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The Nelore hologenome: implications in beef quality and feed efficiency

Grant number: 19/04089-2
Support Opportunities:Research Grants - eScience and Data Science Program - Thematic Grants
Duration: December 01, 2019 - November 30, 2025
Field of knowledge:Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
Principal Investigator:Luciana Correia de Almeida Regitano
Grantee:Luciana Correia de Almeida Regitano
Host Institution: Embrapa Pecuária Sudeste. Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA). Ministério da Agricultura, Pecuária e Abastecimento (Brasil). São Carlos , SP, Brazil
Pesquisadores principais:
Adhemar Zerlotini Neto ; Gerson Barreto Mourão ; Luiz Lehmann Coutinho
Associated researchers:Alexandre Berndt ; Aline Silva Mello Cesar ; Ana Rita de Araujo Nogueira ; Antonio Reverter-Gomez ; Bastiaan Elie Dutilh ; Bruna Pena Sollero ; Christine G Elsik ; Cintia Righetti Marcondes ; Daniel Rodrigues Cardoso ; Danísio Prado Munari ; Fabiane Siqueira ; Gota Morota ; Haithem Afli ; Haja Kadarmideen ; Heidge Fukumasu ; James E Koltes ; James Reecy ; Jeremy Francis Taylor ; João Oiano Neto ; Juliana Petrini ; Juliano Coelho da Silveira ; Julio Cesar Pascale Palhares ; Laercio Ribeiro Porto neto ; Leandro Carrijo Cintra ; Luis Artur Loyola Chardulo ; Luiz Alberto Colnago ; Marcos Roberto Chiaratti ; Marina Rufino Salinas Fortes ; Matthew Lee Spangler ; Mauricio de Alvarenga Mudadu ; Patricia Tholon ; Paul Walsh ; Paula Regina Kuser Falcão ; Polyana Cristine Tizioto ; Rafael Ricardo de Castro Cuadrat ; Renata Tieko Nassu ; Robert David Schnabel ; Sergio Raposo de Medeiros ; Sónia Cristina da Silva Andrade ; William Tadeu Lara Festuccia
Associated scholarship(s):23/18079-4 - Multi-omics information on Nelore structural and functional genome, BP.TT
23/08402-2 - LIVER TISSUE GENE COEXPRESSION NETWORKS ASSOCIATED WITH MEAT AND CARCASS QUALITY PHENOTYPES IN NELLORE CATTLE, BP.MS
21/08079-1 - Rumen metatranscriptomics of Nellore cattle and its relationship to feedlot performance, BP.DR
+ associated scholarships 23/01149-0 - Omics integration of different tissues from Nelore steers submitted to different diets and its association with feed efficiency, beef quality, and methane emission, BP.PD
21/14321-0 - Construction of gene co-expression networks correlated to ruminal microorganisms profile, feed efficiency and intramuscular fat deposition in Nelore cattle, BP.DR
20/07181-4 - Lipidomics of bovine skeletal muscle as biomarkers for meat quality and feed efficiency, BP.PD
20/01369-1 - Identification of variants with regulatory potential on meat quality traits in Nellore cattle, BP.DR
20/15565-7 - Application of shotgun metagenomics to detail the taxonomic and functional diversity of the Nelore microbiome associated with dietary and phenotypic factors, BP.PD
19/25639-0 - Predicted state of H3K27me3 histone modification in Nellore cattle muscle as an indicator of gene modulation associated with mineral amount and meat quality traits, BP.PD
20/00340-0 - The effect of copy number variations on gene expression and bovine meat quality, BP.PD
18/11953-2 - Variations in regulatory regions associated with meat production and quality characteristics in the Nelore breed, BP.PD - associated scholarships

Abstract

Hologenome is an evolutionary concept that both the host and its associated microorganisms (microbiota) form a cohesive biological entity known as holobionte, whose interaction affects the development and general fitness of the so-called hologenome, such that it has been considered as an independent level of selection. Particularly in ruminants, in addition to allowing to break down complex polysaccharides found in pastures, microbial fermentation in the rumen produces methane as a byproduct, a greenhouse gas with high environmental impact. As well as the reduction of cost and environmental impact, quality improvement is a fundamental factor for the conquest of new markets for Brazilian beef. In a previous thematic project, we produced structural and functional genomic data in a Nelore reference population, thus revealing the main actors in the regulation of gene expression and biological processes relevant to beef quality and food efficiency traits. In the current proposal, we will expand the data analysis to further integrate the different levels of genomic and phenotypic information, searching for causal mutations that explain the observed differences in gene expression. We will also investigate the metagenomics and metabolomics of the rumen of a new sample of Nelore cattle. The addition of the meta-omic layer to the functional genomic of the host will allow to answer critical questions about the inter-relation of functional diversity of the microbiota and the host environment. In addition, the construction of a relational database should facilitate the exploration of this unique set of multi-omic data from Bos indicus and its future integration into international efforts to understand the bovine functional genome. (AU)

