Selecting sequence variants to improve genomic predictions for dairy cattle

Table 6 Coefficients for regression of validation data on genomic predictions when adding real sequence variants to HD or 60 k

Trait	PA	HD SNPs only	HD SNPs + 481,904 candidate SNPs	HD SNPs + 481,904 candidate SNPs + InDels	60 k SNPs only	60 k SNPs + 16,648 candidate SNPs^a
Milk	0.81	1.03	1.06	1.06	1.04	1.05
Fat	0.68	0.92	0.95	0.94	0.94	0.93
Protein	0.75	0.93	0.96	0.95	0.94	0.95
Fat percentage	0.97	1.14	1.13	1.12	1.12	1.09
Protein percentage	0.77	0.96	0.98	0.97	0.95	0.96
Productive life	1.24	1.30	1.32	1.25	1.27	1.25
Somatic cell score	0.89	1.09	1.10	1.06	1.08	1.06
Daughter pregnancy rate	1.20	1.47	1.49	1.48	1.43	1.43
Cow conception rate	0.72	0.94	0.95	0.92	0.91	0.91
Heifer conception rate	0.75	0.97	1.03	0.98	0.94	0.92
Sire calving ease	0.65	0.83	0.83	0.81	0.82	0.84
Daughter calving ease	0.80	1.04	1.03	1.02	1.04	1.02
Sire stillbirth	0.84	0.75	0.76	0.78	0.77	0.76
Daughter stillbirth	0.77	1.15	1.16	1.15	1.12	1.16
Final score	0.71	0.93	0.92	0.92	0.91	0.88
Stature	0.84	1.04	1.02	1.01	1.01	1.00
Strength	0.80	1.05	1.03	1.02	1.01	0.99
Dairy form	0.82	1.10	1.08	1.08	1.07	1.05
Foot angle	0.71	0.84	0.82	0.82	0.81	0.79
Rear legs (side view)	0.87	1.01	0.99	0.99	0.98	0.96
Body depth	0.76	1.01	0.99	0.99	0.97	0.96
Rump angle	0.80	1.08	1.07	1.05	1.06	1.05
Rump width	0.78	1.01	0.99	0.98	0.98	0.96
Fore udder attachment	0.80	1.06	1.04	1.03	1.03	1.01
Rear udder height	0.78	0.97	0.96	0.96	0.94	0.93
Udder depth	0.76	1.11	1.09	1.08	1.07	1.06
Udder cleft	0.87	1.00	0.99	0.99	0.98	0.95
Front teat placement	0.80	1.05	1.03	1.01	1.02	0.99
Teat length	0.91	1.06	1.06	1.04	1.04	1.03
Rear legs (rear view)	0.58	0.86	0.85	0.83	0.83	0.80
Feet and leg score	0.54	0.74	0.72	0.72	0.71	0.68
Rear teat placement	0.90	1.13	1.10	1.09	1.09	1.04
Net merit	0.85	0.82	0.84	0.81	0.83	0.81
Average	0.81	1.01	1.01	1.00	0.99	0.98

ISSN: 1297-9686