Efficient computation of the genomic relationship matrix and other matrices used in single‐step evaluation
- 27 January 2011
- journal article
- research article
- Published by Wiley in Journal of Animal Breeding and Genetics
- Vol. 128 (6), 422-428
- https://doi.org/10.1111/j.1439-0388.2010.00912.x
Abstract
Genomic evaluations can be calculated using a unified procedure that combines phenotypic, pedigree and genomic information. Implementation of such a procedure requires the inverse of the relationship matrix based on pedigree and genomic relationships. The objective of this study was to investigate efficient computing options to create relationship matrices based on genomic markers and pedigree information as well as their inverses. SNP maker information was simulated for a panel of 40 K SNPs, with the number of genotyped animals up to 30 000. Matrix multiplication in the computation of the genomic relationship was by a simple ‘do’ loop, by two optimized versions of the loop, and by a specific matrix multiplication subroutine. Inversion was by a generalized inverse algorithm and by a LAPACK subroutine. With the most efficient choices and parallel processing, creation of matrices for 30 000 animals would take a few hours. Matrices required to implement a unified approach can be computed efficiently. Optimizations can be either by modifications of existing code or by the use of efficient automatic optimizations provided by open source or third-party libraries.Keywords
This publication has 15 references indexed in Scilit:
- Variance component model to account for sample structure in genome-wide association studiesNature Genetics, 2010
- Hot topic: A unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final scoreJournal of Dairy Science, 2010
- Genomic prediction when some animals are not genotypedGenetics Selection Evolution, 2010
- Population Structure and Cryptic Relatedness in Genetic Association StudiesStatistical Science, 2009
- A relationship matrix including full pedigree and genomic informationJournal of Dairy Science, 2009
- Invited review: Genomic selection in dairy cattle: Progress and challengesJournal of Dairy Science, 2009
- An indirect approach to the extensive calculation of relationship coefficientsGenetics Selection Evolution, 2002
- A set of level 3 basic linear algebra subprogramsACM Transactions on Mathematical Software, 1990
- An extended set of FORTRAN basic linear algebra subprogramsACM Transactions on Mathematical Software, 1988
- SYSTEMATIC PROCEDURES FOR CALCULATING INBREEDING COEFFICIENTSJournal of Heredity, 1949