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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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Andrade BGN, de Souza MM, Amat S, Regitano LCA, de Oliveira PSN. Editorial: Microbiome genomics for livestock production. Front Genet 2022; 13:1000749. [PMID: 36159982 PMCID: PMC9501712 DOI: 10.3389/fgene.2022.1000749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Bruno G. N. Andrade
- Computer Science Department, Munster Technological University, MTU/ADAPT, Cork, Ireland
- *Correspondence: Bruno G. N. Andrade,
| | | | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
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Andrade BGN, Bressani FA, Cuadrat RRC, Cardoso TF, Malheiros JM, de Oliveira PSN, Petrini J, Mourão GB, Coutinho LL, Reecy JM, Koltes JE, Neto AZ, R de Medeiros S, Berndt A, Palhares JCP, Afli H, Regitano LCA. Stool and Ruminal Microbiome Components Associated With Methane Emission and Feed Efficiency in Nelore Beef Cattle. Front Genet 2022; 13:812828. [PMID: 35656319 PMCID: PMC9152269 DOI: 10.3389/fgene.2022.812828] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 11/10/2021] [Accepted: 03/02/2022] [Indexed: 12/27/2022] Open
Abstract
Background: The impact of extreme changes in weather patterns on the economy and human welfare is one of the biggest challenges our civilization faces. From anthropogenic contributions to climate change, reducing the impact of farming activities is a priority since it is responsible for up to 18% of global greenhouse gas emissions. To this end, we tested whether ruminal and stool microbiome components could be used as biomarkers for methane emission and feed efficiency in bovine by studying 52 Brazilian Nelore bulls belonging to two feed intervention treatment groups, that is, conventional and by-product-based diets. Results: We identified a total of 5,693 amplicon sequence variants (ASVs) in the Nelore bulls’ microbiomes. A Differential abundance analysis with the ANCOM approach identified 30 bacterial and 15 archaeal ASVs as differentially abundant (DA) among treatment groups. An association analysis using Maaslin2 software and a linear mixed model indicated that bacterial ASVs are linked to the host’s residual methane emission (RCH4) and residual feed intake (RFI) phenotype variation, suggesting their potential as targets for interventions or biomarkers. Conclusion: The feed composition induced significant differences in both abundance and richness of ruminal and stool microbial populations in ruminants of the Nelore breed. The industrial by-product-based dietary treatment applied to our experimental groups influenced the microbiome diversity of bacteria and archaea but not of protozoa. ASVs were associated with RCH4 emission and RFI in ruminal and stool microbiomes. While ruminal ASVs were expected to influence CH4 emission and RFI, the relationship of stool taxa, such as Alistipes and Rikenellaceae (gut group RC9), with these traits was not reported before and might be associated with host health due to their link to anti-inflammatory compounds. Overall, the ASVs associated here have the potential to be used as biomarkers for these complex phenotypes.
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Affiliation(s)
- Bruno G N Andrade
- Embrapa Southeast Livestock, São Carlos, Brazil.,Department of Computer Science, Munster Technological University, MTU/ADAPT, Cork, Ireland
| | | | - Rafael R C Cuadrat
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
| | | | | | | | - Juliana Petrini
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | | | | | | | | | - Haithem Afli
- Department of Computer Science, Munster Technological University, MTU/ADAPT, Cork, Ireland
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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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Andrade BGN, Bressani FA, Cuadrat RRC, Tizioto PC, de Oliveira PSN, Mourão GB, Coutinho LL, Reecy JM, Koltes JE, Walsh P, Berndt A, Palhares JCP, Regitano LCA. The structure of microbial populations in Nelore GIT reveals inter-dependency of methanogens in feces and rumen. J Anim Sci Biotechnol 2020; 11:6. [PMID: 32123563 PMCID: PMC7038601 DOI: 10.1186/s40104-019-0422-x] [Citation(s) in RCA: 21] [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: 09/13/2019] [Accepted: 12/23/2019] [Indexed: 12/18/2022] Open
Abstract
Background The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose, a complex polysaccharide found in leaves and grass. Ruminants rely on a complex and diverse microbial community, or microbiota, in a unique compartment known as the rumen to break down this polysaccharide. Changes in microbial populations of the rumen can affect the host’s development, health, and productivity. However, accessing the rumen is stressful for the animal. Therefore, the development and use of alternative sampling methods are needed if this technique is to be routinely used in cattle breeding. To this end, we tested if the fecal microbiome could be used as a proxy for the rumen microbiome due to its accessibility. We investigated the taxonomic composition, diversity and inter-relations of two different GIT compartments, rumen and feces, of 26 Nelore (Bos indicus) bulls, using Next Generation Sequencing (NGS) metabarcoding of bacteria, archaea and ciliate protozoa. Results We identified 4265 Amplicon Sequence Variants (ASVs) from bacteria, 571 from archaea, and 107 from protozoa, of which 143 (96 bacteria and 47 archaea) were found common between both microbiomes. The most prominent bacterial phyla identified were Bacteroidetes (41.48%) and Firmicutes (56.86%) in the ruminal and fecal microbiomes, respectively, with Prevotella and Ruminococcaceae UCG-005 the most relatively abundant genera identified in each microbiome. The most abundant archaeal phylum identified was Euryarchaeota, of which Methanobrevibacter gottschalkii, a methanogen, was the prevalent archaeal species identified in both microbiomes. Protozoa were found exclusively identified in the rumen with Bozasella/Triplumaria being the most frequent genus identified. Co-occurrence among ruminal and fecal ASVs reinforces the relationship of microorganisms within a biological niche. Furthermore, the co-occurrence of shared archaeal ASVs between microbiomes indicates a dependency of the predominant fecal methanogen population on the rumen population. Conclusions Co-occurring microorganisms were identified within the rumen and fecal microbiomes, which revealed a strong association and inter-dependency between bacterial, archaeal and protozoan populations of the same microbiome. The archaeal ASVs identified as co-occurring between GIT compartments corresponded to the methanogenic genera Methanobrevibacter and Methanosphaera and represented 26.34% of the overall archaeal sequencesdiversity in the rumen and 42.73% in feces. Considering that these archaeal ASVs corresponded to a significant part of the overall diversity of both microbiomes, which is much higher if one includes the interactions of these co-occurring with other rumen archaea ASVs, we suggest that fecal methanogens could be used as a proxy of ruminal methanogens.
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Affiliation(s)
| | | | - Rafael R C Cuadrat
- 2Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
| | | | | | - Gerson B Mourão
- 4Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Luiz L Coutinho
- 4Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - James M Reecy
- 5Department of Animal Science, Iowa State University, Ames, IA USA
| | - James E Koltes
- 5Department of Animal Science, Iowa State University, Ames, IA USA
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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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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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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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