Prediction of breeding values in a experimental mice population using selective genotyping

• Grant number: 13/20091-0
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: February 01, 2014
• End date: November 04, 2017
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Danísio Prado Munari
• Grantee: Rodrigo Pelicioni Savegnago
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil

Abstract

Generally only few animals from a reference population are genotyped due to the high costs of genotyping. The aim of this research will be to evaluate which animals must be genotyped in order to get the best predictions of the genetic merit using genome-enabled prediction models. The public data from a heterogeneous population of mice will be used in this study. Public data sets of genotyped animals allows to carried out this kind of study without cost of genotyping. The data set will be divided randomly in 70% to train the models and 30% to validate them. Six selective genotyping strategies will be used: (1) 40% of the animals from the training population will be chosen at random (it will be used as a control case to compare the prediction of genetic merit with other strategies); (2) 40% of the animals with the greatest breeding values obtained by pedigree-based model via BLUP; (3) 40% of the animals with the lowest breeding values obtained by pedigree-based model via BLUP; (4) 20% of the animals with the greatest breeding values and 20% with the lowest breeding values (extremes of the population); (5) 40% of the less related animals and (6) 40% of the most related animals. These strategies will be evaluated for the body mass index (BMI, h2=0.13) and total cholesterol (CHOL, h2=0.38). The Bayesian Lasso and GBLUP will be used to predict the genetic merit of the animals. Accuracy of predictions will be assessed using Pearson's correlation between predictions and observations of genetic merits for each studied trait.

Scientific publications

(15)

(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)

NICOLE COLUCCI TRAMONTE; NATALIA VINHAL GRUPIONI; NEDENIA BONVINO STAFUZZA; DIEGO GOMES FREIRE GUIDOLIN; RODRIGO PELICIONI SAVEGNAGO; LUIZ ANTONIO FRAMARTINO BEZERRA; RAYSILDO BARBOSA LÔBO; DANÍSIO PRADO MUNARI. Genetic parameters, genetic trends, and principal component analysis for productive and reproductive traits of Guzera beef cattle. REVISTA BRASILEIRA DE ZOOTECNIA-BRAZILIAN JOURNAL OF ANIMAL SCIENCE, v. 48, 2019-09-12. (13/20091-0, 11/07124-1)

HEVERTON LUIS MOREIRA; RODRIGO PELICIONI SAVEGNAGO; LUARA AFONSO DE FREITAS; RAYSILDO BARBOSA LÔBO; LUIZ ANTONIO FRAMARTINO BEZERRA; CLAUDIA CRISTINA PARO DE PAZ. Breeding goals and economic values for Nellore cattle in a full-cycle production system. Acta Sci., Anim. Sci., v. 41, 2019-02-25. (13/20091-0, 16/10583-1)

SAVEGNAGO, RODRIGO PELICIONI; DO NASCIMENTO, GUILHERME BATISTA; DE MAGALHAES ROSA, GUILHERME JORDAO; RESENDE DE CARNEIRO, RAUL LARA; SESANA, ROBERTA CRISTINA; EL FARO, LENIRA; MUNARI, DANISIO PRADO. Cluster analyses to explore the genetic curve pattern for milk yield of Holstein. LIVESTOCK SCIENCE, v. 183, p. 28-32, JAN 2016. (12/16087-5, 13/20091-0, 10/05148-8, 12/23384-6)

RAMOS, S. B.; CAETANO, S. L.; ROSA, G. J. M.; SAVEGNAGO, R. P.; KERN, E. L.; BERNANRDES, P. A.; LOBO, R. B.; MUNARI, D. P.. Estimation of genetic parameters for cow age at last calving under different censorship criteria. LIVESTOCK SCIENCE, v. 208, p. 40-43, FEB 2018. (15/25096-6, 13/20091-0, 10/05903-0)

OLIVEIRA, ELISA JUNQUEIRA; SAVEGNAGO, RODRIGO PELICIONI; DE FREITAS, LUARA AFONSO; FREITASO, ANIELLY PAULA; MAIA, SUELLEN RODRIGUES; SIMILI, FLAVIA FERNANDA; EL FARO, LENIRA; DIAS DA COSTA, RICARDO LOPES; SANTANA JUNIOR, MARIO LUIZ; PARO DE RAZ, CLAUDIA CRISTINA. Estimativas de parâmetros genéticos e análise de agrupamento para resistência e resiliência à verminose em ovinos de corte Santa Inês. Pesquisa Agropecuária Brasileira, v. 53, n. 12, p. 1338-1345, DEC 2018. (16/10583-1, 13/20091-0, 12/15982-0)

BUZANSKAS, M. E.; PIRES, P. S.; CHUD, T. C. S.; BERNARDES, P. A.; ROLA, L. D.; SAVEGNAGO, R. P.; LOBO, R. B.; MUNARI, D. P.. Parameter estimates for reproductive and carcass traits in Nelore beef cattle. Theriogenology, v. 92, p. 204-209, APR 1 2017. (13/20091-0, 15/08939-0, 13/13972-0, 13/19335-2, 15/25096-6)

