Convergence behavior of single-step GBLUP and SNPBLUP for different termination criteria

Autor: R. Bergsma, Jérémie Vandenplas, Mario P. L. Calus, Herwin Eding, Cornelis Vuik, Mathijs van Pelt
Přispěvatelé: Wageningen University and Research [Wageningen] (WUR), Delft University of Technology (TU Delft)
Jazyk: angličtina
Rok vydání: 2021
Předmět:
0301 basic medicine
lcsh:QH426-470
Biology
Best linear unbiased prediction
Animal Breeding and Genomics
Breeding
Residual
System of linear equations
Polymorphism
Single Nucleotide
03 medical and health sciences
Approximation error
Conjugate gradient method
Convergence (routing)
Genetics
Life Science
Applied mathematics
Animals
Fokkerij en Genomica
Fokkerij & Genomica
Ecology
Evolution
Behavior and Systematics
lcsh:SF1-1100
Models
Genetic
Preconditioner
0402 animal and dairy science
04 agricultural and veterinary sciences
General Medicine
040201 dairy & animal science
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
lcsh:Genetics
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics
030104 developmental biology
Iterated function
WIAS
Animal Science and Zoology
Cattle
lcsh:Animal culture
Animal Breeding & Genomics
Research Article
Genome-Wide Association Study
Zdroj: Genetics, Selection, Evolution : GSE
Genetics Selection Evolution
Genetics Selection Evolution, BioMed Central, 2021, 53 (1), pp.34. ⟨10.1186/s12711-021-00626-1⟩
Genetics Selection Evolution, 53(1)
Genetics Selection Evolution, Vol 53, Iss 1, Pp 1-15 (2021)
Genetics Selection Evolution 53 (2021) 1
ISSN: 1297-9686
0999-193X
Popis: Background The preconditioned conjugate gradient (PCG) method is the current method of choice for iterative solving of genetic evaluations. The relative difference between two successive iterates and the relative residual of the system of equations are usually chosen as a termination criterion for the PCG method in animal breeding. However, our initial analyses showed that these two commonly used termination criteria may report that a PCG method applied to a single-step single nucleotide polymorphism best linear unbiased prediction (ssSNPBLUP) is not converged yet, whereas the solutions are accurate enough for practical use. Therefore, the aim of this study was to propose two termination criteria that have been (partly) developed in other fields, but are new in animal breeding, and to compare their behavior to that of the two termination criteria widely used in animal breeding for the PCG method applied to ssSNPBLUP. The convergence patterns of ssSNPBLUP were also compared to the convergence patterns of single-step genomic BLUP (ssGBLUP). Results Building upon previous work, we propose two termination criteria that take the properties of the system of equations into account. These two termination criteria are directly related to the relative error of the iterates with respect to the true solutions. Based on pig and dairy cattle datasets, we show that the preconditioned coefficient matrices of ssSNPBLUP and ssGBLUP have similar properties when using a second-level preconditioner for ssSNPBLUP. Therefore, the PCG method applied to ssSNPBLUP and ssGBLUP converged similarly based on the relative error of the iterates with respect to the true solutions. This similar convergence behavior between ssSNPBLUP and ssGBLUP was observed for both proposed termination criteria. This was, however, not the case for the termination criterion defined as the relative residual when applied to the dairy cattle evaluations. Conclusion Our results showed that the PCG method can converge similarly when applied to ssSNPBLUP and to ssGBLUP. The two proposed termination criteria always depicted these similar convergence behaviors, and we recommend them for comparing convergence properties of different models and for routine evaluations.
Databáze: OpenAIRE
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