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Mutch JL, Neupane M, Seabury CM, Neibergs HL, Tizioto PC, Garrick DJ, Kerley MS, Shike DW, Beever JE, Taylor JF, Johnson KA. 1496 Identification of biological pathways involved in residual feed intake in Hereford cattle through gene set enrichment analysis. J Anim Sci 2016. [DOI: 10.2527/jam2016-1496] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- J. L. Mutch
- Department of Animal Sciences, Washington State University, Pullman
| | - M. Neupane
- Department of Animal Sciences, Washington State University, Pullman
| | - C. M. Seabury
- College of Veterinary Medicine, Texas A&M University, College Station
| | - H. L. Neibergs
- Department of Animal Sciences, Washington State University, Pullman
| | | | - D. J. Garrick
- Department of Animal Science, Iowa State University, Ames
| | | | | | | | | | - K. A. Johnson
- Department of Animal Sciences, Washington State University, Pullman
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Oliveira PSN, Tizioto PC, Oliveira GB, Cesar ASM, Diniz WJS, Lima AOD, Reecy JM, Coutinho LL, Regitano LCA. 0340 Differentially expressed miRNAs in skeletal muscle related to feed efficiency in Nellore cattle. J Anim Sci 2016. [DOI: 10.2527/jam2016-0340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Taylor JF, Neibergs HL, Seabury CM, Vaneenennaam A, Decker JE, Hoff JL, Tizioto PC, Womack JE, Schnabel RD. 0286 Identification of causal variants underlying pathogen susceptibility and translation to genetic improvement. J Anim Sci 2016. [DOI: 10.2527/jam2016-0286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Buss CE, Tizioto PC, Oliveira PSN, Mudadu MA, Cesar ASM, Ventura RV, Afonso J, Lima AOD, Coutinho LL, Tullio RR, Regitano LCA. 0891 Genome-wide efficient mixed-model study for meat quality in Nellore cattle. J Anim Sci 2016. [DOI: 10.2527/jam2016-0891] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Afonso J, Tizioto PC, Oliveira PSN, Diniz WJS, Lima AOD, Souza MMD, Rocha MIP, Silva JVD, Buss CE, Gromboni CF, Mourão GB, Nogueira AR, Coutinho LL, Regitano LCA. 0903 Differentially expressed genes in genetically divergent Nellore steers for calcium content in the Longissimus dorsi muscle. J Anim Sci 2016. [DOI: 10.2527/jam2016-0903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Oliveira PSN, Cesar ASM, Oliveira GB, Tizioto PC, Poleti MD, Diniz WJS, Lima AOD, Reecy JM, Coutinho LL, Regitano LCA. 0341 miRNAs related to fatty acids composition in Nellore cattle. J Anim Sci 2016. [DOI: 10.2527/jam2016-0341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Lima AOD, Oliveira PSN, Tizioto PC, Somavilla AL, Diniz WJS, Silva JVD, Andrade SCS, Boschiero C, Cesar ASM, Souza MM, Rocha MIP, Afonso J, Buss CE, Mudadu MA, Mourao GB, Coutinho LL, Regitano LCA. 0318 PRUNE2 gene has a potential effect on residual feed intake in Nellore cattle. J Anim Sci 2016. [DOI: 10.2527/jam2016-0318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Cesar ASM, Reecy JM, Regitano LCA, Poleto MD, Andrade SCS, Tizioto PC, Oliveira PSN, Lanna DPD, Tullio RR, Nassu RT, Koltes JE, Fritz-Waters E, Coutinho LL. P3032 Association of skeletal muscle transcripts with fatty acid content in Nellore cattle. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement468x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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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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Tizioto PC, Coutinho LL, Mourão GB, Gasparin G, Malagó-Jr W, Bressani FA, Tullio RR, Nassu RT, Taylor JF, Regitano LCA. Variation inmyogenic differentiation 1mRNA abundance is associated with beef tenderness in Nelore cattle. Anim Genet 2016; 47:491-4. [DOI: 10.1111/age.12434] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 01/12/2023]
Affiliation(s)
| | - L. L. Coutinho
- Department of Animal Science; University of São Paulo/ESALQ; Piracicaba SP Brazil
| | - G. B. Mourão
- Department of Animal Science; University of São Paulo/ESALQ; Piracicaba SP Brazil
| | - G. Gasparin
- Department of Animal Science; University of São Paulo/ESALQ; Piracicaba SP Brazil
| | - W. Malagó-Jr
