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Padovani NFA, Santos TS, Almeida P, Dias M, Mendes MA, Cesar ASM, Maffei DF. Salmonella and other Enterobacteriaceae in conventional and organic vegetables grown in Brazilian farms. Braz J Microbiol 2023; 54:1055-1064. [PMID: 36811768 PMCID: PMC10235262 DOI: 10.1007/s42770-023-00934-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
This study aimed to assess the microbiological profile of conventional and organic vegetables grown in Brazilian farms through the detection of Salmonella and other Enterobacteriaceae. A total of 200 samples (100 conventional and 100 organic), including leafy greens, spices/herbs, and other unusual vegetables, were submitted to the enumeration of Enterobacteriaceae by plating on VRBG agar. Moreover, colonies of Enterobacteriaceae were randomly selected and submitted to identification by MALDI-TOF MS. Samples were also tested for Salmonella, using culture-based and PCR-based enrichment methods. The mean counts of Enterobacteriaceae in conventional and organic vegetables were 5.1 ± 1.5 and 5.4 ± 1.4 log CFU/g, respectively (P > 0.05). A total of 18 genera (including 38 species) of Enterobacteriaceae were identified, and the most frequent ones found in samples from both farming systems were Enterobacter (76%) and Pantoea (68%). Salmonella was identified in 17 samples (8.5%): nine (4.5%) in conventional and eight (4.0%) in organic vegetables. These results indicate that the farming system had no impact on the Enterobacteriaceae populations and rates of Salmonella and revealed unsatisfactory microbiological safety of some samples, mainly due to the presence of Salmonella. These findings highlight the need for control measures during vegetable production, regardless of the farming system, to reduce microbial contamination and the risks of foodborne illnesses.
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Affiliation(s)
- Nicolle F A Padovani
- Department of Agri-Food Industry, Food and Nutrition, Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Av. Pádua Dias, 11, Piracicaba, SP, CP9, 13418-900, Brazil
| | - Thiago S Santos
- Department of Agri-Food Industry, Food and Nutrition, Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Av. Pádua Dias, 11, Piracicaba, SP, CP9, 13418-900, Brazil
| | - Priscila Almeida
- Department of Agri-Food Industry, Food and Nutrition, Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Av. Pádua Dias, 11, Piracicaba, SP, CP9, 13418-900, Brazil
| | - Meriellen Dias
- Dempster MS Lab, Department of Chemical Engineering, Polytechnic School, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Maria Anita Mendes
- Dempster MS Lab, Department of Chemical Engineering, Polytechnic School, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Aline S M Cesar
- Department of Agri-Food Industry, Food and Nutrition, Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Av. Pádua Dias, 11, Piracicaba, SP, CP9, 13418-900, Brazil
| | - Daniele F Maffei
- Department of Agri-Food Industry, Food and Nutrition, Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Av. Pádua Dias, 11, Piracicaba, SP, CP9, 13418-900, Brazil.
- Food Research Center (FoRC-CEPID), Sao Paulo, SP, Brazil.
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Buss CE, Afonso J, de Oliveira PSN, Petrini J, Tizioto PC, Cesar ASM, Gustani-Buss EC, Cardoso TF, Rovadoski GA, da Silva Diniz WJ, de Lima AO, Rocha MIP, Andrade BGN, Wolf JB, Coutinho LL, Mourão GB, de Almeida Regitano LC. Bivariate GWAS reveals pleiotropic regions among feed efficiency and beef quality-related traits in Nelore cattle. Mamm Genome 2023; 34:90-103. [PMID: 36463529 DOI: 10.1007/s00335-022-09969-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/16/2022] [Indexed: 12/07/2022]
Abstract
Feed-efficient cattle selection is among the most leading solutions to reduce cost for beef cattle production. However, technical difficulties in measuring feed efficiency traits had limited the application in livestock. Here, we performed a Bivariate Genome-Wide Association Study (Bi-GWAS) and presented candidate biological mechanisms underlying the association between feed efficiency and meat quality traits in a half-sibling design with 353 Nelore steers derived from 34 unrelated sires. A total of 13 Quantitative Trait Loci (QTL) were found explaining part of the phenotypic variations. An important transcription factor of adipogenesis in cattle, the TAL1 (rs133408775) gene located on BTA3 was associated with intramuscular fat and average daily gain (IMF-ADG), and a region located on BTA20, close to CD180 and MAST4 genes, both related to fat accumulation. We observed a low positive genetic correlation between IMF-ADG (r = 0.30 ± 0.0686), indicating that it may respond to selection in the same direction. Our findings contributed to clarifying the pleiotropic modulation of the complex traits, indicating new QTLs for bovine genetic improvement.
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Affiliation(s)
- Carlos Eduardo Buss
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, São Paulo, Brazil
- Mindflow Genomics, Leuven, Flanders, Belgium
| | - Juliana Afonso
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
| | - Priscila S N de Oliveira
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | - Aline S M Cesar
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Emanuele Cristina Gustani-Buss
- Mindflow Genomics, Leuven, Flanders, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium
| | - Tainã Figueiredo Cardoso
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
| | - Gregori A Rovadoski
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | - Andressa Oliveira de Lima
- Division of Medical Genetics, Department of Genomics Science, University of Washington, Seattle, WA, USA
| | | | - Bruno Gabriel Nascimento Andrade
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
- Department of Computer Science, Munster Technological University/MTU, Cork, Ireland
| | - Jason B Wolf
- Department of Biology & Biochemistry, Milner Centre for Evolution Bath, University of Bath, Bath, BA2 7AY, UK
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
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3
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Ribeiro G, Baldi F, Cesar ASM, Alexandre PA, Peripolli E, Ferraz JBS, Fukumasu H. Detection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattle. BMC Genomics 2022; 23:774. [PMID: 36434498 PMCID: PMC9700932 DOI: 10.1186/s12864-022-08958-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/20/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Potential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in beef cattle) using a systems-biology driven approach based on RNA-seq data from physiologically relevant organs. RESULTS The systems-biology coupled with deep molecular phenotyping by RNA-seq of liver, muscle, hypothalamus, pituitary, and adrenal glands of animals with high and low feed efficiency (FE) measured by residual feed intake (RFI) identified 2,000,936 uniquely variants. Among them, 9986 variants were significantly associated with FE and only 78 had a high impact on protein expression and were considered as PFVs. A set of 169 significant uniquely variants were expressed in all five organs, however, only 27 variants had a moderate impact and none of them a had high impact on protein expression. These results provide evidence of tissue-specific effects of high-impact PFVs. The PFVs were enriched (FDR < 0.05) for processing and presentation of MHC Class I and II mediated antigens, which are an important part of the adaptive immune response. The experimental validation of these PFVs was demonstrated by the increased prediction accuracy for RFI using the weighted G matrix (ssGBLUP+wG; Acc = 0.10 and b = 0.48) obtained in the ssGWAS in comparison to the unweighted G matrix (ssGBLUP; Acc = 0.29 and b = 1.10). CONCLUSION Here we identified PFVs for FE in beef cattle using a strategy based on systems-biology and deep molecular phenotyping. This approach has great potential to be used in genetic prediction programs, especially for polygenic phenotypes.
