 3800, Australia.
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13
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Yang Y, Tang Z, Fan X, Xu K, Mu Y, Zhou R, Li K. Transcriptome analysis revealed chimeric RNAs, single nucleotide polymorphisms and allele-specific expression in porcine prenatal skeletal muscle. Sci Rep 2016; 6:29039. [PMID: 27352850 PMCID: PMC4926253 DOI: 10.1038/srep29039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/14/2016] [Indexed: 01/28/2023] Open
Abstract
Prenatal skeletal muscle development genetically determines postnatal muscle characteristics such as growth and meat quality in pigs. However, the molecular mechanisms underlying prenatal skeletal muscle development remain unclear. Here, we performed the first genome-wide analysis of chimeric RNAs, single nuclear polymorphisms (SNPs) and allele-specific expression (ASE) in prenatal skeletal muscle in pigs. We identified 14,810 protein coding genes and 163 high-confidence chimeric RNAs expressed in prenatal skeletal muscle. More than 94.5% of the chimeric RNAs obeyed the canonical GT/AG splice rule and were trans-splicing events. Ten and two RNAs were aligned to human and mouse chimeric transcripts, respectively. We detected 106,457 high-quality SNPs (6,955 novel), which were mostly (89.09%) located within QTLs for production traits. The high proportion of non-exonic SNPs revealed the incomplete annotation status of the current swine reference genome. ASE analysis revealed that 11,300 heterozygous SNPs showed allelic imbalance, whereas 131 ASE variants were located in the chimeric RNAs. Moreover, 4 ASE variants were associated with various economically relevant traits of pigs. Taken together, our data provide a source for studies of chimeric RNAs and biomarkers for pig breeding, while illuminating the complex transcriptional events underlying prenatal skeletal muscle development in mammals.
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Affiliation(s)
- Yalan Yang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China
| | - Zhonglin Tang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China
| | - Xinhao Fan
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Kui Xu
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Yulian Mu
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Rong Zhou
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Kui Li
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China
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14
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Genome-wide DNA methylation profiles changes associated with constant heat stress in pigs as measured by bisulfite sequencing. Sci Rep 2016; 6:27507. [PMID: 27264107 PMCID: PMC4893741 DOI: 10.1038/srep27507] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 05/18/2016] [Indexed: 11/08/2022] Open
Abstract
Heat stress affects muscle development and meat quality in food animals; however, little is known regarding its regulatory mechanisms at the epigenetic level, such as via DNA methylation. In this study, we aimed to compare the DNA methylation profiles between control and heat-stressed pigs to identify candidate genes for skeletal muscle development and meat quality. Whole-genome bisulfite sequencing was used to investigate the genome-wide DNA methylation patterns in the longissimus dorsi muscles of the pigs. Both groups showed similar proportions of methylation at CpG sites but exhibited different proportions at non-CpG sites. A total of 57,147 differentially methylated regions were identified between the two groups, which corresponded to 1,422 differentially methylated genes. Gene ontogeny and KEGG pathway analyses indicated that these were mainly involved in energy and lipid metabolism, cellular defense and stress responses, and calcium signaling pathways. This study revealed the global DNA methylation pattern of pig muscle between normal and heat stress conditions. The result of this study might contribute to a better understanding of epigenetic regulation in pig muscle development and meat quality.
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15
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Welzenbach J, Neuhoff C, Looft C, Schellander K, Tholen E, Große-Brinkhaus C. Different Statistical Approaches to Investigate Porcine Muscle Metabolome Profiles to Highlight New Biomarkers for Pork Quality Assessment. PLoS One 2016; 11:e0149758. [PMID: 26919205 PMCID: PMC4769069 DOI: 10.1371/journal.pone.0149758] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/04/2016] [Indexed: 12/04/2022] Open
Abstract
The aim of this study was to elucidate the underlying biochemical processes to identify potential key molecules of meat quality traits drip loss, pH of meat 1 h post-mortem (pH1), pH in meat 24 h post-mortem (pH24) and meat color. An untargeted metabolomics approach detected the profiles of 393 annotated and 1,600 unknown metabolites in 97 Duroc × Pietrain pigs. Despite obvious differences regarding the statistical approaches, the four applied methods, namely correlation analysis, principal component analysis, weighted network analysis (WNA) and random forest regression (RFR), revealed mainly concordant results. Our findings lead to the conclusion that meat quality traits pH1, pH24 and color are strongly influenced by processes of post-mortem energy metabolism like glycolysis and pentose phosphate pathway, whereas drip loss is significantly associated with metabolites of lipid metabolism. In case of drip loss, RFR was the most suitable method to identify reliable biomarkers and to predict the phenotype based on metabolites. On the other hand, WNA provides the best parameters to investigate the metabolite interactions and to clarify the complex molecular background of meat quality traits. In summary, it was possible to attain findings on the interaction of meat quality traits and their underlying biochemical processes. The detected key metabolites might be better indicators of meat quality especially of drip loss than the measured phenotype itself and potentially might be used as bio indicators.
