Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population

Table 6 Rankings from the BayesA 250-kb haplotype model compared to the BayesA SNP model

Trait	Breed	r_S (All)^a	r_S (Top 100)^b	Top 0.9%^c
Fat	HF	0.97	0.70	23/30
	J	0.97	0.68	41/53
	KX	0.96	0.55	36/55
Lwt	HF	0.96	0.57	10/13
	J	0.95	0.68	12/21
	KX	0.96	0.70	17/22
SCS	HF	0.96	0.58	21/30
	J	0.97	0.64	42/53
	KX	0.96	0.49	36/55

^aSpearman rank correlation for all cows
^bSpearman rank correlation for the joint set of cows that are in the top 100 cows for DGV from the SNP model or the top 100 cows for DGV from the haplotype model
^cNumber of animals with DGV in the top 0.9% for both the SNP model and haplotype model over the number of animals that are in the top 0.9% for the SNP model

ISSN: 1297-9686