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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