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Scientific publications (9)
(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)
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, . (18/11953-2, 12/23638-8, 19/04089-2)
AFONSO, JULIANA; SHIM, WOO JUN; BODEN, MIKAEL; FORTES, MARINA RUFINO SALINAS; DINIZ, WELLISON JARLES DA SILVA; DE LIMA, ANDRESSA OLIVEIRA; ROCHA, MARINA IBELLI PEREIRA; CARDOSO, TAINA FIGUEIREDO; BRUSCADIN, JENNIFER JESSICA; GROMBONI, CAIO FERNANDO; et al. Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle. BIOCHEMISTRY AND BIOPHYSICS REPORTS, v. 33, p. 9-pg., . (19/25639-0, 19/04089-2)
DE SOUZA, MARCELA MARIA; NICIURA, SIMONE CRISTINA MEO; ROCHA, MARINA IBELLI PEREIRA; PAN, ZHANGYUAN; ZHOU, HUAIJUN; BRUSCADIN, JENNIFER JESSICA; DA SILVA DINIZ, WELLISON JARLES; AFONSO, JULIANA; DE OLIVEIRA, PRISCILA SILVA NEUBERN; MOURAO, GERSON B.; et al. DNA methylation may affect beef tenderness through signal transduction in Bos indicus. EPIGENETICS & CHROMATIN, v. 15, n. 1, p. 16-pg., . (19/04089-2, 12/23638-8)
SILVA-VIGNATO, BARBARA; CESAR, ALINE SILVA MELLO; AFONSO, JULIANA; MOREIRA, GABRIEL COSTA MONTEIRO; POLETI, MIRELE DAIANA; PETRINI, JULIANA; GARCIA, INGRID SOARES; CLEMENTE, LUAN GASPAR; MOURAO, GERSON BARRETO; REGITANO, LUCIANA CORREIA DE ALMEIDA; et al. Integrative Analysis Between Genome-Wide Association Study and Expression Quantitative Trait Loci Reveals Bovine Muscle Gene Expression Regulatory Polymorphisms Associated With Intramuscular Fat and Backfat Thickness. FRONTIERS IN GENETICS, v. 13, p. 15-pg., . (19/04089-2)
DE NOVAIS, FRANCISCO JOSE; YU, HAIPENG; CESAR, ALINE SILVA MELLO; MOMEN, MEHDI; POLETI, MIRELE DAIANA; PETRY, BRUNA; MOURAO, GERSON BARRETO; REGITANO, LUCIANA CORREIA DE ALMEIDA; MOROTA, GOTA; COUTINHO, LUIZ LEHMANN. Multi-omic data integration for the study of production, carcass, and meat quality traits in Nellore cattle. FRONTIERS IN GENETICS, v. 13, p. 14-pg., . (12/23638-8, 19/04089-2)
MALHEIROS, JESSICA MORAES; BARBOSA CORREIA, BANNY SILVA; CERIBELI, CAROLINE; CARDOSO, DANIEL RODRIGUES; COLNAGO, LUIZ ALBERTO; BOGUSZ JUNIOR, STANISLAU; REECY, JAMES MARK; MOURAO, GERSON BARRETO; COUTINHO, LUIZ LEHMANN; PASCALE PALHARES, JULIO CESAR; et al. Comparative untargeted metabolome analysis of ruminal fluid and feces of Nelore steers (Bos indicus). SCIENTIFIC REPORTS, v. 11, n. 1, . (19/04089-2, 17/26537-1, 17/01189-0)
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, . (12/23638-8, 19/04089-2)
CARDOSO, T. F.; BRUSCADIN, J. J.; AFONSO, J.; PETRINI, J.; ANDRADE, B. G. N.; DE OLIVEIRA, P. S. N.; MALHEIROS, J. M.; ROCHA, M. I. P.; ZERLOTINI, A.; FERRAZ, J. B. S.; et al. EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle. Mammalian Genome, v. 33, n. 4, p. 10-pg., . (18/11953-2, 12/23638-8, 19/04089-2)
LIMA, ANDRESSA OLIVEIRA; MALHEIROS, JESSICA MORAES; AFONSO, JULIANA; PETRINI, JULIANA; COUTINHO, LUIZ LEHMANN; JARLES DA SILVA DINIZ, WELLISON; BRESSANI, FLAVIA ALINE; TIZIOTO, POLYANA CRISTINE; NEUBERN DE OLIVEIRA, PRISCILA SILVA; SILVA RIBEIRO, JANSSEN AYNA; et al. Prune homolog 2 with BCH domain (PRUNE2) gene expression is associated with feed efficiency-related traits in Nelore steers. Mammalian Genome, v. 33, n. 4, p. 13-pg., . (19/04089-2, 12/23638-8)

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