Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost

Table 3 Accuracy of imputation for genotyping scenarios when removing subsets of individuals from the “Other” category

Scenario	Genotyping strategy¹						²Imputation accuracy: R-squared
	³Other	Grandparents		Parents		Testing individuals
		MGS + PGS	MGD + PGD	Sire	Dam
	n2436	n = 63	n = 86	n = 41	n = 73	n = 98	L6k	L3k	L384
s4_100%	100 % H	H	L	H	L	L	.991	.985	.935
s4_50%	50 % H	H	L	H	L	L	.991	.984	.927
s4_25%	25 % H	H	L	H	L	L	.988	.981	.915
s5_100%	100 % H	H	0	H	0	L	.981	.968	.888
s5_50%	50 % H	H	0	H	0	L	.981	.968	.877
s5_25%	25 % H	H	0	H	0	L	.979	.966	.871
s12_100%	100 % H	0	0	0	0	L	.953	.931	.817
s12_50%	50 % H	0	0	0	0	L	.941	.914	.778
s12_25%	25 % H	0	0	0	0	L	.917	.879	.759

¹Animals were split into groups (ordered by generation) of testing individuals, their parents, and their grandparents; grandparents were further divided into two groups: MGS + PGS which included maternal grandsire and paternal grandsire, and MGD + PGD which included maternal granddam and paternal granddam; the remaining individuals were placed in the “Other” category; groups of animals were either genotyped at high density (H), low density (L) or not genotyped (0); ²Imputation accuracy (R-squared) for scenarios using SNP panels L6k, L3k and L384 on animals genotyped at low density; ³100 % H means that all of the individuals in the “Other” category are genotyped at high density, 50 % H means that only a random 50 % of the individuals in the “Other” category are genotyped at high density, 25 % H means that only a random 25 % of the individuals in the “Other” category are genotyped at high density.

ISSN: 1297-9686