Genomics applied to ruminant production

• Grant number: 14/07566-2
• Support Opportunities: Research Projects - Thematic Grants
• Duration: March 01, 2015 - November 30, 2018
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: José Bento Sterman Ferraz
• Grantee: José Bento Sterman Ferraz
• Host Institution: Faculdade de Zootecnia e Engenharia de Alimentos (FZEA). Universidade de São Paulo (USP). Pirassununga , SP, Brazil
• Associated researchers: Felipe Perecin ; Fernando Sebastián Baldi Rey ; Flávio Vieira Meirelles ; Heidge Fukumasu ; Joanir Pereira Eler ; Luiz Lehmann Coutinho ; Marcelo Beltrão Molento ; Rachel Santos Bueno Carvalho ; Ricardo Vieira Ventura
• Associated scholarship(s): 17/21573-0 - Genomic evaluation in composite cattle of the Montana breed using real and simulated data applying the BLUP genomic single-step method, BP.DR; 18/13902-6 - Genome Wide Association Study (GWAS) applied to in vitro embryo production in Nellore cattle, BP.IC; 18/06725-0 - Validation of CNV (copy number variation of genomic regions) by qPCR, BP.IC; + associated scholarships 18/06728-0 - Managing genomic databases, BP.IC; 18/04923-0 - Genomics applied to ruminant production, BP.TT; 17/10493-5 - Genomic-wide association study for gastrointestinal parasites resistance in Santa Inês sheep breed using SNPs and CNVs, BP.PD; 17/10103-2 - Inbreeding effects on progeny uniformity of Nellore sires, BP.MS; 16/11585-8 - Analysis of functional polymorphisms associated with feed efficiency in Nelore cattle, BP.IC; 15/22276-3 - Systems Biology Approach to Determine Molecular Mechanisms Associated with Feed Efficiency in Nelore Cattle, BP.DR; 15/01059-4 - Analysis in serum metabolomic associated with feed efficiency in Nellore, BP.MS - associated scholarships

Abstract

Genomics applied to ruminant production 3The Brazilian beef cattle, besides being one of the main highlights of animal agriculture, have a large importance in the world market, because the country has one of the largest beef herds in the world, with around 200 million heads, predominantly animal origin Bos indicus, wherein Nellore breed influences approximately 90% of the population. Effective data for beef production confirmed in 2011 indicate that 16.5% was exported and the large amount (83.5%) was send to the internal market. (Foram retirados os dados informativos do rebanho de Ovinos) Because of the importance, economic interest and increased food production, improvements are needed for efficient production, especially in the selection of genetically superior animals and resistant to adverse environment of the tropics. With increased demand for food worldwide, the quantity and quality of the production of animal protein is an important target of research. Recent advances in biotechnology, the use of high-density beadchip of single nucleotide polymorphisms (SNP - Single Nucleotide Polymorphisms), allow to develop strategies to identify genes or genomic regions responsible for traits of interest, making the selection process faster and more efficient. GWAS methodology (Genome Wide Association Study) compares results from high-density beadchip with thousands of polymorphic markers found in individuals phenotyped for traits of interest, to identify associations of markers, or genomic regions, with those phenotypes. The objecti ve of this project is a study of molecular genetic systems, addressing genome-wide association study (GWAS), linkage disequilibrium, variations in the number of copies of genomic regions (CNVs) and functional enrichment in measures of growth, reproduction, meat quality and feed efficiency in cattle Nellore (Foram retirados os objetivos dos estudos de Ovinos). Additionally, conduct a study of global gene expression (sequencing of total RNA messenger - RNA-Seq) and epigenetic mechanisms that control the expression of feed efficiency in Nellore cattle. (AU)

Scientific publications

(28)

(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)

BRUNA FOLEGATTI SANTANA; RICARDO DA FONSECA; MATOS MANUEL; GERARDO CORNELIO MAMANI MAMANI; JOANIR PEREIRA ELER; JOSÉ BENTO STERMAN FERRAZ. Viabilidade do uso de características “dias para um peso específico” em programas de melhoramento genético de bovinos da raça Nelore. Rev. bras. saúde prod. anim., v. 18, n. 2, p. 260-268, 2017-06-00. (14/07566-2)

