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

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Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.creatorGouveia Pimentel, Eduardo da Cruz-
Autor(es): dc.creatorSargolzaei, Mehdi-
Autor(es): dc.creatorSimianer, Henner-
Autor(es): dc.creatorSchenkel, Flavio Schramm-
Autor(es): dc.creatorLiu, Zengting-
Autor(es): dc.creatorFries, Luiz Alberto-
Autor(es): dc.creatorde Queiroz, Sandra Aidar-
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Descrição: dc.descriptionBundesministerium für Bildung und Forschung (BMBF)-
Descrição: dc.descriptionForderverein Biotechnologieforschung e.V.-
Descrição: dc.descriptionBonn-
Descrição: dc.descriptionLohmann Tierzucht GmbH, Cuxhaven-
Descrição: dc.descriptionCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)-
Descrição: dc.descriptionThe 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.-
Formato: dc.format198-204-
Idioma: dc.languageen-
Publicador: dc.publisherSoc Brasil Genetica-
Relação: dc.relationGenetics and Molecular Biology-
Relação: dc.relation1.493-
Relação: dc.relation0,638-
Direitos: dc.rightsopenAccess-
Palavras-chave: dc.subjectBreeding value-
Palavras-chave: dc.subjectgenomic selection-
Palavras-chave: dc.subjectmixed model equations-
Palavras-chave: dc.subjectNumerical method-
Título: dc.titleUse of direct and iterative solvers for estimation of SNP effects in genome-wide selection-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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