Use of direct and iterative solvers for estimation of SNP effects in genome-wide selection

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Data

2010-01-01

Autores

Gouveia Pimentel, Eduardo da Cruz [UNESP]
Sargolzaei, Mehdi
Simianer, Henner
Schenkel, Flavio Schramm
Liu, Zengting
Fries, Luiz Alberto
de Queiroz, Sandra Aidar [UNESP]

Título da Revista

ISSN da Revista

Título de Volume

Editor

Soc Brasil Genetica

Resumo

The aim of this study was to compare iterative and direct solvers for estimation of marker effects in genomic selection. One iterative and two direct methods were used: Gauss-Seidel with Residual Update, Cholesky Decomposition and Gentleman-Givens rotations. For resembling different scenarios with respect to number of markers and of genotyped animals, a simulated data set divided into 25 subsets was used. Number of markers ranged from 1,200 to 5,925 and number of animals ranged from 1,200 to 5,865. Methods were also applied to real data comprising 3081 individuals genotyped for 45181 SNPs. Results from simulated data showed that the iterative solver was substantially faster than direct methods for larger numbers of markers. Use of a direct solver may allow for computing (co)variances of SNP effects. When applied to real data, performance of the iterative method varied substantially, depending on the level of ill-conditioning of the coefficient matrix. From results with real data, Gentleman-Givens rotations would be the method of choice in this particular application as it provided an exact solution within a fairly reasonable time frame (less than two hours). It would indeed be the preferred method whenever computer resources allow its use.

Descrição

Palavras-chave

Breeding value, genomic selection, mixed model equations, Numerical method

Como citar

Genetics and Molecular Biology. Ribeirao Pret: Soc Brasil Genetica, v. 33, n. 1, p. 198-204, 2010.