ALEXANDRE, PAMELA A.; KOGELMAN, LISETTE J. A.; SANTANA, MIGUEL H. A.; PASSARELLI, DANIELLE; PULZ, LIDIA H.; FANTINATO-NETO, PAULO; SILVA, PAULO L.; LEME, PAULO R.; STREFEZZI, RICARDO F.; COUTINHO, LUIZ L.; et al. Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle. BMC Genomics, v. 16, DEC 18 2015. (14/02493-7, 14/07566-2, 12/14792-3, 14/00307-1)

GRIGOLETTO, LAIS; BRITO, LUIZ FERNANDO; MATTOS, ELISANGELA C.; ELER, JOANIR PEREIRA; BUSSIMAN, FERNANDO OLIVEIRA; ABREU SILVA, BARBARA DA CONCEICAO; DA SILVA, ROSIANE PEREIRA; CARVALHO, FELIPE EGUTI; BERTON, MARIANA PIATTO; BALDI, FERNANDO; et al. Genome-wide associations and detection of candidate genes for direct and maternal genetic effects influencing growth traits in the Montana Tropical (R) Composite population. LIVESTOCK SCIENCE, v. 229, p. 64-76, NOV 2019. (17/11919-6, 18/20393-0, 14/07566-2)

MACEDO MOTA, LUCIO FLAVIO; BONAFE, CRISTINA MOREIRA; ALEXANDRE, PAMELA ALMEIDA; SANTANA, MIGUEL HENRIQUE; NOVAIS, FRANCISCO JOSE; TORIYAMA, ERIKA; PIRES, ALDRIN VIEIRA; SILVA, SAULO DA LUZ; LEME, PAULO ROBERTO; STERMAN FERRAZ, JOSE BENTO; et al. Circulating leptin and its muscle gene expression in Nellore cattle with divergent feed efficiency. JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY, v. 8, SEP 1 2017. (14/02493-7, 10/05650-5, 14/07566-2)

GRIGOLETTO, LAIS; FERRAZ, JOSE B. S.; OLIVEIRA, HINAYAH R.; ELER, JOANIR P.; BUSSIMAN, FERNANDO O.; ABREU SILVA, BARBARA C.; BALDI, FERNANDO; BRITO, LUIZ F.. Genetic Architecture of Carcass and Meat Quality Traits in Montana Tropical (R) Composite Beef Cattle. FRONTIERS IN GENETICS, v. 11, FEB 27 2020. (14/07566-2, 18/20393-0, 17/11919-6)

BERTON, MARIANA P.; SILVA, ROSIANE P.; CARVALHO, FELIPE E.; CHIAIA, HERMENEGILDO LUCAS JUSTINO; OLIVEIRA, PRISCILA S.; ELER, JOANIR P.; BANCHERO, GEORGGET; FERRAZ, JOSE B. S.; BALDI, FERNANDO. Genetic parameter estimates for gastrointestinal nematode parasite resistance and maternal efficiency indicator traits in Santa Ines breed. JOURNAL OF ANIMAL BREEDING AND GENETICS, v. 136, n. 6, p. 495-504, NOV 2019. (11/00396-6, 17/10493-5, 14/07566-2, 10/05516-7)

CARVALHO, M. E.; BALDI, F. S.; ALEXANDRE, P. A.; SANTANA, M. H. A.; VENTURA, R. V.; BUENO, R. S.; BONIN, M. N.; REZENDE, F. M.; COUTINHO, L. L.; ELER, J. P.; et al. Genomic regions and genes associated with carcass quality in Nelore cattle. Genetics and Molecular Research, v. 18, n. 1, FEB 26 2019. (14/07566-2, 13/13021-6)

