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

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

Vandenplas, Jérémie (Wageningen University & Research)
Calus, Mario P.L. (Wageningen University & Research)
Eding, Herwin (CRV BV)
van Pelt, Mathijs (CRV BV)
Bergsma, Rob (Topigs Norsvin)
Vuik, Cornelis (TU Delft Numerical Analysis)

2021

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.

http://resolver.tudelft.nl/uuid:7ce279bb-d660-4255-93d9-29fbbbe316b2

https://doi.org/10.1186/s12711-021-00626-1

1297-9686

Genetics Selection Evolution, 53 (1), 1-15

Institutional Repository

journal article

© 2021 Jérémie Vandenplas, Mario P.L. Calus, Herwin Eding, Mathijs van Pelt, Rob Bergsma, Cornelis Vuik