Snp_blup_rel: software for calculating individual animal SNP-BLUP model reliabilities

Authors

  • Hafedh Ben Zaabza Natural Resources Institute Finland (Luke)
  • Esa A. Mäntysaari Natural Resources Institute Finland (Luke)
  • Ismo Strandén Natural Resources Institute Finland (Luke)

DOI:

https://doi.org/10.23986/afsci.95617

Keywords:

genomic evaluation, model reliability, SNP markers

Abstract

The snp_blup_rel program computes model reliabilities for genomic breeding values. The program assumes a single trait SNP-BLUP model where the breeding value can include a residual polygenic (RPG) effect. The reliability calculation requires elements of the inverse of the mixed model equations (MME). The calculation has three steps: 1) MME calculation, 2) MME coefficient matrix inversion, and 3) reliability computation. When needed, the inverted matrix can be saved after step 2. Step 3 can be used separately to new genotypes which do not contribute information to Step 2. When an RPG effect is included, an approximate method based on Monte Carlo sampling is applied. This reduces the MME matrix size and allows including many genotyped individuals. The program is written in Fortran 90/95, and uses LAPACK subroutines which enable multi-threaded parallel computing. The program is efficient in terms of computing time and memory requirements, and can be used to analyze even large genomic data. Thus, the program can be used in calculating model reliabilities for large national genomic evaluations.

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Published

2020-09-21

Issue

Vol. 29 No. 4 (2020)

Section

Articles

License

Copyright (c) 2020 Agricultural and Food Science

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How to Cite

Ben Zaabza, H., Mäntysaari, E. A. ., & Strandén, I. . (2020). Snp_blup_rel: software for calculating individual animal SNP-BLUP model reliabilities. Agricultural and Food Science, 29(4), 297–306. https://doi.org/10.23986/afsci.95617
Received 2020-06-11
Accepted 2020-09-01
Published 2020-09-21