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Affiliation(s)
- Gabriela Ribeiro
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| | - Fernando Baldi
- grid.410543.70000 0001 2188 478XDepartment of Animal Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - Aline S. M. Cesar
- grid.11899.380000 0004 1937 0722Escola Superior de Agricultura “Luiz de Queiroz”, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Pâmela A. Alexandre
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil ,CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD 4067 Australia
| | - Elisa Peripolli
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil ,grid.410543.70000 0001 2188 478XDepartment of Animal Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - José B. S. Ferraz
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| | - Heidge Fukumasu
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
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4
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de Lima AO, Koltes JE, Diniz WJS, de Oliveira PSN, Cesar ASM, Tizioto PC, Afonso J, de Souza MM, Petrini J, Rocha MIP, Cardoso TF, Neto AZ, Coutinho LL, Mourão GB, Regitano LCA. Potential Biomarkers for Feed Efficiency-Related Traits in Nelore Cattle Identified by Co-expression Network and Integrative Genomics Analyses. Front Genet 2020; 11:189. [PMID: 32194642 PMCID: PMC7064723 DOI: 10.3389/fgene.2020.00189] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Feed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying co-expression analysis in Longissimus thoracis RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (p-value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs) ELF1, ELK3, ETS1, FLI1, and TCF4, were identified with binding sites in at least one hub gene. Gene expression of CCDC80, FBLN5, SERPINF1, and OGN was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the PCDH18 and SPARCL1 hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle.
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Affiliation(s)
- Andressa O de Lima
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Wellison J S Diniz
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | | | - Aline S M Cesar
- Department of Agroindustry, Food and Nutrition, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Juliana Afonso
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Marcela M de Souza
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Juliana Petrini
- Exact Sciences Institute, Federal University of Alfenas, Alfenas, Brazil
| | - Marina I P Rocha
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Tainã F Cardoso
- Embrapa Pecuária Sudeste, Empresa Brazileira de Pesquisa Agropecuária, São Carlos, Brazil
| | - Adhemar Zerlotini Neto
- Embrapa Informática Agropecuária, Empresa Brazileira de Pesquisa Agropecuária, Campinas, Brazil
| | - Luiz L Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Gerson B Mourão
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Luciana C A Regitano
- Embrapa Pecuária Sudeste, Empresa Brazileira de Pesquisa Agropecuária, São Carlos, Brazil
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5
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Oliveira Júnior GA, Santos DJA, Cesar ASM, Boison SA, Ventura RV, Perez BC, Garcia JF, Ferraz JBS, Garrick DJ. Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires. J Anim Sci Biotechnol 2019; 10:97. [PMID: 31890201 PMCID: PMC6913038 DOI: 10.1186/s40104-019-0403-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/11/2019] [Indexed: 12/26/2022] Open
Abstract
Background Impaired fertility in cattle limits the efficiency of livestock production systems. Unraveling the genetic architecture of fertility traits would facilitate their improvement by selection. In this study, we characterized SNP chip haplotypes at QTL blocks then used whole-genome sequencing to fine map genomic regions associated with reproduction in a population of Nellore (Bos indicus) heifers. Methods The dataset comprised of 1337 heifers genotyped using a GeneSeek® Genomic Profiler panel (74677 SNPs), representing the daughters from 78 sires. After performing marker quality control, 64800 SNPs were retained. Haplotypes carried by each sire at six previously identified QTL on BTAs 5, 14 and 18 for heifer pregnancy and BTAs 8, 11 and 22 for antral follicle count were constructed using findhap software. The significance of the contrasts between the effects of every two paternally-inherited haplotype alleles were used to identify sires that were heterozygous at each QTL. Whole-genome sequencing data localized to the haplotypes from six sires and 20 other ancestors were used to identify sequence variants that were concordant with the haplotype contrasts. Enrichment analyses were applied to these variants using KEGG and MeSH libraries. Results A total of six (BTA 5), six (BTA 14) and five (BTA 18) sires were heterozygous for heifer pregnancy QTL whereas six (BTA 8), fourteen (BTA 11), and five (BTA 22) sires were heterozygous for number of antral follicles’ QTL. Due to inadequate representation of many haplotype alleles in the sequenced animals, fine mapping analysis could only be reliably performed for the QTL on BTA 5 and 14, which had 641 and 3733 concordant candidate sequence variants, respectively. The KEGG “Circadian rhythm” and “Neurotrophin signaling pathway” were significantly associated with the genes in the QTL on BTA 5 whereas 32 MeSH terms were associated with the QTL on BTA 14. Among the concordant sequence variants, 0.2% and 0.3% were classified as missense variants for BTAs 5 and 14, respectively, highlighting the genes MTERF2, RTMB, ENSBTAG00000037306 (miRNA), ENSBTAG00000040351, PRKDC, and RGS20. The potential causal mutations found in the present study were associated with biological processes such as oocyte maturation, embryo development, placenta development and response to reproductive hormones. Conclusions The identification of heterozygous sires by positionally phasing SNP chip data and contrasting haplotype effects for previously detected QTL can be used for fine mapping to identify potential causal mutations and candidate genes. Genomic variants on genes MTERF2, RTBC, miRNA ENSBTAG00000037306, ENSBTAG00000040351, PRKDC, and RGS20, which are known to have influence on reproductive biological processes, were detected.
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Affiliation(s)
- Gerson A Oliveira Júnior
- 1Department of Veterinary Medicine, University of São Paulo (USP), Faculty of Animal Science and Food Engineer, Pirassununga, SP Brazil.,2Department of Animal Bioscience, Center for Genetic Improvement of Livestock, University of Guelph, Guelph, ON Canada
| | - Daniel J A Santos
- 3Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, USA
| | - Aline S M Cesar
- 4Department of Animal Science, University of São Paulo (USP), Piracicaba, SP Brazil
| | - Solomon A Boison
- 5Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ricardo V Ventura
- 2Department of Animal Bioscience, Center for Genetic Improvement of Livestock, University of Guelph, Guelph, ON Canada.,6Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo (USP), Pirassununga, Brazil
| | - Bruno C Perez
- 1Department of Veterinary Medicine, University of São Paulo (USP), Faculty of Animal Science and Food Engineer, Pirassununga, SP Brazil
| | - José F Garcia
- 7Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Araçatuba, SP Brazil
| | - José Bento S Ferraz
- 1Department of Veterinary Medicine, University of São Paulo (USP), Faculty of Animal Science and Food Engineer, Pirassununga, SP Brazil
| | - Dorian J Garrick
- 8School of Agriculture, Massey University, Ruakura Ag Centre, Hamilton, New Zealand
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6
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de Oliveira PSN, Coutinho LL, Cesar ASM, Diniz WJDS, de Souza MM, Andrade BG, Koltes JE, Mourão GB, Zerlotini A, Reecy JM, Regitano LCA. Co-Expression Networks Reveal Potential Regulatory Roles of miRNAs in Fatty Acid Composition of Nelore Cattle. Front Genet 2019; 10:651. [PMID: 31354792 PMCID: PMC6637853 DOI: 10.3389/fgene.2019.00651] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/19/2019] [Indexed: 12/15/2022] Open
Abstract
Fatty acid (FA) content affects the sensorial and nutritional value of meat and plays a significant role in biological processes such as adipogenesis and immune response. It is well known that, in beef, the main FAs associated with these biological processes are oleic acid (C18:1 cis9, OA) and conjugated linoleic acid (CLA-c9t11), which may have beneficial effects on metabolic diseases such as type 2 diabetes and obesity. Here, we performed differential expression and co-expression analyses, weighted gene co-expression network analysis (WGCNA) and partial correlation with information theory (PCIT), to uncover the complex interactions between miRNAs and mRNAs expressed in skeletal muscle associated with FA content. miRNA and mRNA expression data were obtained from skeletal muscle of Nelore cattle that had extreme genomic breeding values for OA and CLA. Insulin and MAPK signaling pathways were identified by WGCNA as central pathways associated with both of these fatty acids. Co-expression network analysis identified bta-miR-33a/b, bta-miR-100, bta-miR-204, bta-miR-365-5p, bta-miR-660, bta-miR-411a, bta-miR-136, bta-miR-30-5p, bta-miR-146b, bta-let-7a-5p, bta-let-7f, bta-let-7, bta-miR 339, bta-miR-10b, bta-miR 486, and the genes ACTA1 and ALDOA as potential regulators of fatty acid synthesis. This study provides evidence and insights into the molecular mechanisms and potential target genes involved in fatty acid content differences in Nelore beef cattle, revealing new candidate pathways of phenotype modulation that could positively benefit beef production and human consumption.