OLIVEIRA JUNIOR, GERSON A.; SANTOS, DANIEL J. A.; CESAR, ALINE S. M.; BOISON, SOLOMON A.; VENTURA, RICARDO V.; PEREZ, BRUNO C.; GARCIA, JOSE F.; FERRAZ, JOSE BENTO S.; GARRICK, DORIAN J.. Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires. JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY, v. 10, n. 1, DEC 16 2019. (13/12097-9, 12/50533-2, 15/12396-1, 14/07566-2)

GEBIM POLIZEL, GUILHERME HENRIQUE; GRIGOLETTO, LAIS; CARVALHO, MINOS ESPERANDIO; ROSSI JUNIOR, PAULO; STERMAN FERRAZ, JOSE BENTO; DE ALMEIDA SANTANA, MIGUEL HENRIQUE. Genetic correlations and heritability estimates for dry matter intake, weight gain and feed efficiency of Nellore cattle in feedlot. LIVESTOCK SCIENCE, v. 214, p. 209-210, AUG 2018. (13/26902-0, 13/20571-2, 14/07566-2, 12/02039-9)

DE ALMEIDA SANTANA, MIGUEL HENRIQUE; GEBIM POLIZEL, GUILHERME HENRIQUE; GRIGOLETTO, LAIS; FERNANDES, ARICIA CHRISTOFARO; BONIN, MARINA DE NADAI; GOMES, RODRIGO DA COSTA; CARVALHO, MINOS ESPERANDIO; DA LUZ E SILVA, SAULO; LEME, PAULO ROBERTO; ROSSI JUNIOR, PAULO; et al. The genetic and genomic effects of Nellore lineages on feed efficiency, intake and performance. LIVESTOCK SCIENCE, v. 228, p. 104-108, OCT 2019. (13/20571-2, 13/26902-0, 14/07566-2, 12/02039-9)

FONSECA, LEYDIANA D.; ELER, JOANIR P.; PEREIRA, MIKAELE A.; ROSA, ALESSANDRA F.; ALEXANDRE, PAMELA A.; MONCAU, CRISTINA T.; SALVATO, FERNANDA; ROSA-FERNANDES, LIVIA; PALMISANO, GIUSEPPE; FERRAZ, JOSE B. S.; et al. Liver proteomics unravel the metabolic pathways related to Feed Efficiency in beef cattle. SCIENTIFIC REPORTS, v. 9, MAR 29 2019. (14/04937-0, 14/12492-8, 14/07566-2, 14/02493-7)

BERTON, MARIANA PIATTO; DE OLIVEIRA SILVA, RAFAEL MEDEIROS; PERIPOLLI, ELISA; STAFUZZA, NEDENIA BONVINO; MARTIN, JESUS FERNANDEZ; ALVAREZ, MARIA SAURA; GAVINA, BEATRIZ VILLANUEVA; TORO, MIGUEL ANGEL; BANCHERO, GEORGGET; OLIVEIRA, PRISCILA SILVA; et al. Genomic regions and pathways associated with gastrointestinal parasites resistance in Santa Ines breed adapted to tropical climate. JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY, v. 8, SEP 4 2017. (11/00396-6, 10/05516-7, 14/07566-2)

PERIPOLLI, ELISA; STAFUZZA, NEDENIA BONVINO; AMORIM, SABRINA THAISE; ANTUNES DE LEMOS, MARCOS VINICIUS; GRIGOLETTO, LAIS; KLUSKA, SABRINA; STERMAN FERRAZ, JOSE BENTO; ELER, JOANIR PEREIRA; MATTOS, ELISANGELA CHICARONI; BALDI, FERNANDO. Genome-wide scan for runs of homozygosity in the composite Montana Tropical (R) beef cattle. JOURNAL OF ANIMAL BREEDING AND GENETICS, v. 137, n. 2, AUG 2019. (14/07566-2)

ALEXANDRE, PAMELA A.; NAVAL-SANCHEZ, MARINA; PORTO-NETO, LAERCIO R.; FERRAZ, JOSE BENTO S.; REVERTER, ANTONIO; FUKUMASU, HEIDGE. Systems Biology Reveals NR2F6 and TGFB1 as Key Regulators of Feed Efficiency in Beef Cattle. FRONTIERS IN GENETICS, v. 10, MAR 22 2019. (17/14707-0, 15/22276-3, 14/07566-2, 14/02493-7)

