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Ridge, Lasso and Bayesian additive-dominance genomic models.
Azevedo, Camila Ferreira; de Resende, Marcos Deon Vilela; E Silva, Fabyano Fonseca; Viana, José Marcelo Soriano; Valente, Magno Sávio Ferreira; Resende, Márcio Fernando Ribeiro; Muñoz, Patricio.
Afiliação
  • Azevedo CF; Department of Statistics, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. camila.azevedo@ufv.br.
  • de Resende MD; Department of Statistics, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. marcos.deon@gmail.com.
  • E Silva FF; Embrapa Forestry, Colombo, Paraná, Brazil. marcos.deon@gmail.com.
  • Viana JM; Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. fabyanofonseca@ufv.br.
  • Valente MS; Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. jmsviana@ufv.br.
  • Resende MF; Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. magnosavio@yahoo.com.br.
  • Muñoz P; RAPiD Genomics, Florida Innovation Hub, Gainesville, Florida, USA. mresende@rapid-genomics.com.
BMC Genet ; 16: 105, 2015 Aug 25.
Article em En | MEDLINE | ID: mdl-26303864
BACKGROUND: A complete approach for genome-wide selection (GWS) involves reliable statistical genetics models and methods. Reports on this topic are common for additive genetic models but not for additive-dominance models. The objective of this paper was (i) to compare the performance of 10 additive-dominance predictive models (including current models and proposed modifications), fitted using Bayesian, Lasso and Ridge regression approaches; and (ii) to decompose genomic heritability and accuracy in terms of three quantitative genetic information sources, namely, linkage disequilibrium (LD), co-segregation (CS) and pedigree relationships or family structure (PR). The simulation study considered two broad sense heritability levels (0.30 and 0.50, associated with narrow sense heritabilities of 0.20 and 0.35, respectively) and two genetic architectures for traits (the first consisting of small gene effects and the second consisting of a mixed inheritance model with five major genes). RESULTS: G-REML/G-BLUP and a modified Bayesian/Lasso (called BayesA*B* or t-BLASSO) method performed best in the prediction of genomic breeding as well as the total genotypic values of individuals in all four scenarios (two heritabilities x two genetic architectures). The BayesA*B*-type method showed a better ability to recover the dominance variance/additive variance ratio. Decomposition of genomic heritability and accuracy revealed the following descending importance order of information: LD, CS and PR not captured by markers, the last two being very close. CONCLUSIONS: Amongst the 10 models/methods evaluated, the G-BLUP, BAYESA*B* (-2,8) and BAYESA*B* (4,6) methods presented the best results and were found to be adequate for accurately predicting genomic breeding and total genotypic values as well as for estimating additive and dominance in additive-dominance genomic models.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Modelos Estatísticos / Genes Dominantes / Modelos Genéticos Tipo de estudo: Prognostic_studies / Risk_factors_studies Idioma: En Revista: BMC Genet Assunto da revista: BIOLOGIA MOLECULAR / BIOTECNOLOGIA Ano de publicação: 2015 Tipo de documento: Article País de afiliação: Brasil País de publicação: Reino Unido

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Modelos Estatísticos / Genes Dominantes / Modelos Genéticos Tipo de estudo: Prognostic_studies / Risk_factors_studies Idioma: En Revista: BMC Genet Assunto da revista: BIOLOGIA MOLECULAR / BIOTECNOLOGIA Ano de publicação: 2015 Tipo de documento: Article País de afiliação: Brasil País de publicação: Reino Unido