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Affiliation(s)
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - Aline S M Cesar
- Department of Agroindustry, Food and Nutrition, University of São Paulo, Piracicaba, Brazil
| | | | - Marcela M de Souza
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Bruno G Andrade
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Carlos, Brazil
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Gerson B Mourão
- Department of Agroindustry, Food and Nutrition, University of São Paulo, Piracicaba, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Luciana C A Regitano
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Carlos, Brazil
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7
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Diniz WJS, Mazzoni G, Coutinho LL, Banerjee P, Geistlinger L, Cesar ASM, Bertolini F, Afonso J, de Oliveira PSN, Tizioto PC, Kadarmideen HN, Regitano LCA. Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle. Front Genet 2019; 10:210. [PMID: 30930938 PMCID: PMC6424907 DOI: 10.3389/fgene.2019.00210] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
Meat quality is a complex trait that is influenced by genetic and environmental factors, which includes mineral concentration. However, the association between mineral concentration and meat quality, and the specific molecular pathways underlying this association, are not well explored. We therefore analyzed gene expression as measured with RNA-seq in Longissimus thoracis muscle of 194 Nelore steers for association with three meat quality traits (intramuscular fat, meat pH, and tenderness) and the concentration of 13 minerals (Ca, Cr, Co, Cu, Fe, K, Mg, Mn, Na, P, S, Se, and Zn). We identified seven sets of co-expressed genes (modules) associated with at least two traits, which indicates that common pathways influence these traits. From pathway analysis of module hub genes, we further found an over-representation for energy and protein metabolism (AMPK and mTOR signaling pathways) in addition to muscle growth, and protein turnover pathways. Among the identified hub genes FASN, ELOV5, and PDE3B are involved with lipid metabolism and were affected by previously identified eQTLs associated to fat deposition. The reported hub genes and over-represented pathways provide evidence of interplay among gene expression, mineral concentration, and meat quality traits. Future studies investigating the effect of different levels of mineral supplementation in the gene expression and meat quality traits could help us to elucidate the regulatory mechanism by which the genes/pathways are affected.
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Affiliation(s)
- Wellison J S Diniz
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil.,Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.,Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil
| | - Gianluca Mazzoni
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Luiz L Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Priyanka Banerjee
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ludwig Geistlinger
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil.,Graduate School of Public Health and Health Policy, The City University of New York, New York, NY, United States
| | - Aline S M Cesar
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Francesca Bertolini
- Department of Aquaculture, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Juliana Afonso
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | | | - Polyana C Tizioto
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Haja N Kadarmideen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Luciana C A Regitano
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil
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8
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Silva-Vignato B, Coutinho LL, Poleti MD, Cesar ASM, Moncau CT, Regitano LCA, Balieiro JCC. Gene co-expression networks associated with carcass traits reveal new pathways for muscle and fat deposition in Nelore cattle. BMC Genomics 2019; 20:32. [PMID: 30630417 PMCID: PMC6329100 DOI: 10.1186/s12864-018-5345-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/30/2018] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Positively correlated with carcass weight and animal growth, the ribeye area (REA) and the backfat thickness (BFT) are economic important carcass traits, which impact directly on producer's payment. The selection of these traits has not been satisfactory since they are expressed later in the animal's life and multigene regulated. So, next-generation technologies have been applied in this area to improve animal's selection and better understand the molecular mechanisms involved in the development of these traits. Correlation network analysis, performed by tools like WGCNA (Weighted Correlation Network Analysis), has been used to explore gene-gene interactions and gene-phenotype correlations. Thus, this study aimed to identify putative candidate genes and metabolic pathways that regulate REA and BFT by constructing a gene co-expression network using WGCNA and RNA sequencing data, to better understand genetic and molecular variations behind these complex traits in Nelore cattle. RESULTS The gene co-expression network analysis, using WGCNA, were built using RNA-sequencing data normalized by transcript per million (TPM) from 43 Nelore steers. Forty-six gene clusters were constructed, between them, three were positively correlated (p-value< 0.1) to the BFT (Green Yellow, Ivory, and Light Yellow modules) and, one cluster was negatively correlated (p-value< 0.1) with REA (Salmon module). The enrichment analysis performed by DAVID and WebGestalt (FDR 5%) identified eight Gene Ontology (GO) terms and three KEGG pathways in the Green Yellow module, mostly associated with immune response and inflammatory mechanisms. The enrichment of the Salmon module demonstrated 19 GO terms and 21 KEGG pathways, related to muscle energy metabolism, lipid metabolism, muscle degradation, and oxidative stress diseases. The Ivory and Light yellow modules have not shown significant results in the enrichment analysis. CONCLUSION With this study, we verified that inflammation and immune response pathways modulate the BFT trait. Energy and lipid metabolism pathways, highlighting fatty acid metabolism, were the central pathways associated with REA. Some genes, as RSAD2, EIF2AK2, ACAT1, and ACSL1 were considered as putative candidate related to these traits. Altogether these results allow us to a better comprehension of the molecular mechanisms that lead to muscle and fat deposition in bovine.
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Affiliation(s)
- Bárbara Silva-Vignato
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
| | - Luiz L Coutinho
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Mirele D Poleti
- College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635-900, Brazil
| | - Aline S M Cesar
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | | | - Júlio C C Balieiro
- College of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, SP, 13635-900, Brazil
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Kappeler BIG, Regitano LCA, Poleti MD, Cesar ASM, Moreira GCM, Gasparin G, Coutinho LL. MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness. BMC Mol Biol 2019; 20:1. [PMID: 30602381 PMCID: PMC6317189 DOI: 10.1186/s12867-018-0118-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/20/2018] [Indexed: 12/16/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs are involved in the regulation of many processes including cell proliferation, differentiation, neurogenesis, angiogenesis, and apoptosis. Beef tenderness is an organoleptic characteristic of great influence in the acceptance of meat by consumers. Previous studies have shown that collagen level, marbling, apoptosis and proteolysis are among the many factors that affect beef tenderness. Considering that miRNAs can modulate gene expression, this study was designed to identify differentially expressed miRNAs that could be modulating biological processes involved with beef tenderness. Results Deep sequence analysis of miRNA libraries from longissimus thoracis muscle allowed the identification of 42 novel and 308 known miRNAs. Among the known miRNAs, seven were specifically expressed in skeletal muscle. Differential expression analysis between animals with high (H) and low (L) estimated breeding values for shear force (EBVSF) revealed bta-mir-182 and bta-mir-183 are up-regulated (q value < 0.05) in animals with L EBVSF, and bta-mir-338 is up-regulated in animals with H EBVSF. The number of bovine predicted targets for bta-mir-182, bta-mir-183 and bta-mir-338 were 811, 281 and 222, respectively, which correspond to 1204 unique target genes. Among these, four of them, MEF2C, MAP3K2, MTDH and TNRC6B were common targets of the three differentially expressed miRNAs. The functional analysis identified important pathways related to tenderness such as apoptosis and the calpain–calpastatin system. Conclusion The results obtained indicate the importance of miRNAs in the regulatory mechanisms that influence muscle proteolysis and meat tenderness and contribute to our better understanding of the role of miRNAs in biological processes associated with beef tenderness. Electronic supplementary material The online version of this article (10.1186/s12867-018-0118-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Berna I G Kappeler
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Mirele D Poleti
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635-900, Brazil
| | - Aline S M Cesar
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Gabriel C M Moreira
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Gustavo Gasparin
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Luiz L Coutinho
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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10
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De Oliveira PSN, Coutinho LL, Tizioto PC, Cesar ASM, de Oliveira GB, Diniz WJDS, De Lima AO, Reecy JM, Mourão GB, Zerlotini A, Regitano LCA. An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle. Sci Rep 2018; 8:17072. [PMID: 30459456 PMCID: PMC6244318 DOI: 10.1038/s41598-018-35315-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/30/2018] [Indexed: 12/21/2022] Open
Abstract
Residual Feed Intake (RFI) is an economically relevant trait in beef cattle. Among the molecular regulatory mechanisms, microRNAs (miRNAs) are an important dimension in post-transcriptional regulation and have been associated with different biological pathways. Here, we performed differential miRNAs expression and weighted gene co-expression network analyses (WGCNA) to better understand the complex interactions between miRNAs and mRNAs expressed in bovine skeletal muscle and liver. MiRNA and mRNA expression data were obtained from Nelore steers that were genetically divergent for RFI (N = 10 [low RFI or feed efficient]; N = 10 [high RFI or feed inefficient]). Differentially expressed and hub miRNAs such as bta-miR-486, bta-miR-7, bta-miR15a, bta-miR-21, bta-miR 29, bta- miR-30b, bta-miR-106b, bta-miR-199a-3p, bta-miR-204, and bta-miR 296 may have a potential role in variation of RFI. Functional enrichment analysis of differentially expressed (DE) miRNA's target genes and miRNA-mRNA correlated modules revealed that insulin, lipid, immune system, oxidative stress and muscle development signaling pathways might potentially be involved in RFI in this population. Our study identified DE miRNAs, miRNA - mRNA regulatory networks and hub miRNAs related to RFI. These findings suggest a possible role of miRNAs in regulation of RFI, providing new insights into the potential molecular mechanisms that control feed efficiency in Nelore cattle.
