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Genetic aspects of meat production quality, efficiency and sustainability in Nelore breed animals

Grant number: 17/10630-2
Support Opportunities:Research Projects - Thematic Grants
Duration: June 01, 2018 - November 30, 2024
Field of knowledge:Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
Principal Investigator:Lucia Galvão de Albuquerque
Grantee:Lucia Galvão de Albuquerque
Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
Pesquisadores principais:
( Atuais )
Josineudson Augusto Ii de Vasconcelos Silva ; Maria Eugênia Zerlotti Mercadante
Pesquisadores principais:
( Anteriores )
Roberto Carvalheiro
Associated researchers:Alexandre Berndt ; Ana Fabrícia Braga Magalhães ; Camila Urbano Braz ; Daiane Cristina Becker Scalez ; Daniel Guariz Pinheiro ; Diercles Francisco Cardoso ; Fernando Sebastián Baldi Rey ; Gerardo Alves Fernandes Júnior ; Guilherme Jordão de Magalhães Rosa ; Henrique Nunes de Oliveira ; Humberto Tonhati ; Jesus Aparecido Ferro ; Joslaine Noely dos Santos Goncalves Cyrillo ; Juliana de Oliveira Santos Marcatto ; Larissa Fernanda Simielli Fonseca ; Luis Artur Loyola Chardulo ; Rafael Espigolan ; Roberta Carrilho Canesin ; Roberto Carvalheiro ; Rosa Toyoko Shiraishi Frighetto
Associated grant(s):23/02356-9 - 56th congress of the international society for applied ethology, AR.EXT
18/20026-8 - Multi-user equipment approved in grant 2017/10630-2: server, AP.EMU
Associated scholarship(s):23/17818-8 - Genome-wide scan to identify selection signatures and candidate genes associated with enteric methane emission and feed efficiency traits in Nellore cattle using sequencing data, BP.DR
23/11176-4 - Mapping candidates for lethal haplotypes and genomic regions associated with the occurrence of abortion and pre-weaning mortality in Nellore cattle, BP.MS
22/11852-7 - Structural equation modeling as a tool to interpret genotype-environment interaction and genome-wide association (GWAS) for growth and reproductive traits in Nellore heifers using whole-genome sequence data, BP.PD
+ associated scholarships 21/09942-5 - Variance of gametic diversity estimation for economically important traits of Nellore cattle, BP.DR
20/03975-6 - Incorporating sequence variants to improve genomic prediction for reproductive traits in Nellore cattle, BP.PD
19/11738-7 - Phenotypic, genetic correlations and genomic wide association between feed efficiency and enteric methane emission of Nellore cattle, BP.DR
20/02392-7 - Determination of enteric methane emission from Nelore cattle, BP.TT
20/02304-0 - Association of ingestive behavior and enteric methane emission in cattle of the Nellore breed, BP.IC
19/06361-1 - Genotype-environment interaction in Nellore cattle for growth traits and visual scores using sequence data, BP.DR
19/15397-0 - GENOME WIDE ASSOCIATION STUDY AND DETECTION OF SELECTION SIGNALS IN THE GENOME OF NELORE CATTLE USING SEQUENCE DATA, BP.PD
19/16732-7 - Bioinformatics application in genome and transcriptome analysis of Nellore cattle, integrating public information, BP.PD
19/05165-4 - Evaluation of ruminal methane emission flows of Nelore cattle, BP.TT
18/12504-7 - Phenotyping for methane emission in Nelore males submitted to feed efficiency test, BP.TT
