SABIIA - Sistema Aberto e Integrado de Informação em Agricultura (Sabiia)

SOUZA, M. M. de; ZERLOTINI NETO, A.; ROCHA, M. I. P.; BRUSCADIN, J. J.; DINIZ, W. J. da S.; CARDOSO, T. F.; CESAR, A. S. M.; AFONSO, J.; ANDRADE, B. G. N.; MUDADU, M. de A.; MOKRY, F. B.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; NICIURA, S. C. M.; COUTINHO, L. L.; REGITANO, L. C. de A..

Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp)....

Allele-specific gene expression in liver of Nelore cattle extremes for feed efficiency.

Palavras-chave: Expressão gênica; Regulação da expressão gênica; Allelic expression; Allele-specific expression; Bos Indicus; Gene expression regulation.

Ano: 2020

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1125395

ROCHA, M. I. P.; SOUZA, M. M. de; ZERLOTINI NETO, A.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; LIMA, A. O. de; AFONSO, J.; COUTINHO, L. L.; REGITANO, L. C. de A.; NICIURA, S. C. M..

Associação entre variantes cis regulatórias do gene KCNJ11e características econômicas em bovinos Nelore.

Palavras-chave: Allele-specific expression; Genome regulation; Genetic improvement.

Ano: 2017

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1073455

OLIVEIRA, K. S. de; LIMA, A. O. de; AFONSO, J.; CARDOSO, T. F.; BRUSCADIN, J. J.; REGITANO, L. C. de A..

Características de produção como eficiência alimentar e de qualidade da carne bovina são de suma importância para o agronegócio, agroindústria e consumidores. Assim, ferramentas biotecnológicas como a genômica podem adicionar informações para identificar potenciais biomarcadores com a finalidade de auxiliar os programas de melhoramento e seleção de bovinos de corte.

Co-expression network analysis identifies genes associated with iron content in bovine muscle.

Palavras-chave: SNP; Expressão gênica; Sítio de ligação de fator de transcriçã0; Ilha CpG; Qualidade da carne; Bos Indicus.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115556

DINIZ, W. J. da S.; CESAR, A. S. M.; GEISTLINGER, L.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; AFONSO, J.; ROCHA, M. I. P.; LIMA, A. O. de; BUSS, C. E.; COUTINHO, L. L.; REGITANO, L. C. de A..

Editores: Luiz Lehmann Coutinho, ESALQ/USP; Luciana Correia de Almeida Regitano, Embrapa Pecuária Sudeste; Gerson Barreto Mourão, ESALQ/USP; Aline Silva Mello Cesar, ESALQ/USP; Bárbara Silva Vignato, FZEA/USP; Mirele Daiana Poleti, ESALQ/USP; Wellison Jarles da Silva Diniz, UFSCar.

Co-expression network analysis identifies genes associated with meat tenderness.

Palavras-chave: Gene expression; Network analysis; Systems biology.

Ano: 2017

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1075630

DINIZ, W. J. da S.; CESAR, A. S. M.; GEISTLINGER, L.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; AFONSO, J.; ROCHA, M. I. P.; LIMA, A. O. de; BUSS, C. E.; COUTINHO, L. L.; REGITANO, L. C. de A..

Tenderness is an important trait of meat quality and is known to be influenced by several factors including genetic composition.

Detection of Co-expressed pathway modules associated with mineral concentration and meat quality in nelore cattle.

Palavras-chave: Gene expression; Network analysis; System biology.

Ano: 2017

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1080848

DINIZ, W. J. S.; MAZZONI, G.; COUTINHO; BANERJEE, P.; GEISTLINGER, L.; CESAR, A. S. M.; BERTOLINI. F.; AFONSO, J.; OLIVEIRA, P. S. N.; TIZIOTO, P. C.; KADARMIDEEN, H. N.; REGITANO, L. C. de A..

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...

Genes diferencialmente expressos no músculo Longissimus dorsi de novilhos nelore divergentes para eficiência bruta.

Palavras-chave: AMPK pathway; Co-expression analysis; RNA sequencing; Tenderness; Gordura Animal; Gado de Corte; Intramuscular fat; Beef quality; Beef cattle.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1107117

SILVA, J. V. da; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; AFONSO, J.; DINIZ, W. J. da S.; LIMA, A. O. de; SOUZA, M. M. de; ROCHA, M. I. P.; BUSS, C. E.; COUTINHO, L. L.; REGITANO, L. C. de A..

2016

Genetic regulators of mineral amount in Nelore cattle muscle predicted by a new co-expression and regulatory impact factor approach.

Palavras-chave: RNA-seq; Bos indicus; Eficiência alimentar.

Ano: 2016

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1054252

AFONSO, J.; FORTES, M. R. S.; REVERTER, A.; DINIZ, W. J. da S.; CESAR, A. S. M.; LIMA, A. O. de; PETRINI, J.; SOUZA, M. de S.; COUTINHO, L. L.; MOURÃO, G. B.; ZERLOTINI NETO, A.; GROMBONI, C. F.; NOGUEIRA, A. R. A.; REGITANO, L. C. de A..

Mineral contents in bovine muscle can affect meat quality, growth, health, and reproductive traits. To better understand the genetic basis of this phenotype in Nelore (Bos indicus) cattle, we analysed genome-wide mRNA and miRNA expression data from 114 muscle samples. The analysis implemented a new application for two complementary algorithms: the partial correlation and information theory (PCIT) and the regulatory impact factor (RIF), in which we included the estimated genomic breeding values (GEBVs) for the phenotypes additionally to the expression levels, originally proposed for these methods. We used PCIT to determine putative regulatory relationships based on significant associations between gene expression and GEBVs for each mineral amount. Then, RIF...