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Affiliation(s)
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Aline S M Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Wellison J da S Diniz
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Andressa O De Lima
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
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11
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Cesar ASM, Regitano LCA, Reecy JM, Poleti MD, Oliveira PSN, de Oliveira GB, Moreira GCM, Mudadu MA, Tizioto PC, Koltes JE, Fritz-Waters E, Kramer L, Garrick D, Beiki H, Geistlinger L, Mourão GB, Zerlotini A, Coutinho LL. Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits. BMC Genomics 2018; 19:499. [PMID: 29945546 PMCID: PMC6020320 DOI: 10.1186/s12864-018-4871-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/14/2018] [Indexed: 12/21/2022] Open
Abstract
Background Integration of high throughput DNA genotyping and RNA-sequencing data allows for the identification of genomic regions that control gene expression, known as expression quantitative trait loci (eQTL), on a whole genome scale. Intramuscular fat (IMF) content and carcass composition play important roles in metabolic and physiological processes in mammals because they influence insulin sensitivity and consequently prevalence of metabolic diseases such as obesity and type 2 diabetes. However, limited information is available on the genetic variants and mechanisms associated with IMF deposition in mammals. Thus, our hypothesis was that eQTL analyses could identify putative regulatory regions and transcription factors (TFs) associated with intramuscular fat (IMF) content traits. Results We performed an integrative eQTL study in skeletal muscle to identify putative regulatory regions and factors associated with intramuscular fat content traits. Data obtained from skeletal muscle samples of 192 animals was used for association analysis between 461,466 SNPs and the transcription level of 11,808 genes. This yielded 1268 cis- and 10,334 trans-eQTLs, among which we identified nine hotspot regions that each affected the expression of > 119 genes. These putative regulatory regions overlapped with previously identified QTLs for IMF content. Three of the hotspots respectively harbored the transcription factors USF1, EGR4 and RUNX1T1, which are known to play important roles in lipid metabolism. From co-expression network analysis, we further identified modules significantly correlated with IMF content and associated with relevant processes such as fatty acid metabolism, carbohydrate metabolism and lipid metabolism. Conclusion This study provides novel insights into the link between genotype and IMF content as evident from the expression level. It thereby identifies genomic regions of particular importance and associated regulatory factors. These new findings provide new knowledge about the biological processes associated with genetic variants and mechanisms associated with IMF deposition in mammals. Electronic supplementary material The online version of this article (10.1186/s12864-018-4871-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aline S M Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.,Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Mirele D Poleti
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | | | - Gabriel C M Moreira
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Polyana C Tizioto
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Elyn Fritz-Waters
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Luke Kramer
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Dorian Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
| | - Hamid Beiki
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | | | - Gerson B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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12
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Rovadoscki GA, Pertile SFN, Alvarenga AB, Cesar ASM, Pértille F, Petrini J, Franzo V, Soares WVB, Morota G, Spangler ML, Pinto LFB, Carvalho GGP, Lanna DPD, Coutinho LL, Mourão GB. Estimates of genomic heritability and genome-wide association study for fatty acids profile in Santa Inês sheep. BMC Genomics 2018; 19:375. [PMID: 29783944 PMCID: PMC5963081 DOI: 10.1186/s12864-018-4777-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 05/10/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity of studies in the literature that report genetic or genomic parameters, especially in the case of sheep populations. To investigate the genetic architecture of fatty acid composition of sheep, we conducted genome-wide association studies (GWAS) and estimated genomic heritabilities for fatty acid profile in Longissimus dorsi muscle of 216 male sheep. RESULTS Genomic heritability estimates for fatty acid content ranged from 0.25 to 0.46, indicating that substantial genetic variation exists for the evaluated traits. Therefore, it is possible to alter fatty acid profiles through selection. Twenty-seven genomic regions of 10 adjacent SNPs associated with fatty acids composition were identified on chromosomes 1, 2, 3, 5, 8, 12, 14, 15, 16, 17, and 18, each explaining ≥0.30% of the additive genetic variance. Twenty-three genes supporting the understanding of genetic mechanisms of fat composition in sheep were identified in these regions, such as DGAT2, TRHDE, TPH2, ME1, C6, C7, UBE3D, PARP14, and MRPS30. CONCLUSIONS Estimates of genomic heritabilities and elucidating important genomic regions can contribute to a better understanding of the genetic control of fatty acid deposition and improve the selection strategies to enhance meat quality and health attributes.
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Affiliation(s)
- G A Rovadoscki
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - S F N Pertile
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - A B Alvarenga
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - A S M Cesar
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - F Pértille
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - J Petrini
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - V Franzo
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - W V B Soares
- Institute of Zootechny (IZ), Nova Odessa, SP, Brazil
| | - G Morota
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - L F B Pinto
- Department of Animal Science, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - G G P Carvalho
- Department of Animal Science, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - D P D Lanna
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - L L Coutinho
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - G B Mourão
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil.
