Impact of genomic preselection on subsequent genetic evaluations with ssGBLUP using real data from pigs

Jibrila, Ibrahim; Vandenplas, Jeremie; ten Napel, Jan; Bergsma, Rob; Veerkamp, Roel F.; Calus, Mario P. L.

doi:10.1186/s12711-022-00727-5

Genetics Selection Evolution

Table 6 Performance of PBLUP^a in the subsequent evaluations in the dam line (SE in brackets)

From: Impact of genomic preselection on subsequent genetic evaluations with ssGBLUP using real data from pigs

Measure/preselection scenario	With records on animals in the validation generation			Without records on animals in the validation generation
Measure/preselection scenario	Reference^b	VGP^c	MGP^d	Reference	VGP	MGP
Average daily gain during performance testing, size of validation population = 2323
Estimated heritability	0.31 (0.01)	0.32 (0.01)	0.40 (0.02)	0.30 (0.01)	0.30 (0.01)	0.38 (0.02)
Validation accuracy^e	0.35 (0.02)	0.30 (0.02)	0.30 (0.02)	0.24 (0.02)	0.24 (0.02)	0.21 (0.02)
Level bias^f	− 0.04 (0.02)	− 0.16 (0.02)	0.01 (0.02)	0.08 (0.02)	0.08 (0.02)	0.13 (0.02)
Dispersion bias^g	0.52 (0.03)	0.45 (0.03)	0.42 (0.03)	0.50 (0.04)	0.50 (0.04)	0.45 (0.04)
Average daily gain throughout life, size of validation population = 2405
Estimated heritability	0.31 (0.01)	0.33 (0.01)	0.43 (0.02)	0.31 (0.01)	0.31 (0.01)	0.44 (0.02)
Validation accuracy	0.48 (0.01)	0.43 (0.02)	0.43 (0.02)	0.34 (0.02)	0.34 (0.02)	0.31 (0.02)
Level bias	− 0.05 (0.01)	− 0.18 (0.01)	− 0.03 (0.01)	0.05 (0.02)	0.05 (0.02)	0.07 (0.01)
Dispersion bias	0.51 (0.02)	0.47 (0.02)	0.44 (0.02)	0.51 (0.03)	0.51 (0.03)	0.44 (0.03)
Backfat thickness thickness, size of validation population = 2312
Estimated heritability	0.51 (0.01)	0.51 (0.01)	0.51 (0.02)	0.51 (0.01)	0.51 (0.01)	0.53 (0.02)
Validation accuracy	0.52 (0.02)	0.50 (0.02)	0.50 (0.02)	0.37 (0.02)	0.37 (0.02)	0.36 (0.02)
Level bias	0.02 (0.01)	0.00 (0.01)	− 0.03 (0.01)	0.04 (0.01)	0.04 (0.01)	0.00 (0.01)
Dispersion bias	0.45 (0.02)	0.43 (0.02)	0.42 (0.02)	0.41 (0.02)	0.41 (0.02)	0.39 (0.02)
Loin depth, size of validation population = 1164
Estimated heritability	0.50 (0.01)	0.50 (0.01)	0.55 (0.02)	0.49 (0.01)	0.49 (0.01)	0.53 (0.02)
Validation accuracy	0.58 (0.02)	0.56 (0.02)	0.56 (0.02)	0.43 (0.02)	0.43 (0.02)	0.41 (0.02)
Level bias	0.00 (0.02)	− 0.01 (0.02)	0.04 (0.02)	− 0.02 (0.02)	− 0.02 (0.02)	0.04 (0.02)
Dispersion bias	0.55 (0.02)	0.54 (0.02)	0.51 (0.02)	0.57 (0.03)	0.57 (0.03)	0.52 (0.03)

^aPedigree-based best linear unbiased prediction
^bIn the reference scenario, the subsequent PBLUP evaluation utilized the entire available data until the validation generation
^cValidation generation preselection (VGP) scenario, in which all animals in the validation generation without progeny in the data were discarded
^dMulti-generation preselection (MGP) scenario, in which all animals in the validation and training generations without progeny in the data were discarded
^eValidation accuracy was computed as weighted Pearson’s correlation coefficient between progeny yield deviation and estimated breeding value of all validation animals
^fLevel bias was computed as the weighted mean difference between progeny yield deviation and half of the estimated breeding value across all validation animals, expressed in additive genetic standard deviation units of the trait
^gDispersion bias was measured by the weighted regression coefficient of progeny yield deviation on estimated breeding value of all validation animals

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ISSN: 1297-9686

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