Multibreed genome wide association can improve precision of mapping causative variants underlying milk production in dairy cattle

Table 1 Results of within breed and within gender genome wide association analysis

Trait	Bulls	Cows	Overlapping	Number of 100 kb intervals containing SNP significant in both breeds
Jerseys
Fat	806	984	25 (3.10)	44 (4.0)
Milk	2117	3969	461 (21.8)	242 (23.5)
Protein	4016	2606	557 (13.9)	504 (24.1)
Fat%	677	5093	66 (9.75)	141 (16.1)
Protein%	692	5444	150 (21.7)	368 (34.2)
Fertility	16	1	0	0
Mamm. Syst.	1721	51	0	0
Survival	4302	206	1 (0.5)	10 (2.9)
SCC	248	3600	42 (16.9)	28 (19.0)
Holsteins
Fat	2100	3899	1543 (73.5)	228 (82.0)
Milk	5321	5488	1529 (28.74)	1023 (31.6)
Protein	3288	8730	2936 (89.3)	178 (90.5)
Fat%	2084	3422	1353 (64.9)	372 (67.3)
Protein%	3378	4374	1644 (48.7)	1512 (54.1)
Fertility	1567	10	0	0
Mamm. Syst.	14770	147	28 (19.0)	79 (24.5)
Survival	3522	220	20 (9.1)	138 (14.5)
SCC	729	701	26 (3.7)	82 (7.0)

The number of SNP which are significant in both genders within Jerseys and Holsteins are presented (percentage of significant SNP that are significant in both genders given in parenthesis), as well as the number of 100 kb intervals containing significant SNP for that trait in both genders (percentage of 100 kb windows with a significant SNP in either gender with significant SNP in both genders given in parenthesis). Milk production traits were tested at P < 10^-8 and reproductive and functional traits at P < 10^-5.

ISSN: 1471-2164