Molecular basis of meat quality in Nelore beef cattle

• Grant number: 12/23638-8
• Support type: Research Projects - Thematic Grants
• Duration: June 01, 2013 - November 30, 2017
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal researcher: Luciana Correia de Almeida Regitano
• Grantee: Luciana Correia de Almeida Regitano
• Home Institution: Embrapa Pecuária Sudeste. Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA). Ministério da Agricultura, Pecuária e Abastecimento (Brasil). São Carlos , SP, Brazil
• Pesquisadores principais:( Últimos ): Adhemar Zerlotini Neto ; Gerson Barreto Mourão
• Pesquisadores principais:( Antigos ): Luiz Lehmann Coutinho
• Assoc. researchers: Ana Rita de Araujo Nogueira ; Andrea Alves Do Egito ; Carlos Alberto Labate ; Cintia Righetti Marcondes ; Danísio Prado Munari ; Fabiane Siqueira ; Felipe Rodrigues da Silva ; Fernando Flores Cardoso ; Gilberto Romeiro de Oliveira Menezes ; Juliana Petrini ; Júlio Cesar de Carvalho Balieiro ; Luiz Lehmann Coutinho ; Marcos Vinicius Gualberto Barbosa da Silva ; Mauricio de Alvarenga Mudadu ; Michel Eduardo Beleza Yamagishi ; Newton Valério Verbisck ; Patricia Tholon ; Paula Regina Kuser Falcão ; Poliana Fernanda Giachetto ; Renata Tieko Nassu ; RICARDO VIEIRA VENTURA ; Roberto Hiroshi Higa ; Simone Cristina Méo Niciura
• Associated grant(s): 17/50044-5 - Integration of genomic resources in beef cattle breeding program: a collaborative effort between UNL and ESALQ, AP.R SPRINT; 17/09312-6 - AMSA 70th Reciprocal Meat Conference, AR.EXT
• Associated scholarship(s): 17/05625-0 - Study of the genes under selection in Nelore and the relation with Bos indicus and Bos taurus based on transcriptomic data, BP.IC; 16/13773-6 - Identification and characterization of euchromatic regions associated with gene expression and intramuscular fat in nelore cattle, BP.MS; 15/09158-1 - Identification of coexpression gene networks and regulatory mechanisms related to mineral composition and meat quality in bovine, BP.DR; + associated scholarships 15/00617-3 - Identification and evaluation of the expression of regulators microRNAs of the intramuscular fat deposition in Nelore cattle, BP.MS; 14/22325-1 - Expression profile of microRNAs extreme animals for feed efficiency in Nelore breed, BP.PD; 14/12652-5 - Differential gene expression related to iron content in Nellore muscle, BP.MS; 14/11871-5 - Identification of eQTLs associated with the deposition and composition of intramuscular fat in Nellore breed, BP.PD; 14/00943-5 - Identification of microRNAs involved in meat tenderness in Nellore cattle, BP.MS; 13/17778-4 - Tanscriptomic profile of extreme animals for feed efficiency of Nelore breed, BP.PD; 13/21017-9 - Study of proteins associated with meat quality phenotypes in Nelore cattle, BP.PD - associated scholarships

Abstract

Brazil is one of the leading producers and exporters of beef and its competitive advantage is mainly attributed to the cost of production of Brazilian beef, which is one of the lowest in the world. To increase its importance in the market, one must adapt its meat production to the standards established by external market. Among the quality attributes, tenderness, amount and composition of intramuscular fat (IMF) can influence the sensory characteristics and nutritional value of beef. Selection for meat quality has not been effective in breeding programs of beef cattle in Brazil. Sequencing, genotyping and expression analysis technologies on a genome-scale have contributed to the knowledge of the genetic basis of variation and for the earlier selection in cattle. A previous project entitled "Genetic Strategies for quality beef production" produced 796 steers, offspring of 34 sires representing the diversity of Nelore. The steers were evaluated for feed efficiency and meat quality and both sires and offspring had their genotypes analyzed in the Illumina SNP BovineHD chip. This project identified genomic regions associated with production characteristics and meat quality. The present project aims to achieve a better understanding of the genetic mechanisms involved in variation in quantitative traits highlighted by the association analysis. Therefore, it is proposed to complement the analysis of genome wide association to include new phenotypes, expanding the functional analysis of the genome (RNA, microRNA and proteins), assess the significance of CNVs and train human resources in the areas of bioinformatics and genomics. (AU)