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13
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Oliveira GB, Regitano LCA, Cesar ASM, Reecy JM, Degaki KY, Poleti MD, Felício AM, Koltes JE, Coutinho LL. Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle. BMC Genomics 2018; 19:126. [PMID: 29415651 PMCID: PMC5804041 DOI: 10.1186/s12864-018-4514-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 01/31/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The amount of intramuscular fat can influence the sensory characteristics and nutritional value of beef, thus the selection of animals with adequate fat deposition is important to the consumer. There is growing knowledge about the genes and pathways that control the biological processes involved in fat deposition in muscle. MicroRNAs (miRNAs) belong to a well-conserved class of non-coding small RNAs that modulate gene expression across a range of biological functions in animal development and physiology. The aim of this study was to identify differentially expressed (DE) miRNAs, regulatory candidate genes and co-expression networks related to intramuscular fat (IMF) deposition. To achieve this, we used mRNA and miRNA expression data from the Longissimus dorsi muscle of 30 Nelore steers with high (H) and low (L) genomic estimated breeding values (GEBV) for IMF deposition. RESULTS Differential miRNA expression analysis between animals with extreme GEBV values for IMF identified six DE miRNAs (FDR 10%). Functional annotation of the target genes for these microRNAs indicated that the PPARs signaling pathway is involved with IMF deposition. Candidate regulatory genes such as SDHAF4, FBXO17, ALDOA and PKM were identified by partial correlation with information theory (PCIT), phenotypic impact factor (PIF) and regulatory impact factor (RIF) co-expression approaches from integrated miRNA-mRNA expression data. Two DE miRNAs (FDR 10%), bta-miR-143 and bta-miR-146b, which were upregulated in the Low IMF group, were correlated with regulatory candidate genes, which were functionally enriched for fatty acid oxidation GO terms. Co-expression patterns obtained by weighted correlation network analysis (WGCNA), which showed possible interaction and regulation between mRNAs and miRNAs, identified several modules related to immune system function, protein metabolism, energy metabolism and glucose catabolism according to in silico analysis performed herein. CONCLUSION In this study, several genes and miRNAs were identified as candidate regulators of IMF by analyzing DE miRNAs using two different miRNA-mRNA co-expression network methods. This study contributes to the understanding of potential regulatory mechanisms of gene signaling networks involved in fat deposition processes measured in muscle. Glucose metabolism and inflammation processes were the main pathways found in silico to influence intramuscular fat deposition in beef cattle in the integrative mRNA-miRNA co-expression analysis.
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Affiliation(s)
- Gabriella B. Oliveira
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | | | - Aline S. M. Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - James M. Reecy
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
| | - Karina Y. Degaki
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Mirele D. Poleti
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Andrezza M. Felício
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - James E. Koltes
- Department of Animal Science, University of Arkansas, Fayetteville, AR 72701 USA
| | - Luiz L. Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
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14
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Silva-Vignato B, Coutinho LL, Cesar ASM, Poleti MD, Regitano LCA, Balieiro JCC. Comparative muscle transcriptome associated with carcass traits of Nellore cattle. BMC Genomics 2017; 18:506. [PMID: 28673252 PMCID: PMC5496360 DOI: 10.1186/s12864-017-3897-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/22/2017] [Indexed: 01/16/2023] Open
Abstract
Background Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measurement of ribeye area (REA) and backfat thickness (BFT) can be used as indirect measures of meat yield. REA and BFT are important traits studied in beef cattle due to their strong implication in technological (carcass yield) and nutritional characteristics of meat products, like the degree of muscularity and total body fat. Thus, the aim of this work was to study the Longissimus dorsi muscle transcriptome of Nellore cattle, associated with REA and BFT, to find differentially expressed (DE) genes, metabolic pathways, and biological processes that may regulate these traits. Results By comparing the gene expression level between groups with extreme genomic estimated breeding values (GEBV), 101 DE genes for REA and 18 for BFT (false discovery rate, FDR 10%) were identified. Functional enrichment analysis for REA identified two KEGG pathways, MAPK (Mitogen-Activated Protein Kinase) signaling pathway and endocytosis pathway, and three biological processes, response to endoplasmic reticulum stress, cellular protein modification process, and macromolecule modification. The MAPK pathway is responsible for fundamental cellular processes, such as growth, differentiation, and hypertrophy. For BFT, 18 biological processes were found to be altered and grouped into 8 clusters of semantically similar terms. The DE genes identified in the biological processes for BFT were ACHE, SRD5A1, RSAD2 and RSPO3. RSAD2 has been previously shown to be associated with lipid droplet content and lipid biosynthesis. Conclusion In this study, we identified genes, metabolic pathways, and biological processes, involved in differentiation, proliferation, protein turnover, hypertrophy, as well as adipogenesis and lipid biosynthesis related to REA and BFT. These results enlighten some of the molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3897-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bárbara Silva-Vignato
- College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635-900, Brazil.
| | - Luiz L Coutinho
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Aline S M Cesar
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Mirele D Poleti
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Júlio C C Balieiro
- College of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, SP, 13635-900, Brazil
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15
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da Silveira JC, Andrade GM, del Collado M, Sampaio RV, Sangalli JR, Silva LA, Pinaffi FVL, Jardim IB, Cesar MC, Nogueira MFG, Cesar ASM, Coutinho LL, Pereira RW, Perecin F, Meirelles FV. Supplementation with small-extracellular vesicles from ovarian follicular fluid during in vitro production modulates bovine embryo development. PLoS One 2017; 12:e0179451. [PMID: 28617821 PMCID: PMC5472319 DOI: 10.1371/journal.pone.0179451] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 05/29/2017] [Indexed: 01/06/2023] Open
Abstract
Pregnancy success results from the interaction of multiple factors, among them are folliculogenesis and early embryonic development. Failure during these different processes can lead to difficulties in conception. Alternatives to overcome these problems are based on assisted reproductive techniques. Extracellular vesicles are cell-secreted vesicles present in different body fluids and contain bioactive materials, such as messenger RNA, microRNAs (miRNAs), and proteins. Thus, our hypothesis is that extracellular vesicles from follicular fluid from 3-6 mm ovarian follicles can modulate bovine embryo development in vitro. To test our hypothesis follicular fluid from bovine ovaries was aspirated and small-extracellular vesicles (<200 nm) were isolated for further analysis. Additionally, small-extracellular vesicles (EVs) were utilized for functional experiments investigating their role in modulating messenger RNA, microRNA as well as global DNA methylation and hydroxymethylation levels of bovine blastocysts. EVs from 3-6 mm follicles were used for RNA-seq and miRNA analysis. Functional annotation analysis of the EVs transcripts revealed messages related to chromatin remodeling and transcriptional regulation. EVs treatment during oocyte maturation and embryo development causes changes in blastocyst rates, as well as changes in the transcription levels of genes related to embryonic metabolism and development. Supplementation with EVs from 3-6 mm follicles during oocyte maturation and early embryo development (until the 4-cell stage) increased the levels of bta-miR-631 (enriched in EVs from 3-6 mm follicles) in embryos. Interestingly, the addition of EVs from 3-6 mm follicles induced changes in global DNA methylation and hydroxymethylation levels compared to embryos produced by the standard in vitro production system. Our results indicate that the supplementation of culture media with EVs isolated from the follicular fluid of 3-6 mm follicles during oocyte maturation and early embryo development can partially modify metabolic and developmental related genes as well as miRNA and global DNA methylation and hydroxymethylation, suggesting that EVs play an important role during oocyte maturation and early embryo development in vitro.