- Embrapa Southeast Livestock; São Carlos SP Brazil
| | | | - R. R. Tullio
- Embrapa Southeast Livestock; São Carlos SP Brazil
| | - R. T. Nassu
- Embrapa Southeast Livestock; São Carlos SP Brazil
| | - J. F. Taylor
- Division of Animal Sciences; University of Missouri; Columbia MO USA
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Veneroni-Gouveia G, Tizioto PC, Meirelles SLC, Santiago AC, Alencar MM, Regitano LCA. Candidate genes for carcass traits in a tropical-adapted Brazilian composite beef breed. Genet Mol Res 2015; 14:16667-74. [PMID: 26681013 DOI: 10.4238/2015.december.11.14] [Citation(s) in RCA: 1] [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
Backfat thickness (BFT) and ribeye area (REA) are important production traits but, because they are measured late in the animal's life, they have not been efficiently included in breeding programs. The aim of this study was to evaluate whether single nucleotide polymorphisms (SNPs) mapped to the leptin, PPARGC1A, PSMC1, CRH, and FABP4 genes, which influence BFT and REA in Canchim cattle, a composite beef breed (5/8 Charolais + 3/8 Zebu). BFT and REA phenotypic records were obtained by ultrasound measurements from 18-month-old animals. All SNP markers were genotyped by restriction fragment length polymorphism-polymerase chain reaction. Restricted maximum likelihood analysis revealed that the non-synonymous SNP located in exon 2 of the FABP4 gene has an additive effect on BFT (P ≤ 0.05). Significant allele substitution effects showed that the substitution of G by A may lead to a decrease of 0.1055 mm in mean BFT. This information can be used for inclusion of this trait-associated marker in commercial SNP panels.
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Affiliation(s)
- G Veneroni-Gouveia
- Colegiado Acadêmico de Zootecnia, Universidade Federal do Vale do São Francisco, Campus Ciências Agrárias, Projeto de Irrigação Nilo Coelho, Petrolina, PE, Brasil
| | - P C Tizioto
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
| | - S L C Meirelles
- Departamento de Zootecnia, Universidade Federal de Lavras, Campus Universitário, Lavras, MG, Brasil
| | - A C Santiago
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
| | - M M Alencar
- Embrapa Pecuária Sudeste, São Carlos, SP, Brasil
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Bressani FA, Tizioto PC, Giglioti R, Meirelles SLC, Coutinho R, Benvenuti CL, Malagó W, Mudadu MA, Vieira LS, Zaros LG, Carrilho E, Regitano LCA. Single nucleotide polymorphisms in candidate genes associated with gastrointestinal nematode infection in goats. Genet Mol Res 2014; 13:8530-6. [PMID: 25366747 DOI: 10.4238/2014.october.20.29] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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
Cytokines are small cell-signaling proteins that play an important role in the immune system, participating in intracellular communication. Four candidate genes of the cytokine family (IL2, IL4, IL13, and IFNG) were selected to identify Single Nucleotide Polymorphisms (SNPs) that might be associated with resistance to gastrointestinal endoparasites in goats. A population of 229 goats, F2 offspring from an F1 intercross was produced by crossing pure Saanen goats, considered as susceptible to gastrointestinal endoparasites, with pure Anglo-Nubian goats, considered resistant. Blood was collected for DNA extraction and fecal samples were also collected for parasite egg count. Polymorphisms were prospected by sequencing animals with extreme phenotype for fecal egg count (FEC) distribution. The association between SNPs and phenotype was determined by using the Fisher exact test with correction for multiple tests. Three of the 10 SNPs were identified as significant (P ≤ 0.03). They were found in intron 1 of IL2 (ENSBTA00000020883), intron 3 of IL13 (ENSBTA00000015953) and exon 3 of IFNG (ENSBTA00000012529), suggesting an association between them and gastrointestinal endoparasite resistance. Further studies will help describe the effects of these markers accurately before implementing them in marker assisted selection. This study is the pioneer in describing such associations in goats.