Scientific publications

(29)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

SOMAVILLA, ADRIANA L.; REGITANO, LUCIANA C. A.; ROSA, GUILHERME J. M.; MOKRY, FABIANA B.; MUDADU, MAURICIO A.; TIZIOTO, POLYANA C.; OLIVEIRA, PRISCILA S. N.; SOUZA, MARCELA M.; COUTINHO, LUIZ L.; MUNARI, DANISIO P.. Genome-Enabled Prediction of Breeding Values for Feedlot Average Daily Weight Gain in Nelore Cattle. G3-GENES, GENOMES, GENETICS, v. 7, n. 6, p. 1855-1859, JUN 2017. (12/23702-8, 12/23638-8, 13/21644-3)

DE SOUZA, MARCELA M.; ZERLOTINI, ADHEMAR; GEISTLINGER, LUDWIG; TIZIOTO, POLYANA C.; TAYLOR, JEREMY F.; ROCHA, MARINA I. P.; DINIZ, WELLISON J. S.; COUTINHO, LUIZ L.; REGITANO, LUCIANA C. A.. A comprehensive manually-curated compendium of bovine transcription factors. SCIENTIFIC REPORTS, v. 8, SEP 13 2018. (12/20328-8, 12/23638-8, 14/15183-6)

GEISTLINGER, LUDWIG; DA SILVA, VINICIUS HENRIQUE; MELLO CESAR, ALINE SILVA; TIZIOTO, POLYANA CRISTINE; WALDRON, LEVI; ZIMMER, RALF; DE ALMEIDA REGITANO, LUCIANA CORREIA; COUTINHO, LUIZ LEHMANN. Widespread modulation of gene expression by copy number variation in skeletal muscle. SCIENTIFIC REPORTS, v. 8, JAN 23 2018. (14/01438-2, 12/23638-8)

CESAR, ALINE S. M.; REGITANO, LUCIANA C. A.; POLETI, MIRELE D.; ANDRADE, SONIA C. S.; TIZIOTO, POLYANA C.; OLIVEIRA, PRISCILA S. N.; FELICIO, ANDREZZA M.; DO NASCIMENTO, MICHELE L.; CHAVES, AMALIA S.; LANNA, DANTE P. D.; et al. Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content. BMC Genomics, v. 17, NOV 22 2016. (14/22884-0, 12/23638-8, 14/11871-5)

BUZANSKAS, MARCOS ELI; VENTURA, RICARDO VIEIRA; SELEGUIM CHUD, TATIANE CRISTINA; BERNARDES, PRISCILA ARRIGUCCI; DE ABREU SANTOS, DANIEL JORDAN; DE ALMEIDA REGITANO, LUCIANA CORREIA; DE ALENCAR, MAURICIO MELLO; MUDADU, MAURICIO DE ALVARENGA; ZANELLA, RICARDO; GUALBERTO BARBOSA DA SILVA, MARCOS VINICIUS; et al. Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers. PLoS One, v. 12, n. 2, FEB 9 2017. (12/23638-8, 15/08939-0, 15/12396-1, 13/19335-2, 15/25096-6)

DE SOUZA, M. M.; NICIURA, S. C. M.; TIZIOTO, P. C.; IBELLI, A. M. G.; GASPARIN, G.; ROCHA, M. I. P.; BRESSANI, F. A.; MALAGO-, JR., W.; DINIZ, W. J. S.; DE OLIVEIRA, P. S. N.; et al. Allele- and parent-of-origin-specific effects on expression of the KCNJ11 gene: A candidate for meat tenderness in cattle. Genetics and Molecular Research, v. 15, n. 3, 2016. (08/03916-8, 12/23638-8)

DA SILVA DINIZ, WELLISON JARLES; COUTINHO, LUIZ LEHMANN; TIZIOTO, POLYANA CRISTINE; MELLO CESAR, ALINE SILVA; GROMBONI, CAIO FERNANDO; ARAUJO NOGUEIRA, ANA RITA; NEUBERN DE OLIVEIRA, PRISCILA SILVA; DE SOUZA, MARCELA MARIA; DE ALMEIDA REGITANO, LUCIANA CORREIA. Iron Content Affects Lipogenic Gene Expression in the Muscle of Nelore Beef Cattle. PLoS One, v. 11, n. 8, AUG 17 2016. (12/23638-8, 14/12652-5)