BUSSIMAN, F. O.; DOS SANTOS, B. A.; ABREU SILVA, B. C.; PEREZ, B. C.; PEREIRA, G. L.; CHARDULO, L. A. L.; ELER, J. P.; FERRAZ, J. B. S.; MATTOS, E. C.; CURI, R. A.; et al. Allelic and genotypic frequencies of the DMRT3 gene in the Brazilian horse breed Mangalarga Marchador and their association with types of gait. Genetics and Molecular Research, v. 18, n. 1, FEB 25 2019. (16/17834-0, 16/19081-9, 14/07566-2)

GRIGOLETTO, LAIS; ALMEIDA SANTANA, MIGUEL HENRIQUE; BRESSAN, FABIANA FERNANDES; ELER, JOANIR PEREIRA; GOUVEIA NOGUEIRA, MARCELO FABIO; KADARMIDEEN, HAJA N.; BARUSELLI, PIETRO SAMPAIO; STERMAN FERRAZ, JOSE BENTO; BRITO, LUIZ F.. Genetic Parameters and Genome-Wide Association Studies for Anti-Mullerian Hormone Levels and Antral Follicle Populations Measured After Estrus Synchronization in Nellore Cattle. ANIMALS, v. 10, n. 7, JUL 2020. (12/50533-2, 14/07566-2, 17/11919-6)

AMORIM, SABRINA THAISE; KLUSKA, SABRINA; BERTON, MARIANA PIATTO; ANTUNES DE LEMOS, MARCOS VINICIUS; PERIPOLLI, ELISA; STAFUZZA, NEDENIA BONVINO; MARTIN, JESUS FERNANDEZ; SAURA ALVAREZ, MARIA; VILLANUEVA GAVINA, BEATRIZ; ANGEL TORO, MIGUEL; et al. Genomic study for maternal related traits in Santa Ines sheep breed. LIVESTOCK SCIENCE, v. 217, p. 76-84, NOV 2018. (11/00396-6, 10/05516-7, 14/07566-2)

ALEXANDRE, PAMELA A.; REVERTER, ANTONIO; BEREZIN, ROBERTA B.; PORTO-NETO, LAERCIO R.; RIBEIRO, GABRIELA; SANTANA, MIGUEL H. A.; FERRAZ, JOSE BENTO S.; FUKUMASU, HEIDGE. Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle. GENES, v. 11, n. 9, SEP 2020. (17/14707-0, 15/22276-3, 14/07566-2)

BERTON, MARIANA P.; SILVA, ROSIANE P.; CARVALHO, FELIPE E.; JUSTINO CHIAIA, HERMENEGILDO LUCAS; OLIVEIRA, PRISCILA S.; ELER, JOANIR P.; BANCHERO, GEORGGET; FERRAZ, JOSE B. S.; BALDI, FERNANDO. Genetic parameter estimates for gastrointestinal nematode parasite resistance and maternal efficiency indicator traits in Santa Ines breed. JOURNAL OF ANIMAL BREEDING AND GENETICS, JULY 2019. (11/00396-6, 17/10493-5, 14/07566-2, 10/05516-7)

FREUA, MATEUS CASTELANI; DE ALMEIDA SANTANA, MIGUEL HENRIQUE; VENTURA, RICARDO VIEIRA; TEDESCHI, LUIS ORLINDO; STERMAN FERRAZ, JOSE BENTO. Using a system of differential equations that models cattle growth to uncover the genetic basis of complex traits. JOURNAL OF APPLIED GENETICS, v. 58, n. 3, p. 393-400, AUG 2017. (13/26902-0, 13/20571-2, 14/07566-2, 12/02039-9)