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Affiliation(s)
- F A Bressani
- Embrapa Pecuária Sudeste, São Carlos, SP, Brasil
| | - P C Tizioto
- Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular, Universidade Federal de São Carlos, São Carlos, SP, Brasil
| | - R Giglioti
- Programa de Pós-Graduação em Genética e Melhoramento Animal, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - S L C Meirelles
- Departamento de Zootecnia, Universidade Federal de Lavras, Lavras, MG, Brasil
| | - R Coutinho
- Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - C L Benvenuti
- Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - W Malagó
- Embrapa Pecuária Sudeste, São Carlos, SP, Brasil
| | - M A Mudadu
- Embrapa Pecuária Sudeste, São Carlos, SP, Brasil
| | - L S Vieira
- Embrapa Caprinos e Ovinos, Sobral, CE, Brasil
| | - L G Zaros
- Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - E Carrilho
- Departamento de Química, Universidade de São Paulo, São Carlos, SP, Brasil
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Tizioto PC, Decker JE, Taylor JF, Schnabel RD, Mudadu MA, Silva FL, Mourão GB, Coutinho LL, Tholon P, Sonstegard TS, Rosa AN, Alencar MM, Tullio RR, Medeiros SR, Nassu RT, Feijó GLD, Silva LOC, Torres RA, Siqueira F, Higa RH, Regitano LCA. Genome scan for meat quality traits in Nelore beef cattle. Physiol Genomics 2013; 45:1012-20. [PMID: 24022219 DOI: 10.1152/physiolgenomics.00066.2013] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Meat quality traits are economically important because they affect consumers' acceptance, which, in turn, influences the demand for beef. However, selection to improve meat quality is limited by the small numbers of animals on which meat tenderness can be evaluated due to the cost of performing shear force analysis and the resultant damage to the carcass. Genome wide-association studies for Warner-Bratzler shear force measured at different times of meat aging, backfat thickness, ribeye muscle area, scanning parameters [lightness, redness (a*), and yellowness] to ascertain color characteristics of meat and fat, water-holding capacity, cooking loss (CL), and muscle pH were conducted using genotype data from the Illumina BovineHD BeadChip array to identify quantitative trait loci (QTL) in all phenotyped Nelore cattle. Phenotype count for these animals ranged from 430 to 536 across traits. Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH. Genomic regions harboring these QTL and the pathways in which the genes from these regions act appear to differ from those identified in taurine cattle for meat quality traits. These results will guide future QTL mapping studies and the development of models for the prediction of genetic merit to implement genomic selection for meat quality in Nelore cattle.
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Affiliation(s)
- P C Tizioto
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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Tizioto PC, Meirelles SL, Tulio RR, Rosa AN, Alencar MM, Medeiros SR, Siqueira F, Feijó GLD, Silva LOC, Torres Junior RAA, Regitano LCA. Candidate genes for production traits in Nelore beef cattle. Genet Mol Res 2012; 11:4138-44. [PMID: 23079978 DOI: 10.4238/2012.september.19.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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
Meat quality is an important trait for the beef industry. Backfat thickness, ribeye area, and shear force are traits measured late in life, and the investigation of molecular markers associated with these traits can help breeding programs. In cattle, some polymorphisms have been related to production traits. Thus, the purpose of this study was to assess the presence of polymorphisms in the candidate genes insulin-like growth factor 1 (IGF1), fatty acid-binding protein 4 (FABP4), and peroxisome proliferative active receptor gamma coactivator 1 A (PPARGC1A) and associate them with production traits in reference families of Nelore cattle. We used 270 steers descendent from 20 sires that were chosen to represent variability in this breed. The investigation of marker effects on the traits was performed using a mixed model under the restricted maximum likelihood method. A significant allele substitution effect was found for IGF1 and yearling weight (P ≤ 0.017). The mean allele substitution effect was 6.9 kg, with the 229 allele associated with reduced yearling weight in this Nelore population.
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Affiliation(s)
- P C Tizioto
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
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Veneroni GB, Meirelles SL, Grossi DA, Gasparin G, Ibelli AMG, Tizioto PC, Oliveira HN, Alencar MM, Regitano LCA. Prospecting candidate SNPs for backfat in Canchim beef cattle. Genet Mol Res 2010; 9:1997-2003. [PMID: 20957603 DOI: 10.4238/vol9-4gmr788] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [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
Canchim is a composite cattle breed developed in Brazil for beef production. One of the breeding objectives is to increase fat deposition. QTLs for fat thickness and/or marbling have been reported on BTA4 and BTA14. The IGFBP3 and DDEF1 genes, mapped to BTA4 and BTA14, respectively, affect adipogenesis. We looked for SNPs in the IGFBP3 and DDEF1 genes that could be associated with backfat thickness in Canchim beef cattle. For SNP identification, sires with the highest accuracy were ranked according to expected breeding value for fat thickness; the 12 extremes (six sires with the highest and six with the lowest expected breeding value for the trait) were chosen. Six regions of the IGFBP3 and 14 regions of the DDEF1 were sequenced using the Sanger method. Nine SNPs were identified in IGFBP3 and 76 in the DDEF1. After an initial analysis, two SNPs were selected to be genotyped for the whole population; these were DDEF1g.279401A>G and IGFBP3c.4394T>C(Trp>Arg). We found a significant effect (P ≤ 0.05) of allele substitution on backfat thickness; however, the IGFBP3 SNP did not significantly affect this trait.
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Affiliation(s)
- G B Veneroni
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
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