CESAR, ALINE S. M.; REGITANO, LUCIANA C. A.; KOLTES, JAMES E.; FRITZ-WATERS, ERIC R.; LANNA, DANTE P. D.; GASPARIN, GUSTAVO; MOURAO, GERSON B.; OLIVEIRA, PRISCILA S. N.; REECY, JAMES M.; COUTINHO, LUIZ L.. Putative Regulatory Factors Associated with Intramuscular Fat Content. PLoS One, v. 10, n. 6, JUN 4 2015. (12/23638-8, 11/00005-7, 12/02383-1)

DINIZ, WELLISON J. S.; MAZZONI, GIANLUCA; COUTINHO, LUIZ L.; BANERJEE, PRIYANKA; GEISTLINGER, LUDWIG; CESAR, ALINE S. M.; BERTOLINI, FRANCESCA; AFONSO, JULIANA; DE OLIVEIRA, PRISCILA S. N.; TIZIOTO, POLYANA C.; et al. Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle. FRONTIERS IN GENETICS, v. 10, MAR 13 2019. (12/23638-8, 15/09158-1, 17/20761-7)

BRUSCADIN, JENNIFER JESSICA; DE SOUZA, MARCELA MARIA; DE OLIVEIRA, KARINA SANTOS; PEREIRA ROCHA, MARINA IBELLI; AFONSO, JULIANA; CARDOSO, TAINA FIGUEIREDO; ZERLOTINI, ADHEMAR; COUTINHO, LUIZ LEHMANN; MEO NICIURA, SIMONE CRISTINA; DE ALMEIDA REGITANO, LUCIANA CORREIA. Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus. SCIENTIFIC REPORTS, v. 11, n. 1, APR 1 2021. (12/23638-8)

POLETI, MIRELE D.; REGITANO, LUCIANA C. A.; SOUZA, GUSTAVO H. M. F.; CESAR, ALINE S. M.; SIMAS, ROSINEIDE C.; SILVA-VIGNATO, BARBARA; MONTENEGRO, HORACIO; PERTILLE, FABIO; BALIEIRO, JULIO C. C.; CAMERON, LUIZ C.; et al. Proteome alterations associated with the oleic acid and cis-9, trans-11 conjugated linoleic acid content in bovine skeletal muscle. JOURNAL OF PROTEOMICS, v. 222, JUN 30 2020. (13/21017-9, 12/23638-8)

DE LIMA, ANDRESSA O.; KOLTES, JAMES E.; DINIZ, WELLISON J. S.; DE OLIVEIRA, PRISCILA S. N.; CESAR, ALINE S. M.; TIZIOTO, POLYANA C.; AFONSO, JULIANA; DE SOUZA, MARCELA M.; PETRINI, JULIANA; ROCHA, MARINA I. P.; et al. Potential Biomarkers for Feed Efficiency-Related Traits in Nelore Cattle Identified by Co-expression Network and Integrative Genomics Analyses. FRONTIERS IN GENETICS, v. 11, MAR 4 2020. (12/23638-8, 19/04089-2)

CESAR, ALINE S. M.; REGITANO, LUCIANA C. A.; REECY, JAMES M.; POLETI, MIRELE D.; OLIVEIRA, PRISCILA S. N.; DE OLIVEIRA, GABRIELLA B.; MOREIRA, GABRIEL C. M.; MUDADU, MAURICIO A.; TIZIOTO, POLYANA C.; KOLTES, JAMES E.; et al. Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits. BMC Genomics, v. 19, JUN 27 2018. (14/22884-0, 12/23638-8, 14/11871-5)

CARDOSO, TAINA FIGUEIREDO; COUTINHO, LUIZ LEHMANN; BRUSCADIN, JENNIFER JESSICA; DA SILVA DINIZ, WELLISON JARLES; PETRINI, JULIANA; ANDRADE, BRUNO GABRIEL NASCIMENTO; DE OLIVEIRA, PRISCILA SILVA NEUBERN; POLETI, MIRELE DAIANA; CESAR, ALINE SILVA MELLO; DA SILVEIRA, JULIANO COELHO; et al. Multi-Omics Approach Reveals miR-SNPs Affecting Muscle Fatty Acids Profile in Nelore Cattle. GENES, v. 12, n. 1, JAN 2021. (12/23638-8, 19/04089-2, 18/11953-2)