18/10109-3 - Identification and analysis of genetic variants obtained from the whole-genome sequencing of Nellore bulls, BP.PD
18/04313-7 - Assessment of inbreeding and study of functional variants using sequenced data in Nelore cattle, BP.PD - associated scholarships

Abstract

In general, Brazilian beef herds need to improve their indexes of efficiency and the final product (meat) quality. Moreover, nowadays, there is a worldwide concern about the animal production sustainability, which could be improved selecting animals with decreased enteric methane emission to the atmosphere. With the evolution of the complete genome sequencing and the decreasing sequencing costs by animal, this technic has been proposed as an alternative to the SNP chips for genomic selection, with various advantages. Therefore, the present project aims to build a data set of enteric methane emission and to use a data set including feed efficiency, meat and carcass quality and reproduction traits already existent to perform genomic studies based in the complete DNA sequence, with the objective of developing technologies to increase the biologic knowledge and the genetic improvement of quality, efficiency and sustainability of Nelore beef cattle production. The following topics will be developed in the project: a) genetic quantitative studies of traits related to enteric methane emission and their genetic associations with feed efficiency traits; b) studies about the accuracy of imputation to the complete DNA sequence from animals genotyped with commercial chips with different SNP numbers and using various methods; c) studies of Nelore genome characterization using sequence data; d) genome wide association studies for economic important traits using genome complete sequence as well as fine mapping candidate genes aiming to identify causal and deleterious mutations for economic traits; e) genomic selection studies for quality, efficiency and sustainability of production traits using sequence data; f) gene expression analysis (transcriptome) for feed efficiency. (AU)

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Scientific publications (27)
(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)
SAKAMOTO, LEANDRO SANNOMIYA; SOUZA, LUANA LELIS; GIANVECCHIO, SARAH BERNARDES; DE OLIVEIRA, MATHEUS HENRIQUE VARGAS; SILVA, JOSINEUDSON AUGUSTO I. I. DE VASCONCELOS; CANESIN, ROBERTA CARRILHO; BRANCO, RENATA HELENA; BACCAN, MELISSA; BERNDT, ALEXANDRE; DE ALBUQUERQUE, LUCIA GALVAO; et al. Phenotypic association among performance, feed efficiency and methane emission traits in Nellore cattle. PLoS One, v. 16, n. 10, . (18/17313-5, 17/50339-5, 19/11738-7, 17/10630-2)
MOTA, LUCIO F. M.; SANTOS, SAMUEL W. B.; JUNIOR, GERARDO A. FERNANDES; BRESOLIN, TIAGO; MERCADANTE, MARIA E. Z.; SILVA, JOSINEUDSON A. V.; CYRILLO, JOSLAINE N. S. G.; MONTEIRO, FABIO M.; CARVALHEIRO, ROBERTO; ALBUQUERQUE, LUCIA G.. Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits. BMC Genomics, v. 23, n. 1, p. 12-pg., . (09/16118-5, 17/10630-2, 17/13411-0, 16/24228-9)