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Affiliation(s)
- Juliano C. da Silveira
- Department of Veterinary Medicine, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Gabriella M. Andrade
- Department of Veterinary Medicine, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Maite del Collado
- Department of Veterinary Medicine, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Rafael V. Sampaio
- Department of Veterinary Medicine, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Juliano R. Sangalli
- Department of Veterinary Medicine, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Luciano A. Silva
- Department of Veterinary Medicine, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Fábio V. L. Pinaffi
- Department of Veterinary Medicine, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Izabelle B. Jardim
- Department of Veterinary Medicine, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Marcelo C. Cesar
- Department of Veterinary Medicine, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Marcelo F. G. Nogueira
- Department of Biological Sciences, University of Sao Paulo State, Assis, Sao Paulo, Brazil
| | - Aline S. M. Cesar
- Department of Animal Sciences, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Luiz L. Coutinho
- Department of Animal Sciences, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Rinaldo W. Pereira
- Department of Biotechnology, Catholic University of Brasilia, Brasília, Brazil
| | - Felipe Perecin
- Department of Veterinary Medicine, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Flávio V. Meirelles
- Department of Veterinary Medicine, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
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16
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Tizioto PC, Coutinho LL, Oliveira PSN, Cesar ASM, Diniz WJS, Lima AO, Rocha MI, Decker JE, Schnabel RD, Mourão GB, Tullio RR, Zerlotini A, Taylor JF, Regitano LCA. Corrigendum: Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake. Sci Rep 2017; 7:44345. [PMID: 28378785 PMCID: PMC5380936 DOI: 10.1038/srep44345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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17
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Tizioto PC, Coutinho LL, Oliveira PSN, Cesar ASM, Diniz WJS, Lima AO, Rocha MI, Decker JE, Schnabel RD, Mourão GB, Tullio RR, Zerlotini A, Taylor JF, Regitano LCA. Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake. Sci Rep 2016; 6:39493. [PMID: 28004777 PMCID: PMC5177880 DOI: 10.1038/srep39493] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/24/2016] [Indexed: 12/18/2022] Open
Abstract
Residual feed intake (RFI), a measure of feed efficiency (FE), is defined as the difference between the observed and the predictable feed intake considering size and growth of the animal. It is extremely important to beef production systems due to its impact on the allocation of land areas to alternative agricultural production, animal methane emissions, food demand and cost of production. Global differential gene expression analysis between high and low RFI groups (HRFI and LRFI: less and more efficient, respectively) revealed 73 differentially expressed (DE) annotated genes in Longissimus thoracis (LT) muscle of Nelore steers. These genes are involved in the overrepresented pathways Metabolism of Xenobiotics by Cytochrome P450 and Butanoate and Tryptophan Metabolism. Among the DE transcripts were several proteins related to mitochondrial function and the metabolism of lipids. Our findings indicate that observed gene expression differences are primarily related to metabolic processes underlying oxidative stress. Genes involved in the metabolism of xenobiotics and antioxidant mechanisms were primarily down-regulated, while genes responsible for lipid oxidation and ketogenesis were up-regulated in HRFI group. By using LT muscle, this study reinforces our previous findings using liver tissue and reveals new genes and likely tissue-specific regulators playing key-roles in these processes.
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Affiliation(s)
- Polyana C Tizioto
- Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | - Aline S M Cesar
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Wellison J S Diniz
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Andressa O Lima
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Marina I Rocha
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA.,Informatics Institute, University of Missouri, Columbia, Missouri, 65211, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA.,Informatics Institute, University of Missouri, Columbia, Missouri, 65211, USA
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | | | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA
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18
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Berton MP, Fonseca LFS, Gimenez DFJ, Utembergue BL, Cesar ASM, Coutinho LL, de Lemos MVA, Aboujaoude C, Pereira ASC, Silva RMDO, Stafuzza NB, Feitosa FLB, Chiaia HLJ, Olivieri BF, Peripolli E, Tonussi RL, Gordo DM, Espigolan R, Ferrinho AM, Mueller LF, de Albuquerque LG, de Oliveira HN, Duckett S, Baldi F. Gene expression profile of intramuscular muscle in Nellore cattle with extreme values of fatty acid. BMC Genomics 2016; 17:972. [PMID: 27884102 PMCID: PMC5123393 DOI: 10.1186/s12864-016-3232-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 11/01/2016] [Indexed: 11/10/2022] Open
Abstract
Background Fatty acid type in beef can be detrimental to human health and has received considerable attention in recent years. The aim of this study was to identify differentially expressed genes in longissimus thoracis muscle of 48 Nellore young bulls with extreme phenotypes for fatty acid composition of intramuscular fat by RNA-seq technique. Results Differential expression analyses between animals with extreme phenotype for fatty acid composition showed a total of 13 differentially expressed genes for myristic (C14:0), 35 for palmitic (C16:0), 187 for stearic (C18:0), 371 for oleic (C18:1, cis-9), 24 for conjugated linoleic (C18:2 cis-9, trans11, CLA), 89 for linoleic (C18:2 cis-9,12 n6), and 110 genes for α-linolenic (C18:3 n3) fatty acids. For the respective sums of the individual fatty acids, 51 differentially expressed genes for saturated fatty acids (SFA), 336 for monounsaturated (MUFA), 131 for polyunsaturated (PUFA), 92 for PUFA/SFA ratio, 55 for ω3, 627 for ω6, and 22 for ω6/ω3 ratio were identified. Functional annotation analyses identified several genes associated with fatty acid metabolism, such as those involved in intra and extra-cellular transport of fatty acid synthesis precursors in intramuscular fat of longissimus thoracis muscle. Some of them must be highlighted, such as: ACSM3 and ACSS1 genes, which work as a precursor in fatty acid synthesis; DGAT2 gene that acts in the deposition of saturated fat in the adipose tissue; GPP and LPL genes that support the synthesis of insulin, stimulating both the glucose synthesis and the amino acids entry into the cells; and the BDH1 gene, which is responsible for the synthesis and degradation of ketone bodies used in the synthesis of ATP. Conclusion Several genes related to lipid metabolism and fatty acid composition were identified. These findings must contribute to the elucidation of the genetic basis to improve Nellore meat quality traits, with emphasis on human health. Additionally, it can also contribute to improve the knowledge of fatty acid biosynthesis and the selection of animals with better nutritional quality. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3232-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mariana P Berton
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Larissa F S Fonseca
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Daniela F J Gimenez
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Bruno L Utembergue
- Departamento de Nutrição e Produção Animal, Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Pirassununga, 13635-900, SP, Brazil
| | - Aline S M Cesar
- Departamento de Zootecnia, Universidade de São Paulo, Piracicaba, 13418-900, SP, Brazil
| | - Luiz L Coutinho
- Departamento de Zootecnia, Universidade de São Paulo, Piracicaba, 13418-900, SP, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico, Lago Sul, 71605-001, DF, Brazil
| | - Marcos Vinicius A de Lemos
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Carolyn Aboujaoude
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Angélica S C Pereira
- Departamento de Nutrição e Produção Animal, Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Pirassununga, 13635-900, SP, Brazil
| | - Rafael M de O Silva
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Nedenia B Stafuzza
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Fabieli L B Feitosa
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Hermenegildo L J Chiaia
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Bianca F Olivieri
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Elisa Peripolli
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Rafael L Tonussi
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Daniel M Gordo
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Rafael Espigolan
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil
| | - Adrielle M Ferrinho
- Departamento de Nutrição e Produção Animal, Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Pirassununga, 13635-900, SP, Brazil
| | - Lenise F Mueller
- Departamento de Zootecnia, Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, 13635-900, SP, Brazil
| | - Lucia G de Albuquerque
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico, Lago Sul, 71605-001, DF, Brazil
| | - Henrique N de Oliveira
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico, Lago Sul, 71605-001, DF, Brazil
| | - Susan Duckett
- Animal and Veterinary Science Department of Clemson University, Clemson, 29634, SC, USA
| | - Fernando Baldi
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, SP, Brazil. .,Conselho Nacional de Desenvolvimento Científico e Tecnológico, Lago Sul, 71605-001, DF, Brazil.
