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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Accuracy of genomic predictions in Bos indicus (Nellore) cattle

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Author(s):
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Neves, Haroldo H. R. [1] ; Carvalheiro, Roberto [1, 2] ; Perez O'Brien, Ana M. [3] ; Utsunomiya, Yuri T. [1] ; do Carmo, Adriana S. [1] ; Schenkel, Flavio S. [4] ; Soelkner, Johann [3] ; McEwan, John C. [5] ; Van Tassell, Curtis P. [6] ; Cole, John B. [7] ; da Silva, Marcos V. G. B. [8] ; Queiroz, Sandra A. [1] ; Sonstegard, Tad S. [6] ; Garcia, Jose Fernando [9]
Total Authors: 14
Affiliation:
[1] Univ Estadual Paulista, UNESP, Fac Ciencias Agr & Vet, BR-14884900 Sao Paulo - Brazil
[2] GenSys Consultores Assoc SC Ltda, BR-90680000 Porto Alegre, RS - Brazil
[3] Univ Nat Resources & Life Sci, Div Livestock Sci, Dept Sustainable Agr Syst BOKU, A-1180 Vienna - Austria
[4] Univ Guelph, Ctr Genet Improvement Livestock, Guelph, ON N1G 2W1 - Canada
[5] AgResearch, Ctr Reprod & Genom, Invermay, Mosgiel - New Zealand
[6] ARS, USDA, Bovine Funct Genom Lab, Beltsville, MD 20705 - USA
[7] ARS, Anim Improvement Programs Lab, USDA, Beltsville, MD 20705 - USA
[8] Embrapa DairyCattle, Bioinformat & Anim Genom Lab, Juiz De Fora, MG - Brazil
[9] Univ Estadual Paulista, UNESP, Fac Med Vet Aracatuba, BR-16050680 Sao Paulo - Brazil
Total Affiliations: 9
Document type: Journal article
Source: GENETICS SELECTION EVOLUTION; v. 46, FEB 27 2014.
Web of Science Citations: 39
Abstract

Background: Nellore cattle play an important role in beef production in tropical systems and there is great interest in determining if genomic selection can contribute to accelerate genetic improvement of production and fertility in this breed. We present the first results of the implementation of genomic prediction in a Bos indicus (Nellore) population. Methods: Influential bulls were genotyped with the Illumina Bovine HD chip in order to assess genomic predictive ability for weight and carcass traits, gestation length, scrotal circumference and two selection indices. 685 samples and 320 238 single nucleotide polymorphisms (SNPs) were used in the analyses. A forward-prediction scheme was adopted to predict the genomic breeding values (DGV). In the training step, the estimated breeding values (EBV) of bulls were deregressed (dEBV) and used as pseudo-phenotypes to estimate marker effects using four methods: genomic BLUP with or without a residual polygenic effect (GBLUP20 and GBLUP0, respectively), a mixture model (Bayes C) and Bayesian LASSO (BLASSO). Empirical accuracies of the resulting genomic predictions were assessed based on the correlation between DGV and dEBV for the testing group. Results: Accuracies of genomic predictions ranged from 0.17 (navel at weaning) to 0.74 (finishing precocity). Across traits, Bayesian regression models (Bayes C and BLASSO) were more accurate than GBLUP. The average empirical accuracies were 0.39 (GBLUP0), 0.40 (GBLUP20) and 0.44 (Bayes C and BLASSO). Bayes C and BLASSO tended to produce deflated predictions (i. e. slope of the regression of dEBV on DGV greater than 1). Further analyses suggested that higher-than-expected accuracies were observed for traits for which EBV means differed significantly between two breeding subgroups that were identified in a principal component analysis based on genomic relationships. Conclusions: Bayesian regression models are of interest for future applications of genomic selection in this population, but further improvements are needed to reduce deflation of their predictions. Recurrent updates of the training population would be required to enable accurate prediction of the genetic merit of young animals. The technical feasibility of applying genomic prediction in a Bos indicus (Nellore) population was demonstrated. Further research is needed to permit cost-effective selection decisions using genomic information. (AU)

FAPESP's process: 10/52030-2 - Genome wide association study for reproductive traits in zebu bulls (Bos indicus) using high-density SNP chip
Grantee:José Fernando Garcia
Support Opportunities: Regular Research Grants
FAPESP's process: 11/16643-2 - Genome-wide association study for detection of chromosomal regions related to scrotal circumference in Nellore cattle
Grantee:Yuri Tani Utsunomiya
Support Opportunities: Scholarships in Brazil - Master
FAPESP's process: 10/06185-4 - Strategies to improve efficiency of genomic selection in animal breeding programs
Grantee:Haroldo Henrique de Rezende Neves
Support Opportunities: Scholarships in Brazil - Doctorate