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

Table 3 Results of within breed genome wide association analysis

Trait	Holsteins	Jerseys	Overlapping	Number of 100 kbintervals containing SNP significant in both breeds
Fat	2654	5718	124 (4.7)	633 (7.5)
Milk	23808	17573	1210 (6.9)	6341(14.2)
Protein	33671	21065	1327 (6.3)	8804 (14.9)
Fat%	7688	12141	2996 (38.9)	2416 (43.1)
Protein%	12141	7434	2032 (27.3)	3243 (33.4)
Fertility	2276	125	0	1 (0.8)
Mamm. Sys	12088	3032	130 (4.3)	707 (11.1)
Survival	3930	6263	300 (7.6)	739 (12.3)
SCC	1693	3507	36 (2.1)	101 (6.1)

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

ISSN: 1471-2164