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Cesar ASM, Regitano LCA, Poleti MD, Andrade SCS, Tizioto PC, Oliveira PSN, Felício AM, do Nascimento ML, Chaves AS, Lanna DPD, Tullio RR, Nassu RT, Koltes JE, Fritz-Waters E, Mourão GB, Zerlotini-Neto A, Reecy JM, Coutinho LL. Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content. BMC Genomics 2016; 17:961. [PMID: 27875996 PMCID: PMC5120530 DOI: 10.1186/s12864-016-3306-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 11/17/2016] [Indexed: 12/19/2022] Open
Abstract
Background Lipids are a class of molecules that play an important role in cellular structure and metabolism in all cell types. In the last few decades, it has been reported that long-chain fatty acids (FAs) are involved in several biological functions from transcriptional regulation to physiological processes. Several fatty acids have been both positively and negatively implicated in different biological processes in skeletal muscle and other tissues. To gain insight into biological processes associated with fatty acid content in skeletal muscle, the aim of the present study was to identify differentially expressed genes (DEGs) and functional pathways related to gene expression regulation associated with FA content in cattle. Results Skeletal muscle transcriptome analysis of 164 Nellore steers revealed no differentially expressed genes (DEGs, FDR 10%) for samples with extreme values for linoleic acid (LA) or stearic acid (SA), and only a few DEGs for eicosapentaenoic acid (EPA, 5 DEGs), docosahexaenoic acid (DHA, 4 DEGs) and palmitic acid (PA, 123 DEGs), while large numbers of DEGs were associated with oleic acid (OA, 1134 DEGs) and conjugated linoleic acid cis9 trans11 (CLA-c9t11, 872 DEGs). Functional annotation and functional enrichment from OA DEGs identified important genes, canonical pathways and upstream regulators such as SCD, PLIN5, UCP3, CPT1, CPT1B, oxidative phosphorylation mitochondrial dysfunction, PPARGC1A, and FOXO1. Two important genes associated with lipid metabolism, gene expression and cancer were identified as DEGs between animals with high and low CLA-c9t11, specifically, epidermal growth factor receptor (EGFR) and RNPS. Conclusion Only two out of seven classes of molecules of FA studied were associated with large changes in the expression profile of skeletal muscle. OA and CLA-c9t11 content had significant effects on the expression level of genes related to important biological processes associated with oxidative phosphorylation, and cell growth, survival, and migration. These results contribute to our understanding of how some FAs modulate metabolism and may have protective health function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3306-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aline S M Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.,Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | | | - Mirele D Poleti
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Sónia C S Andrade
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.,Departament of Genetics and Evolutionary Biology-IB, USP, São Paulo, SP, 05508-090, Brazil
| | | | | | - Andrezza M Felício
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Amália S Chaves
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Dante P D Lanna
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Rymer R Tullio
- Embrapa Pecuária Sudeste, São Carlos, SP, 13560-970, Brazil
| | - Renata T Nassu
- Embrapa Pecuária Sudeste, São Carlos, SP, 13560-970, Brazil
| | - James E Koltes
- Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Eric Fritz-Waters
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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20
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de Oliveira PSN, Tizioto PC, Malago W, do Nascimento ML, Cesar ASM, Diniz WJS, de Souza MM, Lanna DPD, Tullio RR, Mourão GB, de A Mudadu M, Coutinho LL, de A Regitano LC. A single nucleotide polymorphism in NEUROD1 is associated with production traits in Nelore beef cattle. Genet Mol Res 2016; 15:gmr8161. [PMID: 27420997 DOI: 10.4238/gmr.15028161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Feed efficiency and carcass characteristics are late-measured traits. The detection of molecular markers associated with them can help breeding programs to select animals early in life, and to predict breeding values with high accuracy. The objective of this study was to identify polymorphisms in the functional and positional candidate gene NEUROD1 (neurogenic differentiation 1), and investigate their associations with production traits in reference families of Nelore cattle. A total of 585 steers were used, from 34 sires chosen to represent the variability of this breed. By sequencing 14 animals with extreme residual feed intake (RFI) values, seven single nucleotide polymorphisms (SNPs) in NEUROD1 were identified. The investigation of marker effects on the target traits RFI, backfat thickness (BFT), ribeye area (REA), average body weight (ABW), and metabolic body weight (MBW) was performed with a mixed model using the restricted maximum likelihood method. SNP1062, which changes cytosine for guanine, had no significant association with RFI or REA. However, we found an additive effect on ABW (P ≤ 0.05) and MBW (P ≤ 0.05), with an estimated allele substitution effect of -1.59 and -0.93 kg0.75, respectively. A dominant effect of this SNP for BFT was also found (P ≤ 0.010). Our results are the first that identify NEUROD1 as a candidate that affects BFT, ABW, and MBW. Once confirmed, the inclusion of this SNP in dense panels may improve the accuracy of genomic selection for these traits in Nelore beef cattle as this SNP is not currently represented on SNP chips.
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Affiliation(s)
| | - P C Tizioto
- Embrapa Pecuária Sudeste, São Carlos, SP, Brasil
| | - W Malago
- Embrapa Pecuária Sudeste, São Carlos, SP, Brasil
| | - M L do Nascimento
- Departamento de Zootecnia, Universidade de São Paulo, São Paulo, SP, Brasil
| | - A S M Cesar
- Departamento de Zootecnia, Universidade de São Paulo, São Paulo, SP, Brasil
| | - W J S Diniz
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
| | - M M de Souza
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
| | - D P D Lanna
- Departamento de Zootecnia, Universidade de São Paulo, São Paulo, SP, Brasil
| | - R R Tullio
- Embrapa Pecuária Sudeste, São Carlos, SP, Brasil
| | - G B Mourão
- Departamento de Zootecnia, Universidade de São Paulo, São Paulo, SP, Brasil
| | | | - L L Coutinho
- Departamento de Zootecnia, Universidade de São Paulo, São Paulo, SP, Brasil
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21
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Cesar ASM, Regitano LCA, Koltes JE, Fritz-Waters ER, Lanna DPD, Gasparin G, Mourão GB, Oliveira PSN, Reecy JM, Coutinho LL. Putative regulatory factors associated with intramuscular fat content. PLoS One 2015; 10:e0128350. [PMID: 26042666 PMCID: PMC4456163 DOI: 10.1371/journal.pone.0128350] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 04/26/2015] [Indexed: 01/12/2023] Open
Abstract
Intramuscular fat (IMF) content is related to insulin resistance, which is an important prediction factor for disorders, such as cardiovascular disease, obesity and type 2 diabetes in human. At the same time, it is an economically important trait, which influences the sensorial and nutritional value of meat. The deposition of IMF is influenced by many factors such as sex, age, nutrition, and genetics. In this study Nellore steers (Bos taurus indicus subspecies) were used to better understand the molecular mechanisms involved in IMF content. This was accomplished by identifying differentially expressed genes (DEG), biological pathways and putative regulatory factors. Animals included in this study had extreme genomic estimated breeding value (GEBV) for IMF. RNA-seq analysis, gene set enrichment analysis (GSEA) and co-expression network methods, such as partial correlation coefficient with information theory (PCIT), regulatory impact factor (RIF) and phenotypic impact factor (PIF) were utilized to better understand intramuscular adipogenesis. A total of 16,101 genes were analyzed in both groups (high (H) and low (L) GEBV) and 77 DEG (FDR 10%) were identified between the two groups. Pathway Studio software identified 13 significantly over-represented pathways, functional classes and small molecule signaling pathways within the DEG list. PCIT analyses identified genes with a difference in the number of gene-gene correlations between H and L group and detected putative regulatory factors involved in IMF content. Candidate genes identified by PCIT include: ANKRD26, HOXC5 and PPAPDC2. RIF and PIF analyses identified several candidate genes: GLI2 and IGF2 (RIF1), MPC1 and UBL5 (RIF2) and a host of small RNAs, including miR-1281 (PIF). These findings contribute to a better understanding of the molecular mechanisms that underlie fat content and energy balance in muscle and provide important information for the production of healthier beef for human consumption.