AFONSO, JULIANA; COUTINHO, LUIZ LEHMANN; TIZIOTO, POLYANA CRISTINE; DA SILVA DINIZ, WELLISON JARLES; DE LIMA, ANDRESSA OLIVEIRA; PEREIRA ROCHA, MARINA IBELLI; BUSS, CARLOS EDUARDO; NASCIMENTO ANDRADE, BRUNO GABRIEL; PIAYA, OTAVIO; DA SILVA, JULIANA VIRGINIO; et al. Muscle transcriptome analysis reveals genes and metabolic pathways related to mineral concentration in Bos indices. SCIENTIFIC REPORTS, v. 9, SEP 3 2019. (12/23638-8)

SILVA-VIGNATO, BARBARA; COUTINHO, LUIZ L.; POLETI, MIRELE D.; CESAR, ALINE S. M.; MONCAU, CRISTINA T.; REGITANO, LUCIANA C. A.; BALIEIRO, JULIO C. C.. Gene co-expression networks associated with carcass traits reveal new pathways for muscle and fat deposition in Nelore cattle. BMC Genomics, v. 20, JAN 10 2019. (12/23638-8)

KAPPELER, BERNA I. G.; REGITANO, LUCIANA C. A.; POLETI, MIRELE D.; CESAR, ALINE S. M.; MOREIRA, GABRIEL C. M.; GASPARIN, GUSTAVO; COUTINHO, LUIZ L.. MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness. BMC MOLECULAR BIOLOGY, v. 20, JAN 3 2019. (12/23638-8, 13/21017-9, 14/00943-5, 14/11871-5)

POLETI, MIRELE D.; REGITANO, LUCIANA C. A.; SOUZA, GUSTAVO H. M. F.; CESAR, ALINE S. M.; SIMAS, ROSINEIDE C.; SILVA-VIGNATO, BARBARA; OLIVEIRA, GABRIELLA B.; ANDRADE, SONIA C. S.; CAMERON, LUIZ C.; COUTINHO, LUIZ L.. Data from proteomic analysis of bovine Longissimus dorsi muscle associated with intramuscular fat content. DATA IN BRIEF, v. 19, p. 1314-1317, AUG 2018. (12/23638-8, 13/21017-9)

AFONSO, JULIANA; SALINAS FORTES, MARINA RUFINO; REVERTER, ANTONIO; DA SILVA DINIZ, WELLISON JARLES; MELLO CESAR, ALINE SILVA; DE LIMA, ANDRESSA OLIVEIRA; PETRINI, JULIANA; DE SOUZA, MARCELA M.; COUTINHO, LUIZ LEHMANN; MOURAO, GERSON BARRETO; et al. Genetic regulators of mineral amount in Nelore cattle muscle predicted by a new co-expression and regulatory impact factor approach. SCIENTIFIC REPORTS, v. 10, n. 1, MAY 21 2020. (12/23638-8)

DA SILVA DINIZ, WELLISON JARLES; BANERJEE, PRIYANKA; MAZZONI, GIANLUCA; COUTINHO, LUIZ LEHMANN; MELLO CESAR, ALINE SILVA; AFONSO, JULIANA; GROMBONI, CAIO FERNANDO; ARAUJO NOGUEIRA, ANA RITA; KADARMIDEEN, HAJA N.; DE ALMEIDA REGITANO, LUCIANA CORREIA. Interplay among miR-29 family, mineral metabolism, and gene regulation in Bos indicus muscle. Molecular Genetics and Genomics, v. 295, n. 5, p. 1113-1127, SEP 2020. (17/20761-7, 12/23638-8, 15/09158-1)

BERNARDES, PRISCILA ARRIGUCCI; DO NASCIMENTO, GUILHERME BATISTA; SAVEGNAGO, RODRIGO PELICIONI; BUZANSKAS, MARCOS ELI; WATANABE, RAFAEL NAKAMURA; DE ALMEIDA REGITANO, LUCIANA CORREIA; COUTINHO, LUIZ LEHMANN; GONDRO, CEDRIC; MUNARI, DANISIO PRADO. Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle. SCIENTIFIC REPORTS, v. 9, NOV 29 2019. (13/20091-0, 12/23638-8, 16/22940-3, 15/25096-6, 13/19335-2)

