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

Table 4 Accuracy and regression coefficients of predicted number of haplotype copies for ungenotyped animals

Haplotype method	Accuracy nhc(se)		Regression¹ true nhc on predicted nhc(se)
NM	0.643	(0.003)	1.005	(0.004)
HAP2	0.630	(0.007)	0.994	(0.022)
HAP4	0.595	(0.012)	0.914	(0.038)

Accuracy of number of haplotype copies (nhc) and regression of true nhc on predicted nhc for neighboring marker (NM), 2-marker haplotype (HAP2) and 4-marker haplotypes (HAP4) for ungenotyped animals in the last generation (females) (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)
¹Regressions where the variance of the predicted nhc was smaller than 0.0001 were omitted (denominator of regression coefficient)

ISSN: 1297-9686