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Affiliation(s)
- Julia Welzenbach
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Christiane Neuhoff
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Christian Looft
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Karl Schellander
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Ernst Tholen
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
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16
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Sautron V, Terenina E, Gress L, Lippi Y, Billon Y, Larzul C, Liaubet L, Villa-Vialaneix N, Mormède P. Time course of the response to ACTH in pig: biological and transcriptomic study. BMC Genomics 2015; 16:961. [PMID: 26578410 PMCID: PMC4650497 DOI: 10.1186/s12864-015-2118-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/20/2015] [Indexed: 11/10/2022] Open
Abstract
Background HPA axis plays a major role in physiological homeostasis. It is also involved in stress and adaptive response to the environment. In farm animals in general and specifically in pigs, breeding strategies have highly favored production traits such as lean growth rate, feed efficiency and prolificacy at the cost of robustness. On the hypothesis that the HPA axis could contribute to the trade-off between robustness and production traits, we have designed this experiment to explore individual variation in the biological response to the main stress hormone, cortisol, in pigs. We used ACTH injections to trigger production of cortisol in 120 juvenile Large White (LW) pigs from 28 litters and the kinetics of the response was measured with biological variables and whole blood gene expression at 4 time points. A multilevel statistical analysis was used to take into account the longitudinal aspect of the data. Results Cortisol level reached its peak 1 h after ACTH injection. White blood cell composition was modified with a decrease of lymphocytes and monocytes and an increase of granulocytes (FDR<0.05). Basal level of cortisol was correlated with birth and weaning weights. Microarray analysis identified 65 unique genes of which expression responded to the injection of ACTH (adjusted P<0.05). These genes were classified into 4 clusters with distinctive kinetics in response to ACTH injection. The first cluster identified genes strongly correlated to cortisol and previously reported as being regulated by glucocorticoids. In particular, DDIT4, DUSP1, FKBP5, IL7R, NFKBIA, PER1, RGS2 and RHOB were shown to be connected to each other by the glucocorticoid receptor NR3C1. Most of the differentially expressed genes that encode transcription factors have not been described yet as being important in transcription networks involved in stress response. Their co-expression may mean co-regulation and they could thus provide new patterns of biomarkers of the individual sensitivity to cortisol. Conclusions We identified 65 genes as biological markers of HPA axis activation at the gene expression level. These genes might be candidates for a better understanding of the molecular mechanisms of the stress response. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2118-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valérie Sautron
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, F-31076, France.
| | - Elena Terenina
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, F-31076, France.
| | - Laure Gress
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, F-31076, France.
| | | | - Yvon Billon
- INRA, UE 1372 GenESI, Surgeres, F-17700, France.
| | - Catherine Larzul
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, F-31076, France.
| | - Laurence Liaubet
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, F-31076, France.
| | - Nathalie Villa-Vialaneix
- INRA, UR 0875 MIAT Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, F-31326, France.
| | - Pierre Mormède
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, F-31326, France. .,Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, F-31076, France.