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Affiliation(s)
- Aline S. M. Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
| | | | - James E. Koltes
- Department of Animal Science, Iowa State University, Ames, IA, 50011, United States of America
| | - Eric R. Fritz-Waters
- Department of Animal Science, Iowa State University, Ames, IA, 50011, United States of America
| | - Dante P. D. Lanna
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
| | - Gustavo Gasparin
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
| | - Gerson B. Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
| | - Priscila S. N. Oliveira
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, 13565–905, Brazil
| | - James M. Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, United States of America
| | - Luiz L. Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
- * E-mail:
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22
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de Oliveira PSN, Cesar ASM, do Nascimento ML, Chaves AS, Tizioto PC, Tullio RR, Lanna DPD, Rosa AN, Sonstegard TS, Mourao GB, Reecy JM, Garrick DJ, Mudadu MA, Coutinho LL, Regitano LCA. Identification of genomic regions associated with feed efficiency in Nelore cattle. BMC Genet 2014; 15:100. [PMID: 25257854 PMCID: PMC4198703 DOI: 10.1186/s12863-014-0100-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 09/10/2014] [Indexed: 01/17/2023] Open
Abstract
Background Feed efficiency is jointly determined by productivity and feed requirements, both of which are economically relevant traits in beef cattle production systems. The objective of this study was to identify genes/QTLs associated with components of feed efficiency in Nelore cattle using Illumina BovineHD BeadChip (770 k SNP) genotypes from 593 Nelore steers. The traits analyzed included: average daily gain (ADG), dry matter intake (DMI), feed-conversion ratio (FCR), feed efficiency (FE), residual feed intake (RFI), maintenance efficiency (ME), efficiency of gain (EG), partial efficiency of growth (PEG) and relative growth rate (RGR). The Bayes B analysis was completed with Gensel software parameterized to fit fewer markers than animals. Genomic windows containing all the SNP loci in each 1 Mb that accounted for more than 1.0% of genetic variance were considered as QTL region. Candidate genes within windows that explained more than 1% of genetic variance were selected by putative function based on DAVID and Gene Ontology. Results Thirty-six QTL (1-Mb SNP window) were identified on chromosomes 1, 2, 3, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 18, 19, 20, 21, 22, 24, 25 and 26 (UMD 3.1). The amount of genetic variance explained by individual QTL windows for feed efficiency traits ranged from 0.5% to 9.07%. Some of these QTL minimally overlapped with previously reported feed efficiency QTL for Bos taurus. The QTL regions described in this study harbor genes with biological functions related to metabolic processes, lipid and protein metabolism, generation of energy and growth. Among the positional candidate genes selected for feed efficiency are: HRH4, ALDH7A1, APOA2, LIN7C, CXADR, ADAM12 and MAP7. Conclusions Some genomic regions and some positional candidate genes reported in this study have not been previously reported for feed efficiency traits in Bos indicus. Comparison with published results indicates that different QTLs and genes may be involved in the control of feed efficiency traits in this Nelore cattle population, as compared to Bos taurus cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0100-0) contains supplementary material, which is available to authorized users.
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23
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Cesar ASM, Regitano LCA, Mourão GB, Tullio RR, Lanna DPD, Nassu RT, Mudado MA, Oliveira PSN, do Nascimento ML, Chaves AS, Alencar MM, Sonstegard TS, Garrick DJ, Reecy JM, Coutinho LL. Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle. BMC Genet 2014; 15:39. [PMID: 24666668 PMCID: PMC4230646 DOI: 10.1186/1471-2156-15-39] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/28/2014] [Indexed: 01/01/2023] Open
Abstract
Background Meat from Bos taurus and Bos indicus breeds are an important source of nutrients for humans and intramuscular fat (IMF) influences its flavor, nutritional value and impacts human health. Human consumption of fat that contains high levels of monounsaturated fatty acids (MUFA) can reduce the concentration of undesirable cholesterol (LDL) in circulating blood. Different feeding practices and genetic variation within and between breeds influences the amount of IMF and fatty acid (FA) composition in meat. However, it is difficult and costly to determine fatty acid composition, which has precluded beef cattle breeding programs from selecting for a healthier fatty acid profile. In this study, we employed a high-density single nucleotide polymorphism (SNP) chip to genotype 386 Nellore steers, a Bos indicus breed and, a Bayesian approach to identify genomic regions and putative candidate genes that could be involved with deposition and composition of IMF. Results Twenty-three genomic regions (1-Mb SNP windows) associated with IMF deposition and FA composition that each explain ≥ 1% of the genetic variance were identified on chromosomes 2, 3, 6, 7, 8, 9, 10, 11, 12, 17, 26 and 27. Many of these regions were not previously detected in other breeds. The genes present in these regions were identified and some can help explain the genetic basis of deposition and composition of fat in cattle. Conclusions The genomic regions and genes identified contribute to a better understanding of the genetic control of fatty acid deposition and can lead to DNA-based selection strategies to improve meat quality for human consumption.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba SP 13418-900, Brazil.
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Ripamonte P, Baccaglini M, Cesar ASM, Figueiredo LGG, Balieiro JCC, Caetano AR, Meirelles FV. Estimation of taurindicine hybridization of American Zebu cattle in Brazil. Genet Mol Res 2012; 11:393-403. [PMID: 22370942 DOI: 10.4238/2012.february.17.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Our objective was to estimate Bos primigenius taurus introgression in American Zebu cattle. One hundred and four American Zebu (Nellore) cattle were submitted to mtDNA, microsatellite and satellite analysis. Twenty-three alleles were detected in microsatellite analysis, averaging 4.6 ± 1.82/locus. Variance component comparisons of microsatellite allele sizes allowed the construction of two clusters separating taurus and indicus. No significant variation was observed when indicus and taurus mtDNA were compared. Three possible genotypes of 1711b satellite DNA were identified. All European animals showed the same restriction pattern, suggesting a Zebu-specific restriction pattern. The frequencies of B. primigenius indicus-specific microsatellite alleles and 1711b satellite DNA restriction patterns lead to an estimate of 14% taurine contribution in purebred Nellore.
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Affiliation(s)
- P Ripamonte
- Departamento de Ciências Básicas, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brasil
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Silveira ACP, Braga TF, Almeida JF, Antunes RC, Freitas PFA, Cesar ASM, Guimarães EC. PIT1 gene polymorphism in Pietrain and Large White pigs after divergent selection. Genet Mol Res 2009; 8:1008-12. [PMID: 19731221 DOI: 10.4238/vol8-3gmr609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We examined the polymorphisms in the PIT1 gene of 103 pigs and compared their frequencies in the maternal and paternal lineages of the Pietrain and Large White breeds, which have undergone divergent selection for over 30 years. DNA samples extracted from the blood of these animals were amplified by PCR and genotyped by RFLP, using the restriction enzyme RsaI. The data were analyzed with the chi-square test. We found that 57.3% of the animals were genotype AB, among which 26.2% were of the Large White paternal lineage, 18.5% the Pietrain paternal lineage and 12.6% the Pietrain maternal lineage. The AA genotype appeared in 20.4%, of which 7.8% were Large White, 4.8% the Pietrain paternal lineage and 7.8% the Pietrain maternal lineage. BB was observed in 22.3% (6.8% were of the Large White paternal lineage, 9.7% of the Pietrain paternal lineage and 5.8% of the Pietrain maternal lineage). The allele frequencies were 49.0% A and 51.0% B allele. When we examined the Pietrain maternal and paternal lineages, we found that the PIT1 gene had been fixed in the paternal lineage, suggesting that the B allele is associated with low body fat and improved muscle development when compared to the maternal lineage. However, no significant differences were found between the Pietrain and Large White paternal lineages.
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Affiliation(s)
- A C P Silveira
- Universidade Federal de Uberlândia, Faculdade de Medicina Veterinária, Programa de Pós-Graduação em Ciências Veterinárias, Uberlândia, MG, Brasil.
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