FILHO, IVAN CARVALHO; SILVA, DELVAN A.; TEIXEIRA, CAIO S.; SILVA, THALES L.; MOTA, LUCIO F. M.; ALBUQUERQUE, LUCIA G.; CARVALHEIRO, ROBERTO. Heteroscedastic Reaction Norm Models Improve the Assessment of Genotype by Environment Interaction for Growth, Reproductive, and Visual Score Traits in Nellore Cattle. ANIMALS, v. 12, n. 19, p. 24-pg., . (18/20026-8, 19/06361-1, 17/10630-2)
TORO OSPINA, ALEJANDRA MARIA; AGUILAR, IGNACIO; VARGAS DE OLIVEIRA, MATHEUS HENRIQUE; CRUZ DOS SANTOS CORREIA, LUIZ EDUARDO; VERCESI FILHO, ANIBAL EUGENIO; ALBUQUERQUE, LUCIA GALVAO; II DE VASCONCELOS SILVA, JOSINEUDSON AUGUSTO. Assessing the accuracy of imputation in the Gyr breed using different SNP panels. GENOME, v. 64, n. 10, p. 893-899, . (15/06686-7, 17/10630-2)
MAGALHAES MUNIZ, MARIA MALANE; SIMIELLI FONSECA, LARISSA FERNANDA; BECKER SCALEZ, DAIANE CRISTINA; VEGA, AROA SUAREZ; DOS SANTOS SILVA, DANIELLY BERALDO; FERRO, JESUS APARECIDO; CHARDULO, ARTUR LOYOLA; BALDI, FERNANDO; CANOVAS, ANGELA; DE ALBUQUERQUE, LUCIA GALVAO. Characterization of novel lncRNA muscle expression profiles associated with meat quality in beef cattle. EVOLUTIONARY APPLICATIONS, v. 15, n. 4, p. 13-pg., . (18/11154-2, 18/20026-8, 09/16118-5, 17/10630-2, 11/21241-0)
MUNIZ, MALANE M.; SIMIELLI FONSECA, LARISSA FERNANDA; CANOVAS, ANGELA; DOS SANTOS SILVA, DANIELLY BERALDO; FERRO, JESUS APARECIDO; CHARDULO, ARTUR LOYOLA; BALDI, FERNANDO; DE ALBUQUERQUE, LUCIA GALVAO. Structural variants affecting mRNAs isoforms splice sites associated with marbling in Nellore cattle. JOURNAL OF ANIMAL SCIENCE, v. 98, p. 2-pg., . (18/11154-2, 11/21241-0, 09/16118-5, 18/20026-8, 17/10630-2)
MAGALHAES MUNIZ, MARIA MALANE; SIMIELLI FONSECA, LARISSA FERNANDA; DOS SANTOS SILVA, DANIELLY BERALDO; DE OLIVEIRA, HINAYAH ROJAS; BALDI, FERNANDO; CHARDULO, ARTUR LOYOLA; FERRO, JESUS APARECIDO; CANOVAS, ANGELA; DE ALBUQUERQUE, LUCIA GALVAO. Identification of novel mRNA isoforms associated with meat tenderness using RNA sequencing data in beef cattle. MEAT SCIENCE, v. 173, . (18/20026-8, 11/21241-0, 18/11154-2, 09/16118-5, 17/10630-2)
ALVES, A. A. C.; ESPIGOLAN, R.; BRESOLIN, T.; COSTA, R. M.; FERNANDES JUNIOR, G. A.; VENTURA, R. V.; CARVALHEIRO, R.; ALBUQUERQUE, L. G.. Genome-enabled prediction of reproductive traits in Nellore cattle using parametric models and machine learning methods. ANIMAL GENETICS, v. 52, n. 1, . (17/10630-2, 09/16118-5, 18/20026-8, 16/24227-2)
MARIN-GARZON, N. A.; MAGALHAES, A. F. B.; SCHMIDT, P. I.; SERNA, M.; FONSECA, L. F. S.; SALATTA, B. M.; FREZARIM, G. B.; FERNANDES-JUNIOR, G. A.; BRESOLIN, T.; CARVALHEIRO, R.; et al. Genome-wide scan reveals genomic regions and candidate genes underlying direct and maternal effects of preweaning calf mortality in Nellore cattle. Genomics, v. 113, n. 3, p. 1386-1395, . (17/10630-2, 18/20026-8)
SILVA, DANIELLY B. S.; FONSECA, LARISSA F. S.; PINHEIRO, DANIEL G.; MAGALHAES, ANA F. B.; MUNIZ, MARIA M. M.; FERRO, JESUS A.; BALDI, FERNANDO; CHARDULO, LUIS A. L.; SCHNABEL, ROBERT D.; TAYLOR, JEREMY F.; et al. Spliced genes in muscle from Nelore Cattle and their association with carcass and meat quality. SCIENTIFIC REPORTS, v. 10, n. 1, . (17/10630-2, 15/16850-9, 09/16118-5, 16/22894-1, 18/20026-8)