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Poleti MD, DeRijk RH, Rosa AF, Moncau CT, Oliveira PS, Coutinho LL, Eler JP, Balieiro JCC. Genetic variants in glucocorticoid and mineralocorticoid receptors are associated with concentrations of plasma cortisol, muscle glycogen content, and meat quality traits in male Nellore cattle. Domest Anim Endocrinol 2015; 51:105-13. [PMID: 25617989 DOI: 10.1016/j.domaniend.2014.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 11/23/2022]
Abstract
The glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) are key components in the regulation of the hypothalamic-pituitary-adrenal neuroendocrine axis and coordinate the physiological response to stress agents to reestablish homeostasis. Genetic variations of GR (NR3C1) and MR (NR3C2) genes could explain the alterations in animals to adapt to challenges, and therefore, their influence on production traits. The present study aimed to identify single-nucleotide polymorphisms (SNPs) in the bovine NR3C1 and NR3C2 genes and explore their associations to relevant traits of beef cattle production. Genotypes and phenotypes were collected from 241 male Nellore cattle (119 noncastrated and 122 castrated surgically) with an average of 24 ± 1.2 mo of age and live weight of 508 ± 39 kg. The traits evaluated were concentrations of plasma adrenocorticotropic hormone (ACTH) and cortisol, muscle glycogen and lactate content, and pH, color, cooking loss, and shear force of longissimus thoracis measured on the 1st, 7th, and 14th days postmortem. Five SNPs were identified, 2 in the NR3C1 gene and 3 in the NR3C2 gene. There was an associative relationship between the SNP NR3C1_1 g.3293A>G and postmortem plasma concentration of cortisol (P = 0.0008). The SNPs NR3C2_1 g.115T>C and NR3C2_2 g.570T>C were associated with muscle glycogen content (P = 0.0306 and P = 0.0158), postmortem plasma concentration of ACTH (P = 0.0118 and P = 0.0095), and cooking loss of the steak aged 1 d (P = 0.0398 and P = 0.0423). Haplotype analysis showed associations of GR haplotypes with postmortem plasma concentrations of cortisol and MR haplotypes with meat color, cooking losses, muscle glycogen content, and plasma concentrations of ACTH. The associations observed in the present study show that SNPs in GR and MR genes are related with changes of hypothalamic-pituitary-adrenal axis activity and metabolic profile in cattle, leading to individual variation in meat quality traits.
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Affiliation(s)
- M D Poleti
- Department of Basic Sciences, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Sao Paulo 13635-900, Brazil.
| | - R H DeRijk
- Division of Medical Pharmacology, Leiden/Amsterdam Center for Drug Research, Leiden University Medical Center, Leiden, The Netherlands; Department of Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
| | - A F Rosa
- Department of Basic Sciences, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Sao Paulo 13635-900, Brazil
| | - C T Moncau
- Department of Basic Sciences, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Sao Paulo 13635-900, Brazil
| | - P S Oliveira
- Department of Basic Sciences, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Sao Paulo 13635-900, Brazil
| | - L L Coutinho
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Sao Paulo 13418-900, Brazil
| | - J P Eler
- Department of Basic Sciences, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Sao Paulo 13635-900, Brazil
| | - J C C Balieiro
- Department of Basic Sciences, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Sao Paulo 13635-900, Brazil
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18
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Lee TK, Lee C, Bischof R, Lambert GW, Clarke IJ, Henry BA. Stress-induced behavioral and metabolic adaptations lead to an obesity-prone phenotype in ewes with elevated cortisol responses. Psychoneuroendocrinology 2014; 47:166-77. [PMID: 25001966 DOI: 10.1016/j.psyneuen.2014.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/26/2014] [Accepted: 05/21/2014] [Indexed: 11/17/2022]
Abstract
The underlying cause of predisposition to obesity is complex but one marker is cortisol responsiveness. Selection of sheep for high (HR) or low (LR) cortisol responses to adrenocorticotropin shows that HR are more likely to become obese. Increased propensity to obesity is associated with reduced skeletal muscle thermogenesis. We sought to determine whether metabolic or behavioral responses to stress also contribute to altered propensity to obesity in LR and HR. Animals (n=5-10/group) were exposed to 3 stressors and we measured food intake and thermogenesis (recorded with dataloggers implanted into muscle). Stressors were hypoglycaemia (0.125 units/kg insulin, IV), a barking dog and immune challenge (200 ng/kg lipopolysaccharide--LPS, IV). LR animals showed a greater catabolic state in response to both immune and psychosocial stressors. LPS reduced (P<0.01) food intake in both groups but LR showed a greater (P<0.05) reduction in food intake and a more substantial (P<0.05) rise in muscle temperature. Introduction of the barking dog reduced (P<0.05) food intake in LR only. These metabolic differences coincided with differences in cortisol responsiveness, where HR animals had increased (P<0.05) cortisol in response to both immune and psychosocial stressors. We also assessed behavior in the following paradigms: 1, isolation in the open field test; 2, response to a human intruder; and 3, food competition. LR had greater (P<0.05) activity, reduced fearfulness and displayed a proactive coping style of behavior. Thus we demonstrate that high cortisol responsiveness identifies animals with stress-induced metabolic and behavioral traits that may contribute to susceptibility to obesity.
