Genomic growth curves of an outbred pig population

Fabyano Fonseca e Silva, Marcos Deon V. de Resende, Gilson Silvério Rocha, Darlene Ana S. Duarte, Paulo Sávio Lopes, Otávio J.B. Brustolini, Sander Thus, José Marcelo S. Viana, Simone E.F. Guimarães

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13 Citations (Scopus)

Abstract

In the current post-genomic era, the genetic basis of pig growth can be understood by assessing SNP marker effects and genomic breeding values (GEBV) based on estimates of these growth curve parameters as phenotypes. Although various statistical methods, such as random regression (RR-BLUP) and Bayesian LASSO (BL), have been applied to genomic selection (GS), none of these has yet been used in a growth curve approach. In this work, we compared the accuracies of RR-BLUP and BL using empirical weight-age data from an outbred F2 (Brazilian Piau X commercial) population. The phenotypes were determined by parameter estimates using a nonlinear logistic regression model and the halothane gene was considered as a marker for evaluating the assumptions of the GS methods in relation to the genetic variation explained by each locus. BL yielded more accurate values for all of the phenotypes evaluated and was used to estimate SNP effects and GEBV vectors. The latter allowed the construction of genomic growth curves, which showed substantial genetic discrimination among animals in the final growth phase. The SNP effect estimates allowed identification of the most relevant markers for each phenotype, the positions of which were coincident with reported QTL regions for growth traits.

Original languageEnglish
Pages (from-to)520-527
JournalGenetics and Molecular Biology
Volume36
Issue number4
DOIs
Publication statusPublished - 19 Dec 2013

Keywords

  • Bayesian LASSO
  • Nonlinear regression
  • SNP effects

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    Fonseca e Silva, F., de Resende, M. D. V., Rocha, G. S., Duarte, D. A. S., Lopes, P. S., Brustolini, O. J. B., Thus, S., Viana, J. M. S., & Guimarães, S. E. F. (2013). Genomic growth curves of an outbred pig population. Genetics and Molecular Biology, 36(4), 520-527. https://doi.org/10.1590/S1415-47572013005000042