SCHETTINI, GUSTAVO PIMENTA; PERIPOLLI, ELISA; ALEXANDRE, PAMELA ALMEIDA; DOS SANTOS, WELLINGTON BIZARRIA; CRAVO PEREIRA, ANGELICA SIMONE; DE ALBUQUERQUE, LUCIA GALVAO; BALDI, FERNANDO; CURI, ROGERIO ABDALLAH. Transcriptome Profile Reveals Genetic and Metabolic Mechanisms Related to Essential Fatty Acid Content of Intramuscular Longissimus thoracis in Nellore Cattle. METABOLITES, v. 12, n. 5, p. 18-pg., . (18/20026-8, 17/10630-2)
SERNA-GARCIA, MARTA; FONSECA, LARISSA FERNANDA SIMIELLI; ROMERO, JOAQUIN JAVIER PANADERO; ASUNCION, JULIAN CARRETERO; SILVA, DANIELLY BERALDO DOS SANTOS; SALATTA, BRUNA MARIA; FREZARIM, GABRIELA BONFA; MERCADANTE, MARIA EUGENIA ZERLOTTI; BONILHA, SARAH FIGUEIREDO MARTINS; FERRO, JESUS APARECIDO; et al. Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups. ANIMALS, v. 13, n. 3, p. 22-pg., . (18/20026-8, 09/16118-5, 17/10630-2)
ALVES, ANDERSON ANTONIO CARVALHO; DA COSTA, REBEKA MAGALHAES; FONSECA, LARISSA FERNANDA SIMIELLI; CARVALHEIRO, ROBERTO; VENTURA, RICARDO VIEIRA; ROSA, GUILHERME JORDAO DE MAGALHAES; ALBUQUERQUE, LUCIA GALVAO. A Random Forest-Based Genome-Wide Scan Reveals Fertility-Related Candidate Genes and Potential Inter-Chromosomal Epistatic Regions Associated With Age at First Calving in Nellore Cattle. FRONTIERS IN GENETICS, v. 13, p. 18-pg., . (18/20026-8, 17/10630-2, 09/16118-5, 16/24227-2)
FERNANDES JUNIOR, GERARDO ALVES; PERIPOLLI, ELISA; SCHMIDT, PATRICIA IANA; CAMPOS, GABRIEL SOARES; MOTA, LUCIO FLAVIO MACEDO; MERCADANTE, MARIA EUGENIA ZERLOTTI; BALDI, FERNANDO; CARVALHEIRO, ROBERTO; DE ALNUQUERQUE, LUCIA GALVAO. Current applications and perspectives of genomic selection in Bos indicus (Nellore) cattle. LIVESTOCK SCIENCE, v. 263, p. 15-pg., . (18/20026-8, 17/10630-2, 18/10109-3)
MAGALHAES MUNIZ, MARIA MALANE; SIMIELLI FONSECA, LARISSA FERNANDA; DOS SANTOS SILVA, DANIELLY BERALDO; BRAGA MAGALHAES, ANA FABRICIA; FERRO, JESUS APARECIDO; LOYOLA CHARDULO, LUIZ ARTUR; BALDI, FERNANDO; CANOVAS, ANGELA; DE ALBUQUERQUE, LUCIA GALVAO. Small genetic variation affecting mRNA isoforms associated with marbling and meat color in beef cattle. FUNCTIONAL & INTEGRATIVE GENOMICS, v. N/A, p. 16-pg., . (09/16118-5, 17/10630-2, 18/11154-2, 11/21241-0, 18/20026-8)
FERNANDES JUNIOR, GERARDO A.; CARVALHEIRO, ROBERTO; DE OLIVEIRA, HENRIQUE N.; SARGOLZAEI, MEHDI; COSTILLA, ROY; VENTURA, RICARDO V.; FONSECA, LARISSA F. S.; NEVES, HAROLDO H. R.; HAYES, BEN J.; DE ALBUQUERQUE, LUCIA G.. Imputation accuracy to whole-genome sequence in Nellore cattle. GENETICS SELECTION EVOLUTION, v. 53, n. 1, . (17/10630-2, 19/12434-1, 09/16118-5, 18/10109-3, 18/20026-8)
FERNANDES JUNIOR, GERARDO ALVES; DE OLIVEIRA, HENRIQUE NUNES; CARVALHEIRO, ROBERTO; CARDOSO, DIERCLES FRANCISCO; FONSECA, LARISSA FERNANDA SIMIELLI; VENTURA, RICARDO VIEIRA; DE ALBUQUERQUE, LUCIA GALVAO. Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus). SCIENTIFIC REPORTS, v. 10, n. 1, . (09/16118-5, 19/12434-1, 18/10109-3, 18/20026-8, 17/10630-2)
BENFICA, LORENA FERREIRA; SAKAMOTO, LEANDRO SANNOMIYA; BRAGA MAGALHAES, ANA FABRICIA; VARGAS DE OLIVEIRA, MATHEUS HENRIQUE; DE ALBUQUERQUE, LUCIA GALVAO; CAVALHEIRO, ROBERTO; BRANCO, RENATA HELENA; DOS SANTOS GONCALVES CYRILLO, JOSLAINE NOELY; ZERLOTTI MERCADANTE, MARIA EUGENIA. Genetic association among feeding behavior, feed efficiency, and growth traits in growing indicine cattle. JOURNAL OF ANIMAL SCIENCE, v. 98, n. 11, . (17/10630-2, 18/04313-7, 17/50339-5, 18/17313-5)