GRIGOLETTO, L.; MATTOS, E. C.; SANTANA, M. H. A.; BALDI, F.; ELER, J. P.; FERRAZ, J. B. S.. Inclusion of cytoplasmic lineage effect and direct-maternal genetic covariance for genetic evaluation of growth traits in Nellore cattle. Genetics and Molecular Research, v. 15, n. 3, 2016. (14/07566-2)

GRIGOLETTO, L.; PEREZ, B. C.; SANTANA, M. H. A.; BALDI, F.; FERRAZ, J. B. S.. Genetic contribution of cytoplasmic lineage effect on feed efficiency in Nellore cattle. LIVESTOCK SCIENCE, v. 198, p. 52-57, APR 2017. (13/20571-2, 14/07566-2, 12/02039-9)

SANTANA, M. H. A.; FREUA, M. C.; DO, D. N.; VENTURA, R. V.; KADARMIDEEN, H. N.; FERRAZ, J. B. S.. Systems genetics and genome-wide association approaches for analysis of feed intake, feed efficiency, and performance in beef cattle. Genetics and Molecular Research, v. 15, n. 4, 2016. (13/20571-2, 12/02039-9, 14/14121-7, 13/26902-0, 14/07566-2)

FREUA, MATEUS CASTELANI; DE ALMEIDA SANTANA, MIGUEL HENRIQUE; STERMAN FERRAZ, JOSE BENTO. A new approach for applied nutritional models: Computing parameters of dynamic mechanistic growth models using genorne-wide prediction. LIVESTOCK SCIENCE, v. 190, p. 131-135, AUG 2016. (13/26902-0, 13/20571-2, 14/07566-2, 12/02039-9)

NOVAIS, FRANCISCO JOSE; LISBOA PIRES, PEDRO RATTO; ALEXANDRE, PAMELA ALMEIDA; DROMMS, ROBERT A.; IGLESIAS, AMADEU HOSHI; STERMAN FERRAZ, JOSE BENTO; STYCZYNSKI, MARK PHILIP-WALTER; FUKUMASU, HEIDGE. Identification of a metabolomic signature associated with feed efficiency in beef cattle. BMC Genomics, v. 20, JAN 7 2019. (15/01059-4, 14/07566-2, 14/02493-7)

MAZZONI, GIANLUCA; PEDERSEN, HANNE S.; DE OLIVEIRA JUNIOR, GERSON A.; ALEXANDRE, PAMELA; RAZZA, EDUARDO M.; CALLESEN, HENRIK; HYTTEL, POUL; NOGUEIRA, MARCELO F. G.; FERRAZ, JOSE BENTO S.; KADARMIDEEN, HAJA N.. Application of integrative genomics and systems biology to conventional and in vitro reproductive traits in cattle. ANIMAL REPRODUCTION, v. 14, n. 3, p. 507-513, JUL-SEP 2017. (12/50533-2, 14/07566-2)

OLIVEIRA JUNIOR, G. A.; PEREZ, B. C.; COLE, J. B.; SANTANA, M. H. A.; SILVEIRA, J.; MAZZONI, G.; VENTURA, R. V.; SANTANA JUNIOR, M. L.; KADARMIDEEN, H. N.; GARRICK, D. J.; et al. Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers. JOURNAL OF ANIMAL SCIENCE, v. 95, n. 11, p. 4796-4812, NOV 2017. (12/50533-2, 13/12097-9, 14/26354-6, 14/07566-2)

OLIVEIRA JUNIOR, GERSON A.; PINHEIRO, VINICIUS G.; FONSECA, PABLO A. S.; COSTA, CAMILA B.; PIOLTINE, ELISA M.; BOTIGELLI, RAMON C.; RAZZA, EDUARDO M.; ERENO, RONALDO L.; FERRAZ, JOSE B. S.; SENEDA, MARCELO M.; et al. enomic and phenotypic analyses of antral follicle count in Aberdeen Angus cow. LIVESTOCK SCIENCE, v. 249, JUL 2021. (14/26354-6, 14/07566-2, 19/10732-5, 12/50533-2, 12/23409-9, 16/16841-2, 13/12097-9)