BERNARDES, P. A.; GROSSI, D. A.; SAVEGNAGO, R. P.; BUZANSKAS, M. E.; RAMOS, S. B.; ROMANZINI, E. P.; GUIDOLIN, D. G. F.; BEZERRA, L. A. F.; LOBO, R. B.; MUNARI, D. P.. Population structure of Tabapua beef cattle using pedigree analysis. LIVESTOCK SCIENCE, v. 187, p. 96-101, MAY 2016. (13/09364-5, 13/20091-0, 13/19335-2)

CAETANO, SABRINA L.; ROSA, GUILHERME J. M.; SAVEGNAGO, RODRIGO P.. Estimation of genetic parameters for longevity considering the cow's age at last calving. JOURNAL OF APPLIED GENETICS, v. 58, n. 1, p. 103-109, FEB 2017. (13/09364-5, 13/20091-0, 10/05903-0)

DE FREITAS, LUARA AFONSO; SAVEGNAGO, RODRIGO PELICIONI; GRUPIONI, NATALIA VINHAL; RAMOS, SALVADOR BOCCALETTI; STAFUZZA, NEDENIA BONVINO; PEREIRA DE FIGUEIREDO, ELSIO ANTONIO; SCHMIDT, GILBERTO SILBER; LEDUR, MONICA CORREA; MUNARI, DANISIO PRADO. Reduced-rank estimation of genetic parameters for egg production traits and cluster analyses with predicted breeding values. ACTA AGRICULTURAE SCANDINAVICA SECTION A-ANIMAL SCIENCE, v. 68, n. 2, p. 81-86, APR 3 2018. (12/16087-5, 16/10583-1, 13/20091-0)

JOAQUIM, LETICIA BORGES; SELEGUIM CHUD, TATIANE CRISTINA; PETROLI MARCHESI, JORGE AUGUSTO; SAVEGNAGO, RODRIGO PELICIONI; BUZANSKAS, MARCOS ELI; ZANELLA, RICARDO; CANTAO, MAURICIO EGIDIO; PEIXOTO, JANE OLIVEIRA; LEDUR, MONICA CORREA; IRGANG, RENATO; et al. Genomic structure of a crossbred Landrace pig population. PLoS One, v. 14, n. 2, FEB 28 2019. (15/08939-0, 13/20091-0)

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)

BERNARDES, P. A.; GROSSI, D. A.; SAVEGNAGO, R. P.; BUZANSKAS, M. E.; URBINATI, I.; BEZERRA, L. A. F.; LOBO, R. B.; MUNARI, D. P.. Estimates of genetic parameters and genetic trends for reproductive traits and weaning weight in Tabapua cattle. JOURNAL OF ANIMAL SCIENCE, v. 93, n. 11, p. 5175-5185, NOV 2015. (13/09050-0, 13/09364-5, 13/20091-0, 13/19335-2)

NASCIMENTO, G. B.; SAVEGNAGO, R. P.; CHUD, T. C. S.; LEDUR, M. C.; FIGUEIREDO, E. A. P.; MUNARI, D. P.. Genetic parameter estimates and principal component analysis on performance and carcass traits of a terminal pig sire line. ACTA AGRICULTURAE SCANDINAVICA SECTION A-ANIMAL SCIENCE, v. 64, n. 3, p. 137-144, JUL 3 2014. (13/20091-0, 10/05148-8, 12/23384-6, 11/06911-0)

MONTEIRO GAMA, MANUELA PIRES; SAVEGNAGO, RODRIGO PELICIONI; VENTURA, HENRIQUE TORRES; PEREIRA, MARIANA ALENCAR; FREITAS, LUARA AFONSO; PARO PAZ, CLAUDIA CRISTINA; EL FARO, LENIRA. stimates of genetic parameters, principal components and cluster analysis for milk yield and body weight in Guzera cattl. ANIMAL PRODUCTION SCIENCE, v. 62, n. 3, NOV 2021. (18/01540-2, 13/20091-0)

TRAMONTE, NICOLE COLUCCI; GRUPIONI, NATALIA VINHAL; STAFUZZA, NEDENIA BONVINO; FREIRE GUIDOLIN, DIEGO GOMES; SAVEGNAGO, RODRIGO PELICIONI; FRAMARTINO BEZERRA, LUIZ ANTONIO; LOBO, RAYSILDO BARBOSA; MUNARI, DANISIO PRADO. Genetic parameters, genetic trends, and principal component analysis for productive and reproductive traits of Guzera beef cattle. REVISTA BRASILEIRA DE ZOOTECNIA-BRAZILIAN JOURNAL OF ANIMAL SCIENCE, v. 48, p. 11-pg., 2019-01-01. (11/07124-1, 13/20091-0)