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Affiliation(s)
- T Kevin Lee
- Department of Physiology, Monash University, Clayton, Victoria 3800, Australia
| | - Caroline Lee
- CSIRO Animal, Food and Health Sciences, Armidale, NSW 2350, Australia
| | - Robert Bischof
- Department of Physiology, Monash University, Clayton, Victoria 3800, Australia
| | - Gavin W Lambert
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia; Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Iain J Clarke
- Department of Physiology, Monash University, Clayton, Victoria 3800, Australia
| | - Belinda A Henry
- Department of Physiology, Monash University, Clayton, Victoria 3800, Australia.
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19
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Gonzales NM, Palmer AA. Fine-mapping QTLs in advanced intercross lines and other outbred populations. Mamm Genome 2014; 25:271-92. [PMID: 24906874 DOI: 10.1007/s00335-014-9523-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 04/25/2014] [Indexed: 12/16/2022]
Abstract
Quantitative genetic studies in model organisms, particularly in mice, have been extremely successful in identifying chromosomal regions that are associated with a wide variety of behavioral and other traits. However, it is now widely understood that identification of the underlying genes will be far more challenging. In the last few years, a variety of populations have been utilized in an effort to more finely map these chromosomal regions with the goal of identifying specific genes. The common property of these newer populations is that linkage disequilibrium spans relatively short distances, which permits fine-scale mapping resolution. This review focuses on advanced intercross lines (AILs) which are the simplest such population. As originally proposed in 1995 by Darvasi and Soller, an AIL is the product of intercrossing two inbred strains beyond the F2 generation. Unlike recombinant inbred strains, AILs are maintained as outbred populations; brother-sister matings are specifically avoided. Each generation of intercrossing beyond the F2 further degrades linkage disequilibrium between adjacent makers, which allows for fine-scale mapping of quantitative trait loci (QTLs). Advances in genotyping technology and techniques for the statistical analysis of AILs have permitted rapid advances in the application of AILs. We review some of the analytical issues and available software, including QTLRel, EMMA, EMMAX, GEMMA, TASSEL, GRAMMAR, WOMBAT, Mendel, and others.
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Affiliation(s)
- Natalia M Gonzales
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
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Lucion AB, Bortolini MC. Mother-pup interactions: rodents and humans. Front Endocrinol (Lausanne) 2014; 5:17. [PMID: 24616713 PMCID: PMC3935307 DOI: 10.3389/fendo.2014.00017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 02/08/2014] [Indexed: 12/14/2022] Open
Abstract
In order to survive after birth, mammalian infants need a caretaker, usually the mother. Several behavioral strategies have evolved to guarantee the transition from a period of intense caregiving to offspring independence. Here, we examine a selection of literature on the genetic, epigenetic, physiological, and behavioral factors relating to development and mother-infant interactions. We intend to show the utility of comparisons between rodent and human models for deepening knowledge regarding this key relationship. Particular attention is paid to the following factors: the distinct developmental stages of the mother-pup relationship as relating to behavior; examples of key genetic components of mammalian mother-infant interactions, specifically those coding for the hormones oxytocin and vasopressin; and the possible functions of gene imprinting in mediating interactions between genetics and environment in the mother-infant relationship. As early mother-infant attachment seems to establish the basic parameters for later social interactions, ongoing investigations in this area are essential. We propose the importance of interdisciplinary collaboration in order to better understand the network of genes, gene regulation, neuropeptide action, physiological processes, and feedback loops essential to understand the complex behaviors of mother-infant interaction.
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Affiliation(s)
- Aldo B. Lucion
- Departamento de Fisiologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- *Correspondence: Aldo B. Lucion, Departamento de Fisiologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite 500, Porto Alegre, Rio Grande do Sul 90050-170, Brazil e-mail:
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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