DE OLIVEIRA, PRISCILA S. N.; COUTINHO, LUIZ L.; TIZIOTO, POLYANA C.; CESAR, ALINE S. M.; DE OLIVEIRA, GABRIELLA B.; DINIZ, WELLISON J. DA S.; DE LIMA, ANDRESSA O.; REECY, JAMES M.; MOURAO, GERSON B.; ZERLOTINI, ADHEMAR; et al. An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle. SCIENTIFIC REPORTS, v. 8, NOV 20 2018. (12/23638-8, 16/03291-4)

POLETI, MIRELE D.; REGITANO, LUCIANA C. A.; SOUZA, GUSTAVO H. M. F.; CESAR, ALINE S. M.; SIMAS, ROSINEIDE C.; SILVA-VIGNATO, BARBARA; OLIVEIRA, GABRIELLA B.; ANDRADE, SONIA C. S.; CAMERON, LUIZ C.; COUTINHO, LUIZ L.. Longissimus dorsi muscle label-free quantitative proteomic reveals biological mechanisms associated with intramuscular fat deposition. JOURNAL OF PROTEOMICS, v. 179, p. 30-41, MAY 15 2018. (13/21017-9, 12/23638-8)

TIZIOTO, POLYANA C.; COUTINHO, LUIZ L.; OLIVEIRA, PRISCILA S. N.; CESAR, ALINE S. M.; DINIZ, WELLISON J. S.; LIMA, ANDRESSA O.; ROCHA, MARINA I.; DECKER, JARED E.; SCHNABEL, ROBERT D.; MOURAO, GERSON B.; et al. Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake. SCIENTIFIC REPORTS, v. 6, DEC 22 2016. (14/13555-3, 12/23638-8, 13/17778-4)

DA SILVA, VINICIUS HENRIQUE; DE ALMEIDA REGITANO, LUCIANA CORREIA; GEISTLINGER, LUDWIG; PERTILLE, FABIO; GIACHETTO, POLIANA FERNANDA; BRASSALOTI, RICARDO AUGUSTO; MOROSINI, NATALIA SILVA; ZIMMER, RALF; COUTINHO, LUIZ LEHMANN. Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. PLoS One, v. 11, n. 6, JUN 27 2016. (12/23638-8, 14/01438-2, 12/23717-5)

MUDADU, MAURICIO A.; PORTO-NETO, LAERCIO R.; MOKRY, FABIANA B.; TIZIOTO, POLYANA C.; OLIVEIRA, PRISCILA S. N.; TULLIO, RYMER R.; NASSU, RENATA T.; NICIURA, SIMONE C. M.; THOLON, PATRICIA; ALENCAR, MAURICIO M.; et al. Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle. BMC Genomics, v. 17, MAR 15 2016. (12/23638-8)

SILVA-VIGNATO, BARBARA; COUTINHO, LUIZ L.; CESAR, ALINE S. M.; POLETI, MIRELE D.; REGITANO, LUCIANA C. A.; BALIEIRO, JULIO C. C.. Comparative muscle transcriptome associated with carcass traits of Nellore cattle. BMC Genomics, v. 18, JUL 3 2017. (12/23638-8)

DE OLIVEIRA, PRISCILA S. N.; COUTINHO, LUIZ L.; CESAR, ALINE S. M.; DA SILVA DINIZ, WELLISON J.; DE SOUZA, MARCELA M.; ANDRADE, BRUNO G.; KOLTES, JAMES E.; MOURAO, GERSON B.; ZERLOTINI, ADHEMAR; REECY, JAMES M.; et al. Co-Expression Networks Reveal Potential Regulatory Roles of miRNAs in Fatty Acid Composition of Nelore Cattle. FRONTIERS IN GENETICS, v. 10, JUL 11 2019. (12/23638-8, 16/03291-4)

DE SOUZA, MARCELA MARIA; ZERLOTINI, ADHEMAR; PEREIRA ROCHA, MARINA IBELLI; BRUSCADIN, JENNIFER JESSICA; DA SILVA DINIZ, WELLISON JARLES; CARDOSO, TAINA FIGUEIREDO; MELLO CESAR, ALINE SILVA; AFONSO, JULIANA; NASCIMENTO ANDRADE, BRUNO GABRIEL; MUDADU, MAURICIO DE ALVARENGA; et al. Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes. SCIENTIFIC REPORTS, v. 10, n. 1, JUN 23 2020. (12/20328-8, 12/23638-8)