Prediction of haplotypes for ungenotyped animals and its effect on marker-assisted breeding value estimation

Table 3 Summary statistics of predicted number of haplotype copies for ungenotyped animals

Haplotype method	True nhc	Mean	SD	MSE
NM	0	0.59	0.08	0.54
	1	0.99	0.09	0.20
	2	1.43	0.08	0.52
HAP2	0	0.34	0.06	0.27
	1	0.76	0.08	0.24
	2	1.24	0.08	0.75
HAP4	0	0.16	0.04	0.11
	1	0.58	0.06	0.32
	2	1.13	0.08	0.90

Mean, standard deviation (SD) and mean square error (MSE) of predicted number of haplotype copies (nhc) for neighboring marker (NM), 2-marker haplotype (HAP2) and 4-marker haplotypes (HAP4) for ungenotyped animals in the last generation (females) as a function of true nhc (sires and males in last generation are genotyped; distance between markers is 0.1 cM, heritability is 0.30, the QTL explains 15% of the genetic variance, results are averages of 200 replicates)

ISSN: 1297-9686