ALVES, JACKELINE SANTOS; DIAZ, IARA DEL PILAR SOLAR; DA CRUZ, VALDECY APARECIDA ROCHA; BASTOS, MARISA SILVA; DE OLIVEIRA, LOUISE SARMENTO MARTINS; DE ALBUQUERQUE, LUCIA GALVAO; DE CAMARGO, GREGORIO MIGUEL FERREIRA; COSTA, RAPHAEL BERMAL. The effect of mitochondrial DNA polymorphisms on cattle reproduction. MOLECULAR BIOLOGY REPORTS, v. 48, n. 1, . (18/20026-8, 17/10630-2, 09/16118-5)
CARVALHEIRO, ROBERTO; COSTILLA, ROY; NEVES, HAROLDO H. R.; ALBUQUERQUE, LUCIA G.; MOORE, STEPHEN; HAYES, BEN J.. Unraveling genetic sensitivity of beef cattle to environmental variation under tropical conditions. GENETICS SELECTION EVOLUTION, v. 51, . (17/18415-3, 17/10630-2)
NEVES, HAROLDO H. R.; VARGAS, GIOVANA; BRITO, LUIZ F.; SCHENKEL, FLAVIO S.; ALBUQUERQUE, LUCIA G.; CARVALHEIRO, ROBERTO. Genetic and genomic analyses of testicular hypoplasia in Nellore cattle. PLoS One, v. 14, n. 1, . (17/10630-2)
SOARES VALENTE, JULIA DE PAULA; DE-SOUSA, KAROLINI TENFFEN; DENIZ, MATHEUS; BONILHA, SARAH FIGUEIREDO MARTINS; MERCADANTE, MARIA EUGENIA ZERLOTTI; DIAS, LAILA TALARICO. Heritability and genetic association of social organization traits with feeding behavior, feed efficiency and growth in Bos indicus. APPLIED ANIMAL BEHAVIOUR SCIENCE, v. 265, p. 6-pg., . (17/50339-5, 17/10630-2)
VALENTE, JULIA DE PAULA SOARES; DENIZ, MATHEUS; DE SOUSA, KAROLINI TENFFEN; MERCADANTE, MARIA EUGENIA ZERLOTTI; DIAS, LAILA TALARICO; YILDIRIM, ARDA. socialh: An R package for determining the social hierarchy of animals using data from individual electronic bins. PLoS One, v. 17, n. 8, p. 15-pg., . (17/50339-5, 17/10630-2)
MAIORANO, AMANDA MARCHI; CARDOSO, DIERCLES FRANCISCO; CARVALHEIRO, ROBERTO; FERNANDES JUNIOR, GERARDO ALVES; DE ALBUQUERQUE, LUCIA GALVAO; DE OLIVEIRA, HENRIQUE NUNES. Signatures of selection in Nelore cattle revealed by whole-genome sequencing data. Genomics, v. 114, n. 2, p. 12-pg., . (17/10630-2, 09/16118-5)
BRAGA MAGALHAES, ANA FABRICIA; ZERLOTTI MERCADANTE, MARIA EUGENIA; DOS SANTOS SILVA, DANIELLY BERALDO; FERNANDES JUNIOR, GERARDO ALVES; HERRERA RIOS, ANA CRISTINA; MACEDO MOTA, LUCIO FLAVIO; ALBUQUERQUE, LUCIA GALVAO. Study of functional variants in homozygous islands in Nelore cattle. JOURNAL OF ANIMAL SCIENCE, v. 97, p. 2-pg., . (17/10630-2, 18/04313-7)
SILVA, THALES DE LIMA; GONDRO, CEDRIC; FONSECA, PABLO AUGUSTO DE SOUZA; DA SILVA, DELVAN ALVES; VARGAS, GIOVANA; NEVES, HAROLDO HENRIQUE DE REZENDE; FILHO, IVAN CARVALHO; TEIXEIRA, CAIO DE SOUZA; DE ALBUQUERQUE, LUCIA GALVAO; CARVALHEIRO, ROBERTO. Feet and legs malformation in Nellore cattle: genetic analysis and prioritization of GWAS results. FRONTIERS IN GENETICS, v. 14, p. 10-pg., . (18/20026-8, 17/10630-2)
FREZARIM, GABRIELA B.; FONSECA, LARISSA F. S.; SALATTA, BRUNA M.; SILVA, DANIELLY B. S.; BRESOLIN, TIAGO; SENO, LEONARDO DE OLIVEIRA; BARUFATTI, ALEXEIA; FERRO, JESUS APARECIDO; ALBUQUERQUE, LUCIA GALVAO. Genes and proteins associated with ribeye area and meat tenderness in a commercial Nellore cattle population. GENOME, v. 65, n. 4, p. 12-pg., . (18/20026-8, 17/10630-2, 16/23937-6)

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