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Table 3 Comparison of computational feasibility of four methods from the two equivalent models with haplotypes and SNPs for GBLUP and GREML

From: Multi-allelic haplotype model based on genetic partition for genomic prediction and variance component estimation using SNP markers

   Method of for calculating GBLUP
  Conditional expectation (CE) Mixed model equations (MME)
Model I, Eqs. 36 and 37 Largest matrix to invert V, phenotypic variance-covariance matrix C, coefficient matrix of MME
Size of largest matrix to invert q × q, assuming one observation per individual c + 2q for C
Largest matrix to store in memory q × q P matrix c + 2q for C
Applicable to singular genomic relationship matrices Yes, inverse relationship matrices avoided No, inverse relationship matrices required
Model II, Eqs. 38 and 39 Largest matrix to invert V, phenotypic variance-covariance matrix C, coefficient matrix of MME
Size of largest matrix to invert q × q, assuming one observation per individual c + nα + nδ for C
Largest matrix to store in memory q × nα and q × nδ T matrices, q × q P matrix c + nα + nδ for C
Applicable to singular genomic relationship matrices Yes, inverse relationship matrices avoided Yes, inverse relationship matrices avoided
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BMC Genomic Data

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