Genome-wide distribution of allele-specific expression in Nelore steers muscle.

Palavras-chave: Expressão gênica; Bos Indicus; Gado Nelore; Cattle; Gene expression.

Ano: 2020

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1124802

Identification of a pleiotropic locus for beef quality and feed efficiency in cattle using bi-trait genome-wide association analysis.

SOUZA, M. M. de; ZERLOTINI NETO, A.; NICIURA, S. C. M.; ROCHA, M. I. P.; DINIZ, W. J.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; LIMA, A. O.; AFONSO, J.; CESAR, A. S. M; COUTINHO, L. L.; REGITANO, L. C. de A..

The difference between the allelic expression of a gene is known as allele-specific expression (ASE), and it is a common event in mammal?s transcriptome. ASE is named genomic imprinting when guided by epigenetics mechanisms regarding the allele parental origin.

Tipo: Artigo em anais de congresso (ALICE)

Palavras-chave: ASE; Allele-specific expression; Polimorfismo Genético; Melhoramento Genético Animal; Gene expression.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1100405

BUSS, C. E.; PETRINI, J.; MOURAO, G. B.; GEISTLINGER, L.; WOLF, J. B.; DINIZ, W. J. da S.; ROCHA, M. I. P.; AFONSO, J.; LIMA, A. O. de; TIZIOTO, P. C.; TULLIO, R. R.; ANDRADE, B. G.; COUTINHO, L. L.; REGITANO, L. C. de A..

Identification of genes associated with copper-deficient fatty acid increase in Nelore cattle.

Palavras-chave: Lipolysis; Feed efficiency; Pleiotropy; Genome?wide association.

Ano: 2017

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1075651

AFONSO, J.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; DINIZ, W. J. da S.; LIMA, A. O. de; SOUZA, M. M. de; ROCHA, M. I. P.; SILVA, J. V. da; BUSS, C. E.; GROMBONI, C. F.; MOURAO, G. B.; NOGUEIRA, A. R. de A.; COUTINHO, L. L.; REGITANO, L. C. de A..

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Identification of pleiotropic loci for daily weight gain and intramuscular fat in cattle using bivariate genome-wide association analysis.

Palavras-chave: Genome regulation; Meat production; Gene expression.

Ano: 2017

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1079227

BUSS, C. E.; DINIZ, W. J. da S.; ANDRADE, B. G.; LIMA, A. O. de; GEISTLINGER, L.; AFONSO, J.; TULLIO, R. R.; TIZIOTO, P. C.; PETRINI, J.; COUTINHO, L. L.; WOLF, J. B.; MOURAO, G. B.; REGITANO, L. C. de A..

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LDHB gene has allele-specific expression in liver of Nelore cattle extremes for feed efficiency.

Palavras-chave: Feed efficiency; Pleiotropy; Transcription factor.

Ano: 2017

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1079239

ROCHA, M. I. P.; SOUZA, M. M. de; ZERLOTINI NETO, A.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; LIMA, A. O. de; AFONSO, J.; DINIZ, W. J. da S.; BUSS, C. E.; COUTINHO, L. L.; REGITANO, L. C. de A.; NICIURA, S. C. M..

Liver DNA methylation profile in Nelore cattle extremes for feed efficiency.

Palavras-chave: Cattle; Residual feed intake; Differential expression; MicroRNA.

Ano: 2017

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1075647

ROCHA, M. I. P.; SOUZA, M. M. de; DINIZ, W. J. S.; LIMA, A. O. de; AFONSO, J.; TIZIOTO, P. C.; OLIVEIRA, P. N. de; REGITANO, L. C. de A.; KOLTES, J. E.; NICIURA, S. C. M..

The production cost of cattle is high, especially the fraction related to animal nutrition. The increase in feed efficiency may provide increased efficiency in beef production, minimizing feed expenditures, methane gas emission and nitrogen excretion.

Muscle transcriptome analysis reveals genes and metabolic pathways related to mineral concentration in Bos indicus.

Palavras-chave: Feed efficiency; RRBS; Differential methylation; Beef production; Gado de Corte; Bovino; Gene expression regulation; Animal nutrition.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1110134

AFONSO, J.; COUTINHO, L. L.; TIZIOTO, P. C.; DINIZ, W. J. da S.; LIMA, A. O. de; ROCHA, M. I. P.; BUSS, C, E.; ANDRADE, B. G. N. A.; PIAYA. O.; SILVA, J. V.; LINS, L. A.; GROMBONI, C. F.; NOGUEIRA, A. R. de A.; FORTES, M. R. S.; MOURÃO, G. B.; REGITANO, L. C. de A..

Mineral content affects the biological processes underlying beef quality. Muscle mineral concentration depends not only on intake-outtake balance and muscle type, but also on age, environment, breed, and genetic factors.

Potential biomarkers for feed efficiency-related traits in nelore cattle identified by co-expression network and integrative genomics analyses.

Palavras-chave: Muscle type; Mineral concentrations; Nelore; Beef quality; Beef cattle.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115486

LIMA, A. O. de; KOLTES, J. E.; DINIZ, W. J. S.; OLIVEIRA, P. S. N. de; CESAR, A. S. M.; TIZIOTO, P. L.; AFONSO, J.; SOUZA, M. de S.; PETRINI, J.; ROCHA, M. I. P.; CARDOSO, T. F.; ZERLOTINI NETO, A.; COUTINHO, L. L.; MOURÃO, G. B.; REGITANO, L. C. de A..

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...