Multi-user equipment approved in grant 2017/10630-2: server

• Grant number: 18/20026-8
• Support Opportunities: Multi-user Equipment Program
• Start date: November 01, 2018
• End date: October 31, 2025
• 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
• Associated research grant: 17/10630-2 - Genetic aspects of meat production quality, efficiency and sustainability in Nelore breed animals, AP.TEM
• EMU web page: http://www.fcav.unesp.br/#!/servicos/equipamentos-multiusuarios/servidor-multiusuario-para-analise-da-dados/
• Type of equipment: Infraestrutura - Tecnologia da Informação - Servidores
• Manufacturer: Intel
• Model: 80 processadores

Abstract

Multi-user equipment approved in grant 2017/10630-2: Server. Abstract of thematic project. 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)

Scientific publications

(17)

(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)

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, NOV 2020. (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, MAY 2021. (17/10630-2, 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., 2022-05-01. (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, MAR 2021. (18/20026-8, 11/21241-0, 18/11154-2, 09/16118-5, 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., 2022-03-25. (18/11154-2, 18/20026-8, 09/16118-5, 17/10630-2, 11/21241-0)

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, SEP 7 2020. (17/10630-2, 15/16850-9, 09/16118-5, 16/22894-1, 18/20026-8)

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., 2022-05-18. (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., 2022-09-01. (18/20026-8, 17/10630-2, 18/10109-3)

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., 2022-10-01. (18/20026-8, 19/06361-1, 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., 2023-02-01. (18/20026-8, 09/16118-5, 17/10630-2)

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., 2020-11-01. (18/11154-2, 11/21241-0, 09/16118-5, 18/20026-8, 17/10630-2)

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, JAN 2021. (18/20026-8, 17/10630-2, 09/16118-5)

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, JUN 10 2020. (09/16118-5, 19/12434-1, 18/10109-3, 18/20026-8, 17/10630-2)

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., 2022-03-19. (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, MAR 12 2021. (17/10630-2, 19/12434-1, 09/16118-5, 18/10109-3, 18/20026-8)

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., 2022-04-01. (18/20026-8, 17/10630-2, 16/23937-6)

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., 2023-08-16. (18/20026-8, 17/10630-2)