Estimation of dam line composition of 3-way crossbred animals using genomic information

Table 2 Different quality measures of the estimated^a line B proportions when compared against true or BOA estimated values for the simulated data^b

Measure	Reference	Lines	BOA	LR	ADM	REL_GP	REL_GP_noF
Accuracy	True	Close	0.986	0.680	0.692	0.949	0.954
		Distant	0.996	0.876	0.902	0.950	0.959
		Unrelated	0.997	0.950	0.967	0.952	0.962
	BOA	Close		0.690	0.704	0.936	0.942
		Distant		0.878	0.903	0.948	0.956
		Unrelated		0.948	0.965	0.951	0.961
Dispersion bias	True	Close	0.958	0.513	0.530	0.928	0.923
		Distant	0.964	0.776	0.820	0.966	0.958
		Unrelated	0.962	0.910	0.934	1.025	1.022
	BOA	Close		0.536	0.555	0.943	0.938
		Distant		0.804	0.849	0.996	0.987
		Unrelated		0.942	0.966	1.061	1.058
Maximum error	True	Close	0.076	0.321	0.317	0.109	0.105
		Distant	0.046	0.172	0.155	0.106	0.098
		Unrelated	0.038	0.109	0.089	0.104	0.094
	BOA	Close		0.312	0.308	0.124	0.120
		Distant		0.178	0.159	0.114	0.105
		Unrelated		0.114	0.089	0.109	0.099
RMSE	True	Close	0.019	0.109	0.106	0.036	0.035
		Distant	0.012	0.061	0.053	0.035	0.032
		Unrelated	0.010	0.037	0.030	0.035	0.032
	BOA	Close		0.108	0.104	0.041	0.039
		Distant		0.060	0.053	0.037	0.034
		Unrelated		0.038	0.031	0.037	0.033

RMSE root mean squared error
^aLine B proportions are estimated from estimated breed-origin-of-alleles (BOA), using linear regression on mean allele counts within line (LR), ADMIXTURE analysis (ADM) after pruning SNPs based on r² > 0.5, the genomic relationship with maternal grandsire (REL_GP), or this relationship after adjusting all self-relationships to be 1 (REL_GP_noF)
^bResults are based on the average 188 A(BC) crossbreds with both maternal grandparents included with genotypes in